#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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
PCDH15	65217	broad.mit.edu	37	10	55581768	55581769	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:55581768_55581769insT	ENST00000320301.6	-	33	6111_6112	c.5717_5718insA	c.(5716-5718)aacfs	p.N1906fs	PCDH15_ENST00000395432.2_Frame_Shift_Ins_p.N1866fs|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000373957.3_Frame_Shift_Ins_p.N760fs|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000361849.3_Frame_Shift_Ins_p.N1908fs|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395433.1_Frame_Shift_Ins_p.N1883fs|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000437009.1_Frame_Shift_Ins_p.N1837fs|PCDH15_ENST00000395430.1_Frame_Shift_Ins_p.N1903fs	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1906					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.N1906fs*26(1)|p.N1913fs*26(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TGCGTAGATAGTTTTTTTCTAT	0.361										HNSCC(58;0.16)																											p.N1837fs												.	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.5511_5512insA	10						.																																			55251775	SO:0001589	frameshift_variant	65217	exon32			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.5718dupA	10.37:g.55581775_55581775dupT	ENSP00000322604:p.Asn1906fs	Somatic		Capture	Illumina HiSeq	Phase_I	55251774	NM_001142765	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Frame_Shift_Ins	INS	ENST00000320301.6	37	CCDS7248.1																																																																																				0.361	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
LOXL4	84171	broad.mit.edu	37	10	100022771	100022771	+	Silent	SNP	C	C	T	rs201076968	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:100022771C>T	ENST00000260702.3	-	2	156	c.6G>A	c.(4-6)gcG>gcA	p.A2A		NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	2						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)	p.A2A(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		GTGGGGACCACGCCATGGTGA	0.587											OREG0020428	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2	0.000399361	0.0	0.0	5008	,	,		17790	0.001		0.001	False		,,,				2504	0.0				p.A2A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G6A	10						.						30.0	33.0	32.0					10																	100022771		2203	4300	6503	100012761	SO:0001819	synonymous_variant	84171	exon2			AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.6G>A	10.37:g.100022771C>T		Somatic	1348	Capture	Illumina HiSeq	Phase_I	100012761	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Silent	SNP	ENST00000260702.3	37	CCDS7473.1																																																																																				0.587	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211	
DNMBP	23268	broad.mit.edu	37	10	101659796	101659796	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:101659796T>C	ENST00000324109.4	-	7	2673	c.2582A>G	c.(2581-2583)gAg>gGg	p.E861G	DNMBP_ENST00000543621.1_Missense_Mutation_p.E107G|DNMBP_ENST00000342239.3_Missense_Mutation_p.E861G|DNMBP_ENST00000540316.1_5'Flank	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	861	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E861G(1)		central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TCCCTCAAGCTCATCCCGGTG	0.413																																					p.E861G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2582G	10						.						157.0	142.0	147.0					10																	101659796		2203	4300	6503	101649786	SO:0001583	missense	23268	exon7			AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.2582A>G	10.37:g.101659796T>C	ENSP00000315659:p.Glu861Gly	Somatic		Capture	Illumina HiSeq	Phase_I	101649786	NM_015221	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	37	CCDS7485.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.117196	0.77323	.	.	ENSG00000107554	ENST00000342239;ENST00000324109;ENST00000393570;ENST00000543621;ENST00000370423;ENST00000422692	T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12	5.48	4.31	0.51392	Dbl homology (DH) domain (5);	0.132041	0.34268	N	0.004115	T	0.58075	0.2097	L	0.45051	1.395	0.80722	D	1	P;B;P	0.41366	0.747;0.253;0.747	B;B;B	0.44108	0.441;0.108;0.441	T	0.55373	-0.8151	10	0.36615	T	0.2	-11.0435	12.7143	0.57107	0.0:0.0:0.1377:0.8623	.	861;107;861	Q6XZF7;Q6XZF7-2;Q5SVK8	DNMBP_HUMAN;.;.	G	861;861;107;107;149;149	ENSP00000344914:E861G;ENSP00000315659:E861G;ENSP00000443657:E107G;ENSP00000409476:E149G	ENSP00000315659:E861G	E	-	2	0	DNMBP	101649786	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	5.021000	0.64072	0.984000	0.38629	0.459000	0.35465	GAG		0.413	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
GTPBP4	23560	broad.mit.edu	37	10	1041911	1041911	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:1041911G>A	ENST00000360803.4	+	3	344	c.262G>A	c.(262-264)Gac>Aac	p.D88N	GTPBP4_ENST00000491635.1_Intron|GTPBP4_ENST00000545048.1_Missense_Mutation_p.D41N|GTPBP4_ENST00000538293.1_Intron	NM_012341.2	NP_036473.2	Q9BZE4	NOG1_HUMAN	GTP binding protein 4	88					GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of collagen binding (GO:0033342)|negative regulation of DNA replication (GO:0008156)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein stabilization (GO:0050821)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.D88N(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(1)	21		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		TATTCTCTACGACAAGGATCA	0.388																																					p.D88N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G262A	10						.						94.0	76.0	82.0					10																	1041911		2203	4300	6503	1031911	SO:0001583	missense	23560	exon3			AK001548	CCDS31132.1	10p15-p14	2007-07-27			ENSG00000107937	ENSG00000107937			21535	protein-coding gene	gene with protein product	"""G protein-binding protein CRFG"", "" GTP-binding protein"""					11316846	Standard	NM_012341		Approved	CRFG, NGB, FLJ10690, FLJ10686, NOG1	uc001ift.3	Q9BZE4	OTTHUMG00000017538	ENST00000360803.4:c.262G>A	10.37:g.1041911G>A	ENSP00000354040:p.Asp88Asn	Somatic		Capture	Illumina HiSeq	Phase_I	1031911	NM_012341	B3KMC5|B4DY13|B7Z7A3|O95446|Q5T3R8|Q9NVJ8	Missense_Mutation	SNP	ENST00000360803.4	37	CCDS31132.1	.	.	.	.	.	.	.	.	.	.	G	33	5.203163	0.95033	.	.	ENSG00000107937	ENST00000360803;ENST00000360059;ENST00000545048	T;T;T	0.13196	2.61;2.61;2.61	5.56	5.56	0.83823	.	0.046931	0.85682	D	0.000000	T	0.34600	0.0903	M	0.67397	2.05	0.80722	D	1	D	0.69078	0.997	P	0.60345	0.873	T	0.01349	-1.1378	10	0.48119	T	0.1	-13.5995	19.5068	0.95121	0.0:0.0:1.0:0.0	.	88	Q9BZE4	NOG1_HUMAN	N	88;41;41	ENSP00000354040:D88N;ENSP00000353168:D41N;ENSP00000445473:D41N	ENSP00000353168:D41N	D	+	1	0	GTPBP4	1031911	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	9.622000	0.98378	2.619000	0.88677	0.555000	0.69702	GAC		0.388	GTPBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046412.1	NM_012341	
SEMA4G	57715	broad.mit.edu	37	10	102737410	102737410	+	Missense_Mutation	SNP	C	C	T	rs145690277		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:102737410C>T	ENST00000370250.4	+	4	731	c.358C>T	c.(358-360)Cgg>Tgg	p.R120W	SEMA4G_ENST00000519756.1_3'UTR|SEMA4G_ENST00000517724.1_Missense_Mutation_p.R120W|RP11-108L7.4_ENST00000447344.1_RNA|SEMA4G_ENST00000210633.3_Missense_Mutation_p.R120W|MIR608_ENST00000384820.1_RNA	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	120	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.R120W(1)		breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		TAACCATGTGCGGTTCCTGCA	0.552																																					p.R120W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C358T	10						.	C	TRP/ARG,TRP/ARG	0,4406		0,0,2203	225.0	189.0	201.0		358,358	4.4	1.0	10	dbSNP_134	201	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SEMA4G	NM_001203244.1,NM_017893.3	101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	120/703,120/844	102737410	1,13005	2203	4300	6503	102727400	SO:0001583	missense	57715	exon4			AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.358C>T	10.37:g.102737410C>T	ENSP00000359270:p.Arg120Trp	Somatic		Capture	Illumina HiSeq	Phase_I	102727400	NM_017893	A1A5C6|A6NJY8|Q58EY1|Q9HCF3	Missense_Mutation	SNP	ENST00000370250.4	37		.	.	.	.	.	.	.	.	.	.	C	26.8	4.776266	0.90195	0.0	1.16E-4	ENSG00000095539	ENST00000519649;ENST00000518124;ENST00000457585;ENST00000370250;ENST00000517724;ENST00000210633	T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16	5.32	4.39	0.52855	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.69780	0.3149	H	0.94734	3.575	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.79490	-0.1782	10	0.87932	D	0	.	14.4117	0.67119	0.1586:0.8414:0.0:0.0	.	120;120;120	Q9NTN9;A1A5C6;Q9NTN9-2	SEM4G_HUMAN;.;.	W	120	ENSP00000428896:R120W;ENSP00000430103:R120W;ENSP00000359270:R120W;ENSP00000430175:R120W;ENSP00000210633:R120W	ENSP00000210633:R120W	R	+	1	2	SEMA4G	102727400	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	4.482000	0.60257	1.160000	0.42584	0.491000	0.48974	CGG		0.552	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2		
LDB1	8861	broad.mit.edu	37	10	103868806	103868806	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:103868806C>T	ENST00000425280.1	-	10	1327	c.985G>A	c.(985-987)Gcc>Acc	p.A329T	LDB1_ENST00000361198.5_Missense_Mutation_p.A293T|LDB1_ENST00000490751.1_5'Flank	NM_001113407.1	NP_001106878.1	Q86U70	LDB1_HUMAN	LIM domain binding 1	329					anterior/posterior axis specification (GO:0009948)|cellular component assembly (GO:0022607)|cerebellar Purkinje cell differentiation (GO:0021702)|epithelial structure maintenance (GO:0010669)|gastrulation with mouth forming second (GO:0001702)|hair follicle development (GO:0001942)|head development (GO:0060322)|histone H3-K4 acetylation (GO:0043973)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of cell adhesion (GO:0045785)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)|Wnt signaling pathway (GO:0016055)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|enzyme binding (GO:0019899)|LIM domain binding (GO:0030274)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|transcription corepressor activity (GO:0003714)	p.A293T(1)		breast(1)|central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)	21		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)		CTGGAGAGGGCGAAGGTGCTA	0.582																																					p.A329T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G985A	10						.						181.0	153.0	162.0					10																	103868806		2203	4300	6503	103858796	SO:0001583	missense	8861	exon10			AF068652	CCDS7528.1, CCDS44472.1	10q24-q25	2008-08-01			ENSG00000198728	ENSG00000198728			6532	protein-coding gene	gene with protein product	"""carboxy terminal LIM domain protein 2"""	603451				9503020, 9799849	Standard	NM_003893		Approved	NLI, CLIM2	uc009xwz.3	Q86U70	OTTHUMG00000018950	ENST00000425280.1:c.985G>A	10.37:g.103868806C>T	ENSP00000392466:p.Ala329Thr	Somatic		Capture	Illumina HiSeq	Phase_I	103858796	NM_001113407	B4DUC4|O75479|O96010|Q1EQX1|Q9UGM4	Missense_Mutation	SNP	ENST00000425280.1	37	CCDS44472.1	.	.	.	.	.	.	.	.	.	.	C	14.29	2.491555	0.44249	.	.	ENSG00000198728	ENST00000361198;ENST00000425280	T;T	0.22134	1.97;1.97	5.59	5.59	0.84812	.	0.100719	0.64402	D	0.000002	T	0.15003	0.0362	N	0.08118	0	0.54753	D	0.999987	B;B	0.28208	0.203;0.145	B;B	0.29440	0.058;0.102	T	0.11792	-1.0573	10	0.49607	T	0.09	0.6531	19.5878	0.95496	0.0:1.0:0.0:0.0	.	329;293	Q86U70;Q86U70-3	LDB1_HUMAN;.	T	293;329	ENSP00000354616:A293T;ENSP00000392466:A329T	ENSP00000354616:A293T	A	-	1	0	LDB1	103858796	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.760000	0.47581	2.651000	0.90000	0.491000	0.48974	GCC		0.582	LDB1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113407	
NOLC1	9221	broad.mit.edu	37	10	103920362	103920362	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:103920362C>T	ENST00000605788.1	+	10	1488	c.1253C>T	c.(1252-1254)aCg>aTg	p.T418M	NOLC1_ENST00000488254.2_Missense_Mutation_p.T419M|NOLC1_ENST00000405356.1_Missense_Mutation_p.T428M|NOLC1_ENST00000603742.1_Missense_Mutation_p.T137M	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	418	11 X 12 AA approximate repeats of an acidic serine cluster.				cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)	p.T418M(2)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		AAGCTTCTGACGAGAAAGGCT	0.562																																					p.T418M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1253T	10						.						58.0	54.0	55.0					10																	103920362		2203	4300	6503	103910352	SO:0001583	missense	9221	exon10			Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.1253C>T	10.37:g.103920362C>T	ENSP00000474710:p.Thr418Met	Somatic		Capture	Illumina HiSeq	Phase_I	103910352	NM_004741	Q15030|Q5VV70|Q9BUV3	Missense_Mutation	SNP	ENST00000605788.1	37	CCDS7530.1	.	.	.	.	.	.	.	.	.	.	C	1.559	-0.537277	0.04082	.	.	ENSG00000166197	ENST00000405356;ENST00000370007	T	0.33216	1.42	5.67	0.57	0.17347	.	0.634938	0.15624	N	0.252749	T	0.25680	0.0625	L	0.54323	1.7	0.09310	N	1	B;B;B	0.22080	0.064;0.064;0.038	B;B;B	0.15870	0.014;0.014;0.006	T	0.17961	-1.0352	10	0.51188	T	0.08	-0.2215	7.7611	0.28953	0.0:0.6168:0.1142:0.269	.	419;428;418	Q14978-3;Q14978-2;Q14978	.;.;NOLC1_HUMAN	M	428;418	ENSP00000385410:T428M	ENSP00000359024:T418M	T	+	2	0	NOLC1	103910352	0.000000	0.05858	0.004000	0.12327	0.000000	0.00434	-0.039000	0.12124	-0.143000	0.11334	-1.756000	0.00673	ACG		0.562	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741	
SFXN2	118980	broad.mit.edu	37	10	104486494	104486494	+	Missense_Mutation	SNP	G	G	A	rs201929596		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:104486494G>A	ENST00000369893.5	+	2	268	c.101G>A	c.(100-102)cGc>cAc	p.R34H	SFXN2_ENST00000602785.1_3'UTR	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	34					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)	p.R34H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		ACGGACCCCCGCACTGTCTTT	0.587																																					p.R34H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G101A	10						.						83.0	83.0	83.0					10																	104486494		2203	4300	6503	104476484	SO:0001583	missense	118980	exon2			AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"""Sideroflexins"""	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.101G>A	10.37:g.104486494G>A	ENSP00000358909:p.Arg34His	Somatic		Capture	Illumina HiSeq	Phase_I	104476484	NM_178858	Q5JSM6	Missense_Mutation	SNP	ENST00000369893.5	37	CCDS7539.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.965729	0.74131	.	.	ENSG00000156398	ENST00000369893	T	0.32272	1.46	5.63	5.63	0.86233	.	0.102918	0.64402	D	0.000005	T	0.61800	0.2376	M	0.87269	2.87	0.80722	D	1	D	0.71674	0.998	D	0.64877	0.93	T	0.66492	-0.5910	10	0.56958	D	0.05	6.0E-4	19.6913	0.96002	0.0:0.0:1.0:0.0	.	34	Q96NB2	SFXN2_HUMAN	H	34	ENSP00000358909:R34H	ENSP00000358909:R34H	R	+	2	0	SFXN2	104476484	1.000000	0.71417	0.999000	0.59377	0.627000	0.37826	6.611000	0.74183	2.654000	0.90174	0.561000	0.74099	CGC		0.587	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359	
PDCD11	22984	broad.mit.edu	37	10	105194592	105194592	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:105194592C>T	ENST00000369797.3	+	25	3799	c.3705C>T	c.(3703-3705)ggC>ggT	p.G1235G		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1235	S1 motif 11. {ECO:0000255|PROSITE- ProRule:PRU00180}.				mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)	p.G1235G(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		TGGCCATGGGCCGAGTGGTGA	0.547																																					p.G1235G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3705T	10						.						68.0	56.0	60.0					10																	105194592		2203	4300	6503	105184582	SO:0001819	synonymous_variant	22984	exon25			D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.3705C>T	10.37:g.105194592C>T		Somatic		Capture	Illumina HiSeq	Phase_I	105184582	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Silent	SNP	ENST00000369797.3	37	CCDS31276.1																																																																																				0.547	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
PDCD11	22984	broad.mit.edu	37	10	105197789	105197789	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:105197789C>T	ENST00000369797.3	+	26	3957	c.3863C>T	c.(3862-3864)aCt>aTt	p.T1288I		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1288	S1 motif 11. {ECO:0000255|PROSITE- ProRule:PRU00180}.				mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)	p.T1288I(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		ATCCTGTCCACTGCAGACAAC	0.488																																					p.T1288I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3863T	10						.						269.0	259.0	263.0					10																	105197789		2203	4300	6503	105187779	SO:0001583	missense	22984	exon26			D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.3863C>T	10.37:g.105197789C>T	ENSP00000358812:p.Thr1288Ile	Somatic		Capture	Illumina HiSeq	Phase_I	105187779	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	C	0.458	-0.890545	0.02491	.	.	ENSG00000148843	ENST00000369797	T	0.17213	2.29	4.6	3.67	0.42095	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);RNA-binding domain, S1 (1);Ribosomal protein S1, RNA-binding domain (1);	0.796636	0.12371	N	0.474753	T	0.04952	0.0133	N	0.01168	-0.975	0.20196	N	0.999925	B	0.09022	0.002	B	0.06405	0.002	T	0.38134	-0.9675	10	0.19590	T	0.45	-0.5948	3.9234	0.09253	0.1691:0.5764:0.1636:0.091	.	1288	Q14690	RRP5_HUMAN	I	1288	ENSP00000358812:T1288I	ENSP00000358812:T1288I	T	+	2	0	PDCD11	105187779	0.008000	0.16893	0.514000	0.27761	0.080000	0.17528	0.623000	0.24447	1.199000	0.43173	0.561000	0.74099	ACT		0.488	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
CFAP43	80217	broad.mit.edu	37	10	105903311	105903311	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:105903311G>A	ENST00000357060.3	-	32	4146	c.4031C>T	c.(4030-4032)gCc>gTc	p.A1344V	WDR96_ENST00000479392.1_5'Flank|WDR96_ENST00000428666.1_Missense_Mutation_p.A1316V	NM_025145.5	NP_079421.5												p.A1344V(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CTGGGCAAAGGCATCCTTATT	0.438																																					p.A1344V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4031T	10						.						143.0	134.0	137.0					10																	105903311		2203	4300	6503	105893301	SO:0001583	missense	80217	exon32																														ENST00000357060.3:c.4031C>T	10.37:g.105903311G>A	ENSP00000349568:p.Ala1344Val	Somatic		Capture	Illumina HiSeq	Phase_I	105893301	NM_025145		Missense_Mutation	SNP	ENST00000357060.3	37	CCDS31281.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.941|5.941	0.357583|0.357583	0.11239|0.11239	.|.	.|.	ENSG00000197748|ENSG00000197748	ENST00000357060;ENST00000428666|ENST00000457071;ENST00000434629	T;T|.	0.15256|.	2.46;2.44|.	6.02|6.02	-3.16|-3.16	0.05217|0.05217	.|.	1.368040|.	0.04512|.	N|.	0.383076|.	T|T	0.34077|0.34077	0.0885|0.0885	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	B;B|.	0.24258|.	0.1;0.098|.	B;B|.	0.26969|.	0.062;0.075|.	T|T	0.41360|0.41360	-0.9513|-0.9513	10|5	0.29301|.	T|.	0.29|.	.|.	12.3049|12.3049	0.54895|0.54895	0.0:0.1724:0.3257:0.5019|0.0:0.1724:0.3257:0.5019	.|.	1316;1344|.	G5E9L1;Q8NDM7|.	.;WDR96_HUMAN|.	V|S	1344;1316|193;676	ENSP00000349568:A1344V;ENSP00000400289:A1316V|.	ENSP00000349568:A1344V|.	A|P	-|-	2|1	0|0	WDR96|WDR96	105893301|105893301	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.292000|0.292000	0.27327|0.27327	-0.167000|-0.167000	0.09940|0.09940	-0.184000|-0.184000	0.10567|0.10567	-0.284000|-0.284000	0.09977|0.09977	GCC|CCT		0.438	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SORCS3	22986	broad.mit.edu	37	10	107022209	107022209	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:107022209T>C	ENST00000369701.3	+	26	3791	c.3564T>C	c.(3562-3564)ccT>ccC	p.P1188P		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	1188					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)	p.P1188P(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TTACGGAGCCTGAGGAGCTGC	0.527																																					p.P1188P	NSCLC(116;1497 1690 7108 13108 14106)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3564C	10						.						73.0	58.0	63.0					10																	107022209		2203	4300	6503	107012199	SO:0001819	synonymous_variant	22986	exon26			AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.3564T>C	10.37:g.107022209T>C		Somatic		Capture	Illumina HiSeq	Phase_I	107012199	NM_014978	Q5VXF9|Q9NQJ2	Silent	SNP	ENST00000369701.3	37	CCDS7558.1																																																																																				0.527	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978	
CELF2	10659	broad.mit.edu	37	10	11207487	11207487	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:11207487A>G	ENST00000379261.4	+	2	184	c.92A>G	c.(91-93)cAc>cGc	p.H31R	CELF2_ENST00000427450.1_Missense_Mutation_p.H7R|CELF2_ENST00000416382.2_Missense_Mutation_p.H31R|CELF2_ENST00000609692.1_Missense_Mutation_p.H7R|CELF2_ENST00000399850.3_Missense_Mutation_p.H7R|CELF2_ENST00000354897.3_Missense_Mutation_p.H7R|CELF2_ENST00000315874.4_Missense_Mutation_p.H7R|CELF2_ENST00000354440.2_Missense_Mutation_p.H7R|CELF2_ENST00000417956.2_Missense_Mutation_p.H7R|CELF2_ENST00000450189.1_Missense_Mutation_p.H38R|CELF2_ENST00000537122.1_5'Flank|CELF2_ENST00000608830.1_Missense_Mutation_p.H7R|CELF2_ENST00000542579.1_Missense_Mutation_p.H38R	NM_001025077.2	NP_001020248.1	O95319	CELF2_HUMAN	CUGBP, Elav-like family member 2	31	Necessary for RNA-binding, TNNT2 exon 5 and NMDA R1 exon 21 inclusion.				mRNA processing (GO:0006397)|regulation of heart contraction (GO:0008016)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.H26R(1)		breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	16						GCTTTGGATCACTCAGACCAA	0.507																																					p.H31R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A92G	10						.						127.0	134.0	131.0					10																	11207487		1973	4155	6128	11247493	SO:0001583	missense	10659	exon2			U69546	CCDS41488.1, CCDS44354.1, CCDS44355.1, CCDS44356.1	10p13	2013-02-12	2010-02-19	2010-02-19	ENSG00000048740	ENSG00000048740		"""RNA binding motif (RRM) containing"""	2550	protein-coding gene	gene with protein product		602538	"""CUG triplet repeat, RNA-binding protein 2"", ""CUG triplet repeat, RNA binding protein 2"""	CUGBP2		7869393, 9887331	Standard	NM_006561		Approved	Etr-3, NAPOR-2, BRUNOL3	uc001ikl.4	O95319	OTTHUMG00000017668	ENST00000379261.4:c.92A>G	10.37:g.11207487A>G	ENSP00000368563:p.His31Arg	Somatic		Capture	Illumina HiSeq	Phase_I	11247493	NM_001025077	B7ZAN9|Q7KYU4|Q8N499|Q92950|Q96NW9|Q96RQ5|Q96RQ6|Q9UL67	Missense_Mutation	SNP	ENST00000379261.4	37	CCDS44354.1	.	.	.	.	.	.	.	.	.	.	A	16.81	3.224600	0.58668	.	.	ENSG00000048740	ENST00000379261;ENST00000416382;ENST00000450189;ENST00000542579;ENST00000399850;ENST00000417956;ENST00000315874;ENST00000354440;ENST00000354897;ENST00000427450	T;T;T;T;T;T;T;T;T	0.41065	1.01;1.01;1.36;1.36;1.01;1.01;1.01;1.01;1.01	5.42	5.42	0.78866	.	0.048997	0.85682	D	0.000000	T	0.49047	0.1534	L	0.27053	0.805	0.80722	D	1	B;B;B;B;D;B;B	0.54207	0.139;0.139;0.08;0.068;0.965;0.342;0.139	B;B;B;B;P;B;B	0.59487	0.05;0.05;0.037;0.018;0.858;0.152;0.05	T	0.53165	-0.8477	10	0.87932	D	0	-15.0414	15.7607	0.78076	1.0:0.0:0.0:0.0	.	15;31;7;26;38;26;31	B4DDE7;B4DS31;B4DSZ2;B2RA86;E9PC62;O95319-3;O95319	.;.;.;.;.;.;CELF2_HUMAN	R	31;31;38;38;7;7;7;7;7;7	ENSP00000368563:H31R;ENSP00000406451:H31R;ENSP00000389951:H38R;ENSP00000443926:H38R;ENSP00000382743:H7R;ENSP00000404834:H7R;ENSP00000315328:H7R;ENSP00000346426:H7R;ENSP00000388530:H7R	ENSP00000315328:H7R	H	+	2	0	CELF2	11247493	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.200000	0.95010	2.189000	0.69895	0.460000	0.39030	CAC		0.507	CELF2-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
SORCS1	114815	broad.mit.edu	37	10	108923836	108923836	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:108923836G>T	ENST00000263054.6	-	1	456	c.449C>A	c.(448-450)gCc>gAc	p.A150D	SORCS1_ENST00000344440.6_Missense_Mutation_p.A150D	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	150					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.A150D(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GAAGCGGGTGGCTTTGTCCGG	0.657																																					p.A150D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C449A	10						.						56.0	54.0	55.0					10																	108923836		2203	4300	6503	108913826	SO:0001583	missense	114815	exon1			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.449C>A	10.37:g.108923836G>T	ENSP00000263054:p.Ala150Asp	Somatic		Capture	Illumina HiSeq	Phase_I	108913826	NM_052918	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.884775	0.72410	.	.	ENSG00000108018	ENST00000263054;ENST00000344440	T;T	0.18016	2.24;2.26	4.96	4.96	0.65561	.	0.409836	0.21143	N	0.079453	T	0.17492	0.0420	N	0.24115	0.695	0.34549	D	0.711122	D;D;D;D;D	0.59357	0.974;0.985;0.985;0.974;0.985	B;P;P;P;P	0.52217	0.416;0.693;0.62;0.497;0.62	T	0.09422	-1.0675	9	.	.	.	-15.9858	10.5188	0.44907	0.0891:0.0:0.9109:0.0	.	150;150;150;150;150	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	D	150	ENSP00000263054:A150D;ENSP00000345964:A150D	.	A	-	2	0	SORCS1	108913826	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.356000	0.44116	2.560000	0.86352	0.655000	0.94253	GCC		0.657	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
USP6NL	9712	broad.mit.edu	37	10	11569532	11569532	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:11569532C>T	ENST00000609104.1	-	3	433	c.39G>A	c.(37-39)caG>caA	p.Q13Q	USP6NL_ENST00000379237.2_Silent_p.Q36Q|USP6NL_ENST00000277575.5_Silent_p.Q30Q	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	13					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)	p.Q30Q(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						CAGCTCGCTCCTGGGCAAGTT	0.323																																					p.Q13Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G39A	10						.						54.0	51.0	52.0					10																	11569532		1857	4104	5961	11609538	SO:0001819	synonymous_variant	9712	exon3			BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"""related to the N terminus of tre"""	605405	"""USP6NL intronic transcript 1 (non-protein coding)"""	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.39G>A	10.37:g.11569532C>T		Somatic		Capture	Illumina HiSeq	Phase_I	11609538	NM_014688	A8KA79|Q15400|Q5VV10|Q7L0K9	Silent	SNP	ENST00000609104.1	37	CCDS53492.1																																																																																				0.323	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688	
VWA2	340706	broad.mit.edu	37	10	116046094	116046094	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:116046094C>T	ENST00000392982.3	+	11	1644	c.1394C>T	c.(1393-1395)gCg>gTg	p.A465V	VWA2_ENST00000603594.1_Missense_Mutation_p.A465V			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	465	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)	p.A465V(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		GCGGGCCCAGCGCGTCACGCA	0.652																																					p.A465V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1394T	10						.						71.0	63.0	66.0					10																	116046094		2203	4300	6503	116036084	SO:0001583	missense	340706	exon11			AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.1394C>T	10.37:g.116046094C>T	ENSP00000376708:p.Ala465Val	Somatic		Capture	Illumina HiSeq	Phase_I	116036084	NM_198496	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		.	.	.	.	.	.	.	.	.	.	C	14.31	2.495995	0.44352	.	.	ENSG00000165816	ENST00000392982;ENST00000298715	T	0.81330	-1.48	5.74	4.83	0.62350	von Willebrand factor, type A (3);	0.124327	0.56097	D	0.000030	T	0.79941	0.4533	M	0.76838	2.35	0.44061	D	0.9968	P;P;P	0.51449	0.945;0.647;0.594	B;B;B	0.39904	0.313;0.156;0.097	D	0.83373	0.0008	10	0.52906	T	0.07	.	14.8379	0.70197	0.0:0.9288:0.0:0.0712	.	161;465;465	Q5GFL6-3;Q5GFL6;Q5GFL6-2	.;VWA2_HUMAN;.	V	465	ENSP00000376708:A465V	ENSP00000298715:A465V	A	+	2	0	VWA2	116036084	1.000000	0.71417	0.053000	0.19242	0.002000	0.02628	5.459000	0.66685	2.712000	0.92718	0.563000	0.77884	GCG		0.652	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
PNLIPRP3	119548	broad.mit.edu	37	10	118220557	118220557	+	Silent	SNP	C	C	T	rs201251164	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:118220557C>T	ENST00000369230.3	+	6	791	c.645C>T	c.(643-645)gaC>gaT	p.D215D		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	215					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)	p.D215D(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		ACTTTGTTGACGTTATTCATA	0.438													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19013	0.0		0.0	False		,,,				2504	0.0				p.D215D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C645T	10						.						140.0	125.0	130.0					10																	118220557		2203	4300	6503	118210547	SO:0001819	synonymous_variant	119548	exon6			BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.645C>T	10.37:g.118220557C>T		Somatic		Capture	Illumina HiSeq	Phase_I	118210547	NM_001011709		Silent	SNP	ENST00000369230.3	37	CCDS31292.1																																																																																				0.438	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
SEC61A2	55176	broad.mit.edu	37	10	12202950	12202950	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:12202950G>A	ENST00000298428.9	+	10	1086	c.997G>A	c.(997-999)Gca>Aca	p.A333T	SEC61A2_ENST00000379033.3_Missense_Mutation_p.A311T|SEC61A2_ENST00000379020.4_Missense_Mutation_p.A267T|SEC61A2_ENST00000495368.1_3'UTR|SEC61A2_ENST00000304267.8_Missense_Mutation_p.A333T	NM_018144.3	NP_060614.2	Q9H9S3	S61A2_HUMAN	Sec61 alpha 2 subunit (S. cerevisiae)	333					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ribosome binding (GO:0043022)	p.A333T(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Renal(717;0.228)				GGGAGGACCCGCACGTTCTTA	0.458																																					p.A333T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G997A	10						.						199.0	182.0	188.0					10																	12202950		2203	4300	6503	12242956	SO:0001583	missense	55176	exon10			AF346603	CCDS7088.1, CCDS44358.1, CCDS44359.1	10p14	2004-01-06			ENSG00000065665	ENSG00000065665			17702	protein-coding gene	gene with protein product							Standard	NM_018144		Approved	FLJ10578	uc001ile.2	Q9H9S3	OTTHUMG00000017679	ENST00000298428.9:c.997G>A	10.37:g.12202950G>A	ENSP00000298428:p.Ala333Thr	Somatic		Capture	Illumina HiSeq	Phase_I	12242956	NM_001142627	A8K8D0|B4DX72|F8W773	Missense_Mutation	SNP	ENST00000298428.9	37	CCDS7088.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.083855	0.76642	.	.	ENSG00000065665	ENST00000379033;ENST00000298428;ENST00000304267;ENST00000379020;ENST00000426560	.	.	.	5.76	5.76	0.90799	SecY subunit domain (2);	0.000000	0.64402	D	0.000002	T	0.66406	0.2786	L	0.56769	1.78	0.80722	D	1	B;B;B	0.20988	0.024;0.05;0.011	B;B;B	0.23018	0.009;0.043;0.018	T	0.60110	-0.7327	9	0.36615	T	0.2	-11.6463	19.3309	0.94288	0.0:0.0:1.0:0.0	.	311;333;333	F8W773;Q9H9S3-2;Q9H9S3	.;.;S61A2_HUMAN	T	311;333;333;267;81	.	ENSP00000298428:A333T	A	+	1	0	SEC61A2	12242956	1.000000	0.71417	0.973000	0.42090	0.737000	0.42083	9.813000	0.99286	2.880000	0.98712	0.650000	0.86243	GCA		0.458	SEC61A2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046795.1	NM_018144	
PNLIPRP3	119548	broad.mit.edu	37	10	118236172	118236172	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:118236172T>G	ENST00000369230.3	+	11	1327	c.1181T>G	c.(1180-1182)cTt>cGt	p.L394R		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	394	PLAT.				lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)	p.L394R(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		AGTGGAAAACTTGAGCCAGGC	0.358																																					p.L394R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1181G	10						.						105.0	103.0	104.0					10																	118236172		2203	4300	6503	118226162	SO:0001583	missense	119548	exon11			BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.1181T>G	10.37:g.118236172T>G	ENSP00000358232:p.Leu394Arg	Somatic		Capture	Illumina HiSeq	Phase_I	118226162	NM_001011709		Missense_Mutation	SNP	ENST00000369230.3	37	CCDS31292.1	.	.	.	.	.	.	.	.	.	.	T	12.46	1.943168	0.34283	.	.	ENSG00000203837	ENST00000369230	T	0.79554	-1.28	4.13	4.13	0.48395	Lipoxygenase, LH2 (2);Lipase/lipooxygenase, PLAT/LH2 (1);	0.332224	0.21185	N	0.078747	D	0.88698	0.6507	M	0.80616	2.505	0.29351	N	0.865356	D	0.89917	1.0	D	0.78314	0.991	D	0.84160	0.0428	10	0.87932	D	0	.	11.3315	0.49479	0.0:0.0:0.0:1.0	.	394	Q17RR3	LIPR3_HUMAN	R	394	ENSP00000358232:L394R	ENSP00000358232:L394R	L	+	2	0	PNLIPRP3	118226162	0.173000	0.23056	0.633000	0.29310	0.140000	0.21249	3.790000	0.55461	1.819000	0.53055	0.533000	0.62120	CTT		0.358	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
MCM10	55388	broad.mit.edu	37	10	13217613	13217613	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:13217613G>T	ENST00000484800.2	+	6	802	c.699G>T	c.(697-699)ggG>ggT	p.G233G	MCM10_ENST00000378694.1_Silent_p.G232G|MCM10_ENST00000378714.3_Silent_p.G232G			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	233					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.G233G(1)		central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						AAATTGTGGGGACCCCAGGAA	0.512																																					p.G232G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G696T	10						.						126.0	126.0	126.0					10																	13217613		2203	4300	6503	13257619	SO:0001819	synonymous_variant	55388	exon6			AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"""MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"""			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.699G>T	10.37:g.13217613G>T		Somatic		Capture	Illumina HiSeq	Phase_I	13257619	NM_018518	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Silent	SNP	ENST00000484800.2	37	CCDS7096.1																																																																																				0.512	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
MCM10	55388	broad.mit.edu	37	10	13251099	13251099	+	Missense_Mutation	SNP	G	G	A	rs544718421	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:13251099G>A	ENST00000484800.2	+	19	2613	c.2510G>A	c.(2509-2511)gGc>gAc	p.G837D	MCM10_ENST00000378694.1_Missense_Mutation_p.G836D|MCM10_ENST00000378714.3_Missense_Mutation_p.G836D			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	837					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.G837D(1)		central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						AGTAACTGTGGCCTCTACAAA	0.478													G|||	3	0.000599042	0.0	0.0	5008	,	,		19888	0.0		0.0	False		,,,				2504	0.0031				p.G836D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2507A	10						.						205.0	186.0	193.0					10																	13251099		2203	4300	6503	13291105	SO:0001583	missense	55388	exon19			AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"""MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"""			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.2510G>A	10.37:g.13251099G>A	ENSP00000418268:p.Gly837Asp	Somatic		Capture	Illumina HiSeq	Phase_I	13291105	NM_018518	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.940993	0.92526	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.32023	1.47;1.47;1.47	5.25	5.25	0.73442	Replication factor Mcm10 (1);	0.000000	0.85682	D	0.000000	T	0.59905	0.2228	M	0.79926	2.475	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.997;1.0;1.0	T	0.63079	-0.6717	10	0.52906	T	0.07	-10.2269	18.479	0.90804	0.0:0.0:1.0:0.0	.	836;836;837	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	D	836;837;837;836	ENSP00000367986:G836D;ENSP00000418268:G837D;ENSP00000367966:G836D	ENSP00000354945:G837D	G	+	2	0	MCM10	13291105	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.405000	0.97313	2.467000	0.83353	0.561000	0.74099	GGC		0.478	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
WDR11	55717	broad.mit.edu	37	10	122649444	122649444	+	Missense_Mutation	SNP	C	C	T	rs199547310		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:122649444C>T	ENST00000263461.6	+	18	2512	c.2266C>T	c.(2266-2268)Cgt>Tgt	p.R756C	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.R756C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						GAGGAAGATTCGTTTTGCTCC	0.408													C|||	1	0.000199681	0.0	0.0	5008	,	,		15839	0.001		0.0	False		,,,				2504	0.0				p.R756C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2266T	10						.						133.0	123.0	126.0					10																	122649444		2203	4300	6503	122639434	SO:0001583	missense	55717	exon18			AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.2266C>T	10.37:g.122649444C>T	ENSP00000263461:p.Arg756Cys	Somatic		Capture	Illumina HiSeq	Phase_I	122639434	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000263461.6	37	CCDS7619.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	c	32	5.163868	0.94727	.	.	ENSG00000120008	ENST00000263461	D	0.91577	-2.87	5.61	5.61	0.85477	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.93638	0.7968	L	0.42245	1.32	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;P	0.79784	0.993;0.993;0.982;0.899	D	0.92986	0.6410	10	0.48119	T	0.1	-17.3051	20.0018	0.97417	0.0:1.0:0.0:0.0	.	756;756;47;285	Q9BZH6;B2RCJ6;Q9NWV7;Q659C9	WDR11_HUMAN;.;.;.	C	756	ENSP00000263461:R756C	ENSP00000263461:R756C	R	+	1	0	WDR11	122639434	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.475000	0.66787	2.793000	0.96121	0.655000	0.94253	CGT		0.408	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
BNIP3	664	broad.mit.edu	37	10	133782052	133782052	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:133782052C>A	ENST00000368636.4	-	6	685	c.561G>T	c.(559-561)ctG>ctT	p.L187L		NM_004052.2	NP_004043.2	Q12983	BNIP3_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 3	187					apoptotic process (GO:0006915)|autophagic cell death (GO:0048102)|brown fat cell differentiation (GO:0050873)|cell death (GO:0008219)|cellular response to cobalt ion (GO:0071279)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|intrinsic apoptotic signaling pathway in response to hypoxia (GO:1990144)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrial protein catabolic process (GO:0035694)|negative regulation of apoptotic process (GO:0043066)|negative regulation of membrane potential (GO:0045837)|negative regulation of mitochondrial fusion (GO:0010637)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane permeability (GO:0046902)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTPase binding (GO:0051020)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.L187L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|skin(1)	7		all_cancers(35;4e-11)|all_epithelial(44;5.07e-08)|Ovarian(717;2.61e-05)|Lung NSC(174;0.00237)|all_lung(145;0.00354)|Breast(234;0.023)|all_neural(114;0.0299)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)		Epithelial(32;1.59e-12)|all cancers(32;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(35;2.57e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		TGGAGGTTGTCAGACGCCTTC	0.423																																					p.L187L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G561T	10						.						96.0	91.0	93.0					10																	133782052		2203	4300	6503	133632042	SO:0001819	synonymous_variant	664	exon6			U15174	CCDS7663.1	10q26.3	2003-11-05	2002-08-29		ENSG00000176171	ENSG00000176171			1084	protein-coding gene	gene with protein product		603293	"""BCL2/adenovirus E1B 19kD-interacting protein 3"""			7954800	Standard	NM_004052		Approved	Nip3	uc001lkv.1	Q12983	OTTHUMG00000019278	ENST00000368636.4:c.561G>T	10.37:g.133782052C>A		Somatic		Capture	Illumina HiSeq	Phase_I	133632042	NM_004052	O14620|Q96GP0	Silent	SNP	ENST00000368636.4	37	CCDS7663.1																																																																																				0.423	BNIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051039.1		
TUBB8	347688	broad.mit.edu	37	10	94002	94002	+	Silent	SNP	C	C	A	rs189074154	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:94002C>A	ENST00000309812.4	-	4	392	c.330G>T	c.(328-330)gcG>gcT	p.A110A	TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000447903.2_Silent_p.A38A|TUBB8_ENST00000332708.5_Missense_Mutation_p.R74L	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	110					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.A110A(1)		NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		CCATCAGCTCCGCGCCTTCGG	0.607																																					p.A38A	Pancreas(192;2041 3010 9013 18103)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G114T	10						.						70.0	60.0	64.0					10																	94002		2203	4300	6503	84002	SO:0001819	synonymous_variant	347688	exon4			AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"""Tubulins"""	20773	protein-coding gene	gene with protein product	"""class VIII beta-tubulin"""						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.330G>T	10.37:g.94002C>A		Somatic		Capture	Illumina HiSeq	Phase_I	84002	NM_001164154	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	C	4.006	-0.001630	0.07819	.	.	ENSG00000173876	ENST00000309812;ENST00000332708	.	.	.	.	.	.	.	.	.	.	.	T	0.55893	0.1949	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54721	-0.8251	4	0.87932	D	0	.	2.6649	0.05041	0.0:0.5123:0.0:0.4877	.	.	.	.	L	118;74	.	ENSP00000311042:R118L	R	-	2	0	RP11-631M21.2	84002	0.000000	0.05858	0.295000	0.24960	0.299000	0.27559	-4.711000	0.00195	0.119000	0.18210	0.121000	0.15741	CGG		0.607	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
LARP4B	23185	broad.mit.edu	37	10	888986	888986	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:888986A>G	ENST00000316157.3	-	6	572	c.532T>C	c.(532-534)Tat>Cat	p.Y178H		NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	178	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.				positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)	p.Y178H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						GATATAAGATACATGTCACTA	0.393																																					p.Y178H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T532C	10						.						141.0	127.0	132.0					10																	888986		2203	4300	6503	878986	SO:0001583	missense	23185	exon6			D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"""La ribonucleoprotein domain containing"""	28987	protein-coding gene	gene with protein product			"""KIAA0217"", ""La ribonucleoprotein domain family, member 5"""	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.532T>C	10.37:g.888986A>G	ENSP00000326128:p.Tyr178His	Somatic		Capture	Illumina HiSeq	Phase_I	878986	NM_015155	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Missense_Mutation	SNP	ENST00000316157.3	37	CCDS31131.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.694224	0.88735	.	.	ENSG00000107929	ENST00000316157	T	0.50548	0.74	5.37	5.37	0.77165	Winged helix-turn-helix transcription repressor DNA-binding (1);RNA-binding protein Lupus La (3);	0.117336	0.64402	D	0.000012	T	0.67249	0.2873	M	0.67569	2.06	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.70846	-0.4761	10	0.72032	D	0.01	-2.6839	15.3799	0.74648	1.0:0.0:0.0:0.0	.	178	Q92615	LAR4B_HUMAN	H	178	ENSP00000326128:Y178H	ENSP00000326128:Y178H	Y	-	1	0	LARP4B	878986	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.210000	0.95106	2.039000	0.60335	0.383000	0.25322	TAT		0.393	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155	
SFMBT2	57713	broad.mit.edu	37	10	7214511	7214511	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:7214511G>A	ENST00000361972.4	-	18	2187	c.2097C>T	c.(2095-2097)ttC>ttT	p.F699F	SFMBT2_ENST00000397167.1_Silent_p.F699F	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	699					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)	p.F699F(1)		NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						TCTTCTGCACGAAAATGGATT	0.607																																					p.F699F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2097T	10						.						48.0	49.0	49.0					10																	7214511		2203	4300	6503	7254517	SO:0001819	synonymous_variant	57713	exon18			AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"""Sterile alpha motif (SAM) domain containing"""	20256	protein-coding gene	gene with protein product		615392	"""Scm-related gene containing four mbt domains 2"""			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.2097C>T	10.37:g.7214511G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7254517	NM_001029880	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	37	CCDS31138.1																																																																																				0.607	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880	
ITIH5	80760	broad.mit.edu	37	10	7605141	7605141	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:7605141C>T	ENST00000256861.6	-	14	2812	c.2734G>A	c.(2734-2736)Gcc>Acc	p.A912T	ITIH5_ENST00000298441.6_Missense_Mutation_p.A698T|ITIH5_ENST00000397146.2_Intron|ITIH5_ENST00000446830.2_Missense_Mutation_p.A694T	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	912					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A912T(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						ATCAGTTTGGCGGCATTGTTC	0.522																																					p.A912T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2734A	10						.						193.0	155.0	168.0					10																	7605141		2203	4300	6503	7645147	SO:0001583	missense	80760	exon14					10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.2734G>A	10.37:g.7605141C>T	ENSP00000256861:p.Ala912Thr	Somatic		Capture	Illumina HiSeq	Phase_I	7645147	NM_030569	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	37		.	.	.	.	.	.	.	.	.	.	C	21.4	4.150437	0.78001	.	.	ENSG00000123243	ENST00000256861;ENST00000298441;ENST00000446830	T;T;T	0.01902	4.78;4.57;4.58	5.79	3.89	0.44902	.	0.501998	0.22734	N	0.056287	T	0.07818	0.0196	.	.	.	0.80722	D	1	D;D	0.71674	0.998;0.995	P;P	0.59056	0.801;0.851	T	0.20739	-1.0266	9	0.34782	T	0.22	-13.3339	12.9549	0.58421	0.1296:0.746:0.1244:0.0	.	912;698	Q86UX2;Q86UX2-3	ITIH5_HUMAN;.	T	912;698;694	ENSP00000256861:A912T;ENSP00000298441:A698T;ENSP00000387969:A694T	ENSP00000256861:A912T	A	-	1	0	ITIH5	7645147	1.000000	0.71417	0.059000	0.19551	0.800000	0.45204	4.508000	0.60441	0.736000	0.32559	0.650000	0.86243	GCC		0.522	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
ITIH2	3698	broad.mit.edu	37	10	7769667	7769667	+	Splice_Site	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:7769667C>T	ENST00000358415.4	+	11	1321	c.1155C>T	c.(1153-1155)ggC>ggT	p.G385G	ITIH2_ENST00000379587.4_Splice_Site_p.G374G	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	385	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.G385G(1)		NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						CTTCAACAGGCACAAACATCA	0.458																																					p.G385G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1155T	10						.						176.0	140.0	152.0					10																	7769667		2203	4300	6503	7809673	SO:0001630	splice_region_variant	3698	exon11			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.1154-1C>T	10.37:g.7769667C>T		Somatic		Capture	Illumina HiSeq	Phase_I	7809673	NM_002216	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																				0.458	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	Silent
FRMD4A	55691	broad.mit.edu	37	10	13702338	13702338	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:13702338G>A	ENST00000357447.2	-	20	2244	c.1876C>T	c.(1876-1878)Cgc>Tgc	p.R626C	FRMD4A_ENST00000358621.4_Missense_Mutation_p.R611C|FRMD4A_ENST00000378503.1_Missense_Mutation_p.R626C	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	626					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)		p.R626C(1)		breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						TGAGAGGAGCGCTTCTTGACC	0.507											OREG0020030	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R626C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1876T	10						.						91.0	81.0	85.0					10																	13702338		2203	4300	6503	13742344	SO:0001583	missense	55691	exon20			AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474			25491	protein-coding gene	gene with protein product			"""FERM domain containing 4"""	FRMD4		10718198	Standard	NM_018027		Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.1876C>T	10.37:g.13702338G>A	ENSP00000350032:p.Arg626Cys	Somatic	689	Capture	Illumina HiSeq	Phase_I	13742344	NM_018027	A7E2Y3|Q5T377	Missense_Mutation	SNP	ENST00000357447.2	37	CCDS7101.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.664221	0.88251	.	.	ENSG00000151474	ENST00000358621;ENST00000357447;ENST00000378503	D;D;D	0.84730	-1.89;-1.89;-1.89	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.86698	0.5995	N	0.22421	0.69	0.80722	D	1	D	0.89917	1.0	D	0.67548	0.952	D	0.87967	0.2734	10	0.87932	D	0	-16.5983	15.0593	0.71939	0.0:0.0:0.8581:0.1419	.	626	Q9P2Q2	FRM4A_HUMAN	C	611;626;626	ENSP00000351438:R611C;ENSP00000350032:R626C;ENSP00000367764:R626C	ENSP00000350032:R626C	R	-	1	0	FRMD4A	13742344	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	7.812000	0.86109	2.804000	0.96469	0.462000	0.41574	CGC		0.507	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027	
CUBN	8029	broad.mit.edu	37	10	16942802	16942802	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:16942802C>A	ENST00000377833.4	-	53	8297	c.8232G>T	c.(8230-8232)tgG>tgT	p.W2744C		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2744	CUB 20. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.W2744C(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGACAGAGTCCCAAGCACAAG	0.433																																					p.W2744C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8232T	10						.						93.0	80.0	85.0					10																	16942802		2203	4300	6503	16982808	SO:0001583	missense	8029	exon53			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.8232G>T	10.37:g.16942802C>A	ENSP00000367064:p.Trp2744Cys	Somatic		Capture	Illumina HiSeq	Phase_I	16982808	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.673407	0.47781	.	.	ENSG00000107611	ENST00000377833	T	0.17528	2.27	5.59	4.68	0.58851	CUB (5);	0.179096	0.27518	N	0.019006	T	0.32882	0.0844	L	0.45470	1.425	0.80722	D	1	D	0.76494	0.999	D	0.67382	0.951	T	0.02519	-1.1147	10	0.48119	T	0.1	.	13.8988	0.63790	0.0:0.9256:0.0:0.0744	.	2744	O60494	CUBN_HUMAN	C	2744	ENSP00000367064:W2744C	ENSP00000367064:W2744C	W	-	3	0	CUBN	16982808	1.000000	0.71417	1.000000	0.80357	0.296000	0.27459	4.457000	0.60088	1.463000	0.47967	0.655000	0.94253	TGG		0.433	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
TRDMT1	1787	broad.mit.edu	37	10	17195522	17195522	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:17195522T>C	ENST00000377799.3	-	10	1106	c.1059A>G	c.(1057-1059)ggA>ggG	p.G353G	TRDMT1_ENST00000358282.7_3'UTR|TRDMT1_ENST00000488990.1_Silent_p.G230G|TRDMT1_ENST00000412821.3_Silent_p.G329G|TRDMT1_ENST00000457442.2_Silent_p.G272G|TRDMT1_ENST00000452380.2_5'UTR|TRDMT1_ENST00000351358.4_Silent_p.G307G|TRDMT1_ENST00000377766.5_3'UTR	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	353	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)	p.G353G(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	CTGGAGGAAATCCAAGGAGAT	0.373																																					p.G353G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1059G	10						.						134.0	127.0	129.0					10																	17195522		2203	4300	6503	17235528	SO:0001819	synonymous_variant	1787	exon10			AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"""DNA (cytosine-5-)-methyltransferase 2"""	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.1059A>G	10.37:g.17195522T>C		Somatic		Capture	Illumina HiSeq	Phase_I	17235528	NM_004412	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Silent	SNP	ENST00000377799.3	37	CCDS7114.1																																																																																				0.373	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412	
SPAG6	9576	broad.mit.edu	37	10	22699985	22699985	+	Missense_Mutation	SNP	G	G	A	rs555602708	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:22699985G>A	ENST00000376624.3	+	10	1482	c.1340G>A	c.(1339-1341)cGa>cAa	p.R447Q	SPAG6_ENST00000376601.1_Missense_Mutation_p.R208Q|SPAG6_ENST00000490361.1_3'UTR|RP11-301N24.3_ENST00000422675.1_RNA|SPAG6_ENST00000376603.2_Missense_Mutation_p.R523Q|SPAG6_ENST00000538630.1_Missense_Mutation_p.R422Q|SPAG6_ENST00000313311.6_Intron	NM_001253855.1|NM_012443.3	NP_001240784.1|NP_036575.1	O75602	SPAG6_HUMAN	sperm associated antigen 6	447					cell projection organization (GO:0030030)|spermatid development (GO:0007286)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.R447Q(1)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|prostate(1)|skin(2)	27						AGCAAAGCTCGACGACTTTTT	0.368													G|||	3	0.000599042	0.0	0.0	5008	,	,		18884	0.0		0.0	False		,,,				2504	0.0031				p.R447Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1340A	10						.						73.0	71.0	72.0					10																	22699985		2203	4300	6503	22739991	SO:0001583	missense	9576	exon10			AF079363	CCDS7139.1, CCDS7140.1, CCDS58071.1, CCDS73072.1	10p12.31	2014-01-21			ENSG00000077327	ENSG00000077327		"""Armadillo repeat containing"""	11215	protein-coding gene	gene with protein product	"""axoneme central apparatus protein"""	605730				10493827	Standard	NM_012443		Approved	Repro-SA-1, pf16, CT141	uc001iri.3	O75602	OTTHUMG00000017808	ENST00000376624.3:c.1340G>A	10.37:g.22699985G>A	ENSP00000365811:p.Arg447Gln	Somatic		Capture	Illumina HiSeq	Phase_I	22739991	NM_012443	A8K1I8|B4DXZ4|Q5VUX5|Q5VUX6|Q5VUX7|Q6FI74|Q8NHQ6	Missense_Mutation	SNP	ENST00000376624.3	37	CCDS7139.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.704125	0.88924	.	.	ENSG00000077327	ENST00000376624;ENST00000376603;ENST00000376601;ENST00000538630	T;T;T;T	0.64618	-0.11;-0.11;0.67;-0.11	5.97	4.12	0.48240	Armadillo-like helical (1);Armadillo-type fold (1);	0.109676	0.64402	N	0.000007	T	0.76800	0.4038	M	0.84846	2.72	0.54753	D	0.999984	D;D;D	0.76494	0.996;0.999;0.996	P;P;P	0.62014	0.756;0.897;0.756	T	0.76176	-0.3055	10	0.30078	T	0.28	-14.7083	12.3026	0.54882	0.1357:0.0:0.8643:0.0	.	422;523;447	B4DXZ4;O75602-3;O75602	.;.;SPAG6_HUMAN	Q	447;523;208;422	ENSP00000365811:R447Q;ENSP00000365788:R523Q;ENSP00000365786:R208Q;ENSP00000441325:R422Q	ENSP00000365786:R208Q	R	+	2	0	SPAG6	22739991	1.000000	0.71417	0.644000	0.29465	0.846000	0.48090	5.536000	0.67180	0.866000	0.35629	0.591000	0.81541	CGA		0.368	SPAG6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047187.1		
KIAA1217	56243	broad.mit.edu	37	10	24810770	24810770	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:24810770G>A	ENST00000376454.3	+	12	2398	c.2368G>A	c.(2368-2370)Gtg>Atg	p.V790M	KIAA1217_ENST00000376451.2_Missense_Mutation_p.V473M|KIAA1217_ENST00000430453.2_Intron|KIAA1217_ENST00000376462.1_Missense_Mutation_p.V710M|KIAA1217_ENST00000458595.1_Missense_Mutation_p.V755M|KIAA1217_ENST00000307544.6_Missense_Mutation_p.V473M|KIAA1217_ENST00000396445.1_Missense_Mutation_p.V473M|KIAA1217_ENST00000376452.3_Missense_Mutation_p.V755M|KIAA1217_ENST00000396446.1_Missense_Mutation_p.V473M	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	790					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)		p.V790M(1)		breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						AGTGGAGGCCGTGCGGTTTCT	0.567																																					p.V790M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2368A	10						.						79.0	77.0	78.0					10																	24810770		2203	4300	6503	24850776	SO:0001583	missense	56243	exon12			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.2368G>A	10.37:g.24810770G>A	ENSP00000365637:p.Val790Met	Somatic		Capture	Illumina HiSeq	Phase_I	24850776	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	37	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.773057	0.90108	.	.	ENSG00000120549	ENST00000376462;ENST00000376456;ENST00000458595;ENST00000442879;ENST00000376454;ENST00000376452;ENST00000438429;ENST00000307544;ENST00000450158;ENST00000396445;ENST00000376451;ENST00000396446	T;T;T;T;T;T;T;T;T;T	0.59502	0.26;0.26;0.26;0.26;0.26;0.26;0.26;0.26;0.26;0.26	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.79429	0.4444	M	0.79693	2.465	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.999;0.999;0.999;1.0;1.0;0.999;0.998;0.999	T	0.80457	-0.1374	10	0.87932	D	0	.	20.3802	0.98930	0.0:0.0:1.0:0.0	.	755;755;473;473;473;473;790;790	Q5T5P2-7;A6NLF3;Q5T5P2-4;Q5T5P2-8;Q5T5P2-3;Q5T5P2-6;Q5T5P2;Q5T5P2-2	.;.;.;.;.;.;SKT_HUMAN;.	M	710;755;755;473;790;755;605;473;473;473;473;473	ENSP00000365645:V710M;ENSP00000365639:V755M;ENSP00000392625:V755M;ENSP00000365637:V790M;ENSP00000365635:V755M;ENSP00000404798:V605M;ENSP00000302343:V473M;ENSP00000379722:V473M;ENSP00000365634:V473M;ENSP00000379723:V473M	ENSP00000302343:V473M	V	+	1	0	KIAA1217	24850776	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.062000	0.89475	2.822000	0.97130	0.563000	0.77884	GTG		0.567	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
PDSS1	23590	broad.mit.edu	37	10	27035292	27035292	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:27035292G>A	ENST00000376215.5	+	12	1191	c.1138G>A	c.(1138-1140)Gcc>Acc	p.A380T	PDSS1_ENST00000376203.5_3'UTR|PDSS1_ENST00000470978.1_3'UTR	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1	380					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)	p.A380T(1)		autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						AACCTACCTCGCCCAGCAGTA	0.433																																					p.A380T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1138A	10						.						132.0	115.0	120.0					10																	27035292		2203	4300	6503	27075298	SO:0001583	missense	23590	exon12			AF118395	CCDS31168.1	10p12.2	2006-04-12	2006-02-14	2006-02-14	ENSG00000148459	ENSG00000148459			17759	protein-coding gene	gene with protein product	"""coenzyme Q1 homolog (yeast)"""	607429	"""trans-prenyltransferase"""	TPRT		10972372	Standard	NM_014317		Approved	TPT, COQ1	uc001isv.3	Q5T2R2	OTTHUMG00000017844	ENST00000376215.5:c.1138G>A	10.37:g.27035292G>A	ENSP00000365388:p.Ala380Thr	Somatic		Capture	Illumina HiSeq	Phase_I	27075298	NM_014317	Q53F75|Q6P473|Q86WQ8|Q9Y2W5	Missense_Mutation	SNP	ENST00000376215.5	37	CCDS31168.1	.	.	.	.	.	.	.	.	.	.	G	35	5.517365	0.96416	.	.	ENSG00000148459	ENST00000376215;ENST00000396343	T	0.66638	-0.22	5.54	5.54	0.83059	Terpenoid synthase (2);	0.000000	0.85682	D	0.000000	D	0.88005	0.6321	H	0.95224	3.64	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.91234	0.5016	10	0.87932	D	0	-28.4564	19.4716	0.94965	0.0:0.0:1.0:0.0	.	118;380	B4DJY1;Q5T2R2	.;DPS1_HUMAN	T	380;341	ENSP00000365388:A380T	ENSP00000365388:A380T	A	+	1	0	PDSS1	27075298	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.798000	0.85924	2.585000	0.87301	0.655000	0.94253	GCC		0.433	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047276.1		
ANKRD26	22852	broad.mit.edu	37	10	27328935	27328935	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:27328935C>T	ENST00000376087.4	-	21	2499	c.2334G>A	c.(2332-2334)gaG>gaA	p.E778E	ANKRD26_ENST00000436985.2_Silent_p.E794E|ANKRD26_ENST00000376070.3_Silent_p.E335E	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	777					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)		p.E778E(1)		breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						CTTTTTGATGCTCTAACTGTG	0.299																																					p.E778E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2334A	10						.						182.0	167.0	172.0					10																	27328935		1835	4073	5908	27368941	SO:0001819	synonymous_variant	22852	exon21			AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.2334G>A	10.37:g.27328935C>T		Somatic		Capture	Illumina HiSeq	Phase_I	27368941	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Silent	SNP	ENST00000376087.4	37	CCDS41499.1																																																																																				0.299	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
MASTL	84930	broad.mit.edu	37	10	27454086	27454086	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:27454086G>T	ENST00000375940.4	+	5	704	c.647G>T	c.(646-648)aGc>aTc	p.S216I	MASTL_ENST00000375946.4_Missense_Mutation_p.S216I|MASTL_ENST00000342386.6_Missense_Mutation_p.S216I			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	216	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)	p.S216I(1)		breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCGCTTATCAGCTCGTTGGGA	0.328																																					p.S216I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G647T	10						.						84.0	82.0	82.0					10																	27454086		2203	4300	6503	27494092	SO:0001583	missense	84930	exon5			BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.647G>T	10.37:g.27454086G>T	ENSP00000365107:p.Ser216Ile	Somatic		Capture	Illumina HiSeq	Phase_I	27494092	NM_001172303	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	37	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.881902	0.91740	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	D;D;D	0.82526	-1.62;-1.62;-1.62	5.78	5.78	0.91487	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91365	0.7276	M	0.74258	2.255	0.80722	D	1	D;D;D	0.76494	0.998;0.996;0.999	D;D;D	0.77004	0.977;0.949;0.989	D	0.91430	0.5165	10	0.72032	D	0.01	-13.4539	20.0812	0.97776	0.0:0.0:1.0:0.0	.	216;216;216	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	I	216	ENSP00000365113:S216I;ENSP00000343446:S216I;ENSP00000365107:S216I	ENSP00000343446:S216I	S	+	2	0	MASTL	27494092	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.859000	0.86982	2.744000	0.94065	0.586000	0.80456	AGC		0.328	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844	
RAB18	22931	broad.mit.edu	37	10	27815790	27815790	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:27815790A>G	ENST00000356940.6	+	3	260	c.158A>G	c.(157-159)gAt>gGt	p.D53G	RAB18_ENST00000465772.1_3'UTR|RAB18_ENST00000535776.1_Missense_Mutation_p.D53G|RAB18_ENST00000375802.3_Intron	NM_001256410.1|NM_001256415.1|NM_021252.4	NP_001243339.1|NP_001243344.1|NP_067075.1	Q9NP72	RAB18_HUMAN	RAB18, member RAS oncogene family	53					brain development (GO:0007420)|endoplasmic reticulum tubular network organization (GO:0071786)|eye development (GO:0001654)|GTP catabolic process (GO:0006184)|lipid particle organization (GO:0034389)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.D53G(1)		kidney(1)|large_intestine(1)|lung(1)	3						ATTTCAGTGGATGGAAATAAG	0.269																																					p.D53G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A158G	10						.						79.0	94.0	89.0					10																	27815790		2203	4296	6499	27855796	SO:0001583	missense	22931	exon3			AJ277145	CCDS7155.1, CCDS58073.1, CCDS73080.1, CCDS73081.1	10p12	2011-03-07			ENSG00000099246	ENSG00000099246		"""RAB, member RAS oncogene"""	14244	protein-coding gene	gene with protein product		602207				10648831	Standard	NM_021252		Approved		uc001itw.4	Q9NP72	OTTHUMG00000017861	ENST00000356940.6:c.158A>G	10.37:g.27815790A>G	ENSP00000349415:p.Asp53Gly	Somatic		Capture	Illumina HiSeq	Phase_I	27855796	NM_021252	B3KMC7|B7Z333|D3DRW1|Q53FX8|Q56UN9|Q6FIH1	Missense_Mutation	SNP	ENST00000356940.6	37	CCDS7155.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.102870	0.37145	.	.	ENSG00000099246	ENST00000356940;ENST00000535776	T;T	0.80909	-0.17;-1.43	5.71	5.71	0.89125	Small GTP-binding protein domain (1);	.	.	.	.	T	0.73830	0.3637	L	0.35793	1.09	0.42933	D	0.994329	B;B;B;B	0.33477	0.413;0.028;0.051;0.005	B;B;B;B	0.32393	0.145;0.041;0.139;0.026	T	0.75448	-0.3314	9	0.56958	D	0.05	.	15.1665	0.72833	1.0:0.0:0.0:0.0	.	53;53;53;53	B7Z333;B7Z4P9;Q56UN9;Q9NP72	.;.;.;RAB18_HUMAN	G	53	ENSP00000349415:D53G;ENSP00000439321:D53G	ENSP00000349415:D53G	D	+	2	0	RAB18	27855796	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.076000	0.94009	2.165000	0.68154	0.533000	0.62120	GAT		0.269	RAB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047326.2	NM_021252	
MKX	283078	broad.mit.edu	37	10	28024164	28024164	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:28024164T>A	ENST00000375790.5	-	4	920	c.488A>T	c.(487-489)gAc>gTc	p.D163V	MKX_ENST00000419761.1_Missense_Mutation_p.D163V			Q8IYA7	MKX_HUMAN	mohawk homeobox	163					collagen fibril organization (GO:0030199)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|positive regulation of collagen biosynthetic process (GO:0032967)|tendon cell differentiation (GO:0035990)|tendon sheath development (GO:0002932)	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 negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.D163V(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16						AGAACATGAGTCATCACTGCT	0.363																																					p.D163V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A488T	10						.						115.0	121.0	119.0					10																	28024164		2203	4300	6503	28064170	SO:0001583	missense	283078	exon4			BC036207	CCDS7156.1	10p12.1	2011-06-20	2006-03-31	2006-03-31	ENSG00000150051	ENSG00000150051		"""Homeoboxes / TALE class"""	23729	protein-coding gene	gene with protein product		601332	"""chromosome 10 open reading frame 48"", ""iroquois homeobox protein-like 1"""	C10orf48, IRXL1		16408284	Standard	NM_173576		Approved	MGC39616	uc001itx.4	Q8IYA7	OTTHUMG00000017862	ENST00000375790.5:c.488A>T	10.37:g.28024164T>A	ENSP00000364946:p.Asp163Val	Somatic		Capture	Illumina HiSeq	Phase_I	28064170	NM_173576	B3KWM5	Missense_Mutation	SNP	ENST00000375790.5	37	CCDS7156.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.373315	0.61624	.	.	ENSG00000150051	ENST00000375790;ENST00000419761	T;T	0.74842	-0.88;-0.88	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.84955	0.5587	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.86575	0.1850	10	0.87932	D	0	-39.9031	15.9966	0.80256	0.0:0.0:0.0:1.0	.	163	Q8IYA7	MKX_HUMAN	V	163	ENSP00000364946:D163V;ENSP00000400896:D163V	ENSP00000364946:D163V	D	-	2	0	MKX	28064170	1.000000	0.71417	0.828000	0.32881	0.749000	0.42624	6.163000	0.71880	2.179000	0.69175	0.460000	0.39030	GAC		0.363	MKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047332.3	NM_173576	
ARMC4	55130	broad.mit.edu	37	10	28149710	28149710	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:28149710A>G	ENST00000305242.5	-	19	2957	c.2865T>C	c.(2863-2865)aaT>aaC	p.N955N	ARMC4_ENST00000537576.1_Silent_p.N647N|ARMC4_ENST00000545014.1_Silent_p.N480N	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	955					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.N955N(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						AGGCCACTCTATTCCTGCCCC	0.468																																					p.N955N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2865C	10						.						178.0	144.0	155.0					10																	28149710		2203	4300	6503	28189716	SO:0001819	synonymous_variant	55130	exon19			AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.2865T>C	10.37:g.28149710A>G		Somatic		Capture	Illumina HiSeq	Phase_I	28189716	NM_018076	A8K906|B7Z7I1|Q9H0C0	Silent	SNP	ENST00000305242.5	37	CCDS7157.1																																																																																				0.468	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	
LYZL1	84569	broad.mit.edu	37	10	29581596	29581596	+	Silent	SNP	C	C	T	rs192018509		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:29581596C>T	ENST00000375500.3	+	3	483	c.426C>T	c.(424-426)gtC>gtT	p.V142V		NM_032517.4	NP_115906.3	Q6UWQ5	LYZL1_HUMAN	lysozyme-like 1	96					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)	p.V142V(1)		central_nervous_system(1)|cervix(2)|large_intestine(2)|lung(5)|skin(1)	11		Breast(68;0.203)				ACTGCCATGTCGCCTGCTCAG	0.537													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20321	0.0		0.0	False		,,,				2504	0.0				p.V142V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C426T	10						.						162.0	137.0	146.0					10																	29581596		2203	4300	6503	29621602	SO:0001819	synonymous_variant	84569	exon3				CCDS31174.1	10p12.1	2004-08-02			ENSG00000120563	ENSG00000120563	3.2.1.1		30502	protein-coding gene	gene with protein product						12477932	Standard	XM_005252627		Approved	MGC33408, LYC2	uc001iul.3	Q6UWQ5	OTTHUMG00000017880	ENST00000375500.3:c.426C>T	10.37:g.29581596C>T		Somatic		Capture	Illumina HiSeq	Phase_I	29621602	NM_032517	Q5T921|Q8WW16	Silent	SNP	ENST00000375500.3	37	CCDS31174.1																																																																																				0.537	LYZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047381.1	NM_032517	
SVIL	6840	broad.mit.edu	37	10	29822201	29822201	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:29822201A>G	ENST00000355867.4	-	8	1847	c.1095T>C	c.(1093-1095)cgT>cgC	p.R365R	SVIL_ENST00000375398.2_Silent_p.R365R|SVIL_ENST00000375400.3_Intron	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	365					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.R365R(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GGACATAGCCACGGATTGGCT	0.567																																					p.R365R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1095C	10						.						89.0	75.0	79.0					10																	29822201		2203	4300	6503	29862207	SO:0001819	synonymous_variant	6840	exon8			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.1095T>C	10.37:g.29822201A>G		Somatic		Capture	Illumina HiSeq	Phase_I	29862207	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																				0.567	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
ZEB1	6935	broad.mit.edu	37	10	31815671	31815671	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:31815671C>T	ENST00000320985.10	+	9	2964	c.2854C>T	c.(2854-2856)Cga>Tga	p.R952*	ZEB1_ENST00000361642.5_Nonsense_Mutation_p.R953*|ZEB1_ENST00000542815.3_Nonsense_Mutation_p.R885*|ZEB1_ENST00000560721.2_Nonsense_Mutation_p.R932*|ZEB1_ENST00000446923.2_Nonsense_Mutation_p.R936*			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	952					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R952*(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				TGAACACATGCGATTACATTC	0.363																																					p.R932X	Ovarian(40;423 959 14296 36701 49589)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2794T	10						.						93.0	85.0	88.0					10																	31815671		2203	4300	6503	31855677	SO:0001587	stop_gained	6935	exon8			AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	11642	protein-coding gene	gene with protein product		189909	"""transcription factor 8 (represses interleukin 2 expression)"", ""posterior polymorphous corneal dystrophy 3"""	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.2854C>T	10.37:g.31815671C>T	ENSP00000319248:p.Arg952*	Somatic		Capture	Illumina HiSeq	Phase_I	31855677	NM_001174093	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Nonsense_Mutation	SNP	ENST00000320985.10	37	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	C	38	7.267156	0.98175	.	.	ENSG00000148516	ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000543514;ENST00000446923	.	.	.	5.24	4.3	0.51218	.	0.000000	0.50627	D	0.000119	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.8987	14.7696	0.69665	0.1457:0.8543:0.0:0.0	.	.	.	.	X	734;952;953;947;885;952;932;843;936	.	ENSP00000319248:R952X	R	+	1	2	ZEB1	31855677	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	3.872000	0.56085	1.154000	0.42482	0.585000	0.79938	CGA		0.363	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751	
ITGB1	3688	broad.mit.edu	37	10	33221461	33221461	+	Silent	SNP	A	A	G	rs200000349		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:33221461A>G	ENST00000396033.2	-	3	270	c.135T>C	c.(133-135)tgT>tgC	p.C45C	ITGB1_ENST00000423113.1_Silent_p.C45C|ITGB1_ENST00000302278.3_Silent_p.C45C|ITGB1_ENST00000484088.1_5'UTR|ITGB1_ENST00000374956.4_Silent_p.C45C	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	45					axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)	p.C45C(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	TGCACCACCCACAATTTGGCC	0.383													A|||	1	0.000199681	0.0	0.0014	5008	,	,		16769	0.0		0.0	False		,,,				2504	0.0				p.C45C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T135C	10						.						245.0	204.0	218.0					10																	33221461		2203	4300	6503	33261467	SO:0001819	synonymous_variant	3688	exon3			BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"""CD molecules"", ""Integrins"""	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.135T>C	10.37:g.33221461A>G		Somatic		Capture	Illumina HiSeq	Phase_I	33261467	NM_133376	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Silent	SNP	ENST00000396033.2	37	CCDS7174.1																																																																																				0.383	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211	
RET	5979	broad.mit.edu	37	10	43604533	43604533	+	Missense_Mutation	SNP	C	C	T	rs546866208	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:43604533C>T	ENST00000355710.3	+	6	1350	c.1118C>T	c.(1117-1119)gCg>gTg	p.A373V	RET_ENST00000340058.5_Missense_Mutation_p.A373V	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	373					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.A373V(1)	CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	ATGCAGCTGGCGGTGCTGGTC	0.622		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				C|||	4	0.000798722	0.0	0.0	5008	,	,		20426	0.0		0.0	False		,,,				2504	0.0041				p.A373V	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	RET,ovary,NS,Substitution - coding silent,-1 	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1118T	10	GRCh37	CM065437	RET	M		.						78.0	70.0	73.0					10																	43604533		2203	4300	6503	42924539	SO:0001583	missense	5979	exon6	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.1118C>T	10.37:g.43604533C>T	ENSP00000347942:p.Ala373Val	Somatic		Capture	Illumina HiSeq	Phase_I	42924539	NM_020975	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	.	.	.	.	.	.	.	.	.	.	C	7.952	0.745142	0.15710	.	.	ENSG00000165731	ENST00000355710;ENST00000340058;ENST00000535749	T;T	0.77877	-1.02;-1.13	5.17	0.288	0.15719	.	0.551162	0.20663	N	0.087995	T	0.63570	0.2522	L	0.51422	1.61	0.19300	N	0.99997	B;B;B	0.15141	0.007;0.007;0.012	B;B;B	0.11329	0.001;0.002;0.006	T	0.43475	-0.9389	10	0.25106	T	0.35	.	2.9989	0.06007	0.4385:0.3406:0.1291:0.0917	.	119;373;373	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	V	373	ENSP00000347942:A373V;ENSP00000344798:A373V	ENSP00000344798:A373V	A	+	2	0	RET	42924539	0.706000	0.27856	0.116000	0.21606	0.308000	0.27856	1.284000	0.33249	0.510000	0.28216	0.561000	0.74099	GCG		0.622	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
GDF2	2658	broad.mit.edu	37	10	48413584	48413584	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:48413584G>A	ENST00000249598.1	-	2	1443	c.1284C>T	c.(1282-1284)tgC>tgT	p.C428C		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	428					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.C428C(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						GATACTACCTGCACCCACACT	0.597																																					p.C428C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1284T	10						.						42.0	38.0	40.0					10																	48413584		2202	4300	6502	48033590	SO:0001819	synonymous_variant	2658	exon2			AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"""Endogenous ligands"""	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.1284C>T	10.37:g.48413584G>A		Somatic		Capture	Illumina HiSeq	Phase_I	48033590	NM_016204	Q5VSQ9|Q9Y571	Silent	SNP	ENST00000249598.1	37	CCDS7219.1																																																																																				0.597	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204	
ANK3	288	broad.mit.edu	37	10	61831943	61831943	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:61831943G>A	ENST00000280772.2	-	37	8887	c.8696C>T	c.(8695-8697)tCt>tTt	p.S2899F	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2899					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.S2899F(1)		NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CTCAGTCACAGACATAAATTC	0.353																																					p.S2899F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C8696T	10						.						62.0	63.0	63.0					10																	61831943		2201	4299	6500	61501949	SO:0001583	missense	288	exon37			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.8696C>T	10.37:g.61831943G>A	ENSP00000280772:p.Ser2899Phe	Somatic		Capture	Illumina HiSeq	Phase_I	61501949	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	15.96	2.985658	0.53934	.	.	ENSG00000151150	ENST00000280772	T	0.63744	-0.06	5.73	3.83	0.44106	.	0.368413	0.19877	N	0.104064	T	0.44222	0.1283	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31641	-0.9936	10	0.66056	D	0.02	.	10.3372	0.43856	0.0701:0.0:0.7905:0.1395	.	2899	Q12955	ANK3_HUMAN	F	2899	ENSP00000280772:S2899F	ENSP00000280772:S2899F	S	-	2	0	ANK3	61501949	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	3.124000	0.50461	0.728000	0.32382	0.555000	0.69702	TCT		0.353	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
ANK3	288	broad.mit.edu	37	10	62039361	62039361	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:62039361C>A	ENST00000280772.2	-	2	342	c.151G>T	c.(151-153)Gct>Tct	p.A51S	ANK3_ENST00000503366.1_Missense_Mutation_p.A34S|ANK3_ENST00000373827.2_Missense_Mutation_p.A45S	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	51					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.A51S(1)		NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						AGGTGTCCAGCTCGAGCTGCT	0.328																																					p.A51S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G151T	10						.						113.0	124.0	120.0					10																	62039361		2203	4300	6503	61709367	SO:0001583	missense	288	exon2			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.151G>T	10.37:g.62039361C>A	ENSP00000280772:p.Ala51Ser	Somatic		Capture	Illumina HiSeq	Phase_I	61709367	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.071204	0.36566	.	.	ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000503366;ENST00000395299;ENST00000373817;ENST00000503925	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.22	5.22	0.72569	Ankyrin repeat-containing domain (3);	0.000000	0.41938	D	0.000796	T	0.45498	0.1345	N	0.02802	-0.49	0.80722	D	1	B;B;P	0.36753	0.042;0.303;0.568	B;B;B	0.43950	0.015;0.437;0.166	T	0.54200	-0.8329	10	0.45353	T	0.12	.	13.8846	0.63702	0.1522:0.8478:0.0:0.0	.	34;45;51	E9PE32;Q5CZH9;Q12955	.;.;ANK3_HUMAN	S	51;45;34;13;34;25	ENSP00000280772:A51S;ENSP00000362933:A45S;ENSP00000425236:A34S;ENSP00000426011:A25S	ENSP00000280772:A51S	A	-	1	0	ANK3	61709367	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.482000	0.60257	2.713000	0.92767	0.655000	0.94253	GCT		0.328	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
EGR2	1959	broad.mit.edu	37	10	64573268	64573268	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:64573268C>T	ENST00000242480.3	-	2	1455	c.1130G>A	c.(1129-1131)cGc>cAc	p.R377H	EGR2_ENST00000411732.1_Missense_Mutation_p.R327H|EGR2_ENST00000493899.2_5'Flank|EGR2_ENST00000439032.1_Missense_Mutation_p.R377H	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	377					brain development (GO:0007420)|brain segmentation (GO:0035284)|cell death (GO:0008219)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|facial nerve structural organization (GO:0021612)|fat cell differentiation (GO:0045444)|learning or memory (GO:0007611)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein sumoylation (GO:0016925)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ossification (GO:0030278)|response to insulin (GO:0032868)|rhombomere 3 formation (GO:0021660)|rhombomere 5 formation (GO:0021666)|rhythmic behavior (GO:0007622)|Schwann cell differentiation (GO:0014037)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.R377H(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	36	Prostate(12;0.0297)|all_hematologic(501;0.228)					GCTGAAGTTGCGCATGCAGAT	0.612																																					p.R377H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1130A	10						.						131.0	123.0	126.0					10																	64573268		2203	4300	6503	64243274	SO:0001583	missense	1959	exon2			BC035625	CCDS7267.1, CCDS44409.1	10q21.1	2014-09-17	2009-04-23		ENSG00000122877	ENSG00000122877		"""Zinc fingers, C2H2-type"""	3239	protein-coding gene	gene with protein product	"""Krox-20 homolog, Drosophila"""	129010	"""early growth response 2 (Krox-20 homolog, Drosophila)"""	KROX20			Standard	NM_000399		Approved		uc001jmi.3	P11161	OTTHUMG00000018308	ENST00000242480.3:c.1130G>A	10.37:g.64573268C>T	ENSP00000242480:p.Arg377His	Somatic		Capture	Illumina HiSeq	Phase_I	64243274	NM_000399	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Missense_Mutation	SNP	ENST00000242480.3	37	CCDS7267.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.396879	0.83120	.	.	ENSG00000122877	ENST00000242480;ENST00000439032;ENST00000411732	T;T;T	0.03920	3.76;3.76;3.76	4.84	4.84	0.62591	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.18923	0.0454	L	0.58583	1.82	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.00161	-1.1972	10	0.87932	D	0	-18.1132	16.8725	0.86043	0.0:1.0:0.0:0.0	.	327;377	P11161-2;P11161	.;EGR2_HUMAN	H	377;377;327	ENSP00000242480:R377H;ENSP00000402040:R377H;ENSP00000387634:R327H	ENSP00000242480:R377H	R	-	2	0	EGR2	64243274	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.609000	0.82925	2.495000	0.84180	0.655000	0.94253	CGC		0.612	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399	
JMJD1C	221037	broad.mit.edu	37	10	64953121	64953121	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:64953121A>G	ENST00000399262.2	-	15	6064	c.5846T>C	c.(5845-5847)aTg>aCg	p.M1949T	JMJD1C_ENST00000402544.1_Missense_Mutation_p.M1730T|JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000542921.1_Missense_Mutation_p.M1767T	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1949					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)	p.M1949T(1)|p.M1730T(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					TACACCATTCATTGTAGGAAA	0.303																																					p.M1730T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T5189C	10						.						109.0	98.0	102.0					10																	64953121		1796	4061	5857	64623127	SO:0001583	missense	221037	exon12			L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.5846T>C	10.37:g.64953121A>G	ENSP00000382204:p.Met1949Thr	Somatic		Capture	Illumina HiSeq	Phase_I	64623127	NM_004241	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.293|5.293	0.239375|0.239375	0.10023|0.10023	.|.	.|.	ENSG00000171988|ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921|ENST00000327520	T;T;T|.	0.50277|.	1.15;0.75;1.15|.	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	0.093046|.	0.85682|.	D|.	0.000000|.	T|.	0.47002|.	0.1422|.	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	D|D	1|1	B;B;B|.	0.06786|.	0.0;0.001;0.0|.	B;B;B|.	0.06405|.	0.001;0.002;0.001|.	T|.	0.44605|.	-0.9317|.	10|.	0.02654|.	T|.	1|.	-3.7541|-3.7541	15.5814|15.5814	0.76445|0.76445	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1490;1949;1767|.	A6PW35;Q15652;A0T124|.	.;JHD2C_HUMAN;.|.	T|R	1949;1730;1767|496	ENSP00000382204:M1949T;ENSP00000384990:M1730T;ENSP00000444682:M1767T|.	ENSP00000382204:M1949T|.	M|X	-|-	2|1	0|0	JMJD1C|JMJD1C	64623127|64623127	0.999000|0.999000	0.42202|0.42202	0.972000|0.972000	0.41901|0.41901	0.996000|0.996000	0.88848|0.88848	4.653000|4.653000	0.61462|0.61462	2.161000|2.161000	0.67846|0.67846	0.533000|0.533000	0.62120|0.62120	ATG|TGA		0.303	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
SIRT1	23411	broad.mit.edu	37	10	69672723	69672723	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:69672723C>T	ENST00000212015.6	+	8	1903	c.1850C>T	c.(1849-1851)gCt>gTt	p.A617V	SIRT1_ENST00000403579.1_Missense_Mutation_p.A314V|SIRT1_ENST00000432464.1_Missense_Mutation_p.A322V|SIRT1_ENST00000406900.1_Missense_Mutation_p.A314V	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	617					angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.A617V(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						ACTTCAGTGGCTGGAACAGTG	0.413																																					p.A322V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C965T	10						.						64.0	71.0	68.0					10																	69672723		2202	4300	6502	69342729	SO:0001583	missense	23411	exon7			AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1"", ""sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"""			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	ENST00000212015.6:c.1850C>T	10.37:g.69672723C>T	ENSP00000212015:p.Ala617Val	Somatic		Capture	Illumina HiSeq	Phase_I	69342729	NM_001142498	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Missense_Mutation	SNP	ENST00000212015.6	37	CCDS7273.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496107	0.44352	.	.	ENSG00000096717	ENST00000212015;ENST00000432464;ENST00000406900;ENST00000403579	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	6.03	3.87	0.44632	.	0.386363	0.26528	N	0.023875	T	0.30103	0.0754	L	0.29908	0.895	0.30603	N	0.760265	B;B	0.12013	0.001;0.005	B;B	0.08055	0.003;0.001	T	0.14090	-1.0485	10	0.28530	T	0.3	-7.112	5.2912	0.15727	0.1604:0.6223:0.0:0.2173	.	314;617	B0QZ35;Q96EB6	.;SIRT1_HUMAN	V	617;322;314;314	ENSP00000212015:A617V;ENSP00000409208:A322V;ENSP00000384508:A314V;ENSP00000384063:A314V	ENSP00000212015:A617V	A	+	2	0	SIRT1	69342729	0.994000	0.37717	1.000000	0.80357	0.974000	0.67602	1.418000	0.34782	1.556000	0.49512	0.655000	0.94253	GCT		0.413	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1		
MYPN	84665	broad.mit.edu	37	10	69957213	69957213	+	Missense_Mutation	SNP	G	G	A	rs71584501		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:69957213G>A	ENST00000358913.5	+	16	3751	c.3263G>A	c.(3262-3264)cGc>cAc	p.R1088H	MYPN_ENST00000354393.2_Missense_Mutation_p.R813H|MYPN_ENST00000540630.1_Missense_Mutation_p.R1088H	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	1088	Ig-like 4.|Interaction with ACTN.		R -> H (in CMD1KK; dbSNP:rs71584501). {ECO:0000269|PubMed:18006477}.		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.R1088H(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						CATGAGGGGCGCCTCTGTCGG	0.468																																					p.R1088H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3263A	10	GRCh37	CM086686	MYPN	M	rs71584501	.						102.0	105.0	104.0					10																	69957213		2203	4300	6503	69627219	SO:0001583	missense	84665	exon16			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.3263G>A	10.37:g.69957213G>A	ENSP00000351790:p.Arg1088His	Somatic		Capture	Illumina HiSeq	Phase_I	69627219	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.622085	0.87460	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.72282	-0.64;-0.64;-0.64	5.16	5.16	0.70880	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.158697	0.39687	N	0.001288	T	0.77785	0.4182	L	0.35487	1.065	0.46954	D	0.999268	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.996;0.995;0.997	T	0.76085	-0.3088	9	.	.	.	.	18.6276	0.91347	0.0:0.0:1.0:0.0	.	1088;813;1088	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	H	813;813;1088;1088	ENSP00000346369:R813H;ENSP00000351790:R1088H;ENSP00000441668:R1088H	.	R	+	2	0	MYPN	69627219	0.997000	0.39634	0.998000	0.56505	0.997000	0.91878	5.715000	0.68430	2.403000	0.81681	0.655000	0.94253	CGC		0.468	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
UNC5B	219699	broad.mit.edu	37	10	73044511	73044511	+	Silent	SNP	G	G	A	rs374918405	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:73044511G>A	ENST00000335350.6	+	3	755	c.339G>A	c.(337-339)tcG>tcA	p.S113S	UNC5B_ENST00000373192.4_Silent_p.S113S	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	113	Ig-like.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)		p.S113S(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						TCGAGGTGTCGCGGCAGCAGG	0.667													G|||	6	0.00119808	0.0	0.0	5008	,	,		14631	0.006		0.0	False		,,,				2504	0.0				p.S113S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G339A	10						.	G		0,4406		0,0,2203	82.0	75.0	77.0		339	-9.5	0.0	10		77	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	UNC5B	NM_170744.4		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		113/946	73044511	2,13004	2203	4300	6503	72714517	SO:0001819	synonymous_variant	219699	exon3			AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"""Immunoglobulin superfamily / I-set domain containing"""	12568	protein-coding gene	gene with protein product		607870	"""unc5 (C.elegans homolog) b"""				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.339G>A	10.37:g.73044511G>A		Somatic		Capture	Illumina HiSeq	Phase_I	72714517	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Silent	SNP	ENST00000335350.6	37	CCDS7309.1																																																																																				0.667	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
MRPS16	51021	broad.mit.edu	37	10	75010658	75010658	+	Silent	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:75010658A>T	ENST00000372945.3	-	3	576	c.366T>A	c.(364-366)tcT>tcA	p.S122S	MRPS16_ENST00000479005.1_5'UTR|MRPS16_ENST00000372940.3_Intron|MRPS16_ENST00000416782.2_Intron|RP11-152N13.5_ENST00000457758.1_RNA|DNAJC9-AS1_ENST00000440197.2_RNA|RP11-152N13.5_ENST00000457147.1_RNA|RP11-152N13.5_ENST00000394864.2_RNA|DNAJC9_ENST00000372950.4_5'Flank|TTC18_ENST00000493787.1_5'Flank|DNAJC9-AS1_ENST00000513954.1_RNA	NM_016065.3	NP_057149.1	Q9Y3D3	RT16_HUMAN	mitochondrial ribosomal protein S16	122					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	structural constituent of ribosome (GO:0003735)	p.S122S(1)		large_intestine(2)|lung(2)	4	Prostate(51;0.0119)					CTGTTTTCTGAGAAGCTAACA	0.448																																					p.S122S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T366A	10						.						195.0	175.0	182.0					10																	75010658		2203	4300	6503	74680664	SO:0001819	synonymous_variant	51021	exon3			AB051351	CCDS7323.1	10q22.1	2012-09-13			ENSG00000182180	ENSG00000182180		"""Mitochondrial ribosomal proteins / small subunits"""	14048	protein-coding gene	gene with protein product		609204				10810093	Standard	NM_016065		Approved	CGI-132	uc001jts.1	Q9Y3D3	OTTHUMG00000018454	ENST00000372945.3:c.366T>A	10.37:g.75010658A>T		Somatic		Capture	Illumina HiSeq	Phase_I	74680664	NM_016065	B4E032|Q96Q60	Silent	SNP	ENST00000372945.3	37	CCDS7323.1																																																																																				0.448	MRPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048616.1		
USP54	159195	broad.mit.edu	37	10	75276685	75276685	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:75276685C>T	ENST00000339859.4	-	19	3599	c.3499G>A	c.(3499-3501)Gat>Aat	p.D1167N	RP11-137L10.6_ENST00000593790.1_RNA|USP54_ENST00000428547.1_Missense_Mutation_p.D1017N|USP54_ENST00000408019.1_Missense_Mutation_p.D1167N|RP11-137L10.6_ENST00000597958.1_RNA|USP54_ENST00000394811.2_Missense_Mutation_p.D255N|RP11-137L10.6_ENST00000600206.1_RNA|RP11-137L10.6_ENST00000595069.1_RNA|USP54_ENST00000422491.2_Missense_Mutation_p.D349N|USP54_ENST00000497106.1_5'UTR			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	1167					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)	p.D1167N(1)|p.D255N(1)		breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					GGCTTAGAATCAGAAGGGGAA	0.502																																					p.D1167N	Colon(195;880 2046 8854 25025 38456)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3499A	10						.						126.0	128.0	127.0					10																	75276685		2203	4300	6503	74946691	SO:0001583	missense	159195	exon18			AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"""Ubiquitin-specific peptidases"""	23513	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 29"", ""ubiquitin specific protease 54"""	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.3499G>A	10.37:g.75276685C>T	ENSP00000345216:p.Asp1167Asn	Somatic		Capture	Illumina HiSeq	Phase_I	74946691	NM_152586	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Missense_Mutation	SNP	ENST00000339859.4	37	CCDS7329.2	.	.	.	.	.	.	.	.	.	.	C	10.64	1.407544	0.25378	.	.	ENSG00000166348	ENST00000339859;ENST00000408019;ENST00000428547;ENST00000394811;ENST00000422491	T;T;T;T;T	0.33865	1.61;1.61;1.58;1.39;1.44	5.83	3.98	0.46160	.	.	.	.	.	T	0.27313	0.0670	L	0.32530	0.975	0.80722	D	1	B;B	0.27140	0.169;0.009	B;B	0.25884	0.064;0.006	T	0.06285	-1.0835	9	0.34782	T	0.22	-1.8237	11.8017	0.52130	0.0:0.8599:0.0:0.1401	.	349;1167	E7EW90;Q70EL1	.;UBP54_HUMAN	N	1167;1167;1017;255;349	ENSP00000345216:D1167N;ENSP00000386080:D1167N;ENSP00000408714:D1017N;ENSP00000378290:D255N;ENSP00000407368:D349N	ENSP00000345216:D1167N	D	-	1	0	USP54	74946691	0.882000	0.30256	0.989000	0.46669	0.564000	0.35744	1.432000	0.34936	1.473000	0.48159	0.655000	0.94253	GAT		0.502	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586	
ZSWIM8	23053	broad.mit.edu	37	10	75557175	75557175	+	Silent	SNP	G	G	A	rs548106870		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:75557175G>A	ENST00000605216.1	+	18	3676	c.3459G>A	c.(3457-3459)tcG>tcA	p.S1153S	ZSWIM8_ENST00000398706.2_Silent_p.S1158S|RP11-574K11.31_ENST00000603027.1_3'UTR|ZSWIM8_ENST00000604729.1_Silent_p.S1158S|ZSWIM8_ENST00000603114.1_Silent_p.S1120S|ZSWIM8-AS1_ENST00000456638.2_RNA|ZSWIM8_ENST00000604524.1_Silent_p.S1153S	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	1153	Ser-rich.						zinc ion binding (GO:0008270)	p.S1153S(1)|p.S1158S(1)									AAACAACATCGGATAGTTCCC	0.567																																					p.S1158S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G3474A	10						.						72.0	74.0	73.0					10																	75557175		2006	4177	6183	75227181	SO:0001819	synonymous_variant	23053	exon18			BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"""Zinc fingers, SWIM-type"""	23528	protein-coding gene	gene with protein product			"""KIAA0913"""	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.3459G>A	10.37:g.75557175G>A		Somatic		Capture	Illumina HiSeq	Phase_I	75227181	NM_015037	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Silent	SNP	ENST00000605216.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.15|10.15	1.271724|1.271724	0.23221|0.23221	.|.	.|.	ENSG00000214655|ENSG00000214655	ENST00000433366|ENST00000412198	.|.	.|.	.|.	4.86|4.86	2.01|2.01	0.26516|0.26516	.|.	.|.	.|.	.|.	.|.	T|T	0.46386|0.46386	0.1390|0.1390	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.25433|0.25433	-1.0132|-1.0132	4|4	.|.	.|.	.|.	-3.067|-3.067	4.0451|4.0451	0.09770|0.09770	0.4126:0.0:0.4199:0.1674|0.4126:0.0:0.4199:0.1674	.|.	.|.	.|.	.|.	R|Q	869|428	.|.	.|.	G|R	+|+	1|2	0|0	KIAA0913|KIAA0913	75227181|75227181	0.029000|0.029000	0.19370|0.19370	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	-1.028000|-1.028000	0.03589|0.03589	0.268000|0.268000	0.21939|0.21939	-0.208000|-0.208000	0.12717|0.12717	GGA|CGG		0.567	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487	
C10orf55	414236	broad.mit.edu	37	10	75675129	75675129	+	Intron	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:75675129A>G	ENST00000409178.1	-	2	268				PLAU_ENST00000372764.3_Missense_Mutation_p.D364G|C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000372762.4_Missense_Mutation_p.D328G|PLAU_ENST00000446342.1_Missense_Mutation_p.D347G	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55									p.D364G(1)		endometrium(1)	1	Prostate(51;0.0112)					TGTGCTGCTGACCCACAGTGG	0.537																																					p.D364G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1091G	10						.						79.0	76.0	77.0					10																	75675129		2203	4300	6503	75345135	SO:0001627	intron_variant	5328	exon10				CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.72+1147T>C	10.37:g.75675129A>G		Somatic		Capture	Illumina HiSeq	Phase_I	75345135	NM_002658	Q3KRG4|Q8NAK4	Missense_Mutation	SNP	ENST00000409178.1	37	CCDS53541.1	.	.	.	.	.	.	.	.	.	.	A	15.38	2.815339	0.50527	.	.	ENSG00000122861	ENST00000446342;ENST00000372764;ENST00000372762;ENST00000372761	D;D;D	0.87809	-2.3;-2.3;-2.3	5.95	3.59	0.41128	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.236125	0.50627	N	0.000117	T	0.79233	0.4411	N	0.20845	0.615	0.09310	N	0.999997	P;P;P;B	0.41643	0.715;0.758;0.525;0.073	B;P;B;B	0.44732	0.329;0.459;0.233;0.089	T	0.70691	-0.4802	10	0.66056	D	0.02	.	6.3175	0.21199	0.7814:0.0:0.0772:0.1415	.	347;328;364;364	E7ET40;E7ESM2;B2R7F2;P00749	.;.;.;UROK_HUMAN	G	347;364;328;328	ENSP00000388474:D347G;ENSP00000361850:D364G;ENSP00000361848:D328G	ENSP00000361847:D328G	D	+	2	0	PLAU	75345135	0.088000	0.21588	0.927000	0.36925	0.968000	0.65278	2.584000	0.46102	0.484000	0.27630	0.533000	0.62120	GAC		0.537	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791	
DLG5	9231	broad.mit.edu	37	10	79601761	79601761	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:79601761G>A	ENST00000372391.2	-	7	1320	c.1315C>T	c.(1315-1317)Cgt>Tgt	p.R439C	DLG5_ENST00000372388.2_Missense_Mutation_p.R439C	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	439					apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)	p.R439C(1)		breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			ACCTGGTCACGCTCACTCATG	0.562																																					p.R439C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1315T	10						.						157.0	113.0	128.0					10																	79601761		2203	4300	6503	79271767	SO:0001583	missense	9231	exon7			U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.1315C>T	10.37:g.79601761G>A	ENSP00000361467:p.Arg439Cys	Somatic		Capture	Illumina HiSeq	Phase_I	79271767	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	37	CCDS7353.2	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122556	0.77436	.	.	ENSG00000151208	ENST00000372391;ENST00000372388	T;T	0.15603	2.42;2.41	5.71	4.75	0.60458	.	0.000000	0.37437	N	0.002095	T	0.39708	0.1088	M	0.65975	2.015	0.47698	D	0.999493	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.997	T	0.14117	-1.0484	10	0.87932	D	0	.	13.9935	0.64380	0.0:0.0:0.7762:0.2238	.	329;439;439	Q8TDM6-4;Q8TDM6;Q8TDM6-2	.;DLG5_HUMAN;.	C	439	ENSP00000361467:R439C;ENSP00000361464:R439C	ENSP00000361464:R439C	R	-	1	0	DLG5	79271767	1.000000	0.71417	0.999000	0.59377	0.912000	0.54170	2.902000	0.48703	2.711000	0.92665	0.563000	0.77884	CGT		0.562	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
GRID1	2894	broad.mit.edu	37	10	87898605	87898605	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:87898605G>T	ENST00000327946.7	-	4	782	c.697C>A	c.(697-699)Cca>Aca	p.P233T		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	233					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.P233T(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						GCTCCCTGTGGGCTGAGCAGC	0.612										Multiple Myeloma(13;0.14)																											p.P233T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C697A	10						.						121.0	108.0	112.0					10																	87898605		2203	4300	6503	87888585	SO:0001583	missense	2894	exon4			AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.697C>A	10.37:g.87898605G>T	ENSP00000330148:p.Pro233Thr	Somatic		Capture	Illumina HiSeq	Phase_I	87888585	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	g	16.14	3.037425	0.54896	.	.	ENSG00000182771	ENST00000327946	D	0.83075	-1.68	5.17	5.17	0.71159	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.85366	0.5680	L	0.59436	1.845	0.80722	D	1	P	0.45348	0.856	P	0.51055	0.657	T	0.82343	-0.0504	10	0.20046	T	0.44	.	17.6915	0.88269	0.0:0.0:1.0:0.0	.	233	Q9ULK0	GRID1_HUMAN	T	233	ENSP00000330148:P233T	ENSP00000330148:P233T	P	-	1	0	GRID1	87888585	1.000000	0.71417	0.997000	0.53966	0.850000	0.48378	7.945000	0.87732	2.413000	0.81919	0.550000	0.68814	CCA		0.612	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	
OPN4	94233	broad.mit.edu	37	10	88418262	88418262	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:88418262G>A	ENST00000241891.5	+	4	613	c.446G>A	c.(445-447)tGt>tAt	p.C149Y	OPN4_ENST00000372071.2_Missense_Mutation_p.C160Y	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	149					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)	p.C160Y(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						TATGCCTTCTGTGGAGCTCTC	0.617																																					p.C160Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G479A	10						.						93.0	77.0	83.0					10																	88418262		2203	4300	6503	88408242	SO:0001583	missense	94233	exon5			AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"""GPCR / Class A : Opsin receptors"""	14449	protein-coding gene	gene with protein product	"""melanopsin"""	606665	"""opsin 4 (melanopsin)"""			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.446G>A	10.37:g.88418262G>A	ENSP00000241891:p.Cys149Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	88408242	NM_001030015	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	37	CCDS7376.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.993714	0.93167	.	.	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.37235	1.21;1.21;1.21	5.32	5.32	0.75619	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67429	0.2892	H	0.94698	3.57	0.80722	D	1	P;P;P	0.46512	0.879;0.879;0.851	P;P;P	0.54590	0.756;0.756;0.629	T	0.77520	-0.2557	10	0.72032	D	0.01	.	18.9964	0.92815	0.0:0.0:1.0:0.0	.	160;149;160	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	Y	160;149;160	ENSP00000361141:C160Y;ENSP00000241891:C149Y;ENSP00000393132:C160Y	ENSP00000241891:C149Y	C	+	2	0	OPN4	88408242	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.828000	0.99408	2.482000	0.83794	0.511000	0.50034	TGT		0.617	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	
GLUD1	2746	broad.mit.edu	37	10	88813110	88813110	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:88813110G>A	ENST00000277865.4	-	12	1642	c.1546C>T	c.(1546-1548)Cgt>Tgt	p.R516C	GLUD1_ENST00000544149.1_Missense_Mutation_p.R383C|GLUD1_ENST00000537649.1_Missense_Mutation_p.R349C	NM_005271.3	NP_005262.1	P00367	DHE3_HUMAN	glutamate dehydrogenase 1	516					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamine metabolic process (GO:0006541)|positive regulation of insulin secretion (GO:0032024)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|tricarboxylic acid metabolic process (GO:0072350)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|leucine binding (GO:0070728)|NAD+ binding (GO:0070403)	p.R516C(1)		endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(11)|prostate(1)	22					Hexachlorophene(DB00756)	CTGGCAGAACGCTCCATTGTG	0.473																																					p.R516C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1546T	10						.						142.0	101.0	115.0					10																	88813110		2203	4300	6503	88803090	SO:0001583	missense	2746	exon12			M20867	CCDS7382.1	10q23.2	2010-03-17			ENSG00000148672	ENSG00000148672	1.4.1.3		4335	protein-coding gene	gene with protein product		138130		GLUD		2757358	Standard	NM_005271		Approved	GDH	uc001keh.3	P00367	OTTHUMG00000018666	ENST00000277865.4:c.1546C>T	10.37:g.88813110G>A	ENSP00000277865:p.Arg516Cys	Somatic		Capture	Illumina HiSeq	Phase_I	88803090	NM_005271	B3KV55|B4DGN5|Q5TBU3	Missense_Mutation	SNP	ENST00000277865.4	37	CCDS7382.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.514408	0.44763	.	.	ENSG00000148672	ENST00000277865;ENST00000394415;ENST00000537649;ENST00000535802;ENST00000513510;ENST00000544149	D;D;D	0.96491	-4.03;-4.03;-4.03	5.58	3.72	0.42706	Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.053288	0.64402	D	0.000001	D	0.97911	0.9313	M	0.90542	3.125	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.63877	0.857;0.919	D	0.97707	1.0188	10	0.87932	D	0	-2.5094	10.8066	0.46520	0.0682:0.0:0.8006:0.1311	.	383;516	B4DGN5;P00367	.;DHE3_HUMAN	C	516;473;349;215;448;383	ENSP00000277865:R516C;ENSP00000439291:R349C;ENSP00000444732:R383C	ENSP00000277865:R516C	R	-	1	0	GLUD1	88803090	1.000000	0.71417	0.976000	0.42696	0.165000	0.22458	2.377000	0.44300	0.715000	0.32103	-0.218000	0.12543	CGT		0.473	GLUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049188.1	NM_005271	
STAMBPL1	57559	broad.mit.edu	37	10	90668503	90668503	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:90668503G>A	ENST00000371926.3	+	4	1251	c.293G>A	c.(292-294)tGt>tAt	p.C98Y	STAMBPL1_ENST00000371927.3_Missense_Mutation_p.C98Y|STAMBPL1_ENST00000371924.1_Missense_Mutation_p.C98Y	NM_020799.3	NP_065850.1	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1	98						membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)	p.C98Y(2)		breast(2)|endometrium(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(1)	11		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)		TACCAGCAATGTGCAGTACCT	0.378																																					p.C98Y												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G293A	10						.						171.0	152.0	159.0					10																	90668503		2203	4300	6503	90658483	SO:0001583	missense	57559	exon4			AB037794	CCDS7391.1	10q23.32	2006-11-08			ENSG00000138134	ENSG00000138134			24105	protein-coding gene	gene with protein product	"""associated molecule with the SH3 domain of STAM (AMSH) like protein"", ""associated molecule with the SH3 domain of STAM (AMSH) - Family Protein"""	612352				12810066, 12943674	Standard	NM_020799		Approved	AMSH-LP, KIAA1373, AMSH-FP, FLJ31524, ALMalpha, bA399O19.2	uc001kfk.4	Q96FJ0	OTTHUMG00000018702	ENST00000371926.3:c.293G>A	10.37:g.90668503G>A	ENSP00000360994:p.Cys98Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	90658483	NM_020799	B3KPA7|Q5T9N4|Q5T9N9|Q7Z420|Q9P2H4	Missense_Mutation	SNP	ENST00000371926.3	37	CCDS7391.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.388845	0.42308	.	.	ENSG00000138134	ENST00000371926;ENST00000371927;ENST00000371924	T;T;T	0.22539	1.97;1.95;1.97	5.86	5.86	0.93980	.	0.043340	0.85682	D	0.000000	T	0.11836	0.0288	N	0.17474	0.49	0.80722	D	1	B;B	0.15141	0.002;0.012	B;B	0.12837	0.007;0.008	T	0.11108	-1.0601	10	0.07175	T	0.84	-2.8132	12.1106	0.53838	0.0789:0.0:0.9211:0.0	.	98;98	Q96FJ0-2;Q96FJ0	.;STALP_HUMAN	Y	98	ENSP00000360994:C98Y;ENSP00000360995:C98Y;ENSP00000360992:C98Y	ENSP00000360992:C98Y	C	+	2	0	STAMBPL1	90658483	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.485000	0.53208	2.775000	0.95449	0.563000	0.77884	TGT		0.378	STAMBPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049283.1	NM_020799	
LIPA	3988	broad.mit.edu	37	10	90984947	90984947	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:90984947delT	ENST00000336233.5	-	6	899	c.577delA	c.(577-579)aggfs	p.R193fs	LIPA_ENST00000371837.1_Frame_Shift_Del_p.R137fs|LIPA_ENST00000456827.1_Frame_Shift_Del_p.R193fs			P38571	LICH_HUMAN	lipase A, lysosomal acid, cholesterol esterase	193					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cytokine production (GO:0001816)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|lung development (GO:0030324)|tissue remodeling (GO:0048771)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	lipase activity (GO:0016298)|sterol esterase activity (GO:0004771)	p.R193fs*24(1)		endometrium(1)|large_intestine(2)|lung(3)	6		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		ATTTTAATCCTTTTAGCCAGC	0.428																																					p.R193fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.577delA	10						.						155.0	173.0	167.0					10																	90984947		2203	4300	6503	90974927	SO:0001589	frameshift_variant	3988	exon6			M74775	CCDS7401.1, CCDS73160.1	10q23.2-q23.3	2012-07-13	2008-08-01		ENSG00000107798	ENSG00000107798	3.1.1.13		6617	protein-coding gene	gene with protein product	"""Wolman disease"""	613497				8432549	Standard	NM_000235		Approved	LAL, CESD	uc009xtq.3	P38571	OTTHUMG00000018716	ENST00000336233.5:c.577delA	10.37:g.90984947delT	ENSP00000337354:p.Arg193fs	Somatic		Capture	Illumina HiSeq	Phase_I	90974927	NM_001127605	B2RBH5|D3DR29|Q16529|Q53H21|Q5T074|Q5T771|Q96EJ0	Frame_Shift_Del	DEL	ENST00000336233.5	37	CCDS7401.1																																																																																				0.428	LIPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049308.1	NM_000235	
PCGF5	84333	broad.mit.edu	37	10	93011160	93011160	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:93011160T>C	ENST00000336126.5	+	6	669	c.437T>C	c.(436-438)tTa>tCa	p.L146S	PCGF5_ENST00000543648.1_Missense_Mutation_p.L146S	NM_001257101.1|NM_032373.4	NP_001244030.1|NP_115749.2	Q86SE9	PCGF5_HUMAN	polycomb group ring finger 5	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)	zinc ion binding (GO:0008270)	p.L146S(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)	12						CTAGATTGTTTACGAAATAAT	0.338																																					p.L146S	Colon(178;732 2696 46441 50370)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T437C	10						.						129.0	122.0	124.0					10																	93011160		2203	4300	6503	93001140	SO:0001583	missense	84333	exon6			AL832003	CCDS7413.1	10q23.33	2013-01-09	2005-01-17	2005-01-19	ENSG00000180628	ENSG00000180628		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	28264	protein-coding gene	gene with protein product			"""ring finger protein (C3HC4 type) 159"""	RNF159		8076819	Standard	NM_001256549		Approved	MGC16202	uc001khh.4	Q86SE9	OTTHUMG00000018740	ENST00000336126.5:c.437T>C	10.37:g.93011160T>C	ENSP00000337500:p.Leu146Ser	Somatic		Capture	Illumina HiSeq	Phase_I	93001140	NM_032373	B7Z892|D3DR33|Q6PK47|Q86TD0	Missense_Mutation	SNP	ENST00000336126.5	37	CCDS7413.1	.	.	.	.	.	.	.	.	.	.	T	15.91	2.971812	0.53614	.	.	ENSG00000180628	ENST00000543648;ENST00000336126	T;T	0.45668	0.89;0.89	6.06	6.06	0.98353	.	0.264556	0.33534	N	0.004819	T	0.38427	0.1040	L	0.50333	1.59	0.80722	D	1	B	0.26876	0.162	B	0.17979	0.02	T	0.13656	-1.0501	10	0.23302	T	0.38	-9.3049	16.6245	0.84952	0.0:0.0:0.0:1.0	.	146	Q86SE9	PCGF5_HUMAN	S	146	ENSP00000445704:L146S;ENSP00000337500:L146S	ENSP00000337500:L146S	L	+	2	0	PCGF5	93001140	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.375000	0.79646	2.323000	0.78572	0.528000	0.53228	TTA		0.338	PCGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049363.1	NM_032373	
BTAF1	9044	broad.mit.edu	37	10	93786498	93786498	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:93786498G>A	ENST00000265990.6	+	36	5533	c.5225G>A	c.(5224-5226)cGc>cAc	p.R1742H	BTAF1_ENST00000544642.1_Missense_Mutation_p.R570H	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	1742	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R1742H(1)		central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				CGGGCCCATCGCATTGGGCAG	0.468																																					p.R1742H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5225A	10						.						64.0	59.0	61.0					10																	93786498		2203	4300	6503	93776478	SO:0001583	missense	9044	exon36			AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"""Mot1 homolog (S. cerevisiae)"""	605191	"""BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"""			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.5225G>A	10.37:g.93786498G>A	ENSP00000265990:p.Arg1742His	Somatic		Capture	Illumina HiSeq	Phase_I	93776478	NM_003972	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	37	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	G	35	5.462206	0.96240	.	.	ENSG00000095564	ENST00000265990;ENST00000544642;ENST00000538688	D;D	0.97850	-4.57;-4.57	5.65	5.65	0.86999	Helicase, C-terminal (3);	0.055783	0.64402	D	0.000003	D	0.99438	0.9801	H	0.99379	4.54	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98038	1.0380	10	0.87932	D	0	-0.8151	19.7072	0.96079	0.0:0.0:1.0:0.0	.	1742	O14981	BTAF1_HUMAN	H	1742;570;592	ENSP00000265990:R1742H;ENSP00000439924:R570H	ENSP00000265990:R1742H	R	+	2	0	BTAF1	93776478	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.869000	0.99810	2.662000	0.90505	0.591000	0.81541	CGC		0.468	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972	
MYOF	26509	broad.mit.edu	37	10	95083095	95083095	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:95083095C>A	ENST00000359263.4	-	47	5291	c.5292G>T	c.(5290-5292)gtG>gtT	p.V1764V	MYOF_ENST00000485212.1_5'Flank|MYOF_ENST00000358334.5_Silent_p.V1751V|MYOF_ENST00000371501.4_Silent_p.V1764V|MYOF_ENST00000371502.4_Intron	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1764					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)	p.V1764V(1)		NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						GGAAAACATCCACCCACATCT	0.428																																					p.V1751V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G5253T	10						.						81.0	81.0	81.0					10																	95083095		1845	4091	5936	95073085	SO:0001819	synonymous_variant	26509	exon46			AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.5292G>T	10.37:g.95083095C>A		Somatic		Capture	Illumina HiSeq	Phase_I	95073085	NM_133337	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Silent	SNP	ENST00000359263.4	37	CCDS41551.1																																																																																				0.428	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
PDE6C	5146	broad.mit.edu	37	10	95380482	95380482	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:95380482G>A	ENST00000371447.3	+	2	712	c.574G>A	c.(574-576)Gct>Act	p.A192T		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	192	GAF 1.				phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)	p.A192T(1)		breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	GGAGGTTCTTGCTGTGATCAT	0.463																																					p.A192T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G574A	10						.						140.0	132.0	135.0					10																	95380482		2203	4300	6503	95370472	SO:0001583	missense	5146	exon2			U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.574G>A	10.37:g.95380482G>A	ENSP00000360502:p.Ala192Thr	Somatic		Capture	Illumina HiSeq	Phase_I	95370472	NM_006204	A6NCR6|Q5VY29	Missense_Mutation	SNP	ENST00000371447.3	37	CCDS7429.1	.	.	.	.	.	.	.	.	.	.	G	32	5.155145	0.94686	.	.	ENSG00000095464	ENST00000371447	T	0.68479	-0.33	5.23	5.23	0.72850	GAF (2);	0.050201	0.85682	D	0.000000	T	0.81182	0.4769	M	0.84511	2.7	0.58432	D	0.999999	D	0.57571	0.98	P	0.55545	0.778	D	0.84488	0.0609	10	0.87932	D	0	.	18.9873	0.92777	0.0:0.0:1.0:0.0	.	192	P51160	PDE6C_HUMAN	T	192	ENSP00000360502:A192T	ENSP00000360502:A192T	A	+	1	0	PDE6C	95370472	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	9.657000	0.98554	2.719000	0.93026	0.655000	0.94253	GCT		0.463	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204	
PLCE1	51196	broad.mit.edu	37	10	96066217	96066217	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:96066217A>G	ENST00000371380.3	+	25	5891	c.5656A>G	c.(5656-5658)Agc>Ggc	p.S1886G	PLCE1_ENST00000371375.1_Missense_Mutation_p.S1578G|PLCE1_ENST00000371385.3_Missense_Mutation_p.S1578G|PLCE1_ENST00000260766.3_Missense_Mutation_p.S1886G			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	1886	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)	p.S1886G(1)		liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				CCCCAGTAATAGCATGGGAAG	0.517																																					p.S1578G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4732G	10						.						144.0	141.0	142.0					10																	96066217		1992	4159	6151	96056207	SO:0001583	missense	51196	exon25				CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"""nephrosis type 3"""	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.5656A>G	10.37:g.96066217A>G	ENSP00000360431:p.Ser1886Gly	Somatic		Capture	Illumina HiSeq	Phase_I	96056207	NM_001165979	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	A	15.57	2.871713	0.51695	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.10763	2.84;2.84;2.84;2.84	5.43	5.43	0.79202	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.18425	0.0442	N	0.20483	0.58	0.40166	D	0.977126	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.81914	0.995;0.99;0.988	T	0.17501	-1.0367	10	0.21540	T	0.41	.	15.4603	0.75349	1.0:0.0:0.0:0.0	.	1870;1578;1886	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	G	1886;1886;1578;1578	ENSP00000260766:S1886G;ENSP00000360431:S1886G;ENSP00000360438:S1578G;ENSP00000360426:S1578G	ENSP00000260766:S1886G	S	+	1	0	PLCE1	96056207	1.000000	0.71417	0.999000	0.59377	0.186000	0.23388	6.050000	0.71063	2.197000	0.70478	0.533000	0.62120	AGC		0.517	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
PDLIM1	9124	broad.mit.edu	37	10	97023724	97023724	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:97023724A>G	ENST00000329399.6	-	4	538	c.430T>C	c.(430-432)Tac>Cac	p.Y144H	PDLIM1_ENST00000477757.1_5'UTR	NM_020992.2	NP_066272.1	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	144					regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.Y144H(1)		endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|skin(2)	10		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		GGGTTGTTGTACTGGTTTGTG	0.567																																					p.Y144H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T430C	10						.						114.0	98.0	104.0					10																	97023724		2203	4300	6503	97013714	SO:0001583	missense	9124	exon4			U90878	CCDS7441.1	10q23.1	2008-07-29	2008-07-29		ENSG00000107438	ENSG00000107438			2067	protein-coding gene	gene with protein product	"""carboxyl terminal LIM domain protein 1"", ""elfin"""	605900	"""PDZ and LIM domain 1 (elfin)"""	CLIM1		10861853	Standard	NM_020992		Approved	CLP-36, hCLIM1, CLP36	uc001kkh.4	O00151	OTTHUMG00000018810	ENST00000329399.6:c.430T>C	10.37:g.97023724A>G	ENSP00000360305:p.Tyr144His	Somatic		Capture	Illumina HiSeq	Phase_I	97013714	NM_020992	B2RBS6|Q5VZH5|Q9BPZ9	Missense_Mutation	SNP	ENST00000329399.6	37	CCDS7441.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.907887	0.92107	.	.	ENSG00000107438	ENST00000329399	T	0.66460	-0.21	5.93	5.93	0.95920	ZASP (1);	0.108371	0.64402	D	0.000004	T	0.66086	0.2754	M	0.67569	2.06	0.80722	D	1	P	0.34934	0.476	B	0.33890	0.172	T	0.67589	-0.5632	10	0.48119	T	0.1	-20.1251	15.5755	0.76380	1.0:0.0:0.0:0.0	.	144	O00151	PDLI1_HUMAN	H	144	ENSP00000360305:Y144H	ENSP00000360305:Y144H	Y	-	1	0	PDLIM1	97013714	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.281000	0.76405	0.533000	0.62120	TAC		0.567	PDLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049508.1		
TM9SF3	56889	broad.mit.edu	37	10	98287002	98287002	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:98287002G>A	ENST00000371142.4	-	14	1886	c.1670C>T	c.(1669-1671)gCg>gTg	p.A557V		NM_020123.3	NP_064508.3	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3	557						integral component of membrane (GO:0016021)		p.A557V(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)	15		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)		GCTAAATACCGCCATATATCC	0.313																																					p.A557V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1670T	10						.						50.0	47.0	48.0					10																	98287002		2203	4291	6494	98276992	SO:0001583	missense	56889	exon14			AF160213, AF269150	CCDS7450.1	10q24.2	2006-04-12			ENSG00000077147	ENSG00000077147			21529	protein-coding gene	gene with protein product						11530251, 11595169	Standard	NM_020123		Approved	SMBP	uc001kmm.4	Q9HD45	OTTHUMG00000018834	ENST00000371142.4:c.1670C>T	10.37:g.98287002G>A	ENSP00000360184:p.Ala557Val	Somatic		Capture	Illumina HiSeq	Phase_I	98276992	NM_020123	Q5TB57|Q6UWE7|Q9NWL8|Q9P0G9|Q9UHW8	Missense_Mutation	SNP	ENST00000371142.4	37	CCDS7450.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.784502	0.70222	.	.	ENSG00000077147	ENST00000371142	T	0.48836	0.8	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.51160	0.1658	M	0.85462	2.755	0.80722	D	1	D	0.54964	0.969	B	0.37304	0.246	T	0.62604	-0.6819	10	0.34782	T	0.22	-7.2861	17.5679	0.87926	0.0:0.0:1.0:0.0	.	557	Q9HD45	TM9S3_HUMAN	V	557	ENSP00000360184:A557V	ENSP00000360184:A557V	A	-	2	0	TM9SF3	98276992	1.000000	0.71417	0.996000	0.52242	0.963000	0.63663	9.772000	0.98984	2.470000	0.83445	0.467000	0.42956	GCG		0.313	TM9SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049610.2	NM_020123	
SLIT1	6585	broad.mit.edu	37	10	98807498	98807498	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:98807498C>A	ENST00000266058.4	-	16	1828	c.1583G>T	c.(1582-1584)aGc>aTc	p.S528I	SLIT1_ENST00000371070.4_Missense_Mutation_p.S528I|ARHGAP19-SLIT1_ENST00000453547.2_3'UTR	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	528	LRRNT 3.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.S528I(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		GAGCTTCAGGCTGGAGCACTC	0.632																																					p.S528I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1583T	10						.						79.0	76.0	77.0					10																	98807498		2203	4300	6503	98797488	SO:0001583	missense	6585	exon16			AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.1583G>T	10.37:g.98807498C>A	ENSP00000266058:p.Ser528Ile	Somatic		Capture	Illumina HiSeq	Phase_I	98797488	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	37	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.669020	0.67814	.	.	ENSG00000187122	ENST00000266058;ENST00000371057;ENST00000371070;ENST00000314867	D;D;D	0.96587	-4.06;-4.06;-4.06	4.87	3.88	0.44766	Leucine-rich repeat-containing N-terminal (2);	0.088292	0.85682	D	0.000000	D	0.95092	0.8410	M	0.76433	2.335	0.80722	D	1	B;B	0.32031	0.352;0.029	B;B	0.40410	0.328;0.035	D	0.93483	0.6829	10	0.72032	D	0.01	.	3.9161	0.09224	0.0:0.6834:0.0:0.3166	.	538;528	E7EWQ8;O75093	.;SLIT1_HUMAN	I	528;538;528;521	ENSP00000266058:S528I;ENSP00000360109:S528I;ENSP00000315005:S521I	ENSP00000266058:S528I	S	-	2	0	SLIT1	98797488	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.589000	0.53972	2.517000	0.84864	0.563000	0.77884	AGC		0.632	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061	
RRP12	23223	broad.mit.edu	37	10	99150243	99150243	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:99150243G>A	ENST00000370992.4	-	6	801	c.690C>T	c.(688-690)ggC>ggT	p.G230G	RRP12_ENST00000536831.1_Silent_p.G36G|RRP12_ENST00000315563.6_Intron|RRP12_ENST00000414986.1_Silent_p.G169G	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	230						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.G230G(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		TCACGGGGTAGCCCCAGGCCT	0.612																																					p.G230G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C690T	10						.						54.0	53.0	54.0					10																	99150243		2203	4300	6503	99140233	SO:0001819	synonymous_variant	23223	exon6				CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.690C>T	10.37:g.99150243G>A		Somatic		Capture	Illumina HiSeq	Phase_I	99140233	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																				0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
UBTD1	80019	broad.mit.edu	37	10	99330059	99330059	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:99330059C>A	ENST00000370664.3	+	3	799	c.463C>A	c.(463-465)Ctg>Atg	p.L155M	ANKRD2_ENST00000370655.1_5'Flank|ANKRD2_ENST00000298808.5_5'Flank|ANKRD2_ENST00000455090.1_5'Flank|ANKRD2_ENST00000307518.5_5'Flank	NM_024954.3	NP_079230.1	Q9HAC8	UBTD1_HUMAN	ubiquitin domain containing 1	155	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.							p.L155M(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		Colorectal(252;0.162)		Epithelial(162;3.04e-10)|all cancers(201;2.86e-08)		GAAGGTGCGCCTGTCCACGGG	0.697																																					p.L155M	Pancreas(100;169 2668 32720)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C463A	10						.						46.0	46.0	46.0					10																	99330059		2203	4299	6502	99320049	SO:0001583	missense	80019	exon3			BC007331	CCDS7465.1	10q24.2	2005-09-22			ENSG00000165886	ENSG00000165886			25683	protein-coding gene	gene with protein product						12477932	Standard	NM_024954		Approved	FLJ11807	uc001knv.1	Q9HAC8	OTTHUMG00000018856	ENST00000370664.3:c.463C>A	10.37:g.99330059C>A	ENSP00000359698:p.Leu155Met	Somatic		Capture	Illumina HiSeq	Phase_I	99320049	NM_024954	D3DR57|Q53HI3	Missense_Mutation	SNP	ENST00000370664.3	37	CCDS7465.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.472508	0.63737	.	.	ENSG00000165886	ENST00000370664	T	0.73789	-0.78	5.34	5.34	0.76211	Ubiquitin supergroup (1);Ubiquitin (1);	0.000000	0.85682	D	0.000000	D	0.87661	0.6233	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88118	0.2830	10	0.54805	T	0.06	-31.3325	19.0508	0.93043	0.0:1.0:0.0:0.0	.	155	Q9HAC8	UBTD1_HUMAN	M	155	ENSP00000359698:L155M	ENSP00000359698:L155M	L	+	1	2	UBTD1	99320049	1.000000	0.71417	1.000000	0.80357	0.112000	0.19704	4.872000	0.63050	2.687000	0.91594	0.655000	0.94253	CTG		0.697	UBTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049701.1	NM_024954	
ANKRD2	26287	broad.mit.edu	37	10	99338064	99338064	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:99338064A>G	ENST00000307518.5	+	3	605	c.338A>G	c.(337-339)cAg>cGg	p.Q113R	ANKRD2_ENST00000370655.1_Missense_Mutation_p.Q86R|ANKRD2_ENST00000298808.5_Missense_Mutation_p.Q113R|ANKRD2_ENST00000455090.1_Missense_Mutation_p.Q86R			Q9GZV1	ANKR2_HUMAN	ankyrin repeat domain 2 (stretch responsive muscle)	113	May mediate interaction with PML, p53/TP53 and YBX1.				muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|euchromatin (GO:0000791)|I band (GO:0031674)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	protein kinase B binding (GO:0043422)|structural constituent of muscle (GO:0008307)	p.Q113R(1)		breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7		all_hematologic(284;1.95e-06)|Colorectal(252;0.0163)		Epithelial(162;1.18e-94)|all cancers(201;9.31e-86)|BRCA - Breast invasive adenocarcinoma(275;0.0233)|STAD - Stomach adenocarcinoma(243;0.181)|KIRC - Kidney renal clear cell carcinoma(50;0.206)|Kidney(138;0.241)		GGCGGGATCCAGAACCTCATC	0.672																																					p.Q113R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A338G	10						.						30.0	30.0	30.0					10																	99338064		2203	4299	6502	99328054	SO:0001583	missense	26287	exon3			AJ304805	CCDS7466.1, CCDS44468.1	10q23	2013-01-10			ENSG00000165887	ENSG00000165887		"""Ankyrin repeat domain containing"""	495	protein-coding gene	gene with protein product		610734				10873377, 15136035, 15677738	Standard	NM_001129981		Approved	ARPP	uc001knw.3	Q9GZV1	OTTHUMG00000018860	ENST00000307518.5:c.338A>G	10.37:g.99338064A>G	ENSP00000306163:p.Gln113Arg	Somatic		Capture	Illumina HiSeq	Phase_I	99328054	NM_020349	Q3B778|Q5T456|Q70EZ9|Q8WUD7|Q96MG0|Q9NQC9	Missense_Mutation	SNP	ENST00000307518.5	37	CCDS7466.1	.	.	.	.	.	.	.	.	.	.	A	28.7	4.941469	0.92526	.	.	ENSG00000165887	ENST00000307518;ENST00000298808;ENST00000370655;ENST00000455090	T;T;T;T	0.54675	0.8;0.56;0.76;0.56	5.35	5.35	0.76521	.	0.000000	0.64402	D	0.000007	T	0.57989	0.2091	L	0.34521	1.04	0.41569	D	0.988675	D;D	0.60575	0.988;0.981	P;D	0.67900	0.829;0.954	T	0.52139	-0.8615	10	0.10636	T	0.68	-36.3726	15.317	0.74089	1.0:0.0:0.0:0.0	.	113;113	Q9GZV1-2;Q9GZV1	.;ANKR2_HUMAN	R	113;113;86;86	ENSP00000306163:Q113R;ENSP00000298808:Q113R;ENSP00000359689:Q86R;ENSP00000403114:Q86R	ENSP00000298808:Q113R	Q	+	2	0	ANKRD2	99328054	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.523000	0.73787	2.015000	0.59207	0.402000	0.26972	CAG		0.672	ANKRD2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SLC25A28	81894	broad.mit.edu	37	10	101373473	101373473	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:101373473delC	ENST00000370495.4	-	2	528	c.500delG	c.(499-501)ggcfs	p.G167fs	SLC25A28_ENST00000496035.1_5'UTR	NM_031212.3	NP_112489.3	Q96A46	MFRN2_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 28	167					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.G167fs*22(1)		endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|stomach(1)	11		Colorectal(252;0.234)		Epithelial(162;2.57e-10)|all cancers(201;2.01e-08)		ATGGCTATTGCCCCCAGGGTG	0.512																																					p.G167fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.500delG	10						.						54.0	59.0	58.0					10																	101373473		1906	4128	6034	101363463	SO:0001589	frameshift_variant	81894	exon2			AF327402	CCDS41559.1	10q24.2	2013-05-22	2012-03-29		ENSG00000155287	ENSG00000155287		"""Solute carriers"""	23472	protein-coding gene	gene with protein product	"""mitoferrin 2"""	609767	"""solute carrier family 25, member 28"""			11297739	Standard	NM_031212		Approved	MRS3/4, MRS4L	uc001kpx.2	Q96A46	OTTHUMG00000018886	ENST00000370495.4:c.500delG	10.37:g.101373473delC	ENSP00000359526:p.Gly167fs	Somatic		Capture	Illumina HiSeq	Phase_I	101363463	NM_031212	Q4VBZ0|Q5T777|Q86VX5|Q969G8|Q9H2J3	Frame_Shift_Del	DEL	ENST00000370495.4	37	CCDS41559.1																																																																																				0.512	SLC25A28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049801.1	NM_031212	
ABCC2	1244	broad.mit.edu	37	10	101544462	101544462	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:101544462delC	ENST00000370449.4	+	2	244	c.131delC	c.(130-132)gccfs	p.A44fs	ABCC2_ENST00000370434.1_Frame_Shift_Del_p.A44fs	NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	44					cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.W46fs*33(1)		NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TGGCTCCTGGCCCCCTGGCAG	0.502																																					p.A44fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.131delC	10						.						125.0	117.0	119.0					10																	101544462		2203	4300	6503	101534452	SO:0001589	frameshift_variant	1244	exon2			U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.131delC	10.37:g.101544462delC	ENSP00000359478:p.Ala44fs	Somatic		Capture	Illumina HiSeq	Phase_I	101534452	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Frame_Shift_Del	DEL	ENST00000370449.4	37	CCDS7484.1																																																																																				0.502	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
TCF7L2	6934	broad.mit.edu	37	10	114849161	114849161	+	Intron	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:114849161delC	ENST00000355995.4	+	5	1059				TCF7L2_ENST00000545257.1_Intron|TCF7L2_ENST00000534894.1_Intron|TCF7L2_ENST00000542695.1_Intron|TCF7L2_ENST00000369395.1_Frame_Shift_Del_p.S163fs|TCF7L2_ENST00000543371.1_Intron|TCF7L2_ENST00000352065.5_Intron|TCF7L2_ENST00000349937.2_Intron|TCF7L2_ENST00000355717.4_Frame_Shift_Del_p.S162fs|TCF7L2_ENST00000369397.4_Intron|TCF7L2_ENST00000536810.1_Intron|TCF7L2_ENST00000538897.1_Intron			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)						blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.L164fs*29(1)	VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		GGCAGCAGAGCCCCCTCCCTT	0.587			T	VTI1A	colorectal																																p.S162fs			Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.486delC	10						.						42.0	38.0	40.0					10																	114849161		1568	3582	5150	114839151	SO:0001627	intron_variant	6934	exon5			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.552+49276C>-	10.37:g.114849161delC		Somatic		Capture	Illumina HiSeq	Phase_I	114839151	NM_001146283	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Frame_Shift_Del	DEL	ENST00000355995.4	37																																																																																					0.587	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756	
KNDC1	85442	broad.mit.edu	37	10	135015094	135015094	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr10:135015094C>T	ENST00000304613.3	+	17	3100	c.3079C>T	c.(3079-3081)Cgg>Tgg	p.R1027W	KNDC1_ENST00000368571.2_Missense_Mutation_p.R962W|KNDC1_ENST00000368572.2_Missense_Mutation_p.R1029W			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1027					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.R1027W(1)		NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CGCACTGTCACGGGGAAACTT	0.637																																					p.R1027W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3079T	10						.						57.0	65.0	62.0					10																	135015094		2203	4300	6503	134865084	SO:0001583	missense	85442	exon17			AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.3079C>T	10.37:g.135015094C>T	ENSP00000304437:p.Arg1027Trp	Somatic		Capture	Illumina HiSeq	Phase_I	134865084	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.754929	0.49362	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.11495	2.77;2.77;2.77	5.06	4.13	0.48395	.	1.833290	0.02827	N	0.126290	T	0.27419	0.0673	L	0.44542	1.39	0.09310	N	1	D;D;D	0.76494	0.999;0.998;0.999	P;P;P	0.59948	0.866;0.736;0.841	T	0.33240	-0.9876	10	0.66056	D	0.02	-13.8131	12.757	0.57341	0.1657:0.8343:0.0:0.0	.	1027;962;1027	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	W	1027;1029;962	ENSP00000304437:R1027W;ENSP00000357561:R1029W;ENSP00000357560:R962W	ENSP00000304437:R1027W	R	+	1	2	KNDC1	134865084	0.022000	0.18835	0.002000	0.10522	0.006000	0.05464	0.604000	0.24164	1.218000	0.43458	0.313000	0.20887	CGG		0.637	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
HBE1	3046	broad.mit.edu	37	11	5291281	5291282	+	De_novo_Start_InFrame	INS	-	-	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:5291281_5291282insT	ENST00000380237.1	-	0	183_184				HBG2_ENST00000380252.1_Intron|HBE1_ENST00000292896.2_De_novo_Start_InFrame|HBG2_ENST00000380259.2_Intron			P02100	HBE_HUMAN	hemoglobin, epsilon 1						blood coagulation (GO:0007596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein heterooligomerization (GO:0051291)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|skin(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.34e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTGTCCCTCAGGGGTGGAGTC	0.505											OREG0002361	type=REGULATORY REGION|Gene=HBB gene family|Dataset=CRMs in the HBB locus|EvidenceSubtype=Literature derived																									.												.	.	0			.	11						.																																			5247858			3046	.			BC015537	CCDS7756.1	11p15.5	2012-10-02			ENSG00000213931	ENSG00000213931			4830	protein-coding gene	gene with protein product		142100				2649166	Standard	NM_005330		Approved	HBE	uc001mal.1	P02100	OTTHUMG00000066675		11.37:g.5291281_5291282insT		Somatic	625	Capture	Illumina HiSeq	Phase_I	5247857	.	Q6FH44	De_novo_Start_OutOfFrame	INS	ENST00000380237.1	37	CCDS7756.1																																																																																				0.505	HBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142973.2	NM_005330	
MMP1	4312	broad.mit.edu	37	11	102662182	102662182	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:102662182A>G	ENST00000315274.6	-	8	1145	c.1078T>C	c.(1078-1080)Tac>Cac	p.Y360H	WTAPP1_ENST00000525739.2_RNA	NM_001145938.1|NM_002421.3	NP_001139410.1|NP_002412.1	P03956	MMP1_HUMAN	matrix metallopeptidase 1 (interstitial collagenase)	360					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|proteolysis (GO:0006508)|viral process (GO:0016032)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.Y360H(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)	Marimastat(DB00786)	TCCTTGGGGTATCCGTGTAGC	0.443																																					p.Y294H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T880C	11						.						249.0	229.0	236.0					11																	102662182		2203	4299	6502	102167392	SO:0001583	missense	4312	exon8			X54925	CCDS8322.1	11q21-q22	2014-01-30	2005-08-08		ENSG00000196611	ENSG00000196611	3.4.24.7	"""Endogenous ligands"""	7155	protein-coding gene	gene with protein product		120353	"""matrix metalloproteinase 1 (interstitial collagenase)"""	CLG			Standard	NM_002421		Approved		uc001phi.2	P03956	OTTHUMG00000048192	ENST00000315274.6:c.1078T>C	11.37:g.102662182A>G	ENSP00000322788:p.Tyr360His	Somatic		Capture	Illumina HiSeq	Phase_I	102167392	NM_001145938	P08156	Missense_Mutation	SNP	ENST00000315274.6	37	CCDS8322.1	.	.	.	.	.	.	.	.	.	.	a	19.48	3.836184	0.71373	.	.	ENSG00000196611	ENST00000315274	T	0.23950	1.88	5.62	5.62	0.85841	Hemopexin/matrixin (2);	0.000000	0.56097	D	0.000036	T	0.56775	0.2008	M	0.91354	3.2	0.50171	D	0.999855	D	0.76494	0.999	D	0.76071	0.987	T	0.65537	-0.6144	10	0.87932	D	0	.	10.1868	0.43002	0.9246:0.0:0.0754:0.0	.	360	P03956	MMP1_HUMAN	H	360	ENSP00000322788:Y360H	ENSP00000322788:Y360H	Y	-	1	0	MMP1	102167392	1.000000	0.71417	1.000000	0.80357	0.768000	0.43524	6.212000	0.72188	2.250000	0.74265	0.533000	0.62120	TAC		0.443	MMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109632.1	NM_002421	
KBTBD3	143879	broad.mit.edu	37	11	105923933	105923933	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:105923933G>T	ENST00000526793.1	-	3	1642	c.1483C>A	c.(1483-1485)Caa>Aaa	p.Q495K	KBTBD3_ENST00000531837.1_Missense_Mutation_p.Q495K|KBTBD3_ENST00000534815.1_Missense_Mutation_p.Q416K	NM_152433.3	NP_689646.2	Q8NAB2	KBTB3_HUMAN	kelch repeat and BTB (POZ) domain containing 3	491								p.Q495K(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	25		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		TGAAAAAATTGCCCAAACTCT	0.353																																					p.Q495K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1483A	11						.						62.0	61.0	62.0					11																	105923933		2200	4295	6495	105429143	SO:0001583	missense	143879	exon3			AK055247	CCDS8334.1	11q22.3	2013-01-08	2003-12-12	2003-12-17		ENSG00000182359		"""BTB/POZ domain containing"""	22934	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 3"""	BKLHD3			Standard	NM_198439		Approved		uc001pjb.3	Q8NAB2		ENST00000526793.1:c.1483C>A	11.37:g.105923933G>T	ENSP00000436262:p.Gln495Lys	Somatic		Capture	Illumina HiSeq	Phase_I	105429143	NM_152433	Q6N066|Q86X38|Q96NK5	Missense_Mutation	SNP	ENST00000526793.1	37	CCDS8334.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.314678	0.40996	.	.	ENSG00000182359	ENST00000534815;ENST00000526793;ENST00000531837	T;T;T	0.65732	-0.17;-0.17;-0.17	5.97	5.97	0.96955	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.69753	0.3146	L	0.27053	0.805	0.58432	D	0.999999	P;D	0.63880	0.94;0.993	P;D	0.67548	0.514;0.952	T	0.66408	-0.5931	10	0.35671	T	0.21	.	20.4135	0.99023	0.0:0.0:1.0:0.0	.	495;491	A8K1K0;Q8NAB2	.;KBTB3_HUMAN	K	416;495;495	ENSP00000431910:Q416K;ENSP00000436262:Q495K;ENSP00000432163:Q495K	ENSP00000436262:Q495K	Q	-	1	0	KBTBD3	105429143	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.476000	0.97823	2.835000	0.97688	0.591000	0.81541	CAA		0.353	KBTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388705.2	NM_152433	
ACAT1	38	broad.mit.edu	37	11	108017065	108017065	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:108017065T>C	ENST00000265838.4	+	11	1233	c.1142T>C	c.(1141-1143)gTt>gCt	p.V381A		NM_000019.3	NP_000010.1	P24752	THIL_HUMAN	acetyl-CoA acetyltransferase 1	381					adipose tissue development (GO:0060612)|brain development (GO:0007420)|branched-chain amino acid catabolic process (GO:0009083)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular nitrogen compound metabolic process (GO:0034641)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|metanephric proximal convoluted tubule development (GO:0072229)|protein homooligomerization (GO:0051260)|response to hormone (GO:0009725)|response to organic cyclic compound (GO:0014070)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acetyl-CoA C-acetyltransferase activity (GO:0003985)|coenzyme binding (GO:0050662)|metal ion binding (GO:0046872)	p.V381A(1)		endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|prostate(2)	10		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)	GGAGGAGCTGTTTCTCTGGGA	0.363																																					p.V381A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1142C	11						.						87.0	96.0	93.0					11																	108017065		2201	4298	6499	107522275	SO:0001583	missense	38	exon11			D90228	CCDS8339.1	11q22.3	2010-04-30	2010-04-30		ENSG00000075239	ENSG00000075239	2.3.1.9		93	protein-coding gene	gene with protein product	"""acetoacetyl Coenzyme A thiolase"""	607809	"""acetyl-Coenzyme A acetyltransferase 1"""	ACAT		1979337	Standard	NM_000019		Approved	THIL	uc001pjy.3	P24752	OTTHUMG00000166381	ENST00000265838.4:c.1142T>C	11.37:g.108017065T>C	ENSP00000265838:p.Val381Ala	Somatic		Capture	Illumina HiSeq	Phase_I	107522275	NM_000019	B2R6H1|G3XAB4|Q96FG8	Missense_Mutation	SNP	ENST00000265838.4	37	CCDS8339.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.894643	0.91962	.	.	ENSG00000075239	ENST00000265838	D	0.93811	-3.29	5.86	5.86	0.93980	Thiolase-like, subgroup (1);Thiolase-like (1);Thiolase, conserved site (1);Thiolase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.97399	0.9149	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98262	1.0499	10	0.87932	D	0	-1.4681	16.2644	0.82568	0.0:0.0:0.0:1.0	.	381	P24752	THIL_HUMAN	A	381	ENSP00000265838:V381A	ENSP00000265838:V381A	V	+	2	0	ACAT1	107522275	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.799000	0.85936	2.244000	0.73946	0.528000	0.53228	GTT		0.363	ACAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389474.1	NM_000019	
ZC3H12C	85463	broad.mit.edu	37	11	110036419	110036419	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:110036419T>G	ENST00000278590.3	+	6	2660	c.2609T>G	c.(2608-2610)cTc>cGc	p.L870R	ZC3H12C_ENST00000453089.2_Missense_Mutation_p.L839R|ZC3H12C_ENST00000528673.1_Missense_Mutation_p.L871R	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	870							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)	p.L870R(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		GCCCAGCAGCTCGCCGCAGCC	0.438																																					p.L870R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2609G	11						.						25.0	26.0	26.0					11																	110036419		1929	4131	6060	109541629	SO:0001583	missense	85463	exon6				CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.2609T>G	11.37:g.110036419T>G	ENSP00000278590:p.Leu870Arg	Somatic		Capture	Illumina HiSeq	Phase_I	109541629	NM_033390	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	37	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	T	18.91	3.724345	0.68959	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.56275	0.47;0.47;0.5	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.71837	0.3387	M	0.68593	2.085	0.58432	D	0.999994	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	T	0.74500	-0.3645	10	0.87932	D	0	-18.0352	16.5655	0.84588	0.0:0.0:0.0:1.0	.	871;870;870	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	R	870;871;839	ENSP00000278590:L870R;ENSP00000431821:L871R;ENSP00000413094:L839R	ENSP00000278590:L870R	L	+	2	0	ZC3H12C	109541629	1.000000	0.71417	0.957000	0.39632	0.697000	0.40408	8.040000	0.89188	2.302000	0.77476	0.533000	0.62120	CTC		0.438	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
ARHGAP20	57569	broad.mit.edu	37	11	110454448	110454448	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:110454448G>C	ENST00000260283.4	-	14	1713	c.1429C>G	c.(1429-1431)Ctt>Gtt	p.L477V	ARHGAP20_ENST00000528829.1_Missense_Mutation_p.L441V|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.L451V|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.L454V|ARHGAP20_ENST00000529591.1_Missense_Mutation_p.L20V|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.L451V|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.L441V	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	477	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.L477V(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		GCTCTCGGAAGCTGGTCTAAT	0.378																																					p.L477V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1429G	11						.						80.0	69.0	73.0					11																	110454448		2201	4298	6499	109959658	SO:0001583	missense	57569	exon14			AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"""Rho GTPase activating proteins"""	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.1429C>G	11.37:g.110454448G>C	ENSP00000260283:p.Leu477Val	Somatic		Capture	Illumina HiSeq	Phase_I	109959658	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.093022	0.76756	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99	5.56	5.56	0.83823	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.077679	0.52532	D	0.000074	T	0.74344	0.3704	M	0.92738	3.34	0.46241	D	0.998947	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.79108	0.98;0.992;0.98	T	0.80320	-0.1432	10	0.87932	D	0	.	19.8892	0.96923	0.0:0.0:1.0:0.0	.	451;477;454	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	V	477;451;20;454;441;451;441	ENSP00000260283:L477V;ENSP00000349660:L451V;ENSP00000437905:L20V;ENSP00000432076:L454V;ENSP00000436319:L441V;ENSP00000436522:L451V;ENSP00000431399:L441V	ENSP00000260283:L477V	L	-	1	0	ARHGAP20	109959658	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.042000	0.76565	2.777000	0.95525	0.591000	0.81541	CTT		0.378	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809	
HTR3B	9177	broad.mit.edu	37	11	113813713	113813713	+	Missense_Mutation	SNP	C	C	T	rs150117061		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:113813713C>T	ENST00000260191.2	+	7	963	c.706C>T	c.(706-708)Cgc>Tgc	p.R236C	HTR3B_ENST00000537778.1_Missense_Mutation_p.R225C	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	236					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)	p.R236C(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	GGTGGTGATGCGCAGGCACCC	0.547																																					p.R236C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C706T	11						.	C	CYS/ARG	0,4402		0,0,2201	73.0	61.0	65.0		706	5.3	1.0	11	dbSNP_134	65	2,8590	2.2+/-6.3	0,2,4294	yes	missense	HTR3B	NM_006028.4	180	0,2,6495	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	236/442	113813713	2,12992	2201	4296	6497	113318923	SO:0001583	missense	9177	exon7			AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5298	protein-coding gene	gene with protein product		604654	"""5-hydroxytryptamine (serotonin) receptor 3B"""			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.706C>T	11.37:g.113813713C>T	ENSP00000260191:p.Arg236Cys	Somatic		Capture	Illumina HiSeq	Phase_I	113318923	NM_006028	B0YJ23|Q0VJC3	Missense_Mutation	SNP	ENST00000260191.2	37	CCDS8364.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.364590	0.61513	0.0	2.33E-4	ENSG00000149305	ENST00000260191;ENST00000537778	T;T	0.80824	-1.42;-1.42	5.32	5.32	0.75619	Neurotransmitter-gated ion-channel ligand-binding (3);	0.053906	0.85682	D	0.000000	D	0.92909	0.7744	M	0.94142	3.5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	D	0.94659	0.7846	10	0.87932	D	0	-11.154	18.9886	0.92782	0.0:1.0:0.0:0.0	.	225;236	O95264-2;O95264	.;5HT3B_HUMAN	C	236;225	ENSP00000260191:R236C;ENSP00000443118:R225C	ENSP00000260191:R236C	R	+	1	0	HTR3B	113318923	1.000000	0.71417	0.995000	0.50966	0.051000	0.14879	4.676000	0.61627	2.501000	0.84356	0.585000	0.79938	CGC		0.547	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028	
PCSK7	9159	broad.mit.edu	37	11	117100205	117100205	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:117100205G>A	ENST00000320934.3	-	3	986	c.356C>T	c.(355-357)gCt>gTt	p.A119V		NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	119					peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.A119V(1)		NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		AGCCAACACAGCCTCCACCTG	0.657			T	IGH@	MLCLS																																p.A119V			Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C356T	11						.						60.0	63.0	62.0					11																	117100205		2201	4296	6497	116605415	SO:0001583	missense	9159	exon3			U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.356C>T	11.37:g.117100205G>A	ENSP00000325917:p.Ala119Val	Somatic		Capture	Illumina HiSeq	Phase_I	116605415	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Missense_Mutation	SNP	ENST00000320934.3	37	CCDS8382.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.628620	0.28978	.	.	ENSG00000160613	ENST00000320934;ENST00000543900;ENST00000525027	T;T	0.30448	1.53;1.53	4.06	3.15	0.36227	Proteinase inhibitor, propeptide (1);	0.352460	0.28927	N	0.013689	T	0.21307	0.0513	L	0.40543	1.245	0.23889	N	0.996553	B	0.18013	0.025	B	0.15484	0.013	T	0.13656	-1.0501	10	0.33940	T	0.23	-8.3474	6.0717	0.19893	0.0991:0.0:0.7155:0.1854	.	119	Q16549	PCSK7_HUMAN	V	119	ENSP00000325917:A119V;ENSP00000431181:A119V	ENSP00000325917:A119V	A	-	2	0	PCSK7	116605415	0.846000	0.29590	0.285000	0.24819	0.758000	0.43043	3.229000	0.51278	0.928000	0.37168	0.462000	0.41574	GCT		0.657	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
DSCAML1	57453	broad.mit.edu	37	11	117392072	117392072	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:117392072C>T	ENST00000321322.6	-	6	1167	c.1166G>A	c.(1165-1167)gGc>gAc	p.G389D	DSCAML1_ENST00000527706.1_Missense_Mutation_p.G119D	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	329	Ig-like C2-type 4.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.G389D(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GACCGTGCTGCCAATGCCGGT	0.612																																					p.G389D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1166A	11						.						44.0	41.0	42.0					11																	117392072		2201	4296	6497	116897282	SO:0001583	missense	57453	exon6				CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.1166G>A	11.37:g.117392072C>T	ENSP00000315465:p.Gly389Asp	Somatic		Capture	Illumina HiSeq	Phase_I	116897282	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.869589	0.91587	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.80566	-1.39;-1.39	4.5	4.5	0.54988	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.90655	0.7069	M	0.89658	3.05	0.58432	D	0.999997	D;D	0.58268	0.982;0.975	P;D	0.63113	0.856;0.911	D	0.92412	0.5938	9	0.56958	D	0.05	.	17.3845	0.87413	0.0:1.0:0.0:0.0	.	119;329	G3V1B5;Q8TD84	.;DSCL1_HUMAN	D	119;389;96	ENSP00000434335:G119D;ENSP00000315465:G389D	ENSP00000315465:G389D	G	-	2	0	DSCAML1	116897282	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.562000	0.82300	2.333000	0.79357	0.609000	0.83330	GGC		0.612	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
DSCAML1	57453	broad.mit.edu	37	11	117395707	117395707	+	Silent	SNP	C	C	T	rs142205484	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:117395707C>T	ENST00000321322.6	-	5	931	c.930G>A	c.(928-930)tcG>tcA	p.S310S	DSCAML1_ENST00000527706.1_Silent_p.S40S	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	250					axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.S310S(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		TAGGGTAGCCCGAGGCGGTGC	0.677																																					p.S310S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G930A	11						.	C		0,4400		0,0,2200	21.0	21.0	21.0		930	-9.9	0.2	11	dbSNP_134	21	2,8584		0,2,4291	no	coding-synonymous	DSCAML1	NM_020693.2		0,2,6491	TT,TC,CC		0.0233,0.0,0.0154		310/2114	117395707	2,12984	2200	4293	6493	116900917	SO:0001819	synonymous_variant	57453	exon5				CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.930G>A	11.37:g.117395707C>T		Somatic		Capture	Illumina HiSeq	Phase_I	116900917	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																				0.677	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
CD3G	917	broad.mit.edu	37	11	118222367	118222367	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:118222367C>T	ENST00000532917.1	+	5	532	c.464C>T	c.(463-465)cCc>cTc	p.P155L	CD3G_ENST00000392883.2_Missense_Mutation_p.P51L|CD3G_ENST00000532903.1_3'UTR	NM_000073.2	NP_000064.1	P09693	CD3G_HUMAN	CD3g molecule, gamma (CD3-TCR complex)	155	ITAM. {ECO:0000255|PROSITE- ProRule:PRU00379}.				cell surface receptor signaling pathway (GO:0007166)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|protein transport (GO:0015031)|regulation of immune response (GO:0050776)|regulation of lymphocyte apoptotic process (GO:0070228)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|receptor signaling complex scaffold activity (GO:0030159)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)	p.P155L(1)		breast(2)|kidney(1)|large_intestine(2)|skin(1)	6	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)	Muromonab(DB00075)	ACTCTGTTGCCCAATGACCAG	0.393																																					p.P155L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C464T	11						.						156.0	152.0	153.0					11																	118222367		2200	4296	6496	117727577	SO:0001583	missense	917	exon5			X60491	CCDS8395.1	11q23	2014-09-17	2006-03-28		ENSG00000160654	ENSG00000160654		"""CD molecules"""	1675	protein-coding gene	gene with protein product		186740	"""CD3g antigen, gamma polypeptide (TiT3 complex)"""				Standard	NM_000073		Approved		uc001psu.2	P09693	OTTHUMG00000166971	ENST00000532917.1:c.464C>T	11.37:g.118222367C>T	ENSP00000431445:p.Pro155Leu	Somatic		Capture	Illumina HiSeq	Phase_I	117727577	NM_000073	Q2HIZ6	Missense_Mutation	SNP	ENST00000532917.1	37	CCDS8395.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.233887	0.39498	.	.	ENSG00000160654	ENST00000392883;ENST00000532917	T;T	0.56275	1.0;0.47	5.74	3.81	0.43845	.	0.679567	0.14861	N	0.294061	T	0.32585	0.0834	N	0.19112	0.55	0.40838	D	0.983648	P	0.38922	0.651	B	0.30401	0.115	T	0.04481	-1.0948	10	0.25106	T	0.35	.	11.2815	0.49197	0.3442:0.6558:0.0:0.0	.	155	P09693	CD3G_HUMAN	L	51;155	ENSP00000376621:P51L;ENSP00000431445:P155L	ENSP00000376621:P51L	P	+	2	0	CD3G	117727577	0.996000	0.38824	0.999000	0.59377	0.990000	0.78478	1.677000	0.37576	0.723000	0.32274	0.650000	0.86243	CCC		0.393	CD3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392135.1	NM_000073	
UBE4A	9354	broad.mit.edu	37	11	118245939	118245939	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:118245939T>C	ENST00000431736.2	+	9	1538	c.1466T>C	c.(1465-1467)aTg>aCg	p.M489T	UBE4A_ENST00000252108.3_Missense_Mutation_p.M482T					ubiquitination factor E4A									p.M489T(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		AATGTACACATGAGAGGTAGG	0.423																																					p.M489T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1466C	11						.						43.0	40.0	41.0					11																	118245939		2200	4296	6496	117751149	SO:0001583	missense	9354	exon9			D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"""U-box domain containing"""	12499	protein-coding gene	gene with protein product		603753	"""ubiquitination factor E4A (homologous to yeast UFD2)"", ""ubiquitination factor E4A (UFD2 homolog, yeast)"""			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.1466T>C	11.37:g.118245939T>C	ENSP00000387362:p.Met489Thr	Somatic		Capture	Illumina HiSeq	Phase_I	117751149	NM_004788		Missense_Mutation	SNP	ENST00000431736.2	37	CCDS8396.1	.	.	.	.	.	.	.	.	.	.	T	13.46	2.244524	0.39697	.	.	ENSG00000110344	ENST00000252108;ENST00000431736	T;T	0.43294	0.95;0.95	5.85	5.85	0.93711	Ubiquitin conjugation factor E4, core (1);	0.200098	0.64402	D	0.000007	T	0.38931	0.1059	L	0.52905	1.665	0.80722	D	1	B;B	0.23990	0.01;0.095	B;B	0.21917	0.01;0.037	T	0.23547	-1.0185	10	0.12430	T	0.62	-18.6432	16.2268	0.82300	0.0:0.0:0.0:1.0	.	482;489	Q14139;Q14139-2	UBE4A_HUMAN;.	T	482;489	ENSP00000252108:M482T;ENSP00000387362:M489T	ENSP00000252108:M482T	M	+	2	0	UBE4A	117751149	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.716000	0.61916	2.242000	0.73789	0.402000	0.26972	ATG		0.423	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788	
KMT2A	4297	broad.mit.edu	37	11	118392685	118392685	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:118392685G>A	ENST00000389506.5	+	36	11708	c.11708G>A	c.(11707-11709)cGc>cAc	p.R3903H	RP11-770J1.3_ENST00000554407.1_RNA|KMT2A_ENST00000354520.4_Missense_Mutation_p.R3865H|RP11-770J1.3_ENST00000528578.1_RNA|RP11-770J1.3_ENST00000556583.1_RNA|RP11-770J1.3_ENST00000525992.2_RNA|RP11-770J1.3_ENST00000532597.1_RNA|KMT2A_ENST00000534358.1_Missense_Mutation_p.R3906H			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3903	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.R3903H(1)									AATGCTGCACGCTTCATCAAT	0.468																																					p.R3903H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G11708A	11						.						178.0	140.0	153.0					11																	118392685		2200	4295	6495	117897895	SO:0001583	missense	4297	exon36			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.11708G>A	11.37:g.118392685G>A	ENSP00000374157:p.Arg3903His	Somatic		Capture	Illumina HiSeq	Phase_I	117897895	NM_005933	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.085105	0.76642	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.85955	-2.05;-2.05;-2.05	5.5	5.5	0.81552	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.94321	0.8175	M	0.91038	3.17	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94834	0.7999	10	0.87932	D	0	.	19.5916	0.95514	0.0:0.0:1.0:0.0	.	3906;3903	E9PQG7;Q03164	.;MLL1_HUMAN	H	3906;3903;3865;2813	ENSP00000436786:R3906H;ENSP00000374157:R3903H;ENSP00000346516:R3865H	ENSP00000346516:R3865H	R	+	2	0	MLL	117897895	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.657000	0.98554	2.861000	0.98227	0.655000	0.94253	CGC		0.468	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
FOXR1	283150	broad.mit.edu	37	11	118851224	118851224	+	Silent	SNP	G	G	A	rs372574100		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:118851224G>A	ENST00000317011.3	+	5	861	c.636G>A	c.(634-636)acG>acA	p.T212T		NM_181721.2	NP_859072.1	Q6PIV2	FOXR1_HUMAN	forkhead box R1	212					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T212T(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		TTTTCCGGACGGCCCCGGAAG	0.552																																					p.T212T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G636A	11						.	G		0,4400		0,0,2200	62.0	67.0	65.0		636	1.4	1.0	11		65	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	FOXR1	NM_181721.2		0,1,6494	AA,AG,GG		0.0116,0.0,0.0077		212/293	118851224	1,12989	2200	4295	6495	118356434	SO:0001819	synonymous_variant	283150	exon5			AB094092	CCDS31688.1	11q23.3	2008-02-05			ENSG00000176302	ENSG00000176302		"""Forkhead boxes"""	29980	protein-coding gene	gene with protein product		615755				15067358	Standard	XM_005271514		Approved	DLNB13, FOXN5	uc001pui.3	Q6PIV2	OTTHUMG00000166347	ENST00000317011.3:c.636G>A	11.37:g.118851224G>A		Somatic		Capture	Illumina HiSeq	Phase_I	118356434	NM_181721	B0YJ15|Q08AS8|Q86UT9|Q8IXX2	Silent	SNP	ENST00000317011.3	37	CCDS31688.1																																																																																				0.552	FOXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389312.1	NM_181721	
TRAPPC4	51399	broad.mit.edu	37	11	118889654	118889654	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:118889654C>T	ENST00000533632.1	+	1	513	c.149C>T	c.(148-150)gCt>gTt	p.A50V	TRAPPC4_ENST00000533058.1_Missense_Mutation_p.A50V|TRAPPC4_ENST00000528230.1_Missense_Mutation_p.A50V|TRAPPC4_ENST00000359005.4_Missense_Mutation_p.A50V|RPS25_ENST00000528547.1_5'Flank|RPS25_ENST00000527673.1_5'Flank|TRAPPC4_ENST00000434101.2_Missense_Mutation_p.A50V|MIR3656_ENST00000577421.1_RNA|TRAPPC4_ENST00000525303.1_Missense_Mutation_p.A50V	NM_016146.4	NP_057230.1	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4	50					dendrite development (GO:0016358)|ER to Golgi vesicle-mediated transport (GO:0006888)|extracellular matrix organization (GO:0030198)	cis-Golgi network (GO:0005801)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi stack (GO:0005795)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)|TRAPP complex (GO:0030008)		p.A50V(1)		NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		GTGTTGGTTGCTTTCGGCCAG	0.627																																					p.A50V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C149T	11						.						72.0	70.0	71.0					11																	118889654		2200	4295	6495	118394864	SO:0001583	missense	51399	exon1			AF078862	CCDS8407.1	11q23.3	2011-10-10				ENSG00000196655		"""Trafficking protein particle complex"""	19943	protein-coding gene	gene with protein product		610971				10810093	Standard	NM_016146		Approved	TRS23, SBDN, PTD009	uc010ryo.2	Q9Y296		ENST00000533632.1:c.149C>T	11.37:g.118889654C>T	ENSP00000436005:p.Ala50Val	Somatic		Capture	Illumina HiSeq	Phase_I	118394864	NM_016146	A8K3A5|B4DME1	Missense_Mutation	SNP	ENST00000533632.1	37	CCDS8407.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.708425	0.68615	.	.	ENSG00000196655	ENST00000533632;ENST00000528230;ENST00000525303;ENST00000434101;ENST00000359005;ENST00000533058	T;T;T;T;T;T	0.81415	-1.37;-1.43;-1.49;1.11;0.96;0.91	5.86	5.86	0.93980	Longin-like (1);	0.100911	0.64402	D	0.000001	T	0.71710	0.3372	L	0.31578	0.945	0.80722	D	1	B;B;B;B	0.30741	0.007;0.011;0.01;0.293	B;B;B;B	0.21546	0.008;0.016;0.003;0.035	T	0.66976	-0.5787	10	0.24483	T	0.36	-10.516	19.79	0.96453	0.0:1.0:0.0:0.0	.	50;50;50;50	B4DF86;B4DME1;Q9Y296;B4DF36	.;.;TPPC4_HUMAN;.	V	50	ENSP00000436005:A50V;ENSP00000436827:A50V;ENSP00000435339:A50V;ENSP00000405033:A50V;ENSP00000351896:A50V;ENSP00000432920:A50V	ENSP00000351896:A50V	A	+	2	0	TRAPPC4	118394864	1.000000	0.71417	0.980000	0.43619	0.991000	0.79684	7.482000	0.81143	2.784000	0.95788	0.655000	0.94253	GCT		0.627	TRAPPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389332.1	NM_016146	
HYOU1	10525	broad.mit.edu	37	11	118922623	118922623	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:118922623C>T	ENST00000404233.3	-	12	1370	c.1246G>A	c.(1246-1248)Gcc>Acc	p.A416T	HYOU1_ENST00000525859.1_Missense_Mutation_p.A416T|HYOU1_ENST00000529972.1_Missense_Mutation_p.A416T|HYOU1_ENST00000543287.1_Missense_Mutation_p.A329T	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	416					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)	p.A416T(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		GCCCCCATGGCGGCTGCTTCA	0.582																																					p.A416T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1246A	11						.						77.0	76.0	76.0					11																	118922623		2200	4295	6495	118427833	SO:0001583	missense	10525	exon12			U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"""Heat shock proteins / HSP70"""	16931	protein-coding gene	gene with protein product	"""glucose-regulated protein 170"""	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.1246G>A	11.37:g.118922623C>T	ENSP00000384144:p.Ala416Thr	Somatic		Capture	Illumina HiSeq	Phase_I	118427833	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Missense_Mutation	SNP	ENST00000404233.3	37	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.816749	0.70912	.	.	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000536103;ENST00000535579;ENST00000525859;ENST00000544701;ENST00000543287;ENST00000530473	T;T;T;T;T	0.01854	4.6;4.6;4.6;4.6;4.6	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.15305	0.0369	M	0.84585	2.705	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79108	0.992;0.98;0.992;0.992	T	0.00383	-1.1774	10	0.48119	T	0.1	-20.2164	18.7611	0.91851	0.0:1.0:0.0:0.0	.	407;460;416;416	B3KXH0;B7Z2N4;Q9Y4L1;A8C1Z0	.;.;HYOU1_HUMAN;.	T	416;407;416;416;265;416;459;329;416	ENSP00000384144:A416T;ENSP00000437313:A416T;ENSP00000433397:A416T;ENSP00000442727:A329T;ENSP00000431874:A416T	ENSP00000278752:A407T	A	-	1	0	HYOU1	118427833	1.000000	0.71417	0.779000	0.31741	0.466000	0.32739	5.537000	0.67186	2.735000	0.93741	0.655000	0.94253	GCC		0.582	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389	
VPS11	55823	broad.mit.edu	37	11	118949547	118949547	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:118949547C>A	ENST00000300793.6	+	14	2145	c.2103C>A	c.(2101-2103)taC>taA	p.Y701*	VPS11_ENST00000527798.1_3'UTR	NM_021729.4	NP_068375.3	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11 homolog (S. cerevisiae)	702					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)	p.Y701*(3)		autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	29	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)		ACGAGCAGTACCGGCAGGTCA	0.607																																					p.T702N												.	.	3	Substitution - Nonsense(3)	endometrium(2)|large_intestine(1)	c.C2105A	11						.																																			118454757	SO:0001587	stop_gained	55823	exon13			AB027508	CCDS73404.1	11q23	2008-02-05	2006-12-19			ENSG00000160695		"""RING-type (C3HC4) zinc fingers"""	14583	protein-coding gene	gene with protein product		608549	"""vacuolar protein sorting 11 (yeast homolog)"""				Standard	NM_021729		Approved	RNF108, PEP5	uc010ryx.2	Q9H270		ENST00000300793.6:c.2103C>A	11.37:g.118949547C>A	ENSP00000475301:p.Tyr701*	Somatic		Capture	Illumina HiSeq	Phase_I	118454757	NM_021729	Q8WY89|Q96EP8|Q9H6D9|Q9HCS6	Nonsense_Mutation	SNP	ENST00000300793.6	37																																																																																					0.607	VPS11-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021729	
NLRX1	79671	broad.mit.edu	37	11	119054600	119054600	+	3'UTR	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:119054600C>T	ENST00000409109.1	+	0	3967				NLRX1_ENST00000525863.1_Missense_Mutation_p.P893S|NLRX1_ENST00000409991.1_3'UTR|NLRX1_ENST00000409265.4_Missense_Mutation_p.P893S|PDZD3_ENST00000525131.1_5'Flank|PDZD3_ENST00000355547.5_5'Flank|PDZD3_ENST00000392817.2_5'Flank|NLRX1_ENST00000292199.2_3'UTR|PDZD3_ENST00000322712.4_5'Flank|PDZD3_ENST00000531114.1_5'Flank	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1						innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)	p.P893S(1)		cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		ACCGAGGATGCCCTCACATTG	0.562																																					p.P893S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2677T	11						.						107.0	108.0	107.0					11																	119054600		2144	4252	6396	118559810	SO:0001624	3_prime_UTR_variant	79671	exon10			AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"""Nucleotide-binding domain and leucine rich repeat containing"""	29890	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat containing X1"", ""NOD-like receptor X1"", ""NLR family, X1"""	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.*452C>T	11.37:g.119054600C>T		Somatic		Capture	Illumina HiSeq	Phase_I	118559810	NM_170722	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	.	.	.	.	.	.	.	.	.	.	C	9.540	1.113180	0.20795	.	.	ENSG00000160703	ENST00000409265;ENST00000525863	T;T	0.69806	-0.43;-0.43	4.62	3.69	0.42338	.	.	.	.	.	T	0.46308	0.1386	.	.	.	0.09310	N	1	P	0.36909	0.573	B	0.33521	0.165	T	0.18903	-1.0322	8	0.13470	T	0.59	.	10.0618	0.42279	0.2012:0.7988:0.0:0.0	.	893	Q86UT6-2	.	S	893	ENSP00000386858:P893S;ENSP00000433442:P893S	ENSP00000386858:P893S	P	+	1	0	NLRX1	118559810	0.254000	0.23992	0.068000	0.19968	0.139000	0.21198	1.090000	0.30902	1.275000	0.44379	0.543000	0.68304	CCC		0.562	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722	
ARHGEF12	23365	broad.mit.edu	37	11	120292555	120292555	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:120292555C>T	ENST00000397843.2	+	6	508	c.342C>T	c.(340-342)atC>atT	p.I114I	ARHGEF12_ENST00000356641.3_Silent_p.I95I|ARHGEF12_ENST00000532993.1_Silent_p.I11I	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	114	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.I114I(1)		NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		GTGATCGAATCATCAAGGTAA	0.328			T	MLL	AML																																p.I95I			Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C285T	11						.						101.0	96.0	98.0					11																	120292555		1862	4109	5971	119797765	SO:0001819	synonymous_variant	23365	exon5			AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"""Rho guanine nucleotide exchange factors"""	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.342C>T	11.37:g.120292555C>T		Somatic		Capture	Illumina HiSeq	Phase_I	119797765	NM_001198665	O15086|Q6P526	Silent	SNP	ENST00000397843.2	37	CCDS41727.1																																																																																				0.328	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313	
MUC5B	727897	broad.mit.edu	37	11	1268596	1268596	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:1268596G>A	ENST00000529681.1	+	31	10544	c.10486G>A	c.(10486-10488)Gca>Aca	p.A3496T	MUC5B_ENST00000447027.1_Missense_Mutation_p.A3499T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3496	7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.A3475T(1)		cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCACACCCCAGCAGCAACCAC	0.652																																					p.A3496T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G10486A	11						.						102.0	121.0	115.0					11																	1268596		2122	4215	6337	1225172	SO:0001583	missense	727897	exon31			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.10486G>A	11.37:g.1268596G>A	ENSP00000436812:p.Ala3496Thr	Somatic		Capture	Illumina HiSeq	Phase_I	1225172	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	g	6.670	0.492233	0.12702	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17691	2.26;2.57	2.14	-2.68	0.06041	.	.	.	.	.	T	0.14657	0.0354	L	0.47716	1.5	0.09310	N	1	P;B	0.39352	0.669;0.01	B;B	0.38458	0.274;0.004	T	0.18493	-1.0335	9	0.87932	D	0	.	8.88	0.35370	0.8099:0.0:0.1901:0.0	.	4024;3499	A7Y9J9;E9PBJ0	.;.	T	3496;3499;3468;3401	ENSP00000436812:A3496T;ENSP00000415793:A3499T	ENSP00000343037:A3468T	A	+	1	0	MUC5B	1225172	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.954000	0.00676	-0.508000	0.06540	0.297000	0.19635	GCA		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
MUC5B	727897	broad.mit.edu	37	11	1269624	1269624	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:1269624C>T	ENST00000529681.1	+	31	11572	c.11514C>T	c.(11512-11514)acC>acT	p.T3838T	MUC5B_ENST00000447027.1_Silent_p.T3841T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3838	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.T3817T(1)		cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CAGTGCTTACCACCACGGCCA	0.637																																					p.T3838T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C11514T	11						.						160.0	187.0	178.0					11																	1269624		2125	4208	6333	1226200	SO:0001819	synonymous_variant	727897	exon31			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.11514C>T	11.37:g.1269624C>T		Somatic		Capture	Illumina HiSeq	Phase_I	1226200	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																				0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
TECTA	7007	broad.mit.edu	37	11	121000423	121000423	+	Missense_Mutation	SNP	C	C	T	rs111759871	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:121000423C>T	ENST00000392793.1	+	10	2715	c.2444C>T	c.(2443-2445)aCg>aTg	p.T815M	TECTA_ENST00000264037.2_Missense_Mutation_p.T815M			O75443	TECTA_HUMAN	tectorin alpha	815	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.		T -> M (in DFNA12). {ECO:0000269|PubMed:21520338}.		cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.T815M(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		AAAAACAGTACGACAGTGGAG	0.453													C|||	3	0.000599042	0.0015	0.0014	5008	,	,		20738	0.0		0.0	False		,,,				2504	0.0				p.T815M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2444T	11						.	C	MET/THR	11,4395	17.9+/-39.9	1,9,2193	163.0	161.0	162.0		2444	5.6	0.9	11	dbSNP_132	162	0,8598		0,0,4299	yes	missense	TECTA	NM_005422.2	81	1,9,6492	TT,TC,CC		0.0,0.2497,0.0846	probably-damaging	815/2156	121000423	11,12993	2203	4299	6502	120505633	SO:0001583	missense	7007	exon9			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.2444C>T	11.37:g.121000423C>T	ENSP00000376543:p.Thr815Met	Somatic		Capture	Illumina HiSeq	Phase_I	120505633	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	22.4	4.285019	0.80803	0.002497	0.0	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.60171	0.21;0.21	5.56	5.56	0.83823	von Willebrand factor, type D domain (3);	0.000000	0.85682	D	0.000000	T	0.74718	0.3753	M	0.69823	2.125	0.53005	D	0.999964	D	0.71674	0.998	D	0.63793	0.918	T	0.74569	-0.3622	10	0.48119	T	0.1	.	19.5308	0.95228	0.0:1.0:0.0:0.0	.	815	O75443	TECTA_HUMAN	M	815	ENSP00000376543:T815M;ENSP00000264037:T815M	ENSP00000264037:T815M	T	+	2	0	TECTA	120505633	1.000000	0.71417	0.891000	0.34965	0.921000	0.55340	5.420000	0.66441	2.630000	0.89119	0.563000	0.77884	ACG		0.453	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
ZNF202	7753	broad.mit.edu	37	11	123600516	123600516	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:123600516G>A	ENST00000529691.1	-	3	639	c.420C>T	c.(418-420)caC>caT	p.H140H	ZNF202_ENST00000336139.4_Silent_p.H140H|ZNF202_ENST00000530393.1_Silent_p.H140H			O95125	ZN202_HUMAN	zinc finger protein 202	140					lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H140H(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		CTTCCTGGCCGTGAACATGGA	0.522																																					p.H140H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C420T	11						.						66.0	60.0	62.0					11																	123600516		2202	4299	6501	123105726	SO:0001819	synonymous_variant	7753	exon5			AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.420C>T	11.37:g.123600516G>A		Somatic		Capture	Illumina HiSeq	Phase_I	123105726	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	De_novo_Start_OutOfFrame	SNP	ENST00000529691.1	37	CCDS8443.1																																																																																				0.522	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455	
OR4D5	219875	broad.mit.edu	37	11	123810333	123810333	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:123810333G>T	ENST00000307033.2	+	1	84	c.10G>T	c.(10-12)Gca>Tca	p.A4S		NM_001001965.1	NP_001001965.1	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D, member 5	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A4S(1)		autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GATGAATCCAGCAAATCATTC	0.413																																					p.A4S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G10T	11						.						84.0	85.0	85.0					11																	123810333		2202	4299	6501	123315543	SO:0001583	missense	219875	exon1			BK004316	CCDS31699.1	11q24.1	2012-08-09			ENSG00000171014	ENSG00000171014		"""GPCR / Class A : Olfactory receptors"""	14852	protein-coding gene	gene with protein product							Standard	NM_001001965		Approved		uc001pzk.1	Q8NGN0	OTTHUMG00000165961	ENST00000307033.2:c.10G>T	11.37:g.123810333G>T	ENSP00000305970:p.Ala4Ser	Somatic		Capture	Illumina HiSeq	Phase_I	123315543	NM_001001965	B9EGZ4|Q6IFE6	Missense_Mutation	SNP	ENST00000307033.2	37	CCDS31699.1	.	.	.	.	.	.	.	.	.	.	G	1.551	-0.539351	0.04053	.	.	ENSG00000171014	ENST00000307033	T	0.20200	2.09	5.01	2.07	0.26955	.	0.849423	0.09992	N	0.729640	T	0.09642	0.0237	N	0.12831	0.26	0.25355	N	0.988835	B	0.06786	0.001	B	0.09377	0.004	T	0.42103	-0.9471	10	0.12103	T	0.63	-0.7981	4.6562	0.12618	0.1861:0.0:0.6416:0.1723	.	4	Q8NGN0	OR4D5_HUMAN	S	4	ENSP00000305970:A4S	ENSP00000305970:A4S	A	+	1	0	OR4D5	123315543	0.000000	0.05858	0.871000	0.34182	0.494000	0.33585	0.002000	0.13061	0.139000	0.18822	-0.253000	0.11424	GCA		0.413	OR4D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387263.1	NM_001001965	
VWA5A	4013	broad.mit.edu	37	11	124012443	124012443	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:124012443G>A	ENST00000456829.2	+	16	2269	c.2018G>A	c.(2017-2019)aGt>aAt	p.S673N	VWA5A_ENST00000360334.4_3'UTR|VWA5A_ENST00000392748.1_Missense_Mutation_p.S673N	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	673								p.S673N(1)		autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						GACCAGCACAGTCCAGGTGAG	0.428																																					p.S673N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2018A	11						.						172.0	144.0	153.0					11																	124012443		2201	4299	6500	123517653	SO:0001583	missense	4013	exon15			AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"""loss of heterozygosity, 11, chromosomal region 2, gene A"""	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.2018G>A	11.37:g.124012443G>A	ENSP00000407726:p.Ser673Asn	Somatic		Capture	Illumina HiSeq	Phase_I	123517653	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Missense_Mutation	SNP	ENST00000456829.2	37	CCDS8444.1	.	.	.	.	.	.	.	.	.	.	G	3.207	-0.162469	0.06502	.	.	ENSG00000110002	ENST00000456829;ENST00000392748	T;T	0.04015	3.73;3.73	3.11	-3.47	0.04753	.	6.438870	0.00357	N	0.000025	T	0.02230	0.0069	N	0.08118	0	0.09310	N	0.999998	B	0.28233	0.204	B	0.23419	0.046	T	0.34750	-0.9816	10	0.18276	T	0.48	15.5635	1.2568	0.01993	0.1425:0.2378:0.3579:0.2617	.	673	O00534	VMA5A_HUMAN	N	673	ENSP00000407726:S673N;ENSP00000376504:S673N	ENSP00000376504:S673N	S	+	2	0	VWA5A	123517653	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-1.551000	0.02178	-0.719000	0.04942	0.313000	0.20887	AGT		0.428	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622	
OR8B4	283162	broad.mit.edu	37	11	124294095	124294095	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:124294095G>T	ENST00000356130.3	-	1	694	c.673C>A	c.(673-675)Ctc>Atc	p.L225I		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L225I(1)		endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GGAATACAGAGGATGTTGGAG	0.453																																					p.L225I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C673A	11						.						82.0	73.0	76.0					11																	124294095		2201	4299	6500	123799305	SO:0001583	missense	283162	exon1			AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.673C>A	11.37:g.124294095G>T	ENSP00000348449:p.Leu225Ile	Somatic		Capture	Illumina HiSeq	Phase_I	123799305	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	.	.	.	.	.	.	.	.	.	.	g	9.444	1.088722	0.20390	.	.	ENSG00000198657	ENST00000356130	T	0.00302	8.2	4.14	4.14	0.48551	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45361	D	0.000372	T	0.00328	0.0010	M	0.76328	2.33	0.09310	N	1	B	0.18013	0.025	B	0.24269	0.052	T	0.38845	-0.9642	10	0.72032	D	0.01	.	13.2434	0.60010	0.0:0.0:0.8402:0.1598	.	225	Q96RC9	OR8B4_HUMAN	I	225	ENSP00000348449:L225I	ENSP00000348449:L225I	L	-	1	0	OR8B4	123799305	0.009000	0.17119	0.940000	0.37924	0.567000	0.35839	0.859000	0.27858	2.610000	0.88304	0.655000	0.94253	CTC		0.453	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
STT3A	3703	broad.mit.edu	37	11	125482587	125482587	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:125482587G>A	ENST00000529196.1	+	13	1516	c.1310G>A	c.(1309-1311)cGt>cAt	p.R437H	STT3A_ENST00000392708.4_Missense_Mutation_p.R437H|STT3A_ENST00000531491.1_Missense_Mutation_p.R345H			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	437					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.R437H(1)		NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		GACATAAGTCGTCCAGACAAG	0.453																																					p.R437H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1310A	11						.						154.0	131.0	139.0					11																	125482587		2201	4299	6500	124987797	SO:0001583	missense	3703	exon12			BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"""dolichyl-diphosphooligosaccharide protein glycotransferase"""	601134	"""integral membrane protein 1"", ""STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)"", ""STT3A, cataylic subunit of the oligosaccharyltransferase complex"""	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.1310G>A	11.37:g.125482587G>A	ENSP00000436962:p.Arg437His	Somatic		Capture	Illumina HiSeq	Phase_I	124987797	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Missense_Mutation	SNP	ENST00000529196.1	37	CCDS8458.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.5|23.5	4.424267|4.424267	0.83667|0.83667	.|.	.|.	ENSG00000134910|ENSG00000134910	ENST00000392708;ENST00000529196;ENST00000531491|ENST00000526726	.|.	.|.	.|.	5.97|5.97	5.97|5.97	0.96955|0.96955	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.54013|0.54013	0.1832|0.1832	N|N	0.16903|0.16903	0.455|0.455	0.80722|0.80722	D|D	1|1	D;B|.	0.54397|.	0.966;0.009|.	P;B|.	0.46026|.	0.501;0.026|.	T|T	0.45716|0.45716	-0.9242|-0.9242	9|5	0.45353|.	T|.	0.12|.	-9.6811|-9.6811	20.0492|20.0492	0.97617|0.97617	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	345;437|.	B4DJ24;P46977|.	.;STT3A_HUMAN|.	H|I	437;437;345|149	.|.	ENSP00000376472:R437H|.	R|V	+|+	2|1	0|0	STT3A|STT3A	124987797|124987797	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.845000|9.845000	0.99498|0.99498	2.836000|2.836000	0.97738|0.97738	0.655000|0.655000	0.94253|0.94253	CGT|GTC		0.453	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713	
TIRAP	114609	broad.mit.edu	37	11	126163000	126163000	+	Intron	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:126163000T>C	ENST00000392680.2	+	5	1051				TIRAP_ENST00000392678.3_Silent_p.S232S|TIRAP_ENST00000392679.1_Intron|RP11-712L6.7_ENST00000533378.1_RNA|RP11-712L6.5_ENST00000528876.1_5'Flank	NM_001039661.1	NP_001034750.1	P58753	TIRAP_HUMAN	toll-interleukin 1 receptor (TIR) domain containing adaptor protein						3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 1 production (GO:2000340)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-15 production (GO:0032738)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of innate immune response (GO:0045088)|regulation of interferon-beta production (GO:0032648)|response to lipopolysaccharide (GO:0032496)|TIRAP-dependent toll-like receptor 4 signaling pathway (GO:0035665)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|Toll-like receptor 2 binding (GO:0035663)|Toll-like receptor 4 binding (GO:0035662)	p.S232S(1)		breast(1)|endometrium(1)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0739)		CTACAGTATCTGATCTACTTT	0.507																																					p.S232S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T696C	11						.						42.0	45.0	44.0					11																	126163000		2087	4237	6324	125668210	SO:0001627	intron_variant	114609	exon5			AF378129	CCDS8472.1, CCDS41731.1	11q24.2	2008-02-05	2002-01-14		ENSG00000150455	ENSG00000150455			17192	protein-coding gene	gene with protein product	"""MyD88 adapter-like"""	606252	"""Toll-interleukin 1 receptor (TIR) domain-containing adaptor protein"""			11526399, 11544529	Standard	XM_005271399		Approved	Mal, wyatt	uc001qdl.1	P58753	OTTHUMG00000140373	ENST00000392680.2:c.646+50T>C	11.37:g.126163000T>C		Somatic		Capture	Illumina HiSeq	Phase_I	125668210	NM_148910	B3KW65|Q56UH9|Q56UI0|Q8N5E5	Silent	SNP	ENST00000392680.2	37	CCDS8472.1																																																																																				0.507	TIRAP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000277092.1	NM_148910	
ST14	6768	broad.mit.edu	37	11	130068463	130068463	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:130068463G>A	ENST00000278742.5	+	14	2049	c.1631G>A	c.(1630-1632)tGc>tAc	p.C544Y		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	544	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.C544Y(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	AGCCAGCAGTGCAATGGGAAG	0.657																																					p.C544Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1631A	11						.						56.0	59.0	58.0					11																	130068463		2201	4297	6498	129573673	SO:0001583	missense	6768	exon14			AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"""Serine peptidases / Transmembrane"""	11344	protein-coding gene	gene with protein product	"""epithin"", ""matriptase"""	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.1631G>A	11.37:g.130068463G>A	ENSP00000278742:p.Cys544Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	129573673	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Missense_Mutation	SNP	ENST00000278742.5	37	CCDS8487.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434901	0.62955	.	.	ENSG00000149418	ENST00000278742;ENST00000525779	D	0.99755	-6.64	4.73	4.73	0.59995	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.41605	D	0.000858	D	0.99898	0.9951	H	0.99404	4.55	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95978	0.8975	10	0.66056	D	0.02	.	17.3042	0.87190	0.0:0.0:1.0:0.0	.	544	Q9Y5Y6	ST14_HUMAN	Y	544;446	ENSP00000278742:C544Y	ENSP00000278742:C544Y	C	+	2	0	ST14	129573673	1.000000	0.71417	0.976000	0.42696	0.232000	0.25224	9.834000	0.99428	2.158000	0.67659	0.462000	0.41574	TGC		0.657	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1		
VPS26B	112936	broad.mit.edu	37	11	134104835	134104835	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:134104835G>A	ENST00000281187.5	+	2	746	c.268G>A	c.(268-270)Gtg>Atg	p.V90M	VPS26B_ENST00000525095.2_Missense_Mutation_p.V90M	NM_052875.3	NP_443107.1	Q4G0F5	VP26B_HUMAN	vacuolar protein sorting 26 homolog B (S. pombe)	90					protein transport (GO:0015031)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)		p.V90M(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)	14	all_hematologic(175;0.127)	all_cancers(12;1.1e-21)|all_epithelial(12;3.77e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;2.43e-10)|all cancers(11;2.94e-09)|BRCA - Breast invasive adenocarcinoma(10;9.57e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00164)|Lung(977;0.216)		TGTGTCCCTGGTGAAGGACCT	0.577																																					p.V90M	Colon(171;1263 1952 15904 45703 47982)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G268A	11						.						98.0	91.0	93.0					11																	134104835		2201	4297	6498	133610045	SO:0001583	missense	112936	exon2				CCDS8495.1	11q25	2008-02-05	2007-01-12		ENSG00000151502	ENSG00000151502			28119	protein-coding gene	gene with protein product		610027	"""vacuolar protein sorting 26 homolog B (yeast)"""			16190980	Standard	NM_052875		Approved	MGC10485, Pep8b	uc001qhe.3	Q4G0F5	OTTHUMG00000167175	ENST00000281187.5:c.268G>A	11.37:g.134104835G>A	ENSP00000281187:p.Val90Met	Somatic		Capture	Illumina HiSeq	Phase_I	133610045	NM_052875	Q96A55	Missense_Mutation	SNP	ENST00000281187.5	37	CCDS8495.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.392405	0.83011	.	.	ENSG00000151502	ENST00000281187	T	0.06608	3.28	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.13457	0.0326	M	0.76328	2.33	0.80722	D	1	B	0.27316	0.175	B	0.27380	0.079	T	0.01810	-1.1269	10	0.49607	T	0.09	-19.475	19.6081	0.95588	0.0:0.0:1.0:0.0	.	90	Q4G0F5	VP26B_HUMAN	M	90	ENSP00000281187:V90M	ENSP00000281187:V90M	V	+	1	0	VPS26B	133610045	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.652000	0.90054	0.591000	0.81541	GTG		0.577	VPS26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393591.1	NM_052875	
IFITM3	10410	broad.mit.edu	37	11	320793	320793	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:320793G>T	ENST00000399808.4	-	1	257	c.21C>A	c.(19-21)acC>acA	p.T7T	RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_Intron|RP11-326C3.11_ENST00000508004.2_RNA|IFITM3_ENST00000526811.1_Intron|RP11-326C3.11_ENST00000602429.1_RNA|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.10_ENST00000534271.1_RNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	7					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)		p.T7T(1)		central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		GAGAGAAGAAGGTTTGGACAG	0.597																																					p.T7T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C21A	11						.						129.0	144.0	140.0					11																	320793		1940	4142	6082	310793	SO:0001819	synonymous_variant	10410	exon1			X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"""interferon induced transmembrane protein 3 (1-8U)"""			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.21C>A	11.37:g.320793G>T		Somatic		Capture	Illumina HiSeq	Phase_I	310793	NM_021034	Q53Y76|Q96HK8|Q96J15	Silent	SNP	ENST00000399808.4	37	CCDS41585.1																																																																																				0.597	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034	
AP2A2	161	broad.mit.edu	37	11	970195	970195	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:970195delA	ENST00000448903.2	+	3	304	c.163delA	c.(163-165)aaafs	p.K57fs	AP2A2_ENST00000332231.5_Frame_Shift_Del_p.K57fs|AP2A2_ENST00000534328.1_Frame_Shift_Del_p.K57fs	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	57	Lipid-binding.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)	p.K57fs*24(1)		breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		TGGCTATAGTAAAAAAAAGTA	0.488																																					p.K55fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.163delA	11						.						132.0	134.0	134.0					11																	970195		1937	4154	6091	960195	SO:0001589	frameshift_variant	161	exon3			AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"""alpha-adaptin C; Huntingtin interacting protein J"", ""adaptin, alpha B"", ""clathrin-associated/assembly/adaptor protein, large, alpha 2"""	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.163delA	11.37:g.970195delA	ENSP00000413234:p.Lys57fs	Somatic		Capture	Illumina HiSeq	Phase_I	960195	NM_012305	O75403|Q53ET1|Q96SI8	Frame_Shift_Del	DEL	ENST00000448903.2	37	CCDS44512.1																																																																																				0.488	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305	
NUP98	4928	broad.mit.edu	37	11	3716707	3716707	+	Missense_Mutation	SNP	C	C	T	rs201757730		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:3716707C>T	ENST00000324932.7	-	26	4559	c.4139G>A	c.(4138-4140)cGc>cAc	p.R1380H	NUP98_ENST00000488828.1_5'UTR|NUP98_ENST00000355260.3_Missense_Mutation_p.R1380H|NUP98_ENST00000359171.4_Missense_Mutation_p.R1380H	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1397					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)	p.R1380H(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		AGCAAAGATGCGCAGTCTCTC	0.478			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML																																p.R1380H			Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4139A	11						.						203.0	207.0	206.0					11																	3716707		2201	4298	6499	3673283	SO:0001583	missense	4928	exon26			AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.4139G>A	11.37:g.3716707C>T	ENSP00000316032:p.Arg1380His	Somatic		Capture	Illumina HiSeq	Phase_I	3673283	NM_139132	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	37	CCDS7746.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.670233	0.88348	.	.	ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260	.	.	.	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.83193	0.5201	M	0.82823	2.61	0.44337	D	0.997229	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76575	0.978;0.988;0.982	D	0.85275	0.1058	9	0.59425	D	0.04	-9.8195	17.8098	0.88612	0.0:1.0:0.0:0.0	.	1380;1380;1294	P52948-2;P52948-5;P52948-6	.;.;.	H	1380	.	ENSP00000316032:R1380H	R	-	2	0	NUP98	3673283	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.383000	0.59600	2.515000	0.84797	0.558000	0.71614	CGC		0.478	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
OR52K2	119774	broad.mit.edu	37	11	4471224	4471224	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:4471224T>A	ENST00000325719.4	+	1	700	c.655T>A	c.(655-657)Tct>Act	p.S219T		NM_001005172.2	NP_001005172.2	Q8NGK3	O52K2_HUMAN	olfactory receptor, family 52, subfamily K, member 2	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S219T(1)		NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|skin(6)	25		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.48e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0821)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGTTATCCTGTCTTATATCTT	0.488																																					p.S219T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T655A	11						.						384.0	315.0	339.0					11																	4471224		2201	4298	6499	4427800	SO:0001583	missense	119774	exon1			AB065791	CCDS31351.1	11p15.4	2012-08-09			ENSG00000181963	ENSG00000181963		"""GPCR / Class A : Olfactory receptors"""	15223	protein-coding gene	gene with protein product							Standard	NM_001005172		Approved		uc001lyz.2	Q8NGK3	OTTHUMG00000165703	ENST00000325719.4:c.655T>A	11.37:g.4471224T>A	ENSP00000318956:p.Ser219Thr	Somatic		Capture	Illumina HiSeq	Phase_I	4427800	NM_001005172	A8MUY8|B2RP35|Q6IFK4	Missense_Mutation	SNP	ENST00000325719.4	37	CCDS31351.1	.	.	.	.	.	.	.	.	.	.	T	10.02	1.235658	0.22626	.	.	ENSG00000181963	ENST00000325719	T	0.42900	0.96	4.02	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000219	T	0.55337	0.1914	M	0.91561	3.22	0.30508	N	0.769747	P	0.47253	0.892	P	0.44860	0.462	T	0.68830	-0.5305	10	0.87932	D	0	.	11.9403	0.52896	0.0:0.0:0.0:1.0	.	219	Q8NGK3	O52K2_HUMAN	T	219	ENSP00000318956:S219T	ENSP00000318956:S219T	S	+	1	0	OR52K2	4427800	0.990000	0.36364	0.457000	0.27056	0.227000	0.25037	3.524000	0.53495	1.690000	0.51089	0.397000	0.26171	TCT		0.488	OR52K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385844.1	NM_001005172	
OR52M1	119772	broad.mit.edu	37	11	4566607	4566607	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:4566607delT	ENST00000360213.1	+	1	187	c.187delT	c.(187-189)tttfs	p.F64fs		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F64fs*100(1)		endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		GCCCATGTACTTTTTCTTGTG	0.517																																					p.F63fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.187delT	11						.						148.0	137.0	141.0					11																	4566607		2201	4298	6499	4523183	SO:0001589	frameshift_variant	119772	exon1			AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790		"""GPCR / Class A : Olfactory receptors"""	15225	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily M, member 1 pseudogene"""	OR52M1P			Standard	NM_001004137		Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.187delT	11.37:g.4566607delT	ENSP00000353343:p.Phe64fs	Somatic		Capture	Illumina HiSeq	Phase_I	4523183	NM_001004137		Frame_Shift_Del	DEL	ENST00000360213.1	37	CCDS31353.1																																																																																				0.517	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137	
TRIM68	55128	broad.mit.edu	37	11	4626437	4626437	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:4626437G>A	ENST00000300747.5	-	2	587	c.298C>T	c.(298-300)Cgc>Tgc	p.R100C		NM_018073.6	NP_060543.5	Q6AZZ1	TRI68_HUMAN	tripartite motif containing 68	100					protein autoubiquitination (GO:0051865)|regulation of androgen receptor signaling pathway (GO:0060765)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|histone acetyltransferase binding (GO:0035035)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R100C(1)		breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		TCCCCATGGCGCTCACACAGG	0.537																																					p.R100C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C298T	11						.						185.0	163.0	171.0					11																	4626437		2201	4298	6499	4583013	SO:0001583	missense	55128	exon2			AF360739	CCDS31356.1	11p15.4	2013-01-09	2011-01-25	2004-11-17		ENSG00000167333		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	21161	protein-coding gene	gene with protein product		613184	"""ring finger protein 137"", ""tripartite motif-containing 68"""	RNF137		11597395	Standard	NM_018073		Approved	SS-56, FLJ10369	uc001lzf.2	Q6AZZ1		ENST00000300747.5:c.298C>T	11.37:g.4626437G>A	ENSP00000300747:p.Arg100Cys	Somatic		Capture	Illumina HiSeq	Phase_I	4583013	NM_018073	A6NI19|A8K551|B3KPM5|B4DVK4|Q8WZ70|Q96LE5|Q96PF7|Q9H9C2|Q9NW18	Missense_Mutation	SNP	ENST00000300747.5	37	CCDS31356.1	.	.	.	.	.	.	.	.	.	.	G	6.203	0.405661	0.11754	.	.	ENSG00000167333	ENST00000300747;ENST00000533021	T;T	0.44482	0.92;0.92	4.67	-4.15	0.03881	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, B-box (3);	1.560660	0.03847	N	0.271627	T	0.45796	0.1360	L	0.55481	1.735	0.09310	N	1	D;B	0.76494	0.999;0.074	P;B	0.56788	0.806;0.037	T	0.48399	-0.9039	10	0.51188	T	0.08	.	1.1568	0.01797	0.2409:0.107:0.3469:0.3052	.	100;100	E9PR29;Q6AZZ1	.;TRI68_HUMAN	C	100	ENSP00000300747:R100C;ENSP00000436112:R100C	ENSP00000300747:R100C	R	-	1	0	TRIM68	4583013	0.177000	0.23109	0.016000	0.15963	0.221000	0.24807	0.079000	0.14782	-0.535000	0.06307	-1.197000	0.01672	CGC		0.537	TRIM68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385948.1	NM_018073	
OR51I2	390064	broad.mit.edu	37	11	5474777	5474777	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:5474777T>G	ENST00000341449.2	+	1	140	c.59T>G	c.(58-60)cTg>cGg	p.L20R	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	20					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L20R(1)		endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATCCCTGGTCTGGAGAGCTCT	0.537																																					p.L20R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T59G	11						.						116.0	99.0	105.0					11																	5474777		2201	4297	6498	5431353	SO:0001583	missense	390064	exon1			BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"""GPCR / Class A : Olfactory receptors"""	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.59T>G	11.37:g.5474777T>G	ENSP00000341987:p.Leu20Arg	Somatic		Capture	Illumina HiSeq	Phase_I	5431353	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	37	CCDS31383.1	.	.	.	.	.	.	.	.	.	.	T	18.83	3.707084	0.68615	.	.	ENSG00000187918	ENST00000341449	T	0.00484	7.08	5.58	5.58	0.84498	.	0.000000	0.50627	D	0.000120	T	0.01387	0.0045	M	0.73962	2.25	0.34109	D	0.662728	D	0.89917	1.0	D	0.71184	0.972	T	0.54153	-0.8336	10	0.87932	D	0	.	14.7227	0.69320	0.0:0.0:0.0:1.0	.	20	Q9H344	O51I2_HUMAN	R	20	ENSP00000341987:L20R	ENSP00000341987:L20R	L	+	2	0	OR51I2	5431353	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.987000	0.56944	2.343000	0.79666	0.533000	0.62120	CTG		0.537	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754	
PRKCDBP	112464	broad.mit.edu	37	11	6340614	6340614	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:6340614G>T	ENST00000303927.3	-	2	735	c.565C>A	c.(565-567)Ctc>Atc	p.L189I	PRKCDBP_ENST00000530979.1_Missense_Mutation_p.L221I	NM_145040.2	NP_659477.2	Q969G5	PRDBP_HUMAN	protein kinase C, delta binding protein	189					cortical actin cytoskeleton organization (GO:0030866)|negative regulation of fermentation (GO:1901003)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	caveola (GO:0005901)|protein complex (GO:0043234)		p.L189I(1)		large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GCCCTTCGGAGGCTCTGTACC	0.711																																					p.L189I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C565A	11						.						24.0	31.0	28.0					11																	6340614		2200	4295	6495	6297190	SO:0001583	missense	112464	exon2			AF339881	CCDS7762.1	11p15.4	2011-04-20			ENSG00000170955	ENSG00000170955			9400	protein-coding gene	gene with protein product	"""sdr-related gene product that binds to c-kinase"""					9054438	Standard	NM_145040		Approved	SRBC, HSRBC, MGC20400, cavin-3, CAVIN3	uc001mcu.1	Q969G5	OTTHUMG00000133378	ENST00000303927.3:c.565C>A	11.37:g.6340614G>T	ENSP00000307292:p.Leu189Ile	Somatic		Capture	Illumina HiSeq	Phase_I	6297190	NM_145040		Missense_Mutation	SNP	ENST00000303927.3	37	CCDS7762.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.364336	0.61513	.	.	ENSG00000170955	ENST00000303927;ENST00000530979	T;T	0.62941	-0.01;-0.01	5.08	3.18	0.36537	.	0.000000	0.64402	D	0.000004	T	0.45316	0.1336	N	0.19112	0.55	0.42141	D	0.991515	P	0.49961	0.93	P	0.45276	0.475	T	0.26780	-1.0093	10	0.22706	T	0.39	-17.7307	8.4924	0.33108	0.1873:0.0:0.8127:0.0	.	189	Q969G5	PRDBP_HUMAN	I	189;221	ENSP00000307292:L189I;ENSP00000432047:L221I	ENSP00000307292:L189I	L	-	1	0	PRKCDBP	6297190	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.602000	0.36783	1.146000	0.42352	0.561000	0.74099	CTC		0.711	PRKCDBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257228.2	NM_145040	
APBB1	322	broad.mit.edu	37	11	6423331	6423331	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:6423331C>T	ENST00000609360.1	-	8	1462	c.1363G>A	c.(1363-1365)Gtc>Atc	p.V455I	APBB1_ENST00000299402.6_Missense_Mutation_p.V455I|APBB1_ENST00000389906.2_Missense_Mutation_p.V455I|APBB1_ENST00000608655.1_Missense_Mutation_p.V235I|APBB1_ENST00000608704.1_Missense_Mutation_p.V196I|APBB1_ENST00000608645.1_Missense_Mutation_p.V196I|APBB1_ENST00000529519.1_5'UTR|APBB1_ENST00000311051.3_Missense_Mutation_p.V455I|APBB1_ENST00000530885.1_Missense_Mutation_p.V235I|APBB1_ENST00000609331.1_Missense_Mutation_p.V220I|APBB1_ENST00000608394.1_Missense_Mutation_p.V196I	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	455	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)	p.V455I(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		TCCCGCCCGACGCCCCACACG	0.577																																					p.V455I	GBM(147;1810 2556 5672 39622)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1363A	11						.						122.0	104.0	110.0					11																	6423331		2201	4296	6497	6379907	SO:0001583	missense	322	exon8			L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.1363G>A	11.37:g.6423331C>T	ENSP00000477213:p.Val455Ile	Somatic		Capture	Illumina HiSeq	Phase_I	6379907	NM_001164	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	37		.	.	.	.	.	.	.	.	.	.	C	19.87	3.906984	0.72868	.	.	ENSG00000166313	ENST00000299402;ENST00000311051;ENST00000389906;ENST00000539758;ENST00000536523;ENST00000544288;ENST00000530885;ENST00000533407	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	4.18	4.18	0.49190	.	0.000000	0.64402	D	0.000014	T	0.26340	0.0643	M	0.81112	2.525	0.58432	D	0.999998	P;P;D	0.54964	0.529;0.796;0.969	B;B;B	0.43386	0.044;0.107;0.418	T	0.26916	-1.0089	10	0.62326	D	0.03	-21.0469	14.0214	0.64558	0.0:1.0:0.0:0.0	.	220;235;455	F5H1C5;B7Z2Y0;O00213-2	.;.;.	I	455;455;455;304;196;220;235;196	ENSP00000299402:V455I;ENSP00000311912:V455I;ENSP00000374556:V455I;ENSP00000433338:V235I;ENSP00000437114:V196I	ENSP00000299402:V455I	V	-	1	0	APBB1	6379907	1.000000	0.71417	1.000000	0.80357	0.677000	0.39632	7.176000	0.77643	2.142000	0.66516	0.313000	0.20887	GTC		0.577	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164	
TRIM3	10612	broad.mit.edu	37	11	6479469	6479469	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:6479469C>T	ENST00000525074.1	-	3	583	c.189G>A	c.(187-189)cgG>cgA	p.R63R	TRIM3_ENST00000345851.3_Silent_p.R63R|TRIM3_ENST00000529058.1_5'Flank|TRIM3_ENST00000536344.1_5'UTR|TRIM3_ENST00000359518.3_Silent_p.R63R|TRIM3_ENST00000537602.1_Silent_p.R63R	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	63					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R63R(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGGACGTCTGCCGGCATACTG	0.582																																					p.R63R	Melanoma(6;5 510 1540 25169 29084)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G189A	11						.						73.0	74.0	74.0					11																	6479469		2201	4296	6497	6436045	SO:0001819	synonymous_variant	10612	exon4			AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10064	protein-coding gene	gene with protein product	"""ring finger protein 22"", ""brain expressed ring finger"", ""tripartite motif protein TRIM3"""	605493	"""tripartite motif-containing 3"""	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.189G>A	11.37:g.6479469C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6436045	NM_006458	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	37	CCDS7764.1																																																																																				0.582	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
OR2D3	120775	broad.mit.edu	37	11	6942839	6942839	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:6942839C>A	ENST00000317834.3	+	1	635	c.607C>A	c.(607-609)Ctg>Atg	p.L203M		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	203						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L203L(1)|p.L203M(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CCTCCTGAAGCTGGCTTCCAT	0.453																																					p.L203M												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	c.C607A	11						.						109.0	93.0	99.0					11																	6942839		2201	4296	6497	6899415	SO:0001583	missense	120775	exon1			BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"""GPCR / Class A : Olfactory receptors"""	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.607C>A	11.37:g.6942839C>A	ENSP00000320560:p.Leu203Met	Somatic		Capture	Illumina HiSeq	Phase_I	6899415	NM_001004684	B2RP06|Q6IFG8|Q96R51	Missense_Mutation	SNP	ENST00000317834.3	37	CCDS31417.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.163620	0.57476	.	.	ENSG00000178358	ENST00000317834	T	0.00402	7.56	5.17	3.27	0.37495	GPCR, rhodopsin-like superfamily (1);	0.227351	0.22536	N	0.058799	T	0.01061	0.0035	M	0.85859	2.78	0.30415	N	0.778642	D	0.57571	0.98	D	0.65573	0.936	T	0.12760	-1.0535	10	0.52906	T	0.07	-17.5437	8.847	0.35177	0.0:0.7586:0.1569:0.0845	.	203	Q8NGH3	OR2D3_HUMAN	M	203	ENSP00000320560:L203M	ENSP00000320560:L203M	L	+	1	2	OR2D3	6899415	0.000000	0.05858	1.000000	0.80357	0.952000	0.60782	0.200000	0.17257	0.852000	0.35287	0.655000	0.94253	CTG		0.453	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
CALCA	796	broad.mit.edu	37	11	14990491	14990491	+	Intron	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:14990491C>A	ENST00000486207.1	-	2	236				CALCA_ENST00000396372.2_Missense_Mutation_p.G94C|CALCA_ENST00000331587.4_Missense_Mutation_p.G94C|CALCB_ENST00000523376.1_Intron|CALCA_ENST00000359642.3_Missense_Mutation_p.G94C|CALCA_ENST00000361010.3_Intron			P06881	CALCA_HUMAN	calcitonin-related polypeptide alpha						activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|cytosolic calcium ion homeostasis (GO:0051480)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|G-protein coupled receptor internalization (GO:0002031)|leukocyte cell-cell adhesion (GO:0007159)|negative regulation of blood pressure (GO:0045776)|negative regulation of bone resorption (GO:0045779)|negative regulation of calcium ion transport into cytosol (GO:0010523)|negative regulation of osteoclast differentiation (GO:0045671)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of vasodilation (GO:0045909)|protein phosphorylation (GO:0006468)|receptor internalization (GO:0031623)|regulation of blood pressure (GO:0008217)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	protein complex binding (GO:0032403)|receptor binding (GO:0005102)	p.G94C(1)		central_nervous_system(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	8						GTGTATGTGCCCAGCATGCAA	0.517																																					p.G94C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G280T	11						.						206.0	171.0	182.0					11																	14990491		2200	4294	6494	14947067	SO:0001627	intron_variant	796	exon4			X00356, M64486	CCDS7819.1, CCDS31432.1	11p15.2	2014-09-17	2008-02-20		ENSG00000110680	ENSG00000110680		"""Endogenous ligands"""	1437	protein-coding gene	gene with protein product	"""calcitonin"""	114130	"""calcitonin 1"""	CALC1		6546550	Standard	NM_001033953		Approved		uc001mlw.1	P01258	OTTHUMG00000159731	ENST00000486207.1:c.227+989G>T	11.37:g.14990491C>A		Somatic		Capture	Illumina HiSeq	Phase_I	14947067	NM_001741	Q93048|Q9UCP0	Missense_Mutation	SNP	ENST00000486207.1	37	CCDS31432.1	.	.	.	.	.	.	.	.	.	.	C	19.99	3.929140	0.73327	.	.	ENSG00000110680	ENST00000359642;ENST00000331587;ENST00000396372	T;T;T	0.22945	1.93;1.93;1.93	4.43	3.52	0.40303	Calcitonin peptide-like (1);Calcitonin, conserved site (1);	0.046771	0.85682	D	0.000000	T	0.50292	0.1607	M	0.78637	2.42	0.58432	D	0.999996	D	0.89917	1.0	D	0.87578	0.998	T	0.55315	-0.8160	10	0.59425	D	0.04	-17.5118	12.9579	0.58441	0.0:0.9211:0.0:0.0789	.	94	P01258	CALC_HUMAN	C	94	ENSP00000352663:G94C;ENSP00000331746:G94C;ENSP00000379657:G94C	ENSP00000331746:G94C	G	-	1	0	CALCA	14947067	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.300000	0.43620	1.226000	0.43582	-0.137000	0.14449	GGC		0.517	CALCA-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357068.1	NM_001741	
ABCC8	6833	broad.mit.edu	37	11	17428993	17428993	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:17428993A>T	ENST00000389817.3	-	24	2896	c.2828T>A	c.(2827-2829)gTc>gAc	p.V943D	ABCC8_ENST00000302539.4_Missense_Mutation_p.V944D			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	943					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)	p.V943D(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	TCTCTCTGTGACAGTCTCCTA	0.537																																					p.V943D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2828A	11						.						105.0	105.0	105.0					11																	17428993		2200	4293	6493	17385569	SO:0001583	missense	6833	exon24			L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"""ATP binding cassette transporters / subfamily C"""	59	protein-coding gene	gene with protein product	"""sulfonylurea receptor (hyperinsulinemia)"""	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.2828T>A	11.37:g.17428993A>T	ENSP00000374467:p.Val943Asp	Somatic		Capture	Illumina HiSeq	Phase_I	17385569	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Missense_Mutation	SNP	ENST00000389817.3	37	CCDS31437.1	.	.	.	.	.	.	.	.	.	.	A	7.847	0.723207	0.15439	.	.	ENSG00000006071	ENST00000389817;ENST00000302539	D;D	0.91894	-2.93;-2.92	5.99	4.8	0.61643	.	0.591181	0.17704	N	0.164836	D	0.85150	0.5631	L	0.36672	1.1	0.22156	N	0.999328	B	0.10296	0.003	B	0.14578	0.011	T	0.68375	-0.5425	10	0.12430	T	0.62	.	7.7351	0.28810	0.7814:0.1419:0.0766:0.0	.	943	Q09428	ABCC8_HUMAN	D	943;944	ENSP00000374467:V943D;ENSP00000303960:V944D	ENSP00000303960:V944D	V	-	2	0	ABCC8	17385569	0.060000	0.20803	0.111000	0.21465	0.900000	0.52787	2.400000	0.44504	2.291000	0.77112	0.533000	0.62120	GTC		0.537	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	
SERGEF	26297	broad.mit.edu	37	11	18017391	18017391	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:18017391G>T	ENST00000265965.5	-	6	725	c.574C>A	c.(574-576)Cag>Aag	p.Q192K	SERGEF_ENST00000528200.1_Missense_Mutation_p.Q192K|SERGEF_ENST00000532265.1_Missense_Mutation_p.Q78K	NM_012139.2	NP_036271.1	Q9UGK8	SRGEF_HUMAN	secretion regulating guanine nucleotide exchange factor	192					negative regulation of protein secretion (GO:0050709)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.Q192K(1)		autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(5)|lung(5)	12						GGAAGAGTCTGCCCAGGGCAC	0.473																																					p.Q192K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C574A	11						.						99.0	82.0	88.0					11																	18017391		2200	4293	6493	17973967	SO:0001583	missense	26297	exon6			AJ243950	CCDS7828.1	11p14.3	2006-03-09			ENSG00000129158	ENSG00000129158			17499	protein-coding gene	gene with protein product		606051				10571079, 12459492	Standard	NM_012139		Approved	DelGEF, Gnefr	uc001mnm.3	Q9UGK8	OTTHUMG00000166420	ENST00000265965.5:c.574C>A	11.37:g.18017391G>T	ENSP00000265965:p.Gln192Lys	Somatic		Capture	Illumina HiSeq	Phase_I	17973967	NM_012139	Q9UGK9	Missense_Mutation	SNP	ENST00000265965.5	37	CCDS7828.1	.	.	.	.	.	.	.	.	.	.	G	6.527	0.465426	0.12402	.	.	ENSG00000129158	ENST00000265965;ENST00000528200;ENST00000525920;ENST00000532265;ENST00000529728;ENST00000530613;ENST00000532389	T;T;T;T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36;-1.36;-1.36;-1.36	5.51	1.05	0.20165	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.723886	0.14029	N	0.346245	T	0.60547	0.2277	N	0.11560	0.145	0.32519	N	0.536518	B;B;B;B	0.06786	0.0;0.0;0.001;0.001	B;B;B;B	0.06405	0.0;0.001;0.002;0.001	T	0.56589	-0.7954	10	0.29301	T	0.29	-0.1696	8.6185	0.33847	0.0:0.2221:0.2558:0.5221	.	78;78;192;192	B4DFC0;E9PMV6;Q9UGK8-2;Q9UGK8	.;.;.;SRGEF_HUMAN	K	192;192;62;78;78;78;78	ENSP00000265965:Q192K;ENSP00000434188:Q192K;ENSP00000436648:Q62K;ENSP00000431314:Q78K;ENSP00000437297:Q78K;ENSP00000436080:Q78K;ENSP00000435898:Q78K	ENSP00000265965:Q192K	Q	-	1	0	SERGEF	17973967	0.369000	0.25039	0.999000	0.59377	0.712000	0.41017	0.856000	0.27818	0.383000	0.24910	-0.314000	0.08810	CAG		0.473	SERGEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389538.1	NM_012139	
E2F8	79733	broad.mit.edu	37	11	19256366	19256366	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:19256366T>C	ENST00000527884.1	-	5	923	c.691A>G	c.(691-693)Atc>Gtc	p.I231V	RP11-428C19.4_ENST00000527978.1_RNA|E2F8_ENST00000250024.4_Missense_Mutation_p.I231V	NM_001256371.1|NM_001256372.1	NP_001243300.1|NP_001243301.1	A0AVK6	E2F8_HUMAN	E2F transcription factor 8	231					cell cycle comprising mitosis without cytokinesis (GO:0033301)|chorionic trophoblast cell differentiation (GO:0060718)|hepatocyte differentiation (GO:0070365)|negative regulation of cytokinesis (GO:0032466)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.I231V(1)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TTTGATTTGATGATATGATCC	0.413																																					p.I231V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A691G	11						.						105.0	96.0	99.0					11																	19256366		2199	4293	6492	19212942	SO:0001583	missense	79733	exon5				CCDS7849.1	11p15	2008-02-05			ENSG00000129173	ENSG00000129173			24727	protein-coding gene	gene with protein product		612047				15722552	Standard	NM_024680		Approved	FLJ23311	uc001mpo.2	A0AVK6	OTTHUMG00000166102	ENST00000527884.1:c.691A>G	11.37:g.19256366T>C	ENSP00000434199:p.Ile231Val	Somatic		Capture	Illumina HiSeq	Phase_I	19212942	NM_024680	A8K9H3|Q2VPJ3|Q3C1U6|Q5BKY4|Q8N340|Q9H5M0	Missense_Mutation	SNP	ENST00000527884.1	37	CCDS7849.1	.	.	.	.	.	.	.	.	.	.	T	10.05	1.244407	0.22796	.	.	ENSG00000129173	ENST00000527884;ENST00000531809;ENST00000396159;ENST00000250024	T;T	0.16457	2.34;2.34	5.52	1.89	0.25635	.	0.602886	0.16581	N	0.208196	T	0.06096	0.0158	N	0.03177	-0.4	0.21325	N	0.999727	B	0.02656	0.0	B	0.04013	0.001	T	0.42378	-0.9455	10	0.13108	T	0.6	-4.956	7.4167	0.27048	0.0:0.4415:0.0:0.5585	.	231	A0AVK6	E2F8_HUMAN	V	231	ENSP00000434199:I231V;ENSP00000250024:I231V	ENSP00000250024:I231V	I	-	1	0	E2F8	19212942	0.969000	0.33509	0.990000	0.47175	0.993000	0.82548	0.707000	0.25704	0.400000	0.25396	0.533000	0.62120	ATC		0.413	E2F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387830.1	NM_024680	
SLC6A5	9152	broad.mit.edu	37	11	20658776	20658776	+	Missense_Mutation	SNP	G	G	A	rs138885115		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:20658776G>A	ENST00000525748.1	+	12	2069	c.1796G>A	c.(1795-1797)cGc>cAc	p.R599H	SLC6A5_ENST00000528440.1_3'UTR	NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	599					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)	p.R599H(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	AAGTACCTACGCACACACAAG	0.483																																					p.R599H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1796A	11						.						180.0	159.0	166.0					11																	20658776		2203	4300	6503	20615352	SO:0001583	missense	9152	exon12			AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.1796G>A	11.37:g.20658776G>A	ENSP00000434364:p.Arg599His	Somatic		Capture	Illumina HiSeq	Phase_I	20615352	NM_004211	O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	37	CCDS7854.1	.	.	.	.	.	.	.	.	.	.	G	35	5.453772	0.96223	.	.	ENSG00000165970	ENST00000525748	T	0.75938	-0.98	5.67	5.67	0.87782	.	0.094954	0.64402	D	0.000001	D	0.86029	0.5835	M	0.72624	2.21	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.85711	0.1319	10	0.52906	T	0.07	.	19.7802	0.96413	0.0:0.0:1.0:0.0	.	599	Q9Y345	SC6A5_HUMAN	H	599	ENSP00000434364:R599H	ENSP00000434364:R599H	R	+	2	0	SLC6A5	20615352	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.618000	0.98365	2.675000	0.91044	0.655000	0.94253	CGC		0.483	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
FANCF	2188	broad.mit.edu	37	11	22646550	22646550	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:22646550C>T	ENST00000327470.3	-	1	837	c.807G>A	c.(805-807)gcG>gcA	p.A269A	AC103801.2_ENST00000428556.2_5'Flank	NM_022725.3	NP_073562.1	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	269					DNA repair (GO:0006281)|ovarian follicle development (GO:0001541)|spermatogenesis (GO:0007283)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)	p.A269A(1)		kidney(3)|large_intestine(3)|lung(6)|skin(1)	13						CAGGAGACAGCGCTGGGTGGC	0.542			"""N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia		OREG0020844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A269A		yes	Rec		Fanconi anaemia F	11	11p15	2188	"""Fanconi anemia, complementation group F"""		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G807A	11						.						51.0	60.0	57.0					11																	22646550		2203	4300	6503	22603126	SO:0001819	synonymous_variant	2188	exon1	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)		CCDS7857.1	11p15	2014-09-17				ENSG00000183161		"""Fanconi anemia, complementation groups"""	3587	protein-coding gene	gene with protein product		613897				9382107	Standard	NM_022725		Approved	FAF	uc001mql.1	Q9NPI8		ENST00000327470.3:c.807G>A	11.37:g.22646550C>T		Somatic	757	Capture	Illumina HiSeq	Phase_I	22603126	NM_022725	Q52LM0	Silent	SNP	ENST00000327470.3	37	CCDS7857.1																																																																																				0.542	FANCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387712.2	NM_022725	
LGR4	55366	broad.mit.edu	37	11	27389933	27389933	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:27389933G>A	ENST00000379214.4	-	18	2780	c.2337C>T	c.(2335-2337)ccC>ccT	p.P779P	LGR4_ENST00000389858.4_Silent_p.P755P	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	779					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.P779P(1)		NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						TCATTATTTCGGGGCTGATAG	0.403																																					p.P779P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2337T	11						.						85.0	89.0	87.0					11																	27389933		2202	4299	6501	27346509	SO:0001819	synonymous_variant	55366	exon18			AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"""GPCR / Class A : Orphans"""	13299	protein-coding gene	gene with protein product		606666	"""G protein-coupled receptor 48"", ""leucine-rich repeat-containing G protein-coupled receptor 4"""	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.2337C>T	11.37:g.27389933G>A		Somatic		Capture	Illumina HiSeq	Phase_I	27346509	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Silent	SNP	ENST00000379214.4	37	CCDS31449.1																																																																																				0.403	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490	
KIF18A	81930	broad.mit.edu	37	11	28098681	28098681	+	Missense_Mutation	SNP	C	C	T	rs200731334		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:28098681C>T	ENST00000263181.6	-	10	1588	c.1298G>A	c.(1297-1299)cGa>cAa	p.R433Q		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	433					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)	p.R433Q(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						AATTTCTTCTCGATTCTGGAA	0.299													C|||	1	0.000199681	0.0	0.0	5008	,	,		14191	0.001		0.0	False		,,,				2504	0.0				p.R433Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1298A	11						.						120.0	119.0	119.0					11																	28098681		2202	4293	6495	28055257	SO:0001583	missense	81930	exon10			AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"""Kinesins"""	29441	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 99"""	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.1298G>A	11.37:g.28098681C>T	ENSP00000263181:p.Arg433Gln	Somatic		Capture	Illumina HiSeq	Phase_I	28055257	NM_031217	Q4VPE3|Q86VS5|Q9H0F3	Missense_Mutation	SNP	ENST00000263181.6	37	CCDS7867.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	34	5.317223	0.95682	.	.	ENSG00000121621	ENST00000263181	T	0.72167	-0.63	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.83390	0.5244	M	0.70275	2.135	0.58432	D	0.999994	D	0.89917	1.0	D	0.87578	0.998	T	0.77645	-0.2510	10	0.19590	T	0.45	.	20.3052	0.98627	0.0:1.0:0.0:0.0	.	433	Q8NI77	KI18A_HUMAN	Q	433	ENSP00000263181:R433Q	ENSP00000263181:R433Q	R	-	2	0	KIF18A	28055257	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	6.045000	0.71020	2.814000	0.96858	0.650000	0.86243	CGA		0.299	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217	
KCNA4	3739	broad.mit.edu	37	11	30032940	30032940	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:30032940delC	ENST00000328224.6	-	2	2519	c.1286delG	c.(1285-1287)ggtfs	p.G430fs	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	430					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)	p.G429fs*53(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	ACCATTGCCACCCCCCTGTTG	0.498																																					p.G429fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1286delG	11						.						71.0	68.0	69.0					11																	30032940		2072	4233	6305	29989516	SO:0001589	frameshift_variant	3739	exon2			M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6222	protein-coding gene	gene with protein product		176266	"""potassium voltage-gated channel, shaker-related subfamily, member 4-like"""	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1286delG	11.37:g.30032940delC	ENSP00000328511:p.Gly430fs	Somatic		Capture	Illumina HiSeq	Phase_I	29989516	NM_002233		Frame_Shift_Del	DEL	ENST00000328224.6	37	CCDS41629.1																																																																																				0.498	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233	
MPPED2	744	broad.mit.edu	37	11	30557686	30557686	+	Silent	SNP	C	C	T	rs369925319		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:30557686C>T	ENST00000358117.5	-	2	287	c.165G>A	c.(163-165)gcG>gcA	p.A55A	MPPED2_ENST00000448418.2_Silent_p.A55A	NM_001584.2	NP_001575.1	Q15777	MPPD2_HUMAN	metallophosphoesterase domain containing 2	55					nervous system development (GO:0007399)		hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.A55A(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(15)|skin(2)|upper_aerodigestive_tract(2)	33						GCGTGTGGCCCGCTGGTTTTG	0.488																																					p.A55A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G165A	11						.	C	,	0,4404		0,0,2202	92.0	91.0	91.0		165,165	5.9	1.0	11		91	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous	MPPED2	NM_001145399.1,NM_001584.2	,	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	,	55/278,55/295	30557686	1,13001	2202	4299	6501	30514262	SO:0001819	synonymous_variant	744	exon2			U57911	CCDS7870.1, CCDS44560.1	11p13	2008-07-18	2005-10-10	2005-10-10	ENSG00000066382	ENSG00000066382			1180	protein-coding gene	gene with protein product		600911	"""chromosome 11 open reading frame 8"""	C11orf8		8666403, 9266672	Standard	NM_001584		Approved	239FB, D11S302E, Hs.46638, FAM1B, dJ873F21.1, dJ1024C24.1	uc001msr.3	Q15777	OTTHUMG00000166159	ENST00000358117.5:c.165G>A	11.37:g.30557686C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30514262	NM_001584	D3DQZ5|E9PB10|Q59GE6	Silent	SNP	ENST00000358117.5	37	CCDS7870.1																																																																																				0.488	MPPED2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388155.2	NM_001584	
QSER1	79832	broad.mit.edu	37	11	32954322	32954322	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:32954322delT	ENST00000399302.2	+	4	1466	c.1131delT	c.(1129-1131)actfs	p.T377fs	QSER1_ENST00000527788.1_Intron	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	377	Ser-rich.							p.S379fs*7(1)		breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					AAACATTGACTTTTTCTGGGT	0.378																																					p.T377fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1131delT	11						.						110.0	101.0	104.0					11																	32954322		1832	4077	5909	32910898	SO:0001589	frameshift_variant	79832	exon4			AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.1131delT	11.37:g.32954322delT	ENSP00000382241:p.Thr377fs	Somatic		Capture	Illumina HiSeq	Phase_I	32910898	NM_001076786	Q6ZU30|Q6ZUR5	Frame_Shift_Del	DEL	ENST00000399302.2	37	CCDS41631.1																																																																																				0.378	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774	
DEPDC7	91614	broad.mit.edu	37	11	33054332	33054332	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:33054332delT	ENST00000241051.3	+	7	1348	c.1256delT	c.(1255-1257)gttfs	p.V419fs	DEPDC7_ENST00000311388.3_Frame_Shift_Del_p.V410fs	NM_001077242.1	NP_001070710.1	Q96QD5	DEPD7_HUMAN	DEP domain containing 7	419					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)		p.F411fs*11(1)		endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17						CAGAAAGATGTTTTTAAGGTA	0.289																																					p.V410fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1229delT	11						.						103.0	105.0	105.0					11																	33054332		1800	4062	5862	33010908	SO:0001589	frameshift_variant	91614	exon7				CCDS41632.1, CCDS41633.1	11p13	2006-03-24			ENSG00000121690	ENSG00000121690			29899	protein-coding gene	gene with protein product		612294				10568747	Standard	NM_001077242		Approved		uc001mub.3	Q96QD5	OTTHUMG00000166242	ENST00000241051.3:c.1256delT	11.37:g.33054332delT	ENSP00000241051:p.Val419fs	Somatic		Capture	Illumina HiSeq	Phase_I	33010908	NM_139160	G5E941|Q8N602|Q8NCU9|Q9UGK5	Frame_Shift_Del	DEL	ENST00000241051.3	37	CCDS41632.1																																																																																				0.289	DEPDC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388655.1	NM_139160	
KIAA1549L	25758	broad.mit.edu	37	11	33680412	33680412	+	Missense_Mutation	SNP	C	C	T	rs368033259		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:33680412C>T	ENST00000321505.4	+	18	5264	c.5084C>T	c.(5083-5085)aCg>aTg	p.T1695M	KIAA1549L_ENST00000389726.3_Missense_Mutation_p.T1701M			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1695						integral component of membrane (GO:0016021)		p.T1695M(1)									GTGTCCGTGACGCAGTTGGAT	0.617													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18067	0.0		0.0	False		,,,				2504	0.0				p.T1695M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5084T	11						.	C	MET/THR	3,3943		0,3,1970	21.0	27.0	25.0		5084	5.0	1.0	11		25	0,8226		0,0,4113	no	missense	C11orf41	NM_012194.2	81	0,3,6083	TT,TC,CC		0.0,0.076,0.0246	benign	1695/1850	33680412	3,12169	1973	4113	6086	33636988	SO:0001583	missense	25758	exon18			U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"""chromosome 11 open reading frame 69"", ""chromosome 11 open reading frame 41"""	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.5084C>T	11.37:g.33680412C>T	ENSP00000315295:p.Thr1695Met	Somatic		Capture	Illumina HiSeq	Phase_I	33636988	NM_012194	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	37	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	C	14.27	2.486500	0.44249	7.6E-4	0.0	ENSG00000110427	ENST00000321505;ENST00000389726;ENST00000536568	.	.	.	5.02	5.02	0.67125	.	0.647217	0.14950	N	0.288982	T	0.24084	0.0583	N	0.14661	0.345	0.25142	N	0.990495	P	0.35793	0.521	B	0.31337	0.128	T	0.20438	-1.0275	9	0.59425	D	0.04	-5.4371	15.3475	0.74350	0.0:0.8503:0.1497:0.0	.	1701	E9PAT2	.	M	1695;1701;1534	.	ENSP00000315295:T1695M	T	+	2	0	C11orf41	33636988	0.994000	0.37717	0.972000	0.41901	0.565000	0.35776	3.032000	0.49736	2.486000	0.83907	0.561000	0.74099	ACG		0.617	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	
FBXO3	26273	broad.mit.edu	37	11	33763464	33763464	+	Missense_Mutation	SNP	C	C	T	rs138194845		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:33763464C>T	ENST00000265651.3	-	11	1424	c.1406G>A	c.(1405-1407)cGc>cAc	p.R469H	FBXO3_ENST00000532057.1_Missense_Mutation_p.R156H|FBXO3_ENST00000526785.1_Missense_Mutation_p.R356H|FBXO3_ENST00000531080.1_Missense_Mutation_p.R156H|FBXO3_ENST00000530401.1_3'UTR	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	469					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)	p.R469H(1)		NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		CTAAAAAAGGCGTGAGCAGCG	0.413																																					p.R469H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1406A	11						.	C	HIS/ARG	0,4404		0,0,2202	156.0	130.0	139.0		1406	4.8	1.0	11	dbSNP_134	139	1,8595	1.2+/-3.3	0,1,4297	no	missense	FBXO3	NM_012175.3	29	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	benign	469/472	33763464	1,12999	2202	4298	6500	33720040	SO:0001583	missense	26273	exon11			AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"""F-boxes /  ""other"""""	13582	protein-coding gene	gene with protein product		609089	"""F-box only protein 3"""			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.1406G>A	11.37:g.33763464C>T	ENSP00000265651:p.Arg469His	Somatic		Capture	Illumina HiSeq	Phase_I	33720040	NM_012175	B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Missense_Mutation	SNP	ENST00000265651.3	37	CCDS7887.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.848967	0.51164	0.0	1.16E-4	ENSG00000110429	ENST00000526785;ENST00000265651;ENST00000531080;ENST00000532057	T;T	0.54866	0.55;0.55	4.78	4.78	0.61160	.	0.063724	0.64402	D	0.000007	T	0.34106	0.0886	N	0.12182	0.205	0.80722	D	1	B	0.15473	0.013	B	0.06405	0.002	T	0.22695	-1.0209	10	0.87932	D	0	-8.3125	10.936	0.47245	0.0:0.9097:0.0:0.0903	.	469	Q9UK99	FBX3_HUMAN	H	356;469;156;156	ENSP00000435680:R356H;ENSP00000265651:R469H	ENSP00000265651:R469H	R	-	2	0	FBXO3	33720040	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.784000	0.47774	2.339000	0.79563	0.561000	0.74099	CGC		0.413	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1	NM_012175	
TRAF6	7189	broad.mit.edu	37	11	36518807	36518807	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:36518807C>A	ENST00000526995.1	-	4	703	c.457G>T	c.(457-459)Gca>Tca	p.A153S	TRAF6_ENST00000529150.1_5'Flank|TRAF6_ENST00000348124.5_Missense_Mutation_p.A153S	NM_004620.3	NP_004611.1	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6, E3 ubiquitin protein ligase	153	Interaction with TAX1BP1.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of protein kinase activity (GO:0032147)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|apoptotic signaling pathway (GO:0097190)|bone resorption (GO:0045453)|cell development (GO:0048468)|cellular response to lipopolysaccharide (GO:0071222)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein autoubiquitination (GO:0051865)|protein complex assembly (GO:0006461)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|regulation of immunoglobulin secretion (GO:0051023)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	histone deacetylase binding (GO:0042826)|ligase activity (GO:0016874)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A153S(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)	27	all_lung(20;0.211)	all_hematologic(20;0.107)				TCACAATGTGCTTGATGATCC	0.363																																					p.A153S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G457T	11						.						55.0	57.0	56.0					11																	36518807		2202	4298	6500	36475383	SO:0001583	missense	7189	exon5				CCDS7901.1	11p12	2013-01-09	2012-02-23		ENSG00000175104	ENSG00000175104		"""RING-type (C3HC4) zinc fingers"""	12036	protein-coding gene	gene with protein product		602355	"""TNF receptor-associated factor 6"""			8837778	Standard	NM_004620		Approved	RNF85	uc001mws.2	Q9Y4K3	OTTHUMG00000166391	ENST00000526995.1:c.457G>T	11.37:g.36518807C>A	ENSP00000433623:p.Ala153Ser	Somatic		Capture	Illumina HiSeq	Phase_I	36475383	NM_145803	A6NKI7|A8KAB3|D3DR16|Q8NEH5	Missense_Mutation	SNP	ENST00000526995.1	37	CCDS7901.1	.	.	.	.	.	.	.	.	.	.	C	7.213	0.595874	0.13875	.	.	ENSG00000175104	ENST00000526995;ENST00000348124	T;T	0.28895	1.59;1.59	5.49	2.18	0.27775	Zinc finger, TRAF-type (1);TRAF-like (1);Seven In Absentia Homolog-type (1);	1.015470	0.07840	N	0.962783	T	0.14527	0.0351	N	0.14661	0.345	0.18873	N	0.999983	B	0.02656	0.0	B	0.04013	0.001	T	0.34279	-0.9835	10	0.09084	T	0.74	-0.3678	3.7879	0.08707	0.3297:0.4101:0.1809:0.0793	.	153	Q9Y4K3	TRAF6_HUMAN	S	153	ENSP00000433623:A153S;ENSP00000337853:A153S	ENSP00000337853:A153S	A	-	1	0	TRAF6	36475383	0.007000	0.16637	0.995000	0.50966	0.959000	0.62525	0.118000	0.15605	1.294000	0.44707	0.650000	0.86243	GCA		0.363	TRAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389530.1	NM_145803	
LRRC4C	57689	broad.mit.edu	37	11	40137660	40137660	+	Silent	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:40137660A>T	ENST00000278198.2	-	2	2146	c.183T>A	c.(181-183)atT>atA	p.I61I	LRRC4C_ENST00000527150.1_Silent_p.I61I|LRRC4C_ENST00000528697.1_Silent_p.I61I|LRRC4C_ENST00000530763.1_Silent_p.I61I			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	61	LRRNT.				regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)		p.I61I(1)		NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				TCCGAACACAAATCACCTTGC	0.537																																					p.I61I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T183A	11						.						83.0	71.0	75.0					11																	40137660		2203	4300	6503	40094236	SO:0001819	synonymous_variant	57689	exon2			AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.183T>A	11.37:g.40137660A>T		Somatic		Capture	Illumina HiSeq	Phase_I	40094236	NM_020929	A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	37	CCDS31464.1																																																																																				0.537	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929	
API5	8539	broad.mit.edu	37	11	43345148	43345148	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:43345148C>T	ENST00000531273.1	+	6	851	c.712C>T	c.(712-714)Ctc>Ttc	p.L238F	API5_ENST00000534600.1_Missense_Mutation_p.L238F|API5_ENST00000455725.2_Missense_Mutation_p.L227F|API5_ENST00000378852.3_Missense_Mutation_p.L238F|API5_ENST00000534695.1_Intron|API5_ENST00000420461.2_Missense_Mutation_p.L184F			Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5	238	ARM-like and Heat-like helical repeats.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fibroblast apoptotic process (GO:2000270)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	fibroblast growth factor binding (GO:0017134)|poly(A) RNA binding (GO:0044822)	p.L238F(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20						TGTGGACAGGCTCTTACAGTG	0.468																																					p.L238F	Pancreas(1;98 122 5625 20895 49453)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C712T	11						.						145.0	141.0	142.0					11																	43345148		2203	4300	6503	43301724	SO:0001583	missense	8539	exon6			U83857	CCDS31465.1, CCDS44572.1, CCDS44573.1	11p12	2010-09-30			ENSG00000166181	ENSG00000166181			594	protein-coding gene	gene with protein product	"""API5-like 1"", ""fibroblast growth factor 2-interacting factor 2"", ""migration-inducing protein MIG8"""	609774				9307294	Standard	NR_024625		Approved	AAC-11, API5L1, AAC11	uc010rfh.1	Q9BZZ5	OTTHUMG00000166395	ENST00000531273.1:c.712C>T	11.37:g.43345148C>T	ENSP00000431391:p.Leu238Phe	Somatic		Capture	Illumina HiSeq	Phase_I	43301724	NM_001142930	B4DGR0|B4DRJ2|D3DR21|O15441|Q9Y4J7	Missense_Mutation	SNP	ENST00000531273.1	37	CCDS44572.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.130734	0.56828	.	.	ENSG00000166181	ENST00000455725;ENST00000531273;ENST00000420461;ENST00000378852;ENST00000534600;ENST00000526394	T;T;T;T;T;T	0.25085	2.59;2.59;2.59;2.59;2.59;1.82	5.62	5.62	0.85841	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.38108	0.1028	L	0.31804	0.96	0.80722	D	1	D;P;B;P;P	0.76494	0.999;0.733;0.316;0.687;0.687	D;B;B;B;B	0.70487	0.969;0.376;0.214;0.259;0.259	T	0.02774	-1.1112	10	0.12766	T	0.61	-12.2469	19.6343	0.95724	0.0:1.0:0.0:0.0	.	184;238;227;238;238	B4DGR0;Q9BZZ5;B4E283;G3V1C3;Q9BZZ5-2	.;API5_HUMAN;.;.;.	F	227;238;184;238;238;88	ENSP00000399341:L227F;ENSP00000431391:L238F;ENSP00000402540:L184F;ENSP00000368129:L238F;ENSP00000434462:L238F;ENSP00000436436:L88F	ENSP00000368129:L238F	L	+	1	0	API5	43301724	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.809000	0.96659	0.655000	0.94253	CTC		0.468	API5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389545.1	NM_006595	
PRDM11	56981	broad.mit.edu	37	11	45204587	45204587	+	Silent	SNP	C	C	T	rs144282810	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:45204587C>T	ENST00000530656.1	+	4	501	c.501C>T	c.(499-501)aaC>aaT	p.N167N	PRDM11_ENST00000528980.1_3'UTR|PRDM11_ENST00000263765.4_Silent_p.N167N|PRDM11_ENST00000424263.2_Silent_p.N133N			Q9NQV5	PRD11_HUMAN	PR domain containing 11	167	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)	p.N167N(1)		endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						GATGTGTAAACGAGGTCATCC	0.617											OREG0020926	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	7	0.00139776	0.003	0.0	5008	,	,		19002	0.0		0.0	False		,,,				2504	0.0031				p.N167N	NSCLC(118;1511 1736 6472 36603 43224)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C501T	11						.	C		14,4392	21.2+/-45.6	0,14,2189	86.0	83.0	84.0		501	-3.8	0.1	11	dbSNP_134	84	0,8598		0,0,4299	no	coding-synonymous	PRDM11	NM_020229.2		0,14,6488	TT,TC,CC		0.0,0.3177,0.1077		167/512	45204587	14,12990	2203	4299	6502	45161163	SO:0001819	synonymous_variant	56981	exon5			AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"""PR-domain containing protein 11"""						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.501C>T	11.37:g.45204587C>T		Somatic	929	Capture	Illumina HiSeq	Phase_I	45161163	NM_020229	Q8N9F1	Silent	SNP	ENST00000530656.1	37																																																																																					0.617	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229	
CHST1	8534	broad.mit.edu	37	11	45672015	45672015	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:45672015G>A	ENST00000308064.2	-	4	1129	c.459C>T	c.(457-459)cgC>cgT	p.R153R	RP11-495O11.1_ENST00000525563.1_RNA|CHST1_ENST00000533673.1_5'Flank	NM_003654.5	NP_003645.1	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	153					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	keratan sulfotransferase activity (GO:0045130)|sulfotransferase activity (GO:0008146)	p.R153R(1)		breast(1)|endometrium(3)|large_intestine(10)|lung(17)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)		TGGCCCCGCGGCGGAAGATCC	0.697																																					p.R153R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C459T	11						.						30.0	37.0	34.0					11																	45672015		2202	4294	6496	45628591	SO:0001819	synonymous_variant	8534	exon4			U65637	CCDS7913.1	11p11.2	2010-04-29			ENSG00000175264	ENSG00000175264		"""Sulfotransferases, membrane-bound"""	1969	protein-coding gene	gene with protein product		603797				9405439, 9639683	Standard	NM_003654		Approved	C6ST, KSGal6ST	uc001mys.2	O43916		ENST00000308064.2:c.459C>T	11.37:g.45672015G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45628591	NM_003654	D3DQP2	Silent	SNP	ENST00000308064.2	37	CCDS7913.1																																																																																				0.697	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	NM_003654	
PHF21A	51317	broad.mit.edu	37	11	45986931	45986931	+	Missense_Mutation	SNP	T	T	C	rs532473580		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:45986931T>C	ENST00000418153.2	-	9	1127	c.928A>G	c.(928-930)Act>Gct	p.T310A	PHF21A_ENST00000323180.6_Missense_Mutation_p.T311A|PHF21A_ENST00000527753.1_5'UTR|PHF21A_ENST00000257821.4_Missense_Mutation_p.T311A			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	310					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.T311A(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						GTCCCTGGAGTAGCTATCACA	0.532											OREG0020936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1	0.000199681	0.0	0.0	5008	,	,		18456	0.0		0.0	False		,,,				2504	0.001				p.T310A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A928G	11						.						125.0	94.0	104.0					11																	45986931		2202	4299	6501	45943507	SO:0001583	missense	51317	exon9			AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"""Zinc fingers, PHD-type"""	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.928A>G	11.37:g.45986931T>C	ENSP00000398824:p.Thr310Ala	Somatic	935	Capture	Illumina HiSeq	Phase_I	45943507	NM_001101802	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Missense_Mutation	SNP	ENST00000418153.2	37	CCDS44578.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077788	0.36662	.	.	ENSG00000135365	ENST00000257821;ENST00000323180;ENST00000418153	T;T;T	0.40225	1.04;1.04;1.04	6.17	5.05	0.67936	.	0.094982	0.64402	D	0.000001	T	0.11410	0.0278	N	0.00801	-1.175	0.42162	D	0.991608	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.25572	-1.0128	10	0.12103	T	0.63	-8.0555	3.5321	0.07781	0.0:0.2962:0.0:0.7038	.	310;311;311	Q96BD5;Q96BD5-2;Q96BD5-3	PF21A_HUMAN;.;.	A	311;311;310	ENSP00000257821:T311A;ENSP00000323152:T311A;ENSP00000398824:T310A	ENSP00000257821:T311A	T	-	1	0	PHF21A	45943507	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.385000	0.44371	2.371000	0.80710	0.533000	0.62120	ACT		0.532	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621	
LRP4	4038	broad.mit.edu	37	11	46921847	46921849	+	In_Frame_Del	DEL	GTT	GTT	-	rs17848224	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	GTT	GTT	GTT	-	GTT	GTT	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:46921847_46921849delGTT	ENST00000378623.1	-	3	522_524	c.280_282delAAC	c.(280-282)aacdel	p.N94del		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	94	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)	p.N94delN(1)		breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		CCTCACAGTCGTTGTCCCCGTCA	0.522																																					p.94_94del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.280_282del	11						.																																			46878425	SO:0001651	inframe_deletion	4038	exon3			AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.280_282delAAC	11.37:g.46921847_46921849delGTT	ENSP00000367888:p.Asn94del	Somatic		Capture	Illumina HiSeq	Phase_I	46878423	NM_002334	B2RN39|Q4AC85|Q5KTZ5	In_Frame_Del	DEL	ENST00000378623.1	37	CCDS31478.1																																																																																				0.522	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
ACP2	53	broad.mit.edu	37	11	47264423	47264423	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:47264423C>T	ENST00000256997.3	-	10	1105	c.989G>A	c.(988-990)cGg>cAg	p.R330Q	ACP2_ENST00000537863.1_Missense_Mutation_p.R143Q|ACP2_ENST00000533929.1_Missense_Mutation_p.R302Q|ACP2_ENST00000525230.1_5'UTR|ACP2_ENST00000527256.1_Missense_Mutation_p.R298Q|ACP2_ENST00000529444.1_Missense_Mutation_p.R267Q	NM_001610.2	NP_001601.1	P11117	PPAL_HUMAN	acid phosphatase 2, lysosomal	330					dephosphorylation (GO:0016311)|lysosome organization (GO:0007040)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)	acid phosphatase activity (GO:0003993)	p.R330Q(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)	10						ACTCTCGTTCCGAAAGTACAT	0.642																																					p.R330Q	Melanoma(90;262 1440 11488 44828 48531)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G989A	11						.						41.0	45.0	44.0					11																	47264423		2201	4297	6498	47220999	SO:0001583	missense	53	exon10			X15525	CCDS7928.1, CCDS44583.1	11p11.2	2008-02-05			ENSG00000134575	ENSG00000134575	3.1.3.2		123	protein-coding gene	gene with protein product		171650				975882	Standard	NM_001610		Approved		uc001nei.3	P11117	OTTHUMG00000166949	ENST00000256997.3:c.989G>A	11.37:g.47264423C>T	ENSP00000256997:p.Arg330Gln	Somatic		Capture	Illumina HiSeq	Phase_I	47220999	NM_001610	E9PCI1|Q561W5|Q9BTU7	Missense_Mutation	SNP	ENST00000256997.3	37	CCDS7928.1	.	.	.	.	.	.	.	.	.	.	C	31	5.098250	0.94197	.	.	ENSG00000134575	ENST00000256997;ENST00000529444;ENST00000527256;ENST00000537863;ENST00000540414;ENST00000533929;ENST00000529663	T;T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94;0.94	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.64227	0.2579	M	0.63169	1.94	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.67209	-0.5728	10	0.87932	D	0	.	18.8188	0.92088	0.0:1.0:0.0:0.0	.	267;298;302;320;330	E9PHY0;B7Z7D2;E9PQY3;F5H1S6;P11117	.;.;.;.;PPAL_HUMAN	Q	330;267;298;143;320;302;297	ENSP00000256997:R330Q;ENSP00000436658:R267Q;ENSP00000432205:R298Q;ENSP00000441933:R143Q;ENSP00000432439:R302Q;ENSP00000436487:R297Q	ENSP00000256997:R330Q	R	-	2	0	ACP2	47220999	1.000000	0.71417	1.000000	0.80357	0.598000	0.36846	5.487000	0.66863	2.438000	0.82558	0.460000	0.39030	CGG		0.642	ACP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392022.2	NM_001610	
MADD	8567	broad.mit.edu	37	11	47348308	47348308	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:47348308A>G	ENST00000311027.5	+	34	4907	c.4742A>G	c.(4741-4743)cAc>cGc	p.H1581R	MADD_ENST00000395336.3_Intron|MADD_ENST00000342922.4_Missense_Mutation_p.H1522R|MADD_ENST00000402192.2_Missense_Mutation_p.H1521R|MADD_ENST00000407859.3_Missense_Mutation_p.H1499R|MADD_ENST00000395344.3_Missense_Mutation_p.H1475R|MADD_ENST00000402799.1_Missense_Mutation_p.H1479R|MADD_ENST00000406482.1_Intron|MADD_ENST00000349238.3_Missense_Mutation_p.H1542R	NM_003682.3	NP_003673.3			MAP-kinase activating death domain									p.H1581R(1)		breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		GAGCTGAATCACATTAAAAAG	0.512																																					p.H1581R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4742G	11						.						112.0	112.0	112.0					11																	47348308		2201	4298	6499	47304884	SO:0001583	missense	8567	exon34			AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.4742A>G	11.37:g.47348308A>G	ENSP00000310933:p.His1581Arg	Somatic		Capture	Illumina HiSeq	Phase_I	47304884	NM_003682		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184213	0.78677	.	.	ENSG00000110514	ENST00000342922;ENST00000402799;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000402192	T;T;T;T;T;T;T	0.06218	3.45;3.33;3.45;3.45;3.33;3.33;3.46	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.20129	0.0484	L	0.47190	1.495	0.80722	D	1	P;D;D;D;P;D;P	0.71674	0.799;0.993;0.996;0.998;0.873;0.995;0.897	B;D;D;D;P;D;P	0.81914	0.343;0.977;0.99;0.995;0.544;0.989;0.645	T	0.00148	-1.1989	10	0.87932	D	0	-20.0063	16.2045	0.82114	1.0:0.0:0.0:0.0	.	1475;1475;1479;1542;1499;1581;1522	B5MEE5;A8K8S7;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;MADD_HUMAN;.	R	1522;1479;1542;1581;1499;1475;1521	ENSP00000343902:H1522R;ENSP00000385585:H1479R;ENSP00000304505:H1542R;ENSP00000310933:H1581R;ENSP00000384204:H1499R;ENSP00000378753:H1475R;ENSP00000384287:H1521R	ENSP00000310933:H1581R	H	+	2	0	MADD	47304884	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.819000	0.91997	2.234000	0.73211	0.459000	0.35465	CAC		0.512	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
NUP160	23279	broad.mit.edu	37	11	47861510	47861510	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:47861510A>G	ENST00000378460.2	-	4	679	c.633T>C	c.(631-633)tcT>tcC	p.S211S	NUP160_ENST00000530326.1_Silent_p.S97S|NUP160_ENST00000532747.1_Intron|NUP160_ENST00000528071.1_Silent_p.S97S|NUP160_ENST00000526870.1_3'UTR	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa	211					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.S211S(1)		NS(1)|biliary_tract(2)|breast(7)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(6)|prostate(2)|skin(2)|urinary_tract(2)	53						TGGAATTAGGAGATATTCCAG	0.458																																					p.S211S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T633C	11						.						119.0	114.0	116.0					11																	47861510		2201	4298	6499	47818086	SO:0001819	synonymous_variant	23279	exon4			D83781	CCDS31484.1	11p11.12	2008-07-21	2002-08-29		ENSG00000030066	ENSG00000030066			18017	protein-coding gene	gene with protein product		607614	"""nucleoporin 160kD"""			11684705	Standard	NM_015231		Approved	KIAA0197, FLJ22583	uc001ngm.3	Q12769	OTTHUMG00000166534	ENST00000378460.2:c.633T>C	11.37:g.47861510A>G		Somatic		Capture	Illumina HiSeq	Phase_I	47818086	NM_015231	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Silent	SNP	ENST00000378460.2	37	CCDS31484.1																																																																																				0.458	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231	
OR4C46	119749	broad.mit.edu	37	11	51515412	51515412	+	Missense_Mutation	SNP	T	T	G	rs372979385|rs545486160	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:51515412T>G	ENST00000328188.1	+	1	131	c.131T>G	c.(130-132)gTg>gGg	p.V44G		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V44G(1)		endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						GTGCTCATTGTGGTCACCATC	0.458																																					p.V44G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T131G	11						.						239.0	230.0	233.0					11																	51515412		2201	4296	6497	51371988	SO:0001583	missense	119749	exon1				CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"""GPCR / Class A : Olfactory receptors"""	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.131T>G	11.37:g.51515412T>G	ENSP00000329056:p.Val44Gly	Somatic		Capture	Illumina HiSeq	Phase_I	51371988	NM_001004703		Missense_Mutation	SNP	ENST00000328188.1	37	CCDS31498.1	.	.	.	.	.	.	.	.	.	.	.	9.486	1.099357	0.20552	.	.	ENSG00000185926	ENST00000328188	T	0.00532	6.75	2.63	1.47	0.22746	GPCR, rhodopsin-like superfamily (1);	0.527164	0.14230	N	0.332801	T	0.01061	0.0035	M	0.92459	3.31	0.18873	N	0.999989	B	0.13145	0.007	B	0.18263	0.021	T	0.34551	-0.9824	10	0.66056	D	0.02	.	5.7887	0.18349	0.0:0.1444:0.0:0.8556	.	44	A6NHA9	O4C46_HUMAN	G	44	ENSP00000329056:V44G	ENSP00000329056:V44G	V	+	2	0	OR4C46	51371988	0.209000	0.23505	0.013000	0.15412	0.093000	0.18481	2.666000	0.46799	0.280000	0.22209	0.113000	0.15668	GTG		0.458	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703	
OR4C11	219429	broad.mit.edu	37	11	55371530	55371530	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:55371530C>T	ENST00000302231.4	-	1	344	c.320G>A	c.(319-321)tGc>tAc	p.C107Y		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C107Y(1)|p.C107F(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						GATCTCCATGCAGCCAAATAA	0.448																																					p.C107Y												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G320A	11						.						109.0	91.0	97.0					11																	55371530		2179	4006	6185	55128106	SO:0001583	missense	219429	exon1			AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"""GPCR / Class A : Olfactory receptors"""	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.320G>A	11.37:g.55371530C>T	ENSP00000306651:p.Cys107Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	55128106	NM_001004700	B9EIL4|Q8NGL8	Missense_Mutation	SNP	ENST00000302231.4	37	CCDS31503.1	.	.	.	.	.	.	.	.	.	.	C	4.975	0.181101	0.09443	.	.	ENSG00000172188	ENST00000302231	T	0.02974	4.09	4.34	1.13	0.20643	GPCR, rhodopsin-like superfamily (1);	0.247001	0.28901	U	0.013773	T	0.03390	0.0098	L	0.52573	1.65	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.34976	-0.9807	10	0.87932	D	0	.	7.9954	0.30265	0.0:0.549:0.3589:0.0921	.	107	Q6IEV9	OR4CB_HUMAN	Y	107	ENSP00000306651:C107Y	ENSP00000306651:C107Y	C	-	2	0	OR4C11	55128106	0.000000	0.05858	0.822000	0.32727	0.322000	0.28314	-1.401000	0.02502	0.126000	0.18424	0.478000	0.44815	TGC		0.448	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700	
OR5D14	219436	broad.mit.edu	37	11	55563435	55563435	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:55563435C>A	ENST00000335605.1	+	1	404	c.404C>A	c.(403-405)aCa>aAa	p.T135K		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	135						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T135K(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				CTGCTTTATACAGTGGCCATG	0.537																																					p.T135K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C404A	11						.						102.0	91.0	94.0					11																	55563435		2200	4296	6496	55320011	SO:0001583	missense	219436	exon1			AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"""GPCR / Class A : Olfactory receptors"""	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.404C>A	11.37:g.55563435C>A	ENSP00000334456:p.Thr135Lys	Somatic		Capture	Illumina HiSeq	Phase_I	55320011	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	37	CCDS31508.1	.	.	.	.	.	.	.	.	.	.	c	11.77	1.737328	0.30774	.	.	ENSG00000186113	ENST00000335605	T	0.00527	6.79	5.08	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.311893	0.23055	N	0.052456	T	0.00695	0.0023	M	0.83012	2.62	0.09310	N	1	B	0.25105	0.118	B	0.24848	0.056	T	0.36480	-0.9746	10	0.59425	D	0.04	-8.249	7.2734	0.26271	0.0:0.7324:0.0:0.2676	.	135	Q8NGL3	OR5DE_HUMAN	K	135	ENSP00000334456:T135K	ENSP00000334456:T135K	T	+	2	0	OR5D14	55320011	0.000000	0.05858	0.947000	0.38551	0.602000	0.36980	-1.208000	0.03005	1.142000	0.42291	0.643000	0.83706	ACA		0.537	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735	
P2RX3	5024	broad.mit.edu	37	11	57135523	57135523	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:57135523C>T	ENST00000263314.2	+	9	917	c.883C>T	c.(883-885)Cgc>Tgc	p.R295C		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	295					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)	p.R295C(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						CAGTGAGTACCGCACCCTCCT	0.572																																					p.R295C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C883T	11						.						98.0	91.0	94.0					11																	57135523		2201	4296	6497	56892099	SO:0001583	missense	5024	exon9			Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.883C>T	11.37:g.57135523C>T	ENSP00000263314:p.Arg295Cys	Somatic		Capture	Illumina HiSeq	Phase_I	56892099	NM_002559	Q6DK37|Q9UQB6	Missense_Mutation	SNP	ENST00000263314.2	37	CCDS7953.1	.	.	.	.	.	.	.	.	.	.	C	32	5.131348	0.94473	.	.	ENSG00000109991	ENST00000439993;ENST00000263314	T	0.14266	2.52	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.49389	0.1554	M	0.92555	3.32	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.58126	-0.7691	10	0.87932	D	0	-25.6283	17.5802	0.87965	0.0:1.0:0.0:0.0	.	295	P56373	P2RX3_HUMAN	C	295	ENSP00000263314:R295C	ENSP00000263314:R295C	R	+	1	0	P2RX3	56892099	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.561000	0.60809	2.894000	0.99253	0.655000	0.94253	CGC		0.572	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559	
OR5B21	219968	broad.mit.edu	37	11	58275211	58275211	+	Missense_Mutation	SNP	G	G	A	rs148173637	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:58275211G>A	ENST00000360374.2	-	1	367	c.368C>T	c.(367-369)gCg>gTg	p.A123V		NM_001005218.1	NP_001005218.1	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B, member 21	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A123V(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CCTACATACCGCTGCATGGCG	0.527													G|||	13	0.00259585	0.0	0.0	5008	,	,		21461	0.001		0.0	False		,,,				2504	0.0123				p.A123V												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C368T	11						.	G	VAL/ALA	1,4401	2.1+/-5.4	0,1,2200	128.0	96.0	107.0		368	4.2	0.5	11	dbSNP_134	107	0,8590		0,0,4295	no	missense	OR5B21	NM_001005218.1	64	0,1,6495	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	123/310	58275211	1,12991	2201	4295	6496	58031787	SO:0001583	missense	219968	exon1				CCDS31552.1	11q12.1	2012-08-09			ENSG00000198283	ENSG00000198283		"""GPCR / Class A : Olfactory receptors"""	19616	protein-coding gene	gene with protein product							Standard	NM_001005218		Approved		uc010rki.2	A6NL26	OTTHUMG00000167519	ENST00000360374.2:c.368C>T	11.37:g.58275211G>A	ENSP00000353537:p.Ala123Val	Somatic		Capture	Illumina HiSeq	Phase_I	58031787	NM_001005218		Missense_Mutation	SNP	ENST00000360374.2	37	CCDS31552.1	.	.	.	.	.	.	.	.	.	.	G	16.46	3.128195	0.56721	2.27E-4	0.0	ENSG00000198283	ENST00000360374	T	0.01228	5.14	5.07	4.17	0.49024	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36703	U	0.002446	T	0.08670	0.0215	H	0.95745	3.715	0.40794	D	0.98328	D	0.71674	0.998	P	0.52454	0.699	T	0.03957	-1.0989	10	0.87932	D	0	-6.2997	12.3366	0.55071	0.0821:0.0:0.9179:0.0	.	123	A6NL26	OR5BL_HUMAN	V	123	ENSP00000353537:A123V	ENSP00000353537:A123V	A	-	2	0	OR5B21	58031787	1.000000	0.71417	0.489000	0.27452	0.061000	0.15899	4.602000	0.61098	1.376000	0.46267	0.655000	0.94253	GCG		0.527	OR5B21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394891.1	NM_001005218	
DTX4	23220	broad.mit.edu	37	11	58959578	58959578	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:58959578C>T	ENST00000227451.3	+	6	1333	c.1229C>T	c.(1228-1230)aCc>aTc	p.T410I	DTX4_ENST00000532982.1_Missense_Mutation_p.T304I|DTX4_ENST00000531902.1_3'UTR	NM_015177.1	NP_055992.1	Q9Y2E6	DTX4_HUMAN	deltex 4, E3 ubiquitin ligase	410					innate immune response (GO:0045087)|Notch signaling pathway (GO:0007219)|positive regulation of type I interferon production (GO:0032481)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.T304I(1)		central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	20		all_epithelial(135;0.125)				CAGGACTGCACCATCTGTATG	0.592																																					p.T410I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1229T	11						.						51.0	52.0	52.0					11																	58959578		2027	4176	6203	58716154	SO:0001583	missense	23220	exon6			AB023154	CCDS44612.1	11q12.2	2014-01-28	2014-01-28		ENSG00000110042	ENSG00000110042		"""RING-type (C3HC4) zinc fingers"""	29151	protein-coding gene	gene with protein product			"""deltex 4 homolog (Drosophila)"", ""deltex homolog 4 (Drosophila)"""			10231032, 22388039	Standard	NM_015177		Approved	KIAA0937, RNF155	uc001nns.2	Q9Y2E6	OTTHUMG00000167336	ENST00000227451.3:c.1229C>T	11.37:g.58959578C>T	ENSP00000227451:p.Thr410Ile	Somatic		Capture	Illumina HiSeq	Phase_I	58716154	NM_015177	Q0VF38	Missense_Mutation	SNP	ENST00000227451.3	37	CCDS44612.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.305637	0.60305	.	.	ENSG00000110042	ENST00000532982;ENST00000227451	T;T	0.42900	0.96;0.96	5.81	5.81	0.92471	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	T	0.50222	0.1603	N	0.21324	0.655	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.31280	-0.9949	10	0.13470	T	0.59	.	18.8417	0.92186	0.0:1.0:0.0:0.0	.	410	Q9Y2E6	DTX4_HUMAN	I	304;410	ENSP00000434055:T304I;ENSP00000227451:T410I	ENSP00000227451:T410I	T	+	2	0	DTX4	58716154	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.693000	0.84214	2.733000	0.93635	0.655000	0.94253	ACC		0.592	DTX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394228.1	XM_166213	
OR10V1	390201	broad.mit.edu	37	11	59480737	59480737	+	Silent	SNP	G	G	A	rs377363304		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:59480737G>A	ENST00000307552.2	-	1	600	c.582C>T	c.(580-582)cgC>cgT	p.R194R	STX3_ENST00000300150.7_5'Flank	NM_001005324.1	NP_001005324.1	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V, member 1	194						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R194R(1)		endometrium(1)|large_intestine(3)|liver(1)|lung(10)|skin(1)	16						TCTTGTGAACGCGTGTGTCTG	0.473																																					p.R194R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C582T	11						.	G		0,4402		0,0,2201	106.0	90.0	95.0		582	-8.9	0.0	11		95	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	OR10V1	NM_001005324.1		0,1,6495	AA,AG,GG		0.0116,0.0,0.0077		194/310	59480737	1,12991	2201	4295	6496	59237313	SO:0001819	synonymous_variant	390201	exon1			AB065807	CCDS31565.1	11q12.1	2012-08-09			ENSG00000172289	ENSG00000172289		"""GPCR / Class A : Olfactory receptors"""	15136	protein-coding gene	gene with protein product							Standard	NM_001005324		Approved		uc001nof.1	Q8NGI7	OTTHUMG00000167406	ENST00000307552.2:c.582C>T	11.37:g.59480737G>A		Somatic		Capture	Illumina HiSeq	Phase_I	59237313	NM_001005324	Q6IFD9|Q96R50	Silent	SNP	ENST00000307552.2	37	CCDS31565.1																																																																																				0.473	OR10V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394517.1	NM_001005324	
CPSF7	79869	broad.mit.edu	37	11	61183649	61183649	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:61183649delG	ENST00000394888.4	-	6	1065	c.893delC	c.(892-894)ccafs	p.P299fs	CPSF7_ENST00000448745.1_Frame_Shift_Del_p.P290fs|CPSF7_ENST00000439958.3_Frame_Shift_Del_p.P290fs|CPSF7_ENST00000340437.4_Frame_Shift_Del_p.P342fs	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa	299	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P298fs*14(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						AGCGTTTGGTGGGGGGAAGAA	0.557																																					p.P298fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.893delC	11						.						59.0	65.0	63.0					11																	61183649		2202	4299	6501	60940225	SO:0001589	frameshift_variant	79869	exon6				CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"""RNA binding motif (RRM) containing"""	30098	protein-coding gene	gene with protein product	"""pre mRNA cleavage factor I, 59 kDa subunit"", ""cleavage factor Im complex 59 kDa subunit"""					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198	ENST00000394888.4:c.893delC	11.37:g.61183649delG	ENSP00000378352:p.Pro299fs	Somatic		Capture	Illumina HiSeq	Phase_I	60940225	NM_001136040	B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Frame_Shift_Del	DEL	ENST00000394888.4	37	CCDS44619.1																																																																																				0.557	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811	
AHNAK	79026	broad.mit.edu	37	11	62287785	62287785	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:62287785C>T	ENST00000378024.4	-	5	14378	c.14104G>A	c.(14104-14106)Gcg>Acg	p.A4702T	AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4702					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.A4702T(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TTTAGTTTCGCATCTGGACCT	0.493																																					p.A4702T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G14104A	11						.						200.0	205.0	203.0					11																	62287785		2202	4299	6501	62044361	SO:0001583	missense	79026	exon5			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.14104G>A	11.37:g.62287785C>T	ENSP00000367263:p.Ala4702Thr	Somatic		Capture	Illumina HiSeq	Phase_I	62044361	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.501111	0.26861	.	.	ENSG00000124942	ENST00000378024	T	0.00686	5.85	5.16	5.16	0.70880	.	0.550337	0.17857	N	0.159662	T	0.03305	0.0096	M	0.68593	2.085	0.09310	N	1	D	0.69078	0.997	D	0.66196	0.942	T	0.56159	-0.8025	10	0.12103	T	0.63	-5.2312	18.2575	0.90024	0.0:1.0:0.0:0.0	.	4702	Q09666	AHNK_HUMAN	T	4702	ENSP00000367263:A4702T	ENSP00000367263:A4702T	A	-	1	0	AHNAK	62044361	0.128000	0.22383	0.006000	0.13384	0.000000	0.00434	3.965000	0.56788	2.397000	0.81536	0.549000	0.68633	GCG		0.493	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
AHNAK	79026	broad.mit.edu	37	11	62294669	62294669	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:62294669T>C	ENST00000378024.4	-	5	7494	c.7220A>G	c.(7219-7221)gAt>gGt	p.D2407G	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2407					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.D2407G(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TTTGGGAACATCTACATCCAC	0.483																																					p.D2407G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A7220G	11						.						73.0	74.0	74.0					11																	62294669		2202	4299	6501	62051245	SO:0001583	missense	79026	exon5			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.7220A>G	11.37:g.62294669T>C	ENSP00000367263:p.Asp2407Gly	Somatic		Capture	Illumina HiSeq	Phase_I	62051245	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	t	8.610	0.888821	0.17540	.	.	ENSG00000124942	ENST00000244934;ENST00000378024	T	0.05258	3.47	4.38	1.81	0.25067	.	.	.	.	.	T	0.08403	0.0209	L	0.52573	1.65	0.09310	N	1	P	0.38729	0.644	B	0.38985	0.287	T	0.19418	-1.0306	9	0.49607	T	0.09	.	11.1827	0.48638	0.0:0.0:0.5274:0.4726	.	2407	Q09666	AHNK_HUMAN	G	496;2407	ENSP00000367263:D2407G	ENSP00000244934:D496G	D	-	2	0	AHNAK	62051245	0.000000	0.05858	0.983000	0.44433	0.552000	0.35366	-0.014000	0.12656	0.547000	0.28938	-0.669000	0.03829	GAT		0.483	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
EML3	256364	broad.mit.edu	37	11	62372618	62372618	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:62372618C>A	ENST00000394773.2	-	16	2256	c.1949G>T	c.(1948-1950)gGg>gTg	p.G650V	EML3_ENST00000529309.1_Missense_Mutation_p.G650V|EML3_ENST00000278845.4_Missense_Mutation_p.G651V|RP11-831H9.3_ENST00000532626.1_RNA|EML3_ENST00000494176.2_Missense_Mutation_p.G622V|EML3_ENST00000438258.1_5'Flank|EML3_ENST00000531557.1_Missense_Mutation_p.G433V	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	650						cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.G650V(1)		biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						CACAACTGCCCCACTCGGGTG	0.582																																					p.G650V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1949T	11						.						95.0	90.0	92.0					11																	62372618		2202	4299	6501	62129194	SO:0001583	missense	256364	exon16			AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"""WD repeat domain containing"""	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.1949G>T	11.37:g.62372618C>A	ENSP00000378254:p.Gly650Val	Somatic		Capture	Illumina HiSeq	Phase_I	62129194	NM_153265	Q6ZQW7|Q8NA55	Missense_Mutation	SNP	ENST00000394773.2	37	CCDS8023.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.8|29.8	5.033240|5.033240	0.93575|0.93575	.|.	.|.	ENSG00000149499|ENSG00000149499	ENST00000394773;ENST00000278845;ENST00000531557;ENST00000494176;ENST00000529309|ENST00000394776	T;T;T;T;T|.	0.56941|.	0.43;0.43;0.97;0.97;0.97|.	5.84|5.84	5.84|5.84	0.93424|0.93424	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80292|0.80292	0.4596|0.4596	M|M	0.84948|0.84948	2.725|2.725	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	0.998;0.988;0.995;0.999;1.0|.	T|T	0.81499|0.81499	-0.0905|-0.0905	10|5	0.87932|.	D|.	0|.	-14.4565|-14.4565	17.6216|17.6216	0.88083|0.88083	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	650;650;433;651;622|.	Q32P44-2;Q32P44;G3V195;B7WPE2;G3V1D0|.	.;EMAL3_HUMAN;.;.;.|.	V|C	650;651;433;622;650|644	ENSP00000378254:G650V;ENSP00000278845:G651V;ENSP00000433417:G433V;ENSP00000435064:G622V;ENSP00000434513:G650V|.	ENSP00000278845:G651V|.	G|W	-|-	2|3	0|0	EML3|EML3	62129194|62129194	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.471000|7.471000	0.80985|0.80985	2.768000|2.768000	0.95171|0.95171	0.561000|0.561000	0.74099|0.74099	GGG|TGG		0.582	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265	
B3GAT3	26229	broad.mit.edu	37	11	62384188	62384188	+	Silent	SNP	G	G	A	rs574558220		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:62384188G>A	ENST00000265471.5	-	4	926	c.699C>T	c.(697-699)gaC>gaT	p.D233D	B3GAT3_ENST00000531383.1_Silent_p.D233D|B3GAT3_ENST00000534026.1_Silent_p.D233D	NM_012200.3	NP_036332.2	O94766	B3GA3_HUMAN	beta-1,3-glucuronyltransferase 3	233					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|glucuronosyltransferase activity (GO:0015020)|metal ion binding (GO:0046872)	p.D233D(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)|urinary_tract(1)	12						CTACCCGGCCGTCCTGTACCT	0.642													g|||	1	0.000199681	0.0	0.0	5008	,	,		17191	0.0		0.001	False		,,,				2504	0.0				p.D233D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C699T	11						.						38.0	38.0	38.0					11																	62384188		2202	4299	6501	62140764	SO:0001819	synonymous_variant	26229	exon4			AB009598	CCDS8025.1	11q12	2014-07-08	2014-07-08		ENSG00000149541	ENSG00000149541	2.4.1.135	"""Beta-1,3-glucuronyltransferases"""	923	protein-coding gene	gene with protein product	"""glucuronosyltransferase I"", ""galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3"""	606374	"""beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)"""			9506957	Standard	NM_012200		Approved	GlcAT-I	uc001ntw.3	O94766	OTTHUMG00000167685	ENST00000265471.5:c.699C>T	11.37:g.62384188G>A		Somatic		Capture	Illumina HiSeq	Phase_I	62140764	NM_012200	B7ZAB3|Q96I06|Q9UEP0	Silent	SNP	ENST00000265471.5	37	CCDS8025.1																																																																																				0.642	B3GAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395588.1	NM_012200	
BSCL2	26580	broad.mit.edu	37	11	62469981	62469981	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:62469981G>A	ENST00000403550.1	-	3	676	c.253C>T	c.(253-255)Cct>Tct	p.P85S	BSCL2_ENST00000407022.3_Missense_Mutation_p.P85S|BSCL2_ENST00000360796.5_Missense_Mutation_p.P149S|HNRNPUL2-BSCL2_ENST00000403734.2_3'UTR|BSCL2_ENST00000537604.1_5'UTR|BSCL2_ENST00000405837.1_Missense_Mutation_p.P149S|BSCL2_ENST00000278893.7_Missense_Mutation_p.P85S|BSCL2_ENST00000433053.1_Missense_Mutation_p.P149S|BSCL2_ENST00000421906.1_Missense_Mutation_p.P85S			Q96G97	BSCL2_HUMAN	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	85					cell death (GO:0008219)|fat cell differentiation (GO:0045444)|lipid catabolic process (GO:0016042)|lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|negative regulation of lipid catabolic process (GO:0050995)	integral component of endoplasmic reticulum membrane (GO:0030176)		p.P85S(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	12						TTGGCAACAGGGAAGGAGCAG	0.473																																					p.P149S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C445T	11						.						187.0	145.0	159.0					11																	62469981		2202	4299	6501	62226557	SO:0001583	missense	26580	exon4				CCDS8031.1, CCDS44627.1, CCDS55769.1	11q13	2014-09-17	2009-07-30		ENSG00000168000	ENSG00000168000			15832	protein-coding gene	gene with protein product		606158	"""spastic paraplegia 17 (Silver syndrome)"""	GNG3LG, SPG17		11479539, 14981520	Standard	NM_001122955		Approved		uc001nur.4	Q96G97	OTTHUMG00000150624	ENST00000403550.1:c.253C>T	11.37:g.62469981G>A	ENSP00000385561:p.Pro85Ser	Somatic		Capture	Illumina HiSeq	Phase_I	62226557	NM_001130702	G3XAE4|Q567S1|Q96SV1|Q9BSQ0	Missense_Mutation	SNP	ENST00000403550.1	37	CCDS8031.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.7|29.7	5.030389|5.030389	0.93575|0.93575	.|.	.|.	ENSG00000168000|ENSG00000168000	ENST00000525000|ENST00000405837;ENST00000433053;ENST00000278893;ENST00000360796;ENST00000403550;ENST00000407022;ENST00000421906;ENST00000448568;ENST00000524862;ENST00000533982	.|D;D;D;D;D;D;D;D;D;D	.|0.96587	.|-4.06;-4.06;-4.06;-4.06;-4.06;-4.06;-4.06;-4.06;-4.06;-4.06	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.000000|0.000000	0.64402|0.64402	U|U	0.000001|0.000001	D|D	0.98302|0.98302	0.9437|0.9437	M|M	0.86953|0.86953	2.85|2.85	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|0.994;0.999;0.999;1.0	D|D	0.98945|0.98945	1.0792|1.0792	6|10	.|0.66056	.|D	.|0.02	-7.6908|-7.6908	17.206|17.206	0.86918|0.86918	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|85;85;149;85	.|Q96G97-3;Q53EN3;G3XAE4;Q96G97	.|.;.;.;BSCL2_HUMAN	L|S	26|149;149;85;149;85;85;85;85;149;85	.|ENSP00000385332:P149S;ENSP00000414002:P149S;ENSP00000278893:P85S;ENSP00000354032:P149S;ENSP00000385561:P85S;ENSP00000384080:P85S;ENSP00000413209:P85S;ENSP00000413340:P85S;ENSP00000433888:P149S;ENSP00000434149:P85S	.|ENSP00000278893:P85S	P|P	-|-	2|1	0|0	BSCL2|BSCL2	62226557|62226557	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.690000|7.690000	0.84178|0.84178	2.681000|2.681000	0.91329|0.91329	0.561000|0.561000	0.74099|0.74099	CCC|CCT		0.473	BSCL2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319185.1	NM_032667	
ZBTB3	79842	broad.mit.edu	37	11	62520758	62520758	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:62520758C>T	ENST00000394807.3	-	2	654	c.529G>A	c.(529-531)Gca>Aca	p.A177T		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	177					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A177T(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						GTACTGTCTGCCTCTGCCAGG	0.552																																					p.A177T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G529A	11						.						96.0	98.0	97.0					11																	62520758		2202	4299	6501	62277334	SO:0001583	missense	79842	exon2			AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.529G>A	11.37:g.62520758C>T	ENSP00000378286:p.Ala177Thr	Somatic		Capture	Illumina HiSeq	Phase_I	62277334	NM_024784		Missense_Mutation	SNP	ENST00000394807.3	37	CCDS8034.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.696788	0.88830	.	.	ENSG00000185670	ENST00000394807	T	0.14766	2.48	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.22399	0.0540	N	0.19112	0.55	0.54753	D	0.999989	D	0.89917	1.0	D	0.83275	0.996	T	0.07751	-1.0756	10	0.13853	T	0.58	.	17.4202	0.87513	0.0:1.0:0.0:0.0	.	177	Q9H5J0	ZBTB3_HUMAN	T	177	ENSP00000378286:A177T	ENSP00000378286:A177T	A	-	1	0	ZBTB3	62277334	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	7.484000	0.81180	2.700000	0.92200	0.561000	0.74099	GCA		0.552	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784	
CHRM1	1128	broad.mit.edu	37	11	62677424	62677424	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:62677424G>T	ENST00000306960.3	-	2	1690	c.1149C>A	c.(1147-1149)atC>atA	p.I383I	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	383					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.I383I(1)		large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	CCAGCACCATGATGTTGTACG	0.587																																					p.I383I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1149A	11						.						110.0	93.0	99.0					11																	62677424		2201	4298	6499	62434000	SO:0001819	synonymous_variant	1128	exon2			Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1950	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 1"""	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.1149C>A	11.37:g.62677424G>T		Somatic		Capture	Illumina HiSeq	Phase_I	62434000	NM_000738	Q96RH1	Silent	SNP	ENST00000306960.3	37	CCDS8040.1																																																																																				0.587	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738	
ESRRA	2101	broad.mit.edu	37	11	64082632	64082632	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:64082632G>A	ENST00000405666.1	+	6	1136	c.902G>A	c.(901-903)gGc>gAc	p.G301D	ESRRA_ENST00000000442.6_Missense_Mutation_p.G301D|ESRRA_ENST00000406310.1_Missense_Mutation_p.G300D|PRDX5_ENST00000265462.4_5'Flank	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	301	Ligand binding domain.				cartilage development (GO:0051216)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.G301D(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						CGGGCAGCTGGCCTGGGGGAA	0.652																																					p.G301D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G902A	11						.						24.0	27.0	26.0					11																	64082632		1995	4163	6158	63839208	SO:0001583	missense	2101	exon6			X51416, L38487	CCDS41667.1, CCDS60830.1	11q12	2013-01-16			ENSG00000173153	ENSG00000173153		"""Nuclear hormone receptors"""	3471	protein-coding gene	gene with protein product		601998		ESRL1		3267207	Standard	NM_004451		Approved	ERR1, ERRalpha, NR3B1, ERRa	uc001nzq.1	P11474	OTTHUMG00000150641	ENST00000405666.1:c.902G>A	11.37:g.64082632G>A	ENSP00000384851:p.Gly301Asp	Somatic		Capture	Illumina HiSeq	Phase_I	63839208	NM_004451	Q14514	Missense_Mutation	SNP	ENST00000405666.1	37	CCDS41667.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.66|19.66	3.868280|3.868280	0.72065|0.72065	.|.	.|.	ENSG00000173153|ENSG00000173153	ENST00000545035|ENST00000406310;ENST00000000442;ENST00000539594;ENST00000405666	.|D;D;T;D	.|0.96685	.|-4.09;-4.09;0.94;-4.09	4.14|4.14	4.14|4.14	0.48551|0.48551	.|Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	.|0.124809	.|0.53938	.|D	.|0.000053	D|D	0.98582|0.98582	0.9526|0.9526	H|H	0.95294|0.95294	3.65|3.65	0.80722|0.80722	D|D	1|1	.|P;D	.|0.89917	.|0.796;1.0	.|B;D	.|0.97110	.|0.072;1.0	D|D	0.99229|0.99229	1.0881|1.0881	5|10	.|0.87932	.|D	.|0	.|.	14.3272|14.3272	0.66528|0.66528	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|300;301	.|P11474-2;P11474	.|.;ERR1_HUMAN	T|D	82|300;301;158;301	.|ENSP00000385971:G300D;ENSP00000000442:G301D;ENSP00000439896:G158D;ENSP00000384851:G301D	.|ENSP00000000442:G301D	A|G	+|+	1|2	0|0	ESRRA|ESRRA	63839208|63839208	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.940000|0.940000	0.58332|0.58332	9.596000|9.596000	0.98267|0.98267	2.309000|2.309000	0.77851|0.77851	0.462000|0.462000	0.41574|0.41574	GCC|GGC		0.652	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	NM_004451	
SLC22A11	55867	broad.mit.edu	37	11	64336209	64336209	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:64336209C>A	ENST00000301891.4	+	8	1715	c.1341C>A	c.(1339-1341)tgC>tgA	p.C447*	SLC22A11_ENST00000377581.3_Nonsense_Mutation_p.C447*|SLC22A11_ENST00000377585.3_Intron	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 11	447					organic anion transport (GO:0015711)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.C447*(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23					Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495)	GCCTAACCTGCCTCACCATCT	0.597																																					p.C447X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1341A	11						.						210.0	166.0	181.0					11																	64336209		2201	4297	6498	64092785	SO:0001587	stop_gained	55867	exon8			AB026116	CCDS8074.1	11q13.3	2013-05-22	2008-01-11		ENSG00000168065	ENSG00000168065		"""Solute carriers"""	18120	protein-coding gene	gene with protein product		607097				10660625, 15576633, 17229912	Standard	NM_018484		Approved	OAT4	uc001oai.3	Q9NSA0	OTTHUMG00000045142	ENST00000301891.4:c.1341C>A	11.37:g.64336209C>A	ENSP00000301891:p.Cys447*	Somatic		Capture	Illumina HiSeq	Phase_I	64092785	NM_018484	A8K426|Q53GR2|Q6ZP72|Q8NBU4	Nonsense_Mutation	SNP	ENST00000301891.4	37	CCDS8074.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.267826	0.59540	.	.	ENSG00000168065	ENST00000301891;ENST00000377581;ENST00000416590	.	.	.	2.53	1.61	0.23674	.	0.061436	0.64402	U	0.000003	.	.	.	.	.	.	0.58432	D	0.999995	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4807	0.16721	0.0:0.8391:0.0:0.1609	.	.	.	.	X	447;447;94	.	ENSP00000301891:C447X	C	+	3	2	SLC22A11	64092785	0.409000	0.25368	0.001000	0.08648	0.029000	0.11900	0.717000	0.25851	0.649000	0.30751	0.555000	0.69702	TGC		0.597	SLC22A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104886.4	NM_018484	
ZFPL1	7542	broad.mit.edu	37	11	64855578	64855578	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:64855578C>A	ENST00000294258.3	+	8	1077	c.925C>A	c.(925-927)Ccc>Acc	p.P309T	AP003068.6_ENST00000525544.2_5'Flank	NM_006782.3	NP_006773.2	O95159	ZFPL1_HUMAN	zinc finger protein-like 1	309					regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.P309T(1)		breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11						CCGCGTGGGCCCCTCCTGAGC	0.652																																					p.P309T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C925A	11						.						56.0	57.0	56.0					11																	64855578		2201	4297	6498	64612154	SO:0001583	missense	7542	exon8				CCDS8092.1	11q13	2013-01-08			ENSG00000162300	ENSG00000162300			12868	protein-coding gene	gene with protein product	"""zinc-finger protein in MEN1 region"""					9653652	Standard	NM_006782		Approved	D11S750, MCG4	uc001ocq.1	O95159	OTTHUMG00000165597	ENST00000294258.3:c.925C>A	11.37:g.64855578C>A	ENSP00000294258:p.Pro309Thr	Somatic		Capture	Illumina HiSeq	Phase_I	64612154	NM_006782	A8K7E9|O14616|Q9UID0	Missense_Mutation	SNP	ENST00000294258.3	37	CCDS8092.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.841474	0.51057	.	.	ENSG00000162300	ENST00000294258	T	0.41400	1.0	4.94	4.94	0.65067	.	0.270224	0.35708	N	0.003039	T	0.43122	0.1233	N	0.22421	0.69	0.80722	D	1	D	0.54207	0.965	P	0.55055	0.767	T	0.35649	-0.9780	10	0.54805	T	0.06	-22.0836	13.5	0.61449	0.0:1.0:0.0:0.0	.	309	O95159	ZFPL1_HUMAN	T	309	ENSP00000294258:P309T	ENSP00000294258:P309T	P	+	1	0	ZFPL1	64612154	.	.	0.985000	0.45067	0.527000	0.34593	.	.	2.563000	0.86464	0.655000	0.94253	CCC		0.652	ZFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385196.1	NM_006782	
SIPA1	6494	broad.mit.edu	37	11	65417251	65417251	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:65417251C>T	ENST00000394224.3	+	12	2957	c.2661C>T	c.(2659-2661)ggC>ggT	p.G887G	SIPA1_ENST00000527525.1_Silent_p.G785G|MIR4489_ENST00000578869.1_RNA|SIPA1_ENST00000534313.1_Silent_p.G887G|SIPA1_ENST00000394227.3_Silent_p.G785G	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	887					cell proliferation (GO:0008283)|cellular response to water deprivation (GO:0042631)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|signal transduction (GO:0007165)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	GTPase activator activity (GO:0005096)|Rap GTPase activator activity (GO:0046582)	p.G887G(1)		cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	10						GTCCCAGTGGCTCTGAGGACA	0.602																																					p.G887G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2661T	11						.						68.0	68.0	68.0					11																	65417251		2201	4297	6498	65173827	SO:0001819	synonymous_variant	6494	exon12			AH006363, BC010492, BM677738	CCDS8108.1	11q13.3	2008-09-12	2008-09-12		ENSG00000213445	ENSG00000213445			10885	protein-coding gene	gene with protein product		602180				9027487	Standard	NM_006747		Approved	SPA1	uc001ofb.2	Q96FS4	OTTHUMG00000166541	ENST00000394224.3:c.2661C>T	11.37:g.65417251C>T		Somatic		Capture	Illumina HiSeq	Phase_I	65173827	NM_006747	O14518|O60484|O60618|Q2YD83	Silent	SNP	ENST00000394224.3	37	CCDS8108.1																																																																																				0.602	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747	
KLC2	64837	broad.mit.edu	37	11	66031649	66031649	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:66031649G>A	ENST00000417856.1	+	8	1318	c.1075G>A	c.(1075-1077)Ggg>Agg	p.G359R	KLC2_ENST00000394066.2_Missense_Mutation_p.G282R|KLC2_ENST00000394078.1_Intron|KLC2_ENST00000394065.2_Missense_Mutation_p.G220R|KLC2_ENST00000316924.5_Missense_Mutation_p.G359R|RP11-755F10.3_ENST00000533576.1_RNA|RP11-867G23.1_ENST00000530805.1_RNA|KLC2_ENST00000421552.1_Missense_Mutation_p.G282R|KLC2_ENST00000394067.2_Missense_Mutation_p.G359R	NM_001134775.1	NP_001128247.1	Q9H0B6	KLC2_HUMAN	kinesin light chain 2	359					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon cargo transport (GO:0008088)|blood coagulation (GO:0007596)|microtubule-based movement (GO:0007018)	ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinesin I complex (GO:0016938)|membrane (GO:0016020)|microtubule (GO:0005874)|neuron projection (GO:0043005)|protein complex (GO:0043234)	kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)	p.G359R(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						TACACGCCTCGGGCCCGATGA	0.597																																					p.G359R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1075A	11						.						28.0	22.0	24.0					11																	66031649		2196	4285	6481	65788225	SO:0001583	missense	64837	exon8			AK022449	CCDS8130.1, CCDS44653.1	11q13.1	2013-01-10			ENSG00000174996	ENSG00000174996		"""Tetratricopeptide (TTC) repeat domain containing"""	20716	protein-coding gene	gene with protein product		611729				9624122	Standard	NM_022822		Approved	FLJ12387	uc001ohb.2	Q9H0B6	OTTHUMG00000133757	ENST00000417856.1:c.1075G>A	11.37:g.66031649G>A	ENSP00000399403:p.Gly359Arg	Somatic		Capture	Illumina HiSeq	Phase_I	65788225	NM_001134775	A8MXL7|B2RDY4|Q9H9C8|Q9HA20	Missense_Mutation	SNP	ENST00000417856.1	37	CCDS8130.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.165478	0.78339	.	.	ENSG00000174996	ENST00000417856;ENST00000394067;ENST00000316924;ENST00000421552;ENST00000394066;ENST00000394065	T;T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29;-0.29	4.24	4.24	0.50183	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.64402	D	0.000001	T	0.82047	0.4952	M	0.79805	2.47	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	D	0.85374	0.1115	10	0.87932	D	0	-30.5119	15.5738	0.76359	0.0:0.0:1.0:0.0	.	220;282;359	A8MZ87;A8MXL7;Q9H0B6	.;.;KLC2_HUMAN	R	359;359;359;282;282;220	ENSP00000399403:G359R;ENSP00000377631:G359R;ENSP00000314837:G359R;ENSP00000408484:G282R;ENSP00000377630:G282R;ENSP00000377629:G220R	ENSP00000314837:G359R	G	+	1	0	KLC2	65788225	1.000000	0.71417	0.966000	0.40874	0.518000	0.34316	9.592000	0.98245	2.212000	0.71576	0.561000	0.74099	GGG		0.597	KLC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258200.1	NM_022822	
B3GNT1	11041	broad.mit.edu	37	11	66113705	66113705	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:66113705C>T	ENST00000311181.4	-	2	1209	c.1063G>A	c.(1063-1065)Gag>Aag	p.E355K	RP11-867G23.8_ENST00000531602.1_5'Flank|BRMS1_ENST00000425825.2_5'Flank|BRMS1_ENST00000359957.3_5'Flank	NM_006876.2	NP_006867.1	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1	355					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)	p.E355K(1)		breast(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	12						ACATGCAGCTCGCAGGCCTGC	0.517																																					p.E355K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1063A	11						.						62.0	66.0	65.0					11																	66113705		2200	4295	6495	65870281	SO:0001583	missense	11041	exon2			AF029893	CCDS8136.1	11q13.2	2014-07-08	2006-04-12	2006-04-12	ENSG00000174684	ENSG00000174684	2.4.1.149	"""Beta 3-glycosyltransferases"""	15685	protein-coding gene	gene with protein product	"""N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase"""	605517	"""UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6"""	B3GNT6		9405606	Standard	NM_006876		Approved	iGNT, iGAT, iGnT, BETA3GNTI, B3GN-T1	uc001ohr.3	O43505	OTTHUMG00000167082	ENST00000311181.4:c.1063G>A	11.37:g.66113705C>T	ENSP00000309096:p.Glu355Lys	Somatic		Capture	Illumina HiSeq	Phase_I	65870281	NM_006876	Q4TTN0	Missense_Mutation	SNP	ENST00000311181.4	37	CCDS8136.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.467350	0.84533	.	.	ENSG00000174684	ENST00000311181;ENST00000538757	T	0.23552	1.9	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.57755	0.2075	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.61874	-0.6973	10	0.40728	T	0.16	-25.0295	16.5318	0.84362	0.0:1.0:0.0:0.0	.	355	O43505	B3GN1_HUMAN	K	355;126	ENSP00000309096:E355K	ENSP00000309096:E355K	E	-	1	0	B3GNT1	65870281	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.335000	0.79234	2.505000	0.84491	0.655000	0.94253	GAG		0.517	B3GNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392959.1	NM_006876	
NPAS4	266743	broad.mit.edu	37	11	66191311	66191311	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:66191311T>C	ENST00000311034.2	+	7	1126	c.950T>C	c.(949-951)aTg>aCg	p.M317T		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	317	PAC.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)	p.M317T(1)		breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						TCCAGTGACATGGAAGCCTGG	0.562																																					p.M317T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T950C	11						.						67.0	68.0	68.0					11																	66191311		2200	4295	6495	65947887	SO:0001583	missense	266743	exon7			AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"""Basic helix-loop-helix proteins"""	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.950T>C	11.37:g.66191311T>C	ENSP00000311196:p.Met317Thr	Somatic		Capture	Illumina HiSeq	Phase_I	65947887	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Missense_Mutation	SNP	ENST00000311034.2	37	CCDS8138.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.166285	0.00318	.	.	ENSG00000174576	ENST00000311034	T	0.39056	1.1	4.71	0.727	0.18254	.	0.919920	0.09131	N	0.844415	T	0.14960	0.0361	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29119	-1.0022	10	0.06625	T	0.88	2.9529	3.7822	0.08684	0.1632:0.4747:0.0:0.3621	.	317	Q8IUM7	NPAS4_HUMAN	T	317	ENSP00000311196:M317T	ENSP00000311196:M317T	M	+	2	0	NPAS4	65947887	0.006000	0.16342	0.367000	0.25926	0.990000	0.78478	1.133000	0.31430	0.045000	0.15804	-0.441000	0.05720	ATG		0.562	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864	
PC	5091	broad.mit.edu	37	11	66617582	66617582	+	Silent	SNP	C	C	T	rs573985170		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:66617582C>T	ENST00000393958.2	-	19	2817	c.2724G>A	c.(2722-2724)acG>acA	p.T908T	PC_ENST00000393960.1_Silent_p.T908T|PC_ENST00000393955.2_Silent_p.T908T|PC_ENST00000529047.1_Silent_p.T28T|PC_ENST00000528224.1_5'Flank	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	908					biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)	p.T908T(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	TGGAGGAGGGCGTCACCTGAG	0.642													C|||	1	0.000199681	0.0	0.0	5008	,	,		19440	0.0		0.0	False		,,,				2504	0.001				p.T908T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2724A	11						.						81.0	78.0	79.0					11																	66617582		2200	4295	6495	66374158	SO:0001819	synonymous_variant	5091	exon20			U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.2724G>A	11.37:g.66617582C>T		Somatic		Capture	Illumina HiSeq	Phase_I	66374158	NM_001040716	B4DN00|Q16705	Silent	SNP	ENST00000393958.2	37	CCDS8152.1																																																																																				0.642	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716	
KDM2A	22992	broad.mit.edu	37	11	66975083	66975083	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:66975083G>A	ENST00000529006.2	+	6	856	c.410G>A	c.(409-411)cGa>cAa	p.R137Q	KDM2A_ENST00000398645.2_Missense_Mutation_p.R137Q|KDM2A_ENST00000526258.1_3'UTR	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	137					histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.R137Q(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						GAGGAGGAGCGAGAGAAACTC	0.493																																					p.R137Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G410A	11						.						64.0	69.0	67.0					11																	66975083		2011	4179	6190	66731659	SO:0001583	missense	22992	exon6			BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13606	protein-coding gene	gene with protein product	"""F-box protein FBL11"", ""jumonji C domain-containing histone demethylase 1A"""	605657	"""F-box and leucine-rich repeat protein 11"""	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.410G>A	11.37:g.66975083G>A	ENSP00000432786:p.Arg137Gln	Somatic		Capture	Illumina HiSeq	Phase_I	66731659	NM_012308	D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Missense_Mutation	SNP	ENST00000529006.2	37	CCDS44657.1	.	.	.	.	.	.	.	.	.	.	G	36	5.643135	0.96704	.	.	ENSG00000173120	ENST00000398645;ENST00000529006	T;T	0.71341	-0.56;-0.56	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.87418	0.6172	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.89899	0.4043	10	0.87932	D	0	-12.1726	18.0888	0.89468	0.0:0.0:1.0:0.0	.	137	Q9Y2K7	KDM2A_HUMAN	Q	137	ENSP00000381640:R137Q;ENSP00000432786:R137Q	ENSP00000381640:R137Q	R	+	2	0	KDM2A	66731659	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.869000	0.99810	2.503000	0.84419	0.591000	0.81541	CGA		0.493	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	NM_012308	
RPS6KB2	6199	broad.mit.edu	37	11	67200478	67200478	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:67200478C>T	ENST00000312629.5	+	8	717	c.672C>T	c.(670-672)gcC>gcT	p.A224A	RPS6KB2_ENST00000539188.1_3'UTR|AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	224	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)	p.A224A(2)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			ATGAGGGCGCCGTCACTCACA	0.622																																					p.A224A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C672T	11						.						40.0	45.0	43.0					11																	67200478		2064	4200	6264	66957054	SO:0001819	synonymous_variant	6199	exon8			AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"""ribosomal protein S6 kinase, 70kD, polypeptide 2"""			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.672C>T	11.37:g.67200478C>T		Somatic		Capture	Illumina HiSeq	Phase_I	66957054	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Silent	SNP	ENST00000312629.5	37	CCDS41677.1																																																																																				0.622	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952	
NDUFV1	4723	broad.mit.edu	37	11	67379389	67379389	+	Missense_Mutation	SNP	G	G	A	rs376958800		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:67379389G>A	ENST00000322776.6	+	8	1255	c.1102G>A	c.(1102-1104)Gcc>Acc	p.A368T	NDUFV1_ENST00000526169.1_3'UTR|NDUFV1_ENST00000529927.1_Missense_Mutation_p.A359T|NDUFV1_ENST00000532303.1_Missense_Mutation_p.A267T|NDUFV1_ENST00000415352.2_Missense_Mutation_p.A361T|DOC2GP_ENST00000495263.1_RNA	NM_001166102.1|NM_007103.3	NP_001159574.1|NP_009034.2	P49821	NDUV1_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 1, 51kDa	368					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.A368T(1)		breast(1)|endometrium(3)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	16						GAAAGCCATCGCCCGCCTCAT	0.627																																					p.A359T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1075A	11						.	G	THR/ALA,THR/ALA	0,4400		0,0,2200	122.0	109.0	113.0		1102,1075	4.7	1.0	11		113	1,8587	1.2+/-3.3	0,1,4293	no	missense,missense	NDUFV1	NM_007103.3,NM_001166102.1	58,58	0,1,6493	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	368/465,359/456	67379389	1,12987	2200	4294	6494	67135965	SO:0001583	missense	4723	exon8			AF092131	CCDS8173.1, CCDS53669.1	11q13	2011-07-04	2002-08-29		ENSG00000167792	ENSG00000167792	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7716	protein-coding gene	gene with protein product	"""complex I 51kDa subunit"", ""NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial"""	161015	"""NADH dehydrogenase (ubiquinone) flavoprotein 1 (51kD)"""			1478657	Standard	NM_007103		Approved	CI-51K	uc001omj.2	P49821	OTTHUMG00000166215	ENST00000322776.6:c.1102G>A	11.37:g.67379389G>A	ENSP00000322450:p.Ala368Thr	Somatic		Capture	Illumina HiSeq	Phase_I	67135965	NM_001166102	O60924|O60940|Q16104|Q6IBR3|Q96BF8|Q96HS7	Missense_Mutation	SNP	ENST00000322776.6	37	CCDS8173.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.040979	0.75732	0.0	1.16E-4	ENSG00000167792	ENST00000322776;ENST00000532303;ENST00000529927;ENST00000415352;ENST00000453836	D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16	4.65	4.65	0.58169	NADH ubiquinone oxidoreductase, F subunit, iron sulphur binding (2);	0.057756	0.64402	D	0.000002	D	0.85733	0.5765	M	0.64404	1.975	0.80722	D	1	P;B;B	0.35793	0.521;0.174;0.408	B;B;B	0.35413	0.052;0.052;0.202	D	0.86491	0.1797	10	0.48119	T	0.1	-20.2166	16.4799	0.84155	0.0:0.0:1.0:0.0	.	361;359;368	G3V0I5;P49821-2;P49821	.;.;NDUV1_HUMAN	T	368;267;359;361;239	ENSP00000322450:A368T;ENSP00000432015:A267T;ENSP00000436766:A359T;ENSP00000395368:A361T	ENSP00000322450:A368T	A	+	1	0	NDUFV1	67135965	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.469000	0.97679	2.302000	0.77476	0.491000	0.48974	GCC		0.627	NDUFV1-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388406.1	NM_007103	
ALDH3B1	221	broad.mit.edu	37	11	67789113	67789113	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:67789113G>A	ENST00000539229.1	+	8	835	c.719G>A	c.(718-720)gGc>gAc	p.G240D	ALDH3B1_ENST00000316367.6_Intron|ALDH3B1_ENST00000434449.1_3'UTR|ALDH3B1_ENST00000342456.6_Missense_Mutation_p.G204D|ALDH3B1_ENST00000007633.8_Missense_Mutation_p.G240D	NM_001161473.1	NP_001154945.1	P43353	AL3B1_HUMAN	aldehyde dehydrogenase 3 family, member B1	241					alcohol metabolic process (GO:0006066)|aldehyde catabolic process (GO:0046185)|cellular response to oxidative stress (GO:0034599)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)										TTCAACGCCGGCCAGACCTGC	0.652											OREG0021141	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G204D												.	.	0			c.G611A	11						.						96.0	106.0	102.0					11																	67789113		2200	4294	6494	67545689	SO:0001583	missense	221	exon6			U10868	CCDS73335.1, CCDS73336.1	11q13	2010-04-27			ENSG00000006534	ENSG00000006534	1.2.1.5	"""Aldehyde dehydrogenases"""	410	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase 7"", ""aldehyde dehydrogenase 3B1"""	600466		ALDH7		9161417, 7828891	Standard	NM_000694		Approved		uc001ona.3	P43353	OTTHUMG00000154910	ENST00000539229.1:c.719G>A	11.37:g.67789113G>A	ENSP00000474034:p.Gly240Asp	Somatic	1102	Capture	Illumina HiSeq	Phase_I	67545689	NM_001030010	A3FMP9|Q53XL5|Q8N515|Q96CK8	Missense_Mutation	SNP	ENST00000539229.1	37																																																																																					0.652	ALDH3B1-204	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000694	
TPCN2	219931	broad.mit.edu	37	11	68854064	68854064	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:68854064A>G	ENST00000294309.3	+	23	2178	c.2077A>G	c.(2077-2079)Att>Gtt	p.I693V	TPCN2_ENST00000542467.1_Intron|TPCN2_ENST00000442692.2_3'UTR	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	693					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)	p.I693V(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TCTGGCCCTGATTCTGGAGGT	0.567																																					p.I693V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2077G	11						.						209.0	165.0	180.0					11																	68854064		2200	4294	6494	68610640	SO:0001583	missense	219931	exon23			AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.2077A>G	11.37:g.68854064A>G	ENSP00000294309:p.Ile693Val	Somatic		Capture	Illumina HiSeq	Phase_I	68610640	NM_139075	Q9NT82	Missense_Mutation	SNP	ENST00000294309.3	37	CCDS8189.1	.	.	.	.	.	.	.	.	.	.	A	7.108	0.575474	0.13623	.	.	ENSG00000162341	ENST00000294309	D	0.98876	-5.2	4.36	3.28	0.37604	Ion transport (1);	0.331184	0.25549	N	0.029920	D	0.96602	0.8891	L	0.39692	1.235	0.80722	D	1	P	0.40302	0.712	B	0.41135	0.348	D	0.94848	0.8011	10	0.51188	T	0.08	-6.488	11.4282	0.50022	0.4682:0.5318:0.0:0.0	.	693	Q8NHX9	TPC2_HUMAN	V	693	ENSP00000294309:I693V	ENSP00000294309:I693V	I	+	1	0	TPCN2	68610640	1.000000	0.71417	0.528000	0.27938	0.188000	0.23474	3.311000	0.51919	0.736000	0.32559	0.459000	0.35465	ATT		0.567	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
FOLR3	2352	broad.mit.edu	37	11	71850756	71850756	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:71850756G>A	ENST00000445078.2	+	5	810	c.739G>A	c.(739-741)Ggc>Agc	p.G247S	FOLR3_ENST00000442948.2_Missense_Mutation_p.G206S|FOLR3_ENST00000456237.1_Missense_Mutation_p.G249S			P41439	FOLR3_HUMAN	folate receptor 3 (gamma)	205					folic acid transport (GO:0015884)	extracellular region (GO:0005576)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)	folic acid binding (GO:0005542)	p.G249S(1)		large_intestine(3)|lung(8)|prostate(2)	13					Folic Acid(DB00158)	TCGAGGGAGCGGCCGCTGCAT	0.602																																					p.R206Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G617A	11						.						40.0	41.0	41.0					11																	71850756		2200	4293	6493	71528404	SO:0001583	missense	2352	exon5			U08471	CCDS73344.1	11q13.4	2012-11-14			ENSG00000110203	ENSG00000110203			3795	protein-coding gene	gene with protein product		602469				8110752	Standard	NM_000804		Approved	FR-G	uc001orx.1	P41439	OTTHUMG00000167870	ENST00000445078.2:c.739G>A	11.37:g.71850756G>A	ENSP00000390338:p.Gly247Ser	Somatic		Capture	Illumina HiSeq	Phase_I	71528404	NM_000804	J3KQ90|Q05C14	Missense_Mutation	SNP	ENST00000445078.2	37		.	.	.	.	.	.	.	.	.	.	N	18.60	3.660025	0.67586	.	.	ENSG00000110203	ENST00000445078;ENST00000456237;ENST00000442948	T;T;T	0.75938	-0.98;-0.98;-0.98	2.94	2.94	0.34122	Folate receptor-like (1);	0.000000	0.64402	U	0.000006	D	0.83580	0.5285	.	.	.	0.53688	D	0.999977	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.979	D	0.84186	0.0442	8	.	.	.	.	11.6457	0.51259	0.0:0.0:1.0:0.0	.	249;205	E9PGT2;P41439	.;FOLR3_HUMAN	S	247;249;206	ENSP00000390338:G247S;ENSP00000399235:G249S;ENSP00000411161:G206S	.	G	+	1	0	FOLR3	71528404	1.000000	0.71417	0.979000	0.43373	0.466000	0.32739	6.456000	0.73501	1.638000	0.50547	0.467000	0.42956	GGC		0.602	FOLR3-001	NOVEL	upstream_ATG|basic	protein_coding	protein_coding	OTTHUMT00000396739.1	NM_000804	
UCP3	7352	broad.mit.edu	37	11	73715570	73715570	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:73715570T>C	ENST00000314032.4	-	5	1154	c.602A>G	c.(601-603)gAc>gGc	p.D201G	UCP3_ENST00000545271.1_5'Flank|UCP3_ENST00000426995.2_Missense_Mutation_p.D201G|UCP3_ENST00000348534.4_Intron	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	201					aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to hormone stimulus (GO:0032870)|fatty acid metabolic process (GO:0006631)|lipid metabolic process (GO:0006629)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|response to activity (GO:0014823)|response to cold (GO:0009409)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)|transporter activity (GO:0005215)	p.D201G(2)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12	Breast(11;2.08e-05)					CTTGAGGATGTCGTAGGTCAC	0.582																																					p.D201G												.	.	2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.A602G	11						.						177.0	131.0	146.0					11																	73715570		2200	4293	6493	73393218	SO:0001583	missense	7352	exon5			AF001787	CCDS8229.1, CCDS44677.1	11q13.4	2013-05-22				ENSG00000175564		"""Solute carriers"""	12519	protein-coding gene	gene with protein product		602044				9480760, 9196039	Standard	NM_003356		Approved	SLC25A9	uc001our.3	P55916		ENST00000314032.4:c.602A>G	11.37:g.73715570T>C	ENSP00000323740:p.Asp201Gly	Somatic		Capture	Illumina HiSeq	Phase_I	73393218	NM_022803	O60475|Q96HL3	Missense_Mutation	SNP	ENST00000314032.4	37	CCDS8229.1	.	.	.	.	.	.	.	.	.	.	T	31	5.099030	0.94197	.	.	ENSG00000175564	ENST00000314032;ENST00000426995	T;T	0.80566	-1.39;-1.39	5.82	5.82	0.92795	Mitochondrial carrier domain (2);	0.085770	0.85682	D	0.000000	D	0.89791	0.6817	M	0.81341	2.54	0.80722	D	1	D	0.67145	0.996	D	0.81914	0.995	D	0.91090	0.4906	10	0.87932	D	0	-6.7037	15.1554	0.72735	0.0:0.0:0.0:1.0	.	201	P55916	UCP3_HUMAN	G	201	ENSP00000323740:D201G;ENSP00000392143:D201G	ENSP00000323740:D201G	D	-	2	0	UCP3	73393218	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.977000	0.88081	2.228000	0.72767	0.533000	0.62120	GAC		0.582	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356	
POLD3	10714	broad.mit.edu	37	11	74331075	74331075	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:74331075G>A	ENST00000263681.2	+	7	803	c.674G>A	c.(673-675)gGc>gAc	p.G225D	POLD3_ENST00000532497.1_Missense_Mutation_p.G119D|POLD3_ENST00000527458.1_Missense_Mutation_p.G186D	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	225					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)	p.G225D(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					TCTGCAGCAGGCAACAAGGCA	0.403																																					p.G225D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G674A	11						.						194.0	184.0	187.0					11																	74331075		2200	4293	6493	74008723	SO:0001583	missense	10714	exon7			D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"""DNA polymerases"""	20932	protein-coding gene	gene with protein product	"""DNA polymerase delta subunit p66"", ""Pol delta C subunit (p66)"", ""protein phosphatase 1, regulatory subunit 128"""	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.674G>A	11.37:g.74331075G>A	ENSP00000263681:p.Gly225Asp	Somatic		Capture	Illumina HiSeq	Phase_I	74008723	NM_006591	B7ZAI6|Q32MZ9|Q32N00	Missense_Mutation	SNP	ENST00000263681.2	37	CCDS8233.1	.	.	.	.	.	.	.	.	.	.	G	8.130	0.782918	0.16189	.	.	ENSG00000077514	ENST00000263681;ENST00000527458;ENST00000532497;ENST00000538052	.	.	.	5.01	4.07	0.47477	.	0.265582	0.43110	D	0.000614	T	0.50429	0.1615	L	0.44542	1.39	0.38031	D	0.935151	B	0.32653	0.379	B	0.38378	0.272	T	0.48293	-0.9048	9	0.14252	T	0.57	-21.2402	13.2542	0.60068	0.0:0.1607:0.8393:0.0	.	225	Q15054	DPOD3_HUMAN	D	225;186;119;225	.	ENSP00000263681:G225D	G	+	2	0	POLD3	74008723	1.000000	0.71417	0.988000	0.46212	0.953000	0.61014	2.540000	0.45727	1.413000	0.46997	0.563000	0.77884	GGC		0.403	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1	NM_006591	
OR2AT4	341152	broad.mit.edu	37	11	74800047	74800047	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:74800047C>A	ENST00000305159.3	-	1	752	c.712G>T	c.(712-714)Gga>Tga	p.G238*		NM_001005285.1	NP_001005285.1	A6NND4	O2AT4_HUMAN	olfactory receptor, family 2, subfamily AT, member 4	238						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G238*(1)		endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	12						TTTGCCCGTCCTTCTAGGGAA	0.572																																					p.G238X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G712T	11						.						52.0	50.0	50.0					11																	74800047		2200	4293	6493	74477695	SO:0001587	stop_gained	341152	exon1			BK004820	CCDS31639.1	11q13.4	2012-08-09			ENSG00000171561	ENSG00000171561		"""GPCR / Class A : Olfactory receptors"""	19620	protein-coding gene	gene with protein product							Standard	NM_001005285		Approved		uc010rro.2	A6NND4	OTTHUMG00000165370	ENST00000305159.3:c.712G>T	11.37:g.74800047C>A	ENSP00000304846:p.Gly238*	Somatic		Capture	Illumina HiSeq	Phase_I	74477695	NM_001005285	B9EGZ8	Nonsense_Mutation	SNP	ENST00000305159.3	37	CCDS31639.1	.	.	.	.	.	.	.	.	.	.	C	16.77	3.215017	0.58452	.	.	ENSG00000171561	ENST00000305159	.	.	.	5.26	5.26	0.73747	.	0.000000	0.33092	U	0.005296	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	16.7481	0.85478	0.0:1.0:0.0:0.0	.	.	.	.	X	238	.	ENSP00000304846:G238X	G	-	1	0	OR2AT4	74477695	0.316000	0.24580	0.982000	0.44146	0.401000	0.30781	1.364000	0.34171	2.617000	0.88574	0.650000	0.86243	GGA		0.572	OR2AT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383734.1	NM_001005285	
RPS3	6188	broad.mit.edu	37	11	75112734	75112734	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:75112734C>A	ENST00000531188.1	+	3	274	c.212C>A	c.(211-213)gCt>gAt	p.A71D	RPS3_ENST00000529285.1_3'UTR|RPS3_ENST00000530164.1_Missense_Mutation_p.A71D|RPS3_ENST00000527446.1_Missense_Mutation_p.A71D|SNORD15B_ENST00000384714.1_RNA|RPS3_ENST00000534440.1_Missense_Mutation_p.A71D|RPS3_ENST00000278572.6_Missense_Mutation_p.A71D|SNORD15A_ENST00000384214.1_RNA|RPS3_ENST00000524851.1_Missense_Mutation_p.A71D|RPS3_ENST00000526608.1_Missense_Mutation_p.A71D	NM_001005.4|NM_001260506.1|NM_001260507.1	NP_000996.2|NP_001247435.1|NP_001247436.1	P23396	RS3_HUMAN	ribosomal protein S3	71	KH type-2. {ECO:0000255|PROSITE- ProRule:PRU00118}.				cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic translation (GO:0002181)|DNA catabolic process, endonucleolytic (GO:0000737)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of DNA repair (GO:0045738)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of DNA N-glycosylase activity (GO:1902546)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ruffle membrane (GO:0032587)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|enzyme binding (GO:0019899)|iron-sulfur cluster binding (GO:0051536)|mRNA binding (GO:0003729)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)	p.A71D(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6						GAACTGACTGCTGTAGTTCAG	0.463																																					p.A71D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C212A	11						.						106.0	103.0	104.0					11																	75112734		2200	4293	6493	74790382	SO:0001583	missense	6188	exon3				CCDS8236.1, CCDS58161.1	11q13.3-q13.5	2011-04-05				ENSG00000149273		"""S ribosomal proteins"""	10420	protein-coding gene	gene with protein product	"""IMR-90 ribosomal protein S3"", ""40S ribosomal protein S3"""	600454				1712897, 7789996	Standard	NM_001005		Approved	FLJ26283, FLJ27450, MGC87870, S3	uc031qcs.1	P23396		ENST00000531188.1:c.212C>A	11.37:g.75112734C>A	ENSP00000434643:p.Ala71Asp	Somatic		Capture	Illumina HiSeq	Phase_I	74790382	NM_001005	B2R7N5|J3KN86|Q498B5|Q8NI95	Missense_Mutation	SNP	ENST00000531188.1	37	CCDS8236.1	.	.	.	.	.	.	.	.	.	.	c	26.0	4.694239	0.88735	.	.	ENSG00000149273	ENST00000531188;ENST00000530164;ENST00000530689;ENST00000278572;ENST00000534440;ENST00000527446;ENST00000526608;ENST00000527273;ENST00000524851	.	.	.	5.9	5.9	0.94986	K Homology (1);K homology domain-like, alpha/beta (1);K Homology, prokaryotic type (1);K Homology, type 2 (2);	0.047553	0.85682	D	0.000000	T	0.71476	0.3344	M	0.76002	2.32	0.80722	D	1	B	0.17465	0.022	B	0.28305	0.088	T	0.69183	-0.5212	9	0.87932	D	0	-5.9286	17.7772	0.88513	0.0:1.0:0.0:0.0	.	71	P23396	RS3_HUMAN	D	71	.	ENSP00000278572:A71D	A	+	2	0	RPS3	74790382	1.000000	0.71417	0.994000	0.49952	0.971000	0.66376	7.815000	0.86186	2.798000	0.96311	0.651000	0.88453	GCT		0.463	RPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384158.2	NM_001005	
SERPINH1	871	broad.mit.edu	37	11	75280084	75280084	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:75280084C>T	ENST00000524558.1	+	4	2257	c.822C>T	c.(820-822)caC>caT	p.H274H	SERPINH1_ENST00000358171.3_Silent_p.H274H|SERPINH1_ENST00000525876.1_Silent_p.H57H|SERPINH1_ENST00000533603.1_Silent_p.H274H|SERPINH1_ENST00000530284.1_Silent_p.H274H			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	274					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.H274H(1)		endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					TGCCCCATCACGTGGAGCCTC	0.547																																					p.H274H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C822T	11						.						86.0	80.0	82.0					11																	75280084		2200	4293	6493	74957732	SO:0001819	synonymous_variant	871	exon4			X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.822C>T	11.37:g.75280084C>T		Somatic		Capture	Illumina HiSeq	Phase_I	74957732	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Silent	SNP	ENST00000524558.1	37	CCDS8239.1																																																																																				0.547	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353	
C11orf30	56946	broad.mit.edu	37	11	76248901	76248901	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:76248901C>T	ENST00000529032.1	+	15	2422	c.2422C>T	c.(2422-2424)Cct>Tct	p.P808S	C11orf30_ENST00000525038.1_Missense_Mutation_p.P823S|C11orf30_ENST00000343878.3_Missense_Mutation_p.P808S|C11orf30_ENST00000334736.3_Missense_Mutation_p.P808S|C11orf30_ENST00000524490.1_Missense_Mutation_p.P724S|C11orf30_ENST00000533248.1_Intron|C11orf30_ENST00000525919.1_Missense_Mutation_p.P809S|C11orf30_ENST00000524767.1_Missense_Mutation_p.P823S			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	808					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.P808S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						AATGGCAGTGCCTATTCAGAT	0.398																																					p.P808S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2422T	11						.						116.0	110.0	112.0					11																	76248901		2200	4292	6492	75926549	SO:0001583	missense	56946	exon16			AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.2422C>T	11.37:g.76248901C>T	ENSP00000432327:p.Pro808Ser	Somatic		Capture	Illumina HiSeq	Phase_I	75926549	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Missense_Mutation	SNP	ENST00000529032.1	37	CCDS8244.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.978595	0.92982	.	.	ENSG00000158636	ENST00000524490;ENST00000334736;ENST00000343878;ENST00000524767;ENST00000525919;ENST00000525038;ENST00000529032	T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.60051	0.2239	L	0.27053	0.805	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	0.83275	0.994;0.994;0.996;0.996;0.994;0.996	T	0.60193	-0.7311	10	0.56958	D	0.05	-8.2546	20.428	0.99075	0.0:1.0:0.0:0.0	.	823;823;176;809;724;808	B7ZKU2;B7ZKU0;B3KWW8;Q17RM7;E9PMC9;Q7Z589	.;.;.;.;.;EMSY_HUMAN	S	724;808;808;823;809;823;808	ENSP00000334130:P808S;ENSP00000344688:P808S;ENSP00000433205:P823S;ENSP00000432010:P809S;ENSP00000432327:P808S	ENSP00000334130:P808S	P	+	1	0	C11orf30	75926549	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.142000	0.77339	2.837000	0.97791	0.655000	0.94253	CCT		0.398	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193	
INTS4	92105	broad.mit.edu	37	11	77602456	77602456	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:77602456G>T	ENST00000534064.1	-	21	2535	c.2501C>A	c.(2500-2502)cCt>cAt	p.P834H	INTS4_ENST00000535943.1_Missense_Mutation_p.P209H|AAMDC_ENST00000532481.1_Intron|AAMDC_ENST00000527134.1_Intron|AAMDC_ENST00000304716.8_Intron	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	834					snRNA processing (GO:0016180)	integrator complex (GO:0032039)		p.P834H(1)	INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			AAACCGCAAAGGGTTGTCTGA	0.522																																					p.P834H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2501A	11						.						43.0	39.0	40.0					11																	77602456		2200	4292	6492	77280104	SO:0001583	missense	92105	exon21			BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.2501C>A	11.37:g.77602456G>T	ENSP00000434466:p.Pro834His	Somatic		Capture	Illumina HiSeq	Phase_I	77280104	NM_033547	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	37	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.281340	0.80692	.	.	ENSG00000149262	ENST00000534064;ENST00000535943	.	.	.	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.78717	0.4327	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.80540	-0.1337	9	0.87932	D	0	-17.8313	18.7604	0.91848	0.0:0.0:1.0:0.0	.	834	Q96HW7	INT4_HUMAN	H	834;209	.	ENSP00000434466:P834H	P	-	2	0	INTS4	77280104	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	9.514000	0.98013	2.667000	0.90743	0.585000	0.79938	CCT		0.522	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547	
TENM4	26011	broad.mit.edu	37	11	78369639	78369639	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:78369639G>A	ENST00000278550.7	-	34	8236	c.7774C>T	c.(7774-7776)Cga>Tga	p.R2592*		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2592					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.R2592*(2)									GCAACCCTTCGCCCATCCTCA	0.527																																					p.R2592X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C7774T	11						.						40.0	42.0	41.0					11																	78369639		2079	4214	6293	78047287	SO:0001587	stop_gained	26011	exon34			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.7774C>T	11.37:g.78369639G>A	ENSP00000278550:p.Arg2592*	Somatic		Capture	Illumina HiSeq	Phase_I	78047287	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Nonsense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	G	50	17.230809	0.99882	.	.	ENSG00000149256	ENST00000278550	.	.	.	5.65	4.73	0.59995	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5376	0.61655	0.0:0.0:0.603:0.397	.	.	.	.	X	2592	.	.	R	-	1	2	ODZ4	78047287	0.994000	0.37717	1.000000	0.80357	0.971000	0.66376	2.571000	0.45990	1.609000	0.50190	0.655000	0.94253	CGA		0.527	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
DLG2	1740	broad.mit.edu	37	11	83252744	83252744	+	Frame_Shift_Del	DEL	C	C	-	rs149247541		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:83252744delC	ENST00000532653.1	-	15	2085	c.1783delG	c.(1783-1785)gtcfs	p.V595fs	DLG2_ENST00000530800.1_Frame_Shift_Del_p.V104fs|DLG2_ENST00000524982.1_Frame_Shift_Del_p.V595fs|DLG2_ENST00000398309.2_Frame_Shift_Del_p.V595fs|DLG2_ENST00000376106.3_Frame_Shift_Del_p.V77fs|DLG2_ENST00000280241.8_Frame_Shift_Del_p.V634fs|DLG2_ENST00000543673.1_Frame_Shift_Del_p.V700fs|DLG2_ENST00000418306.2_Frame_Shift_Del_p.V492fs|DLG2_ENST00000404783.3_Frame_Shift_Del_p.V77fs|DLG2_ENST00000376104.2_Frame_Shift_Del_p.V700fs|DLG2_ENST00000426717.2_Frame_Shift_Del_p.V77fs|DLG2_ENST00000537455.1_Frame_Shift_Del_p.V349fs|DLG2_ENST00000330014.6_Frame_Shift_Del_p.V534fs|DLG2_ENST00000398304.1_Frame_Shift_Del_p.V77fs|DLG2_ENST00000531015.1_Frame_Shift_Del_p.V562fs			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	306					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)	p.V595fs*16(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				CTGGGGATGACCCCCATCTCC	0.468																																					p.V492fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1474delG	11						.						77.0	80.0	79.0					11																	83252744		2060	4220	6280	82930392	SO:0001589	frameshift_variant	1740	exon12			U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	2901	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 58"""	603583	"""discs, large homolog 2, chapsyn-110 (Drosophila)"""			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.1783delG	11.37:g.83252744delC	ENSP00000435849:p.Val595fs	Somatic		Capture	Illumina HiSeq	Phase_I	82930392	NM_001142700	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Frame_Shift_Del	DEL	ENST00000532653.1	37																																																																																					0.468	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364	
DLG2	1740	broad.mit.edu	37	11	83641443	83641443	+	Missense_Mutation	SNP	T	T	C	rs577146407		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:83641443T>C	ENST00000532653.1	-	10	1411	c.1109A>G	c.(1108-1110)gAc>gGc	p.D370G	DLG2_ENST00000524982.1_Missense_Mutation_p.D370G|DLG2_ENST00000398309.2_Missense_Mutation_p.D370G|DLG2_ENST00000376106.3_5'UTR|DLG2_ENST00000280241.8_Missense_Mutation_p.D409G|DLG2_ENST00000543673.1_Missense_Mutation_p.D475G|DLG2_ENST00000418306.2_Intron|DLG2_ENST00000398301.2_Missense_Mutation_p.D409G|DLG2_ENST00000376104.2_Missense_Mutation_p.D475G|DLG2_ENST00000537455.1_Missense_Mutation_p.D124G|DLG2_ENST00000330014.6_Missense_Mutation_p.D309G|DLG2_ENST00000531015.1_Missense_Mutation_p.D337G			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	0					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)	p.D370G(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				GAAGCTTTTGTCACACTCAAC	0.512													T|||	1	0.000199681	0.0	0.0	5008	,	,		19516	0.0		0.001	False		,,,				2504	0.0				p.D370G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1109G	11						.						175.0	185.0	182.0					11																	83641443		2072	4206	6278	83319091	SO:0001583	missense	1740	exon10			U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	2901	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 58"""	603583	"""discs, large homolog 2, chapsyn-110 (Drosophila)"""			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.1109A>G	11.37:g.83641443T>C	ENSP00000435849:p.Asp370Gly	Somatic		Capture	Illumina HiSeq	Phase_I	83319091	NM_001364	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000532653.1	37		.	.	.	.	.	.	.	.	.	.	T	21.6	4.180023	0.78564	.	.	ENSG00000150672	ENST00000398309;ENST00000376104;ENST00000543673;ENST00000280241;ENST00000330014;ENST00000537455;ENST00000524982;ENST00000532653;ENST00000546021;ENST00000531015;ENST00000398301	T;T;T;T;T;T;T;T;T;T	0.20332	2.6;2.6;2.6;2.56;2.51;2.4;2.6;2.56;2.4;2.08	5.88	5.88	0.94601	.	0.000000	0.56097	D	0.000029	T	0.15912	0.0383	N	0.19112	0.55	0.80722	D	1	P;B;B;B;P;P;B	0.41673	0.646;0.39;0.39;0.39;0.664;0.759;0.39	B;B;B;B;B;B;B	0.39503	0.097;0.097;0.097;0.097;0.201;0.301;0.097	T	0.06144	-1.0843	9	.	.	.	.	16.3009	0.82811	0.0:0.0:0.0:1.0	.	337;370;370;309;409;475;370	E9PIW2;B7Z2T4;E9PN83;B7Z264;Q6ZSU2;Q15700-2;Q15700	.;.;.;.;.;.;DLG2_HUMAN	G	370;475;475;409;309;124;370;370;475;337;409	ENSP00000381355:D370G;ENSP00000365272:D475G;ENSP00000441994:D475G;ENSP00000280241:D409G;ENSP00000381353:D309G;ENSP00000443248:D124G;ENSP00000432894:D370G;ENSP00000435849:D370G;ENSP00000433848:D337G;ENSP00000381346:D409G	.	D	-	2	0	DLG2	83319091	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.550000	0.82173	2.246000	0.74042	0.533000	0.62120	GAC		0.512	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364	
TMEM126B	55863	broad.mit.edu	37	11	85347144	85347144	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:85347144G>A	ENST00000358867.6	+	5	587	c.564G>A	c.(562-564)acG>acA	p.T188T	TMEM126B_ENST00000534341.1_3'UTR|TMEM126B_ENST00000393375.1_Silent_p.T158T	NM_018480.4	NP_060950.3	Q8IUX1	T126B_HUMAN	transmembrane protein 126B	188						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.T158T(1)		kidney(1)|large_intestine(2)|lung(3)|prostate(1)	7		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				ATTGGATGACGCTTTGTCAAA	0.353																																					p.T168T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G504A	11						.						111.0	99.0	103.0					11																	85347144		2203	4298	6501	85024792	SO:0001819	synonymous_variant	55863	exon6				CCDS8267.1, CCDS8267.2, CCDS53686.1	11q14.1	2013-05-24				ENSG00000171204		"""Mitochondrial respiratory chain complex assembly factors"""	30883	protein-coding gene	gene with protein product		615533				22982022	Standard	NM_018480		Approved	HT007	uc001pap.4	Q8IUX1		ENST00000358867.6:c.564G>A	11.37:g.85347144G>A		Somatic		Capture	Illumina HiSeq	Phase_I	85024792	NM_001193537	A8K535|A8MSS0|Q32Q09|Q8WVU3|Q96EP3|Q9NZ29	Silent	SNP	ENST00000358867.6	37	CCDS8267.2	.	.	.	.	.	.	.	.	.	.	G	3.392	-0.124049	0.06795	.	.	ENSG00000171204	ENST00000531274	.	.	.	5.65	-2.37	0.06643	.	.	.	.	.	T	0.39410	0.1077	.	.	.	0.49687	D	0.999811	.	.	.	.	.	.	T	0.32268	-0.9913	4	.	.	.	.	1.6466	0.02763	0.431:0.1421:0.2904:0.1366	.	.	.	.	H	106	.	.	R	+	2	0	TMEM126B	85024792	0.004000	0.15560	0.019000	0.16419	0.001000	0.01503	-0.224000	0.09164	-0.259000	0.09432	-0.140000	0.14226	CGC		0.353	TMEM126B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392164.1	NM_018480	
CTSC	1075	broad.mit.edu	37	11	88045626	88045626	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:88045626C>T	ENST00000227266.5	-	3	529	c.415G>A	c.(415-417)Gga>Aga	p.G139R		NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	139			G -> R (in PLS). {ECO:0000269|PubMed:12112662, ECO:0000269|PubMed:14974080}.		aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)	p.G139R(1)		large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ACCTTCTTTCCGGTGAAACAA	0.468																																					p.G139R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G415A	11	GRCh37	CM021254	CTSC	M		.						215.0	206.0	209.0					11																	88045626		2201	4299	6500	87685274	SO:0001583	missense	1075	exon3			AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"""Cathepsins"""	2528	protein-coding gene	gene with protein product	"""dipeptidyl peptidase 1"""	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.415G>A	11.37:g.88045626C>T	ENSP00000227266:p.Gly139Arg	Somatic		Capture	Illumina HiSeq	Phase_I	87685274	NM_001814	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Missense_Mutation	SNP	ENST00000227266.5	37	CCDS8282.1	.	.	.	.	.	.	.	.	.	.	C	34	5.316017	0.95655	.	.	ENSG00000109861	ENST00000393302;ENST00000227266	D	0.90444	-2.67	5.97	5.97	0.96955	Cathepsin C exclusion (1);	0.051717	0.85682	D	0.000000	D	0.96213	0.8765	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.95885	0.8902	9	.	.	.	.	19.2102	0.93751	0.0:1.0:0.0:0.0	.	139	P53634	CATC_HUMAN	R	122;139	ENSP00000227266:G139R	.	G	-	1	0	CTSC	87685274	1.000000	0.71417	0.967000	0.41034	0.983000	0.72400	6.623000	0.74238	2.836000	0.97738	0.655000	0.94253	GGA		0.468	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814	
MMP10	4319	broad.mit.edu	37	11	102649466	102649467	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	AA	AA	AA	-	AA	AA	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:102649466_102649467delAA	ENST00000279441.4	-	4	546_547	c.510_511delTT	c.(508-513)ttttacfs	p.FY170fs		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	170					collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.F170fs*4(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	TCAAAAGAGTAAAAGTCTCCAT	0.381																																					p.170_171del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.510_511del	11						.																																			102154677	SO:0001589	frameshift_variant	4319	exon4			X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"""matrix metalloproteinase 10 (stromelysin 2)"""	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.510_511delTT	11.37:g.102649468_102649469delAA	ENSP00000279441:p.Phe170fs	Somatic		Capture	Illumina HiSeq	Phase_I	102154676	NM_002425	B2R9X9|Q53HH9	Frame_Shift_Del	DEL	ENST00000279441.4	37	CCDS8321.1																																																																																				0.381	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1		
LAYN	143903	broad.mit.edu	37	11	111425991	111425991	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:111425991delA	ENST00000375615.3	+	6	843	c.658delA	c.(658-660)aaafs	p.K221fs	LAYN_ENST00000525126.1_Frame_Shift_Del_p.K221fs|LAYN_ENST00000528924.1_3'UTR|LAYN_ENST00000436913.2_Frame_Shift_Del_p.K68fs|LAYN_ENST00000533265.1_Frame_Shift_Del_p.K213fs|LAYN_ENST00000375614.2_Frame_Shift_Del_p.K213fs	NM_001258390.1	NP_001245319.1	Q6UX15	LAYN_HUMAN	layilin	221						cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|ruffle (GO:0001726)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)	p.T214fs*10(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|skin(1)	14		all_cancers(61;9.06e-10)|all_epithelial(67;1.34e-05)|Melanoma(852;1.74e-05)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.086)		Epithelial(105;1.5e-06)|BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|all cancers(92;2.45e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0476)	Hyaluronan(DB08818)	AGAAGATGCCAAAAAAACATT	0.408																																					p.K212fs	Ovarian(17;551 586 12136 22082 22900)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.634delA	11						.						73.0	70.0	71.0					11																	111425991		2201	4297	6498	110931201	SO:0001589	frameshift_variant	143903	exon5				CCDS31676.1, CCDS58178.1, CCDS58179.1	11q23.1	2006-02-09			ENSG00000204381	ENSG00000204381			29471	protein-coding gene	gene with protein product						15913605	Standard	NM_001258390		Approved	FLJ30977, FLJ31092	uc001plr.2	Q6UX15	OTTHUMG00000166721	ENST00000375615.3:c.658delA	11.37:g.111425991delA	ENSP00000364765:p.Lys221fs	Somatic		Capture	Illumina HiSeq	Phase_I	110931201	NM_178834	A6NJB0|B4DJU0|Q8TAY8|Q96NC5|Q96NF3	Frame_Shift_Del	DEL	ENST00000375615.3	37	CCDS58178.1																																																																																				0.408	LAYN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391187.1	NM_178834	
C11orf57	55216	broad.mit.edu	37	11	111953460	111953460	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:111953460delA	ENST00000280352.9	+	6	1279	c.643delA	c.(643-645)aaafs	p.K216fs	C11orf57_ENST00000420986.2_Frame_Shift_Del_p.K216fs|TIMM8B_ENST00000507614.1_5'Flank|C11orf57_ENST00000393047.3_Frame_Shift_Del_p.K217fs|C11orf57_ENST00000532163.1_Frame_Shift_Del_p.K188fs	NM_001082970.1|NM_018195.3	NP_001076439.1|NP_060665.3	Q6ZUT1	CK057_HUMAN	chromosome 11 open reading frame 57	216	Lys-rich.							p.K216fs*6(1)		autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12		all_cancers(61;9.8e-15)|all_epithelial(67;6.57e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.6e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;7.01e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0521)		AAAGTCTCTCAAAAAACCTGC	0.408																																					p.K216fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.646delA	11						.						72.0	77.0	75.0					11																	111953460		2201	4297	6498	111458670	SO:0001589	frameshift_variant	55216	exon6			BX538107	CCDS8356.2, CCDS41715.1, CCDS73383.1	11q23.1	2006-03-09			ENSG00000150776	ENSG00000150776			25569	protein-coding gene	gene with protein product						12477932	Standard	NM_001082970		Approved	FLJ10726	uc001pmw.4	Q6ZUT1	OTTHUMG00000150213	ENST00000280352.9:c.643delA	11.37:g.111953460delA	ENSP00000339076:p.Lys216fs	Somatic		Capture	Illumina HiSeq	Phase_I	111458670	NM_001082969	Q5RL41|Q6IN53|Q7Z357|Q8N2T3	Frame_Shift_Del	DEL	ENST00000280352.9	37	CCDS41715.1																																																																																				0.408	C11orf57-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316852.1	NM_018195	
TMEM25	84866	broad.mit.edu	37	11	118402960	118402960	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:118402960delG	ENST00000313236.5	+	3	219	c.166delG	c.(166-168)gggfs	p.G57fs	TMEM25_ENST00000544878.1_Frame_Shift_Del_p.G57fs|TMEM25_ENST00000354284.4_Frame_Shift_Del_p.G57fs|TMEM25_ENST00000411589.2_Frame_Shift_Del_p.G57fs|RP11-770J1.3_ENST00000554407.1_RNA|TMEM25_ENST00000359862.4_Frame_Shift_Del_p.G57fs|TMEM25_ENST00000533102.1_Frame_Shift_Del_p.G57fs|RP11-770J1.3_ENST00000528578.1_RNA|RP11-770J1.3_ENST00000556583.1_RNA|TMEM25_ENST00000442938.2_Frame_Shift_Del_p.G57fs|TMEM25_ENST00000529001.1_3'UTR|TMEM25_ENST00000354064.7_Intron|TMEM25_ENST00000524725.1_Frame_Shift_Del_p.G57fs|RP11-770J1.3_ENST00000525992.2_RNA|RP11-770J1.3_ENST00000532597.1_RNA	NM_032780.3	NP_116169.2	Q86YD3	TMM25_HUMAN	transmembrane protein 25	57	Ig-like.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P58fs*23(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|stomach(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		CCGGGTGGCAGGGGGGCCTGG	0.642																																					p.G56fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.166delG	11						.						33.0	37.0	35.0					11																	118402960		2200	4295	6495	117908170	SO:0001589	frameshift_variant	84866	exon3			AK075437	CCDS8398.1, CCDS44745.1, CCDS44746.1, CCDS44747.1, CCDS44748.1	11q23.3	2013-01-11			ENSG00000149582	ENSG00000149582		"""Immunoglobulin superfamily / C2-set domain containing"""	25890	protein-coding gene	gene with protein product		613934				15254712, 12975309	Standard	NM_001144034		Approved	FLJ14399	uc010rye.2	Q86YD3	OTTHUMG00000166339	ENST00000313236.5:c.166delG	11.37:g.118402960delG	ENSP00000315635:p.Gly57fs	Somatic		Capture	Illumina HiSeq	Phase_I	117908170	NM_001144037	A8K8J4|B0YJA6|B0YJA7|B0YJA9|G5E9U4|Q6UW89|Q86UA7|Q8NBL5|Q96KA6|Q96MW9	Frame_Shift_Del	DEL	ENST00000313236.5	37	CCDS8398.1																																																																																				0.642	TMEM25-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389266.1	NM_032780	
CCDC15	80071	broad.mit.edu	37	11	124845049	124845049	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:124845049delA	ENST00000344762.5	+	5	833	c.574delA	c.(574-576)aaafs	p.K194fs	CCDC15_ENST00000529051.1_Frame_Shift_Del_p.K194fs	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	194						centrosome (GO:0005813)		p.K194fs*29(5)|p.S196fs*6(2)		central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(1)	23	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		AACCGTGATTAAAAAAAAGGG	0.373																																					p.K192fs												.	.	7	Deletion - Frameshift(5)|Insertion - Frameshift(2)	large_intestine(7)	c.574delA	11						.																																			124350259	SO:0001589	frameshift_variant	80071	exon5			BC018540	CCDS44756.1	11q24.2	2008-02-05			ENSG00000149548	ENSG00000149548			25798	protein-coding gene	gene with protein product							Standard	NM_025004		Approved	FLJ13215	uc001qbm.4	Q0P6D6	OTTHUMG00000165940	ENST00000344762.5:c.574delA	11.37:g.124845049delA	ENSP00000341684:p.Lys194fs	Somatic		Capture	Illumina HiSeq	Phase_I	124350259	NM_025004	Q9H8U7	Frame_Shift_Del	DEL	ENST00000344762.5	37	CCDS44756.1																																																																																				0.373	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
TMEM218	219854	broad.mit.edu	37	11	124972035	124972035	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:124972035delC	ENST00000279968.4	-	3	426	c.103delG	c.(103-105)gcgfs	p.A36fs	TMEM218_ENST00000532156.1_Frame_Shift_Del_p.A36fs|TMEM218_ENST00000531262.1_Intron|TMEM218_ENST00000527271.1_Frame_Shift_Del_p.A36fs|TMEM218_ENST00000532407.1_Frame_Shift_Del_p.A36fs|TMEM218_ENST00000455225.1_Frame_Shift_Del_p.A36fs|TMEM218_ENST00000529583.1_Frame_Shift_Del_p.A36fs|TMEM218_ENST00000526175.1_Frame_Shift_Del_p.A36fs|TMEM218_ENST00000527766.1_Frame_Shift_Del_p.A36fs|TMEM218_ENST00000528724.1_Frame_Shift_Del_p.A36fs|TMEM218_ENST00000531909.1_Frame_Shift_Del_p.A36fs|TMEM218_ENST00000529609.1_Frame_Shift_Del_p.A36fs			A2RU14	TM218_HUMAN	transmembrane protein 218	36						integral component of membrane (GO:0016021)		p.A35fs*14(1)		breast(1)|large_intestine(2)|lung(1)|prostate(1)	5						TACCTCGCCGCCCCGGAGGCT	0.547																																					p.A35fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.103delG	11						.						47.0	48.0	48.0					11																	124972035		2198	4298	6496	124477245	SO:0001589	frameshift_variant	219854	exon2				CCDS31715.1	11q24.2	2008-08-08			ENSG00000150433	ENSG00000150433			27344	protein-coding gene	gene with protein product							Standard	NM_001258238		Approved		uc031qeu.1	A2RU14		ENST00000279968.4:c.103delG	11.37:g.124972035delC	ENSP00000279968:p.Ala36fs	Somatic		Capture	Illumina HiSeq	Phase_I	124477245	NM_001080546	B7ZM48	Frame_Shift_Del	DEL	ENST00000279968.4	37	CCDS31715.1																																																																																				0.547	TMEM218-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386849.1	NM_001080546	
GLB1L2	89944	broad.mit.edu	37	11	134228984	134228984	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr11:134228984C>A	ENST00000535456.2	+	7	870	c.682C>A	c.(682-684)Ctc>Atc	p.L228I	GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Missense_Mutation_p.L228I|GLB1L2_ENST00000389881.3_Missense_Mutation_p.L228I	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	228					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)	p.L228I(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		TGTGGAACTGCTCCTGACTTC	0.612																																					p.L228I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C682A	11						.						216.0	186.0	196.0					11																	134228984		2201	4297	6498	133734194	SO:0001583	missense	89944	exon7				CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.682C>A	11.37:g.134228984C>A	ENSP00000444628:p.Leu228Ile	Somatic		Capture	Illumina HiSeq	Phase_I	133734194	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Missense_Mutation	SNP	ENST00000535456.2	37	CCDS31724.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.09|18.09	3.547253|3.547253	0.65311|0.65311	.|.	.|.	ENSG00000149328|ENSG00000149328	ENST00000525089;ENST00000533324|ENST00000339772;ENST00000535456;ENST00000389881	.|D;D;D	.|0.98264	.|-4.83;-4.83;-4.83	4.72|4.72	3.81|3.81	0.43845|0.43845	.|Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.98658|0.98658	0.9550|0.9550	M|M	0.85945|0.85945	2.785|2.785	0.50632|0.50632	D|D	0.999883|0.999883	.|D	.|0.69078	.|0.997	.|D	.|0.70016	.|0.967	D|D	0.99104|0.99104	1.0844|1.0844	5|10	.|0.87932	.|D	.|0	-29.8847|-29.8847	8.9267|8.9267	0.35646|0.35646	0.0:0.8195:0.0:0.1804|0.0:0.8195:0.0:0.1804	.|.	.|228	.|Q8IW92	.|GLBL2_HUMAN	D|I	166;55|228	.|ENSP00000344659:L228I;ENSP00000444628:L228I;ENSP00000374531:L228I	.|ENSP00000344659:L228I	A|L	+|+	2|1	0|0	GLB1L2|GLB1L2	133734194|133734194	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.586000|0.586000	0.36452|0.36452	3.616000|3.616000	0.54174|0.54174	1.212000|1.212000	0.43366|0.43366	0.561000|0.561000	0.74099|0.74099	GCT|CTC		0.612	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342	
NFE2	4778	broad.mit.edu	37	12	54686529	54686530	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:54686529_54686530insA	ENST00000540264.2	-	2	1259_1260	c.750_751insT	c.(748-753)tttaatfs	p.N251fs	NFE2_ENST00000435572.2_Frame_Shift_Ins_p.N251fs|NFE2_ENST00000312156.4_Frame_Shift_Ins_p.N251fs|NFE2_ENST00000553070.1_Frame_Shift_Ins_p.N251fs|RP11-968A15.8_ENST00000553061.1_RNA			Q16621	NFE2_HUMAN	nuclear factor, erythroid 2	251					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|hemostasis (GO:0007599)|labyrinthine layer blood vessel development (GO:0060716)|multicellular organismal development (GO:0007275)|negative regulation of bone mineralization (GO:0030502)|negative regulation of syncytium formation by plasma membrane fusion (GO:0034242)|nucleosome disassembly (GO:0006337)|positive regulation of peptidyl-lysine acetylation (GO:2000758)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|WW domain binding (GO:0050699)	p.N251fs*1(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|lung(7)|upper_aerodigestive_tract(2)	16						AATAGCTCATTAAAGTCATCTA	0.574																																					p.N251_E252delinsX												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.751_752insT	12						.																																			52972797	SO:0001589	frameshift_variant	4778	exon3			BC005044	CCDS8876.1	12q13	2013-08-23	2013-08-23			ENSG00000123405		"""basic leucine zipper proteins"""	7780	protein-coding gene	gene with protein product		601490	"""nuclear factor (erythroid-derived 2), 45kD"", ""nuclear factor (erythroid-derived 2), 45kDa"""			8355703	Standard	NM_001136023		Approved	NF-E2	uc001sfr.5	Q16621		ENST00000540264.2:c.751dupT	12.37:g.54686532_54686532dupA	ENSP00000439120:p.Asn251fs	Somatic		Capture	Illumina HiSeq	Phase_I	52972796	NM_006163	Q07720|Q6ICV9	Frame_Shift_Ins	INS	ENST00000540264.2	37	CCDS8876.1																																																																																				0.574	NFE2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405747.1	NM_006163	
GNPTAB	79158	broad.mit.edu	37	12	102158339	102158339	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:102158339G>A	ENST00000299314.7	-	13	2618	c.2356C>T	c.(2356-2358)Cag>Tag	p.Q786*	RNU6-101P_ENST00000410323.1_RNA	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	786	DMAP-interaction.				carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)	p.Q786*(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						GTCAACCTCTGCAATCTTTCA	0.433																																					p.Q786X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2356T	12						.						106.0	101.0	103.0					12																	102158339		2203	4300	6503	100682470	SO:0001587	stop_gained	79158	exon13			AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"""EF-hand domain containing"""	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.2356C>T	12.37:g.102158339G>A	ENSP00000299314:p.Gln786*	Somatic		Capture	Illumina HiSeq	Phase_I	100682470	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Nonsense_Mutation	SNP	ENST00000299314.7	37	CCDS9088.1	.	.	.	.	.	.	.	.	.	.	G	38	6.955483	0.97960	.	.	ENSG00000111670	ENST00000299314	.	.	.	5.56	1.87	0.25490	.	1.236570	0.05235	N	0.511028	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-1.4165	10.6433	0.45604	0.0:0.2706:0.5767:0.1527	.	.	.	.	X	786	.	ENSP00000299314:Q786X	Q	-	1	0	GNPTAB	100682470	0.110000	0.22057	0.010000	0.14722	0.063000	0.16089	0.912000	0.28597	0.482000	0.27582	0.655000	0.94253	CAG		0.433	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1		
KIAA1033	23325	broad.mit.edu	37	12	105538549	105538549	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:105538549C>A	ENST00000332180.5	+	22	2320	c.2233C>A	c.(2233-2235)Ctt>Att	p.L745I		NM_015275.1	NP_056090.1			KIAA1033									p.L745I(1)		breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						AACTGTAGCCCTTCATGACTG	0.393																																					p.L745I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2233A	12						.						112.0	105.0	107.0					12																	105538549		1902	4119	6021	104062679	SO:0001583	missense	23325	exon22			AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.2233C>A	12.37:g.105538549C>A	ENSP00000328062:p.Leu745Ile	Somatic		Capture	Illumina HiSeq	Phase_I	104062679	NM_015275		Missense_Mutation	SNP	ENST00000332180.5	37	CCDS41826.1	.	.	.	.	.	.	.	.	.	.	C	35	5.454317	0.96223	.	.	ENSG00000136051	ENST00000332180	T	0.48522	0.81	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.70055	0.3180	M	0.86178	2.8	0.80722	D	1	D;D	0.59767	0.986;0.986	P;P	0.59115	0.852;0.852	T	0.70745	-0.4788	10	0.40728	T	0.16	.	19.8435	0.96701	0.0:1.0:0.0:0.0	.	746;745	B7ZKT9;Q2M389	.;WASH7_HUMAN	I	745	ENSP00000328062:L745I	ENSP00000328062:L745I	L	+	1	0	KIAA1033	104062679	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.045000	0.71020	2.688000	0.91661	0.585000	0.79938	CTT		0.393	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275	
CRY1	1407	broad.mit.edu	37	12	107393424	107393424	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:107393424G>A	ENST00000008527.5	-	7	1909	c.1042C>T	c.(1042-1044)Cgt>Tgt	p.R348C		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	348					blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)	p.R348C(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						CCCTCCTGACGAAGCTGTGTC	0.502																																					p.R348C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1042T	12						.						95.0	86.0	89.0					12																	107393424		2203	4300	6503	105917554	SO:0001583	missense	1407	exon7			BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"""cryptochrome 1 (photolyase-like)"""	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.1042C>T	12.37:g.107393424G>A	ENSP00000008527:p.Arg348Cys	Somatic		Capture	Illumina HiSeq	Phase_I	105917554	NM_004075		Missense_Mutation	SNP	ENST00000008527.5	37	CCDS9112.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.685045	0.88639	.	.	ENSG00000008405	ENST00000008527	.	.	.	5.79	5.79	0.91817	DNA photolyase, FAD-binding/Cryptochrome, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.78278	0.4258	M	0.88570	2.965	0.80722	D	1	D	0.61080	0.989	P	0.51355	0.667	T	0.82563	-0.0395	9	0.72032	D	0.01	-16.6295	20.0308	0.97536	0.0:0.0:1.0:0.0	.	348	Q16526	CRY1_HUMAN	C	348	.	ENSP00000008527:R348C	R	-	1	0	CRY1	105917554	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.370000	0.59517	2.732000	0.93576	0.585000	0.79938	CGT		0.502	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075	
CRY1	1407	broad.mit.edu	37	12	107393823	107393823	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:107393823G>A	ENST00000008527.5	-	6	1589	c.722C>T	c.(721-723)gCg>gTg	p.A241V		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	241					blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)	p.A241V(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						CAGAGAATTCGCATTCATTCG	0.363																																					p.A241V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C722T	12						.						77.0	78.0	78.0					12																	107393823		2203	4300	6503	105917953	SO:0001583	missense	1407	exon6			BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"""cryptochrome 1 (photolyase-like)"""	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.722C>T	12.37:g.107393823G>A	ENSP00000008527:p.Ala241Val	Somatic		Capture	Illumina HiSeq	Phase_I	105917953	NM_004075		Missense_Mutation	SNP	ENST00000008527.5	37	CCDS9112.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.592531	0.86953	.	.	ENSG00000008405	ENST00000008527	.	.	.	5.85	5.85	0.93711	DNA photolyase, FAD-binding/Cryptochrome, C-terminal (2);	0.044697	0.85682	D	0.000000	T	0.46190	0.1380	N	0.19112	0.55	0.80722	D	1	P	0.46987	0.888	B	0.43445	0.42	T	0.49952	-0.8884	9	0.62326	D	0.03	-17.876	20.1559	0.98114	0.0:0.0:1.0:0.0	.	241	Q16526	CRY1_HUMAN	V	241	.	ENSP00000008527:A241V	A	-	2	0	CRY1	105917953	1.000000	0.71417	0.996000	0.52242	0.962000	0.63368	6.780000	0.75063	2.770000	0.95276	0.650000	0.86243	GCG		0.363	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075	
FICD	11153	broad.mit.edu	37	12	108912203	108912203	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:108912203C>T	ENST00000552695.1	+	3	563	c.328C>T	c.(328-330)Ctg>Ttg	p.L110L	FICD_ENST00000361549.2_3'UTR	NM_007076.2	NP_009007.2	Q9BVA6	FICD_HUMAN	FIC domain containing	110					negative regulation of Rho GTPase activity (GO:0034259)|protein adenylylation (GO:0018117)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein adenylyltransferase activity (GO:0070733)	p.L110L(1)		NS(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|upper_aerodigestive_tract(2)	15						CAGAGCTGCCCTGAACCAGGC	0.622																																					p.L110L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C328T	12						.						51.0	48.0	49.0					12																	108912203		2203	4300	6503	107436333	SO:0001819	synonymous_variant	11153	exon3			AF049611	CCDS9116.1	12q24.1	2007-12-05				ENSG00000198855			18416	protein-coding gene	gene with protein product	"""huntingtin interacting protein 13"", ""fic S-phase protein cell division homolog (E. coli)"""					9700202	Standard	NM_007076		Approved	HYPE, HIP13	uc001tmx.1	Q9BVA6		ENST00000552695.1:c.328C>T	12.37:g.108912203C>T		Somatic		Capture	Illumina HiSeq	Phase_I	107436333	NM_007076	O75406	Silent	SNP	ENST00000552695.1	37	CCDS9116.1																																																																																				0.622	FICD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404842.1	NM_007076	
SART3	9733	broad.mit.edu	37	12	108954661	108954661	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:108954661C>T	ENST00000228284.3	-	1	504	c.270G>A	c.(268-270)gaG>gaA	p.E90E	ISCU_ENST00000535729.1_5'Flank|SART3_ENST00000552221.1_5'UTR|ISCU_ENST00000539593.1_5'Flank|SART3_ENST00000546611.1_Silent_p.E90E|SART3_ENST00000431469.2_Silent_p.E90E|ISCU_ENST00000338291.4_5'Flank|ISCU_ENST00000392807.4_5'Flank|ISCU_ENST00000311893.9_5'Flank|ISCU_ENST00000431221.2_5'Flank|ISCU_ENST00000547005.1_5'Flank	NM_014706.3	NP_055521.1	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T cells 3	90	Poly-Glu.				cell morphogenesis (GO:0000902)|hematopoietic stem cell proliferation (GO:0071425)|homeostasis of number of cells (GO:0048872)|regulation of gene expression (GO:0010468)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E90E(1)		NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|stomach(1)	25						TTTTCTCCTCCTCTTCGTCAT	0.622									Porokeratosis																												p.E90E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G270A	12						.						58.0	59.0	59.0					12																	108954661		2203	4300	6503	107478791	SO:0001819	synonymous_variant	9733	exon1	Familial Cancer Database	incl.: Porokeratosis of Mibelli, Disseminated Superficial Actinic Porokertosis, Porokeratosis Palmaris Plantaris et Disseminata, Porokeratosis Punctata Palmaris et Plantaris, Linear Porokeratosis	AB020880	CCDS9117.1	12q24.11	2013-02-12	2006-12-07			ENSG00000075856		"""RNA binding motif (RRM) containing"""	16860	protein-coding gene	gene with protein product		611684	"""squamous cell carcinoma antigen recognised by T cells 3"""			12032085, 15840095, 20595234	Standard	NM_014706		Approved	KIAA0156, RP11-13G14, TIP110, p110	uc001tmz.1	Q15020	OTTHUMG00000169449	ENST00000228284.3:c.270G>A	12.37:g.108954661C>T		Somatic		Capture	Illumina HiSeq	Phase_I	107478791	NM_014706	A8K2E4|Q2M2H0|Q58F06|Q8IUS1|Q96J95	Silent	SNP	ENST00000228284.3	37	CCDS9117.1																																																																																				0.622	SART3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404094.1		
TCHP	84260	broad.mit.edu	37	12	110346717	110346717	+	Missense_Mutation	SNP	G	G	A	rs367967992		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:110346717G>A	ENST00000312777.5	+	8	1068	c.854G>A	c.(853-855)cGc>cAc	p.R285H	TCHP_ENST00000405876.4_Missense_Mutation_p.R285H	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding									p.R285H(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						CTCAGCAGACGCACACAGCAG	0.423																																					p.R285H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G854A	12						.	G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	67.0	65.0	66.0		854,854	4.5	0.4	12		66	0,8600		0,0,4300	no	missense,missense	TCHP	NM_001143852.1,NM_032300.4	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	285/499,285/499	110346717	1,13005	2203	4300	6503	108831100	SO:0001583	missense	84260	exon8			AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"""mitostatin"""	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.854G>A	12.37:g.110346717G>A	ENSP00000324404:p.Arg285His	Somatic		Capture	Illumina HiSeq	Phase_I	108831100	NM_001143852		Missense_Mutation	SNP	ENST00000312777.5	37	CCDS9137.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.452049	0.84209	2.27E-4	0.0	ENSG00000139437	ENST00000405876;ENST00000312777	T;T	0.11277	2.79;2.79	5.39	4.49	0.54785	.	0.052393	0.64402	D	0.000001	T	0.13200	0.0320	L	0.54323	1.7	0.80722	D	1	P	0.49090	0.919	B	0.43194	0.411	T	0.00766	-1.1575	10	0.59425	D	0.04	-5.7587	11.1897	0.48677	0.0881:0.0:0.9119:0.0	.	285	Q9BT92	TCHP_HUMAN	H	285	ENSP00000384520:R285H;ENSP00000324404:R285H	ENSP00000324404:R285H	R	+	2	0	TCHP	108831100	1.000000	0.71417	0.384000	0.26145	0.955000	0.61496	5.900000	0.69853	2.543000	0.85770	0.650000	0.86243	CGC		0.423	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300	
CUX2	23316	broad.mit.edu	37	12	111779832	111779832	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:111779832G>A	ENST00000261726.6	+	21	3788	c.3634G>A	c.(3634-3636)Gtc>Atc	p.V1212I	RNA5SP373_ENST00000517271.1_RNA	NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	1212					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)	p.V1212I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						GACCAACACCGTCATCAACTG	0.612																																					p.V1212I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3634A	12						.						66.0	75.0	72.0					12																	111779832		2195	4300	6495	110264215	SO:0001583	missense	23316	exon21			AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"""Homeoboxes / CUT class"""	19347	protein-coding gene	gene with protein product		610648	"""cut-like 2 (Drosophila)"""	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.3634G>A	12.37:g.111779832G>A	ENSP00000261726:p.Val1212Ile	Somatic		Capture	Illumina HiSeq	Phase_I	110264215	NM_015267	A7E2Y4	Missense_Mutation	SNP	ENST00000261726.6	37	CCDS41837.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.902732	0.92035	.	.	ENSG00000111249	ENST00000261726	D	0.98512	-4.97	5.24	5.24	0.73138	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97801	0.9278	N	0.21240	0.645	0.80722	D	1	D	0.65815	0.995	D	0.72625	0.978	D	0.98358	1.0547	10	0.38643	T	0.18	-42.6658	18.8282	0.92127	0.0:0.0:1.0:0.0	.	1212	O14529	CUX2_HUMAN	I	1212	ENSP00000261726:V1212I	ENSP00000261726:V1212I	V	+	1	0	CUX2	110264215	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.787000	0.99055	2.446000	0.82766	0.563000	0.77884	GTC		0.612	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267	
ATXN2	6311	broad.mit.edu	37	12	111907981	111907981	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:111907981C>T	ENST00000377617.3	-	20	3408	c.3247G>A	c.(3247-3249)Gcc>Acc	p.A1083T	ATXN2_ENST00000389153.4_Missense_Mutation_p.A820T|ATXN2_ENST00000542287.2_Missense_Mutation_p.A818T|ATXN2_ENST00000535949.1_Missense_Mutation_p.A794T|ATXN2_ENST00000550104.1_3'UTR|ATXN2_ENST00000608853.1_Missense_Mutation_p.A923T	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	1083	Pro-rich.				cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.A1083T(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						CCAGGCTGGGCGTGTGTTGGT	0.443																																					p.A1083T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3247A	12						.						216.0	171.0	186.0					12																	111907981		2203	4300	6503	110392364	SO:0001583	missense	6311	exon20			U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"""Ataxins"""	10555	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 13"""	601517	"""spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"""	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.3247G>A	12.37:g.111907981C>T	ENSP00000366843:p.Ala1083Thr	Somatic		Capture	Illumina HiSeq	Phase_I	110392364	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Missense_Mutation	SNP	ENST00000377617.3	37	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.935695	0.92458	.	.	ENSG00000204842	ENST00000389154;ENST00000389153;ENST00000377617;ENST00000482777;ENST00000542287;ENST00000535949;ENST00000550844	T	0.67171	-0.25	5.46	5.46	0.80206	.	0.052206	0.85682	D	0.000000	T	0.67674	0.2918	L	0.36672	1.1	0.80722	D	1	P;D;P;D;P	0.63046	0.89;0.992;0.688;0.983;0.907	B;P;B;P;B	0.52454	0.422;0.49;0.116;0.699;0.308	T	0.68205	-0.5470	10	0.48119	T	0.1	-9.6556	15.9837	0.80133	0.0:0.8653:0.1347:0.0	.	102;1083;794;818;820	Q99700-3;Q99700;Q24JQ7;F8VQP2;F8WB06	.;ATX2_HUMAN;.;.;.	T	138;820;1083;102;818;794;8	ENSP00000366843:A1083T	ENSP00000366843:A1083T	A	-	1	0	ATXN2	110392364	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	5.602000	0.67612	2.724000	0.93272	0.585000	0.79938	GCC		0.443	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973	
DDX54	79039	broad.mit.edu	37	12	113603709	113603709	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:113603709C>T	ENST00000306014.5	-	13	1570	c.1543G>A	c.(1543-1545)Gcc>Acc	p.A515T	DDX54_ENST00000314045.7_Missense_Mutation_p.A515T	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	515					ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)	p.A515T(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TGCTGCTGGGCGTTATCAGCA	0.662																																					p.A515T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1543A	12						.						60.0	57.0	58.0					12																	113603709		2203	4300	6503	112088092	SO:0001583	missense	79039	exon13			AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"""DEAD-boxes"""	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.1543G>A	12.37:g.113603709C>T	ENSP00000304072:p.Ala515Thr	Somatic		Capture	Illumina HiSeq	Phase_I	112088092	NM_024072	Q86YT8|Q9BRZ1	Missense_Mutation	SNP	ENST00000306014.5	37	CCDS31907.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.197948	0.79015	.	.	ENSG00000123064	ENST00000314045;ENST00000306014	T;T	0.17213	2.31;2.29	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.51500	0.1678	M	0.91663	3.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.989	T	0.64580	-0.6374	10	0.87932	D	0	.	17.4138	0.87494	0.0:1.0:0.0:0.0	.	515;515	Q8TDD1-2;Q8TDD1	.;DDX54_HUMAN	T	515	ENSP00000323858:A515T;ENSP00000304072:A515T	ENSP00000304072:A515T	A	-	1	0	DDX54	112088092	1.000000	0.71417	0.253000	0.24343	0.278000	0.26855	7.297000	0.78799	2.424000	0.82194	0.655000	0.94253	GCC		0.662	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072	
DDX54	79039	broad.mit.edu	37	12	113607630	113607630	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:113607630C>T	ENST00000306014.5	-	12	1386	c.1359G>A	c.(1357-1359)ctG>ctA	p.L453L	DDX54_ENST00000314045.7_Silent_p.L453L	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	453	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)	p.L453L(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						GGAACAGGTGCAGATCCAGCA	0.647																																					p.L453L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1359A	12						.						50.0	45.0	46.0					12																	113607630		2203	4300	6503	112092013	SO:0001819	synonymous_variant	79039	exon12			AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"""DEAD-boxes"""	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.1359G>A	12.37:g.113607630C>T		Somatic		Capture	Illumina HiSeq	Phase_I	112092013	NM_024072	Q86YT8|Q9BRZ1	Silent	SNP	ENST00000306014.5	37	CCDS31907.1																																																																																				0.647	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072	
DDX54	79039	broad.mit.edu	37	12	113610244	113610244	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:113610244G>A	ENST00000306014.5	-	11	1220	c.1193C>T	c.(1192-1194)gCc>gTc	p.A398V	DDX54_ENST00000314045.7_Missense_Mutation_p.A398V	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	398	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)	p.A398V(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						GCCTCGGGCGGCCAGGTCAGT	0.597																																					p.A398V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1193T	12						.						109.0	92.0	97.0					12																	113610244		2203	4300	6503	112094627	SO:0001583	missense	79039	exon11			AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"""DEAD-boxes"""	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.1193C>T	12.37:g.113610244G>A	ENSP00000304072:p.Ala398Val	Somatic		Capture	Illumina HiSeq	Phase_I	112094627	NM_024072	Q86YT8|Q9BRZ1	Missense_Mutation	SNP	ENST00000306014.5	37	CCDS31907.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.840359	0.91117	.	.	ENSG00000123064	ENST00000314045;ENST00000306014	T;T	0.76578	-1.03;-1.03	5.18	4.29	0.51040	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.88786	0.6531	M	0.87328	2.875	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90366	0.4377	10	0.87932	D	0	.	13.3673	0.60692	0.0768:0.0:0.9232:0.0	.	398;398	Q8TDD1-2;Q8TDD1	.;DDX54_HUMAN	V	398	ENSP00000323858:A398V;ENSP00000304072:A398V	ENSP00000304072:A398V	A	-	2	0	DDX54	112094627	1.000000	0.71417	0.957000	0.39632	0.924000	0.55760	9.758000	0.98927	1.192000	0.43071	0.650000	0.86243	GCC		0.597	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072	
RITA1	84934	broad.mit.edu	37	12	113629195	113629195	+	Missense_Mutation	SNP	G	G	A	rs368110690	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:113629195G>A	ENST00000548278.1	+	4	1075	c.383G>A	c.(382-384)cGg>cAg	p.R128Q	C12orf52_ENST00000552495.1_Missense_Mutation_p.R152Q|C12orf52_ENST00000549621.1_Missense_Mutation_p.R128Q|RP11-545P7.4_ENST00000552525.1_RNA	NM_032848.1	NP_116237.1	Q96K30	RITA1_HUMAN		128	Interaction with RBPJ/RBPSUH.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|nuclear export (GO:0051168)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	tubulin binding (GO:0015631)	p.R128Q(1)		large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	5						GGGGCCCCGCGGATGGCGAAG	0.642													G|||	4	0.000798722	0.0	0.0	5008	,	,		14839	0.0		0.0	False		,,,				2504	0.0041				p.R128Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G383A	12						.	G	GLN/ARG	0,4406		0,0,2203	27.0	30.0	29.0		383	3.7	0.0	12		29	1,8599	1.2+/-3.3	0,1,4299	no	missense	C12orf52	NM_032848.1	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	128/270	113629195	1,13005	2203	4300	6503	112113578	SO:0001583	missense	84934	exon4																														ENST00000548278.1:c.383G>A	12.37:g.113629195G>A	ENSP00000449841:p.Arg128Gln	Somatic		Capture	Illumina HiSeq	Phase_I	112113578	NM_032848	B3KVZ4|C9JIN1|F8VRG5|Q53GM3|Q96K25	Missense_Mutation	SNP	ENST00000548278.1	37	CCDS9166.1	.	.	.	.	.	.	.	.	.	.	G	5.660	0.306471	0.10733	0.0	1.16E-4	ENSG00000139405	ENST00000549621;ENST00000548278;ENST00000552495;ENST00000436053;ENST00000299731;ENST00000266813	T;T;T	0.32988	1.45;1.45;1.43	4.6	3.71	0.42584	.	0.364168	0.23708	N	0.045345	T	0.12603	0.0306	N	0.12182	0.205	0.09310	N	1	D;P;D	0.55800	0.973;0.951;0.973	B;B;B	0.35278	0.199;0.199;0.199	T	0.10776	-1.0615	10	0.26408	T	0.33	-2.164	8.434	0.32775	0.1057:0.0:0.8943:0.0	.	128;152;128	Q96K30-2;F8VRG5;Q96K30	.;.;RITA_HUMAN	Q	128;128;152;128;128;125	ENSP00000448289:R128Q;ENSP00000449841:R128Q;ENSP00000448680:R152Q	ENSP00000266813:R125Q	R	+	2	0	C12orf52	112113578	0.993000	0.37304	0.023000	0.16930	0.004000	0.04260	2.374000	0.44274	1.151000	0.42436	-0.136000	0.14681	CGG		0.642	C12orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405239.1		
IQCD	115811	broad.mit.edu	37	12	113645923	113645923	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:113645923T>C	ENST00000416617.2	-	2	239	c.49A>G	c.(49-51)Atc>Gtc	p.I17V	IQCD_ENST00000546692.1_Missense_Mutation_p.I17V|IQCD_ENST00000299732.2_Missense_Mutation_p.I17V			Q96DY2	IQCD_HUMAN	IQ motif containing D	17								p.I17V(1)		endometrium(2)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						ATTCTGTTGATGGCAGGGGCC	0.522																																					p.I17V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A49G	12						.						177.0	177.0	177.0					12																	113645923		2203	4300	6503	112130306	SO:0001583	missense	115811	exon2			BC013151	CCDS9167.1	12q24.21	2014-07-18				ENSG00000166578			25168	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 10"""					23427265, 24804578	Standard	NM_138451		Approved	DRC10, CFAP84	uc001tuu.3	Q96DY2		ENST00000416617.2:c.49A>G	12.37:g.113645923T>C	ENSP00000400669:p.Ile17Val	Somatic		Capture	Illumina HiSeq	Phase_I	112130306	NM_138451	Q6ZSU0	Missense_Mutation	SNP	ENST00000416617.2	37		.	.	.	.	.	.	.	.	.	.	T	12.22	1.873177	0.33069	.	.	ENSG00000166578	ENST00000299732;ENST00000416617;ENST00000546692;ENST00000392574	T;T;T	0.09350	2.99;2.99;2.99	4.58	-1.16	0.09678	.	0.659645	0.13454	N	0.386671	T	0.12774	0.0310	M	0.69823	2.125	0.09310	N	1	P;B	0.43287	0.802;0.206	B;B	0.42495	0.389;0.085	T	0.10154	-1.0642	10	0.56958	D	0.05	-7.436	5.3749	0.16160	0.2863:0.0:0.2964:0.4172	.	17;17	F8VZV9;Q96DY2-2	.;.	V	17	ENSP00000299732:I17V;ENSP00000400669:I17V;ENSP00000446623:I17V	ENSP00000299732:I17V	I	-	1	0	IQCD	112130306	0.000000	0.05858	0.017000	0.16124	0.026000	0.11368	-0.692000	0.05127	-0.365000	0.08076	0.460000	0.39030	ATC		0.522	IQCD-004	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000405327.1	NM_138451	
RBM19	9904	broad.mit.edu	37	12	114380151	114380151	+	Missense_Mutation	SNP	A	A	G	rs529084315		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:114380151A>G	ENST00000545145.2	-	14	1793	c.1715T>C	c.(1714-1716)gTc>gCc	p.V572A	RBM19_ENST00000392561.3_Missense_Mutation_p.V572A|RBM19_ENST00000261741.5_Missense_Mutation_p.V572A	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	572					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.V572A(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					ATCCAGGCTGACCCCGTTGTC	0.627																																					p.V572A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1715C	12						.						43.0	41.0	42.0					12																	114380151		2203	4300	6503	112864534	SO:0001583	missense	9904	exon14			AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1715T>C	12.37:g.114380151A>G	ENSP00000442053:p.Val572Ala	Somatic		Capture	Illumina HiSeq	Phase_I	112864534	NM_016196	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.403529	0.83230	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.09911	2.93;2.93;2.93	4.48	4.48	0.54585	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.40372	0.1114	M	0.92555	3.32	0.80722	D	1	D	0.76494	0.999	D	0.67725	0.953	T	0.54860	-0.8230	10	0.87932	D	0	-34.6837	13.7737	0.63039	1.0:0.0:0.0:0.0	.	572	Q9Y4C8	RBM19_HUMAN	A	572	ENSP00000442053:V572A;ENSP00000376344:V572A;ENSP00000261741:V572A	ENSP00000261741:V572A	V	-	2	0	RBM19	112864534	1.000000	0.71417	0.958000	0.39756	0.841000	0.47740	8.823000	0.92018	1.664000	0.50801	0.397000	0.26171	GTC		0.627	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
RBM19	9904	broad.mit.edu	37	12	114395768	114395768	+	Missense_Mutation	SNP	G	G	A	rs141996636	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:114395768G>A	ENST00000545145.2	-	6	737	c.659C>T	c.(658-660)tCg>tTg	p.S220L	RBM19_ENST00000392561.3_Missense_Mutation_p.S220L|RBM19_ENST00000261741.5_Missense_Mutation_p.S220L	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	220					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S220L(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GGAAGAGGACGACCCAGCCTT	0.552													G|||	15	0.00299521	0.0	0.0	5008	,	,		21384	0.0149		0.0	False		,,,				2504	0.0				p.S220L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C659T	12						.						132.0	117.0	122.0					12																	114395768		2203	4300	6503	112880151	SO:0001583	missense	9904	exon6			AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.659C>T	12.37:g.114395768G>A	ENSP00000442053:p.Ser220Leu	Somatic		Capture	Illumina HiSeq	Phase_I	112880151	NM_016196	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	G	5.609	0.297053	0.10622	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.06371	3.31;3.31;3.31	5.04	1.16	0.20824	.	1.062930	0.07352	N	0.882597	T	0.04048	0.0113	L	0.34521	1.04	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.42832	-0.9428	10	0.38643	T	0.18	0.0491	8.17	0.31249	0.3213:0.0:0.6787:0.0	.	220	Q9Y4C8	RBM19_HUMAN	L	220	ENSP00000442053:S220L;ENSP00000376344:S220L;ENSP00000261741:S220L	ENSP00000261741:S220L	S	-	2	0	RBM19	112880151	0.005000	0.15991	0.000000	0.03702	0.003000	0.03518	1.227000	0.32576	0.043000	0.15746	-0.140000	0.14226	TCG		0.552	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
SRRM4	84530	broad.mit.edu	37	12	119554806	119554806	+	Nonsense_Mutation	SNP	C	C	T	rs200163299	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:119554806C>T	ENST00000267260.4	+	4	818	c.430C>T	c.(430-432)Cga>Tga	p.R144*	RP11-364C11.2_ENST00000537730.1_RNA	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	144	Lys-rich.|Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)	p.R144*(2)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						GAAACACAAGCGACGCAGGTA	0.488																																					p.R144X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C430T	12						.						72.0	67.0	68.0					12																	119554806		1859	4095	5954	118039189	SO:0001587	stop_gained	84530	exon4			AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"""neural-specific SR-related protein of 100 kDa"""	613103	"""KIAA1853"""	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.430C>T	12.37:g.119554806C>T	ENSP00000267260:p.Arg144*	Somatic		Capture	Illumina HiSeq	Phase_I	118039189	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Nonsense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	C	42	9.549168	0.99202	.	.	ENSG00000139767	ENST00000267260	.	.	.	5.46	2.39	0.29439	.	0.135690	0.48286	D	0.000200	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.4484	12.6927	0.56985	0.4975:0.5025:0.0:0.0	.	.	.	.	X	144	.	ENSP00000267260:R144X	R	+	1	2	SRRM4	118039189	0.999000	0.42202	1.000000	0.80357	0.984000	0.73092	0.237000	0.17985	0.729000	0.32403	0.655000	0.94253	CGA		0.488	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
PRKAB1	5564	broad.mit.edu	37	12	120110171	120110171	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:120110171C>A	ENST00000229328.5	+	2	717	c.225C>A	c.(223-225)gcC>gcA	p.A75A	PRKAB1_ENST00000541640.1_Silent_p.A75A|PRKAB1_ENST00000540121.1_5'UTR	NM_006253.4	NP_006244.2	Q9Y478	AAKB1_HUMAN	protein kinase, AMP-activated, beta 1 non-catalytic subunit	75	Glycogen-binding domain. {ECO:0000250}.				cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|insulin receptor signaling pathway (GO:0008286)|membrane organization (GO:0061024)|positive regulation of gene expression (GO:0010628)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein kinase activity (GO:0004672)	p.A75A(1)		endometrium(2)|large_intestine(3)|lung(5)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.166)	Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Metformin(DB00331)	AAGCTCCCGCCCAGGCTCGGC	0.522																																					p.A75A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C225A	12						.						115.0	129.0	124.0					12																	120110171		2203	4300	6503	118594554	SO:0001819	synonymous_variant	5564	exon2			BC001823	CCDS9191.1	12q24.1-q24.3	2008-05-14			ENSG00000111725	ENSG00000111725			9378	protein-coding gene	gene with protein product	"""AMPK beta 1"""	602740				8557660	Standard	NM_006253		Approved		uc001txg.3	Q9Y478	OTTHUMG00000168954	ENST00000229328.5:c.225C>A	12.37:g.120110171C>A		Somatic		Capture	Illumina HiSeq	Phase_I	118594554	NM_006253	Q9UBV0|Q9UE20|Q9UEX2|Q9Y6V8	Silent	SNP	ENST00000229328.5	37	CCDS9191.1																																																																																				0.522	PRKAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401731.2	NM_006253	
CIT	11113	broad.mit.edu	37	12	120210668	120210668	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:120210668C>T	ENST00000261833.7	-	17	2040	c.1988G>A	c.(1987-1989)cGc>cAc	p.R663H	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Missense_Mutation_p.R663H	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	663					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.R663H(1)|p.R664H(1)		breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		CTTTGCCTGGCGGATATTCTG	0.517																																					p.R663H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1988A	12						.						105.0	107.0	106.0					12																	120210668		2203	4300	6503	118695051	SO:0001583	missense	11113	exon17			AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.1988G>A	12.37:g.120210668C>T	ENSP00000261833:p.Arg663His	Somatic		Capture	Illumina HiSeq	Phase_I	118695051	NM_007174	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	CCDS9192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.090890|5.090890	0.94149|0.94149	.|.	.|.	ENSG00000122966|ENSG00000122966	ENST00000392520|ENST00000392521;ENST00000261833	.|T;T	.|0.79141	.|-1.24;-0.23	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	.|0.065016	.|0.64402	.|D	.|0.000008	T|T	0.80454|0.80454	0.4626|0.4626	N|N	0.24115|0.24115	0.695|0.695	0.53688|0.53688	D|D	0.999978|0.999978	.|D;D;D	.|0.71674	.|0.998;0.998;0.997	.|P;P;P	.|0.59288	.|0.7;0.791;0.855	T|T	0.82147|0.82147	-0.0601|-0.0601	5|10	.|0.72032	.|D	.|0.01	.|.	20.4082|20.4082	0.99013|0.99013	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|663;663;196	.|Q2M5E1;O14578;O14578-3	.|.;CTRO_HUMAN;.	T|H	291|663	.|ENSP00000376306:R663H;ENSP00000261833:R663H	.|ENSP00000261833:R663H	A|R	-|-	1|2	0|0	CIT|CIT	118695051|118695051	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.980000|0.980000	0.70556|0.70556	4.686000|4.686000	0.61700|0.61700	2.814000|2.814000	0.96858|0.96858	0.655000|0.655000	0.94253|0.94253	GCC|CGC		0.517	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
GCN1L1	10985	broad.mit.edu	37	12	120597762	120597762	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:120597762G>T	ENST00000300648.6	-	24	2628	c.2616C>A	c.(2614-2616)ggC>ggA	p.G872G		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	872					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)	p.G872G(1)		NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACTGGGTCAGGCCGGACGGGT	0.592																																					p.G872G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2616A	12						.						82.0	95.0	91.0					12																	120597762		2057	4200	6257	119082145	SO:0001819	synonymous_variant	10985	exon24			U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.2616C>A	12.37:g.120597762G>T		Somatic		Capture	Illumina HiSeq	Phase_I	119082145	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																				0.592	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
ANAPC5	51433	broad.mit.edu	37	12	121773516	121773516	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:121773516C>T	ENST00000261819.3	-	7	891	c.770G>A	c.(769-771)aGc>aAc	p.S257N	ANAPC5_ENST00000344395.4_Missense_Mutation_p.S158N|ANAPC5_ENST00000541887.1_Missense_Mutation_p.S257N|ANAPC5_ENST00000544314.1_5'Flank|ANAPC5_ENST00000441917.2_Missense_Mutation_p.S158N|ANAPC5_ENST00000536366.1_Missense_Mutation_p.S136N	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN	anaphase promoting complex subunit 5	257					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)	p.S257N(1)		breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GTTTAAGTAGCTGAGATAATG	0.378																																					p.S158N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G473A	12						.						76.0	78.0	77.0					12																	121773516		2203	4300	6503	120257899	SO:0001583	missense	51433	exon7			AF191339	CCDS9220.1, CCDS45000.1	12q24.31	2014-08-12			ENSG00000089053	ENSG00000089053		"""Anaphase promoting complex subunits"""	15713	protein-coding gene	gene with protein product		606948				9469815	Standard	NM_016237		Approved	APC5	uc001uag.3	Q9UJX4	OTTHUMG00000169157	ENST00000261819.3:c.770G>A	12.37:g.121773516C>T	ENSP00000261819:p.Ser257Asn	Somatic		Capture	Illumina HiSeq	Phase_I	120257899	NM_001137559	E9PFB2|Q8N4H7|Q9BQD4	Missense_Mutation	SNP	ENST00000261819.3	37	CCDS9220.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466359	0.63625	.	.	ENSG00000089053	ENST00000441917;ENST00000541887;ENST00000261819;ENST00000344395;ENST00000536366;ENST00000544442	.	.	.	6.04	6.04	0.98038	.	0.034896	0.85682	D	0.000000	T	0.57621	0.2066	L	0.37850	1.14	0.54753	D	0.999983	B;B	0.29162	0.051;0.235	B;B	0.29524	0.046;0.103	T	0.55503	-0.8131	9	0.59425	D	0.04	.	19.6319	0.95708	0.0:1.0:0.0:0.0	.	158;257	E9PFB2;Q9UJX4	.;APC5_HUMAN	N	158;257;257;158;136;158	.	ENSP00000261819:S257N	S	-	2	0	ANAPC5	120257899	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.336000	0.65935	2.890000	0.99128	0.650000	0.86243	AGC		0.378	ANAPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402582.1		
KDM2B	84678	broad.mit.edu	37	12	122013746	122013746	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:122013746A>G	ENST00000377071.4	-	3	362	c.290T>C	c.(289-291)gTa>gCa	p.V97A	KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000377069.4_Missense_Mutation_p.V66A|KDM2B_ENST00000538046.2_Missense_Mutation_p.V97A	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	97					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)	p.V97A(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						TTCTCTCTGTACGTACTCATA	0.418																																					p.V97A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T290C	12						.						146.0	140.0	142.0					12																	122013746		1855	4083	5938	120498129	SO:0001583	missense	84678	exon3			AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.290T>C	12.37:g.122013746A>G	ENSP00000366271:p.Val97Ala	Somatic		Capture	Illumina HiSeq	Phase_I	120498129	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	37	CCDS41850.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.074601	0.76415	.	.	ENSG00000089094	ENST00000397480;ENST00000377069;ENST00000377071;ENST00000397478;ENST00000261824;ENST00000446152;ENST00000539371	T;T;T	0.71579	-0.58;-0.58;-0.58	5.55	5.55	0.83447	.	0.000000	0.51477	D	0.000092	T	0.77785	0.4182	L	0.37561	1.115	0.80722	D	1	B;B;D	0.58970	0.094;0.302;0.984	B;P;D	0.68192	0.176;0.498;0.956	T	0.80344	-0.1422	10	0.87932	D	0	-18.1561	15.707	0.77592	1.0:0.0:0.0:0.0	.	97;97;66	E7EML5;Q8NHM5;A8MRS1	.;KDM2B_HUMAN;.	A	97;66;97;97;97;60;66	ENSP00000366269:V66A;ENSP00000366271:V97A;ENSP00000398279:V60A	ENSP00000261824:V97A	V	-	2	0	KDM2B	120498129	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.347000	0.90062	2.112000	0.64535	0.383000	0.25322	GTA		0.418	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
LRP6	4040	broad.mit.edu	37	12	12332848	12332848	+	Missense_Mutation	SNP	G	G	A	rs147034749		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:12332848G>A	ENST00000261349.4	-	7	1517	c.1441C>T	c.(1441-1443)Cgt>Tgt	p.R481C	LRP6_ENST00000543091.1_Missense_Mutation_p.R481C	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	481	Beta-propeller 2.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.R481C(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				AATACTACACGGTCAGAACCA	0.403																																					p.R481C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1441T	12						.	G	CYS/ARG	0,4406		0,0,2203	111.0	102.0	105.0		1441	4.9	1.0	12	dbSNP_134	105	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRP6	NM_002336.2	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	481/1614	12332848	1,13005	2203	4300	6503	12224115	SO:0001583	missense	4040	exon7			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.1441C>T	12.37:g.12332848G>A	ENSP00000261349:p.Arg481Cys	Somatic		Capture	Illumina HiSeq	Phase_I	12224115	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.113554	0.77210	0.0	1.16E-4	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.97665	-4.48;-4.48	5.82	4.93	0.64822	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.52532	D	0.000062	D	0.98982	0.9653	H	0.97315	3.98	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	D	0.99087	1.0839	10	0.72032	D	0.01	.	13.2902	0.60267	0.0:0.0:0.5694:0.4306	.	481;481	F5H7J9;O75581	.;LRP6_HUMAN	C	481	ENSP00000261349:R481C;ENSP00000442472:R481C	ENSP00000261349:R481C	R	-	1	0	LRP6	12224115	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.148000	0.58085	1.447000	0.47661	0.655000	0.94253	CGT		0.403	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
DIABLO	56616	broad.mit.edu	37	12	122709075	122709075	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:122709075G>A	ENST00000443649.3	-	3	984	c.167C>T	c.(166-168)gCg>gTg	p.A56V	DIABLO_ENST00000353548.6_Missense_Mutation_p.A56V|RP11-512M8.5_ENST00000535844.1_Intron|DIABLO_ENST00000464942.2_Intron|DIABLO_ENST00000413918.1_Missense_Mutation_p.A56V|DIABLO_ENST00000475784.1_5'Flank|DIABLO_ENST00000267169.6_Intron	NM_019887.4	NP_063940.1	Q9NR28	DBLOH_HUMAN	diablo, IAP-binding mitochondrial protein	56					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)		p.A56V(1)		breast(1)|endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	7	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000302)|Epithelial(86;0.00051)|BRCA - Breast invasive adenocarcinoma(302;0.223)		AATAGGAACCGCACACAGGGT	0.463																																					p.A56V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C167T	12						.						161.0	148.0	152.0					12																	122709075		2203	4300	6503	121275028	SO:0001583	missense	56616	exon3			AF262240	CCDS9228.1, CCDS9229.1, CCDS73541.1	12q24.31	2011-08-02	2011-03-11		ENSG00000184047	ENSG00000184047			21528	protein-coding gene	gene with protein product	"""second mitochondria-derived activator of caspase"""	605219				12749848, 17237824, 21722859	Standard	NM_019887		Approved	SMAC, DIABLO-S, FLJ25049, FLJ10537, DFNA64	uc010tab.2	Q9NR28	OTTHUMG00000157014	ENST00000443649.3:c.167C>T	12.37:g.122709075G>A	ENSP00000398495:p.Ala56Val	Somatic		Capture	Illumina HiSeq	Phase_I	121275028	NM_138929	B2RDQ0|Q6W3F3|Q96LV0|Q9BT11|Q9HAV6	Missense_Mutation	SNP	ENST00000443649.3	37	CCDS9228.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.721561	0.89298	.	.	ENSG00000184047	ENST00000413918;ENST00000443649;ENST00000353548	D;D;D	0.83992	-1.79;-1.79;-1.79	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.91119	0.7204	M	0.78049	2.395	0.49389	D	0.999788	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.90270	0.4307	10	0.44086	T	0.13	-0.4414	17.778	0.88515	0.0:0.0:1.0:0.0	.	56;56	Q6W3F3;Q9NR28	.;DBLOH_HUMAN	V	56	ENSP00000411638:A56V;ENSP00000398495:A56V;ENSP00000320343:A56V	ENSP00000320343:A56V	A	-	2	0	DIABLO	121275028	1.000000	0.71417	0.966000	0.40874	0.911000	0.54048	6.061000	0.71148	2.745000	0.94114	0.555000	0.69702	GCG		0.463	DIABLO-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347102.2	NM_019887	
LOH12CR1	118426	broad.mit.edu	37	12	12618609	12618609	+	Missense_Mutation	SNP	G	G	A	rs199869851	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:12618609G>A	ENST00000314565.4	+	4	821	c.490G>A	c.(490-492)Gac>Aac	p.D164N	LOH12CR1_ENST00000542728.1_Missense_Mutation_p.D145N|LOH12CR1_ENST00000298571.6_Missense_Mutation_p.D116N	NM_058169.3	NP_477517.1	Q969J3	L12R1_HUMAN	loss of heterozygosity, 12, chromosomal region 1	164								p.D164N(1)		kidney(1)|large_intestine(1)|lung(1)|ovary(1)	4		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.0205)		GATGGGCATCGACCAGACTGT	0.607													G|||	4	0.000798722	0.0	0.0014	5008	,	,		19263	0.003		0.0	False		,,,				2504	0.0				p.D164N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G490A	12						.						75.0	59.0	65.0					12																	12618609		2203	4300	6503	12509876	SO:0001583	missense	118426	exon4			AY037865	CCDS8649.1, CCDS73448.1	12p12	2008-07-03			ENSG00000165714	ENSG00000165714			17950	protein-coding gene	gene with protein product						11896457, 15284860	Standard	XR_242885		Approved	LOH1CR12	uc001ral.2	Q969J3	OTTHUMG00000168542	ENST00000314565.4:c.490G>A	12.37:g.12618609G>A	ENSP00000321546:p.Asp164Asn	Somatic		Capture	Illumina HiSeq	Phase_I	12509876	NM_058169	Q96QS5	Missense_Mutation	SNP	ENST00000314565.4	37	CCDS8649.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	G	12.86	2.063343	0.36373	.	.	ENSG00000165714	ENST00000542728;ENST00000314565;ENST00000298571	T;T;T	0.44881	0.91;0.91;0.91	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.19167	0.0460	N	0.22421	0.69	0.58432	D	0.999999	B;P	0.44478	0.433;0.836	B;B	0.33620	0.049;0.167	T	0.07751	-1.0756	10	0.10636	T	0.68	-12.2733	17.9394	0.89022	0.0:0.0:1.0:0.0	.	116;164	Q969J3-2;Q969J3	.;L12R1_HUMAN	N	145;164;116	ENSP00000443023:D145N;ENSP00000321546:D164N;ENSP00000298571:D116N	ENSP00000298571:D116N	D	+	1	0	LOH12CR1	12509876	1.000000	0.71417	0.965000	0.40720	0.396000	0.30629	9.414000	0.97362	2.662000	0.90505	0.557000	0.71058	GAC		0.607	LOH12CR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400150.1		
SBNO1	55206	broad.mit.edu	37	12	123813428	123813428	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:123813428T>G	ENST00000602398.1	-	10	1276	c.1149A>C	c.(1147-1149)aaA>aaC	p.K383N	SBNO1_ENST00000602750.1_Missense_Mutation_p.K382N|SBNO1_ENST00000267176.4_Missense_Mutation_p.K382N|SBNO1_ENST00000420886.2_Missense_Mutation_p.K383N			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	383					regulation of transcription, DNA-templated (GO:0006355)			p.K382N(1)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TGGAAGAAATTTTTCCGTATT	0.328																																					p.K382N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1146C	12						.						61.0	61.0	61.0					12																	123813428		2203	4300	6503	122379381	SO:0001583	missense	55206	exon9			AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.1149A>C	12.37:g.123813428T>G	ENSP00000473665:p.Lys383Asn	Somatic		Capture	Illumina HiSeq	Phase_I	122379381	NM_018183	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.096392	0.56075	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	D;D	0.93906	-3.31;-3.31	5.53	4.4	0.53042	Helicase/UvrB domain (1);	0.000000	0.85682	D	0.000000	D	0.95532	0.8548	M	0.74258	2.255	0.58432	D	0.999998	P;B;D	0.76494	0.774;0.198;0.999	P;B;D	0.80764	0.8;0.34;0.994	D	0.94221	0.7467	10	0.46703	T	0.11	-26.526	8.7534	0.34631	0.0:0.213:0.0:0.787	.	383;382;381	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	N	383;382;382	ENSP00000387361:K383N;ENSP00000267176:K382N	ENSP00000267176:K382N	K	-	3	2	SBNO1	122379381	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	0.587000	0.23909	0.948000	0.37687	0.260000	0.18958	AAA		0.328	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
TMEM132D	121256	broad.mit.edu	37	12	129559372	129559372	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:129559372T>G	ENST00000422113.2	-	9	2674	c.2348A>C	c.(2347-2349)aAg>aCg	p.K783T	TMEM132D_ENST00000389441.4_Missense_Mutation_p.K321T	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	783					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.K783T(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TAACACACTCTTCCGCTTGGA	0.478																																					p.K783T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2348C	12						.						173.0	146.0	155.0					12																	129559372		2203	4300	6503	128125325	SO:0001583	missense	121256	exon9			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.2348A>C	12.37:g.129559372T>G	ENSP00000408581:p.Lys783Thr	Somatic		Capture	Illumina HiSeq	Phase_I	128125325	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	T	12.62	1.993725	0.35131	.	.	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.17691	2.26;2.26	4.2	3.04	0.35103	.	0.000000	0.85682	D	0.000000	T	0.44286	0.1286	M	0.88105	2.93	0.46279	D	0.998965	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.992	T	0.41395	-0.9511	9	.	.	.	-36.2842	9.5387	0.39237	0.0:0.0857:0.0:0.9143	.	783;321	Q14C87;Q14C87-2	T132D_HUMAN;.	T	321;783	ENSP00000374092:K321T;ENSP00000408581:K783T	.	K	-	2	0	TMEM132D	128125325	0.995000	0.38212	0.885000	0.34714	0.191000	0.23601	1.244000	0.32778	0.586000	0.29626	0.379000	0.24179	AAG		0.478	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
TMEM132D	121256	broad.mit.edu	37	12	130185179	130185179	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:130185179G>A	ENST00000422113.2	-	2	470	c.144C>T	c.(142-144)ccC>ccT	p.P48P	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	48					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.P48P(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GGTAGGTCACGGGGAGGTAGG	0.567																																					p.P48P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C144T	12						.						106.0	75.0	85.0					12																	130185179		2203	4300	6503	128751132	SO:0001819	synonymous_variant	121256	exon2			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.144C>T	12.37:g.130185179G>A		Somatic		Capture	Illumina HiSeq	Phase_I	128751132	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																				0.567	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
CACNA1C	775	broad.mit.edu	37	12	2788861	2788861	+	Silent	SNP	C	C	T	rs374858814		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:2788861C>T	ENST00000347598.4	+	44	5487	c.5487C>T	c.(5485-5487)ccC>ccT	p.P1829P	CACNA1C_ENST00000402845.3_Silent_p.P1800P|CACNA1C_ENST00000335762.5_Silent_p.P1806P|CACNA1C_ENST00000399621.1_Silent_p.P1800P|CACNA1C_ENST00000399591.1_Silent_p.P1789P|CACNA1C_ENST00000399638.1_Silent_p.P1809P|CACNA1C_ENST00000399637.1_Silent_p.P1800P|CACNA1C_ENST00000399629.1_Silent_p.P1798P|CACNA1C_ENST00000327702.7_Silent_p.P1781P|CACNA1C_ENST00000344100.3_Silent_p.P1822P|CACNA1C_ENST00000399644.1_Silent_p.P1781P|CACNA1C_ENST00000399603.1_Silent_p.P1781P|CACNA1C_ENST00000406454.3_Silent_p.P1781P|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399655.1_Silent_p.P1781P|CACNA1C_ENST00000399617.1_Silent_p.P1781P|CACNA1C_ENST00000399606.1_Silent_p.P1801P|CACNA1C_ENST00000399597.1_Silent_p.P1781P|CACNA1C_ENST00000399649.1_Silent_p.P1787P|CACNA1C_ENST00000399601.1_Silent_p.P1781P|CACNA1C_ENST00000399641.1_Silent_p.P1781P|CACNA1C_ENST00000399634.1_Silent_p.P1781P|CACNA1C_ENST00000399595.1_Silent_p.P1789P	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1829					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.P1316P(1)|p.P1859P(1)|p.P1822P(1)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TCCCTCGCCCCGCCGGCTACC	0.677													C|||	1	0.000199681	0.0	0.0	5008	,	,		16796	0.001		0.0	False		,,,				2504	0.0				p.P1781P												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C5343T	12						.	C	,,,,,,,,,,,,,,,,,,,,,,	1,4161		0,1,2080	50.0	59.0	56.0		5343,5487,5466,5343,5427,5403,5400,5400,5400,5394,5367,5367,5361,5343,5343,5343,5343,5334,5310,5343,5343,5310,5487	-0.1	0.0	12		56	0,8420		0,0,4210	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1C	NM_000719.6,NM_001129827.1,NM_001129829.1,NM_001129830.1,NM_001129831.1,NM_001129832.1,NM_001129833.1,NM_001129834.1,NM_001129835.1,NM_001129836.1,NM_001129837.1,NM_001129838.1,NM_001129839.1,NM_001129840.1,NM_001129841.1,NM_001129842.1,NM_001129843.1,NM_001129844.1,NM_001129846.1,NM_001167623.1,NM_001167624.1,NM_001167625.1,NM_199460.2	,,,,,,,,,,,,,,,,,,,,,,	0,1,6290	TT,TC,CC		0.0,0.024,0.0079	,,,,,,,,,,,,,,,,,,,,,,	1781/2139,1829/2187,1822/2180,1781/2174,1809/2167,1801/2159,1800/2158,1800/2158,1800/2158,1798/2156,1789/2147,1789/2147,1787/2145,1781/2139,1781/2139,1781/2139,1781/2139,1778/2136,1770/2128,1781/2139,1781/2174,1770/2199,1829/2222	2788861	1,12581	2081	4210	6291	2659122	SO:0001819	synonymous_variant	775	exon42			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5487C>T	12.37:g.2788861C>T		Somatic		Capture	Illumina HiSeq	Phase_I	2659122	NM_001129842	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	37	CCDS44788.1																																																																																				0.677	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
TEAD4	7004	broad.mit.edu	37	12	3131019	3131019	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:3131019C>T	ENST00000397122.2	+	8	631	c.346C>T	c.(346-348)Cac>Tac	p.H116Y	TEAD4_ENST00000358409.2_Missense_Mutation_p.H202Y|TEAD4_ENST00000359864.2_Missense_Mutation_p.H245Y	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4	245					gene expression (GO:0010467)|hippo signaling (GO:0035329)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H245Y(1)		endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)			GTACAACAAGCACCTGTTCGT	0.577																																					p.H245Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C733T	12						.						109.0	102.0	104.0					12																	3131019		2203	4300	6503	3001280	SO:0001583	missense	7004	exon10			X94438	CCDS31729.1, CCDS31730.1, CCDS41737.1	12p13.3-p13.2	2008-05-14				ENSG00000197905			11717	protein-coding gene	gene with protein product		601714		TCF13L1		9889009, 8921372	Standard	NM_003213		Approved	TEF-3, TEFR-1, EFTR-2, RTEF-1	uc010sej.2	Q15561		ENST00000397122.2:c.346C>T	12.37:g.3131019C>T	ENSP00000380311:p.His116Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	3001280	NM_003213	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Missense_Mutation	SNP	ENST00000397122.2	37	CCDS41737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.1|23.1	4.374322|4.374322	0.82573|0.82573	.|.	.|.	ENSG00000197905|ENSG00000197905	ENST00000544666|ENST00000358409;ENST00000359864;ENST00000397122	.|T;T;T	.|0.65916	.|-0.18;-0.18;-0.18	4.19|4.19	4.19|4.19	0.49359|0.49359	.|.	.|0.113369	.|0.64402	.|D	.|0.000013	T|T	0.80138|0.80138	0.4568|0.4568	M|M	0.93594|0.93594	3.435|3.435	0.80722|0.80722	D|D	1|1	.|D	.|0.55800	.|0.973	.|P	.|0.54460	.|0.753	D|D	0.86750|0.86750	0.1960|0.1960	5|10	.|0.87932	.|D	.|0	-16.4999|-16.4999	15.6724|15.6724	0.77289|0.77289	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|245	.|Q15561	.|TEAD4_HUMAN	V|Y	167|202;245;116	.|ENSP00000351184:H202Y;ENSP00000352926:H245Y;ENSP00000380311:H116Y	.|ENSP00000351184:H202Y	A|H	+|+	2|1	0|0	TEAD4|TEAD4	3001280|3001280	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.943000|0.943000	0.58893|0.58893	7.625000|7.625000	0.83145|0.83145	2.167000|2.167000	0.68274|0.68274	0.655000|0.655000	0.94253|0.94253	GCA|CAC		0.577	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213	
C12orf5	57103	broad.mit.edu	37	12	4460504	4460504	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:4460504C>T	ENST00000179259.4	+	5	409	c.342C>T	c.(340-342)tgC>tgT	p.C114C	C12orf5_ENST00000537251.1_3'UTR	NM_020375.2	NP_065108.1	Q9NQ88	TIGAR_HUMAN	chromosome 12 open reading frame 5	114					intestinal epithelial cell development (GO:0060576)|negative regulation of macromitophagy (GO:1901525)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|response to gamma radiation (GO:0010332)|response to xenobiotic stimulus (GO:0009410)	intracellular (GO:0005622)	fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)	p.C114C(1)		endometrium(1)|large_intestine(1)|lung(5)|skin(3)	10			all cancers(3;1.15e-07)|Colorectal(7;0.00165)|OV - Ovarian serous cystadenocarcinoma(31;0.00596)|COAD - Colon adenocarcinoma(12;0.0229)|GBM - Glioblastoma multiforme(3;0.0266)|STAD - Stomach adenocarcinoma(119;0.206)			GGGAAGAGTGCCCTGTGTTTA	0.493																																					p.C114C	Colon(1;100 192 35375 49454 52532)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C342T	12						.						102.0	92.0	96.0					12																	4460504		2203	4300	6503	4330765	SO:0001819	synonymous_variant	57103	exon5			AJ272206	CCDS8525.1	12p13.32	2014-05-29	2009-11-24	2009-11-24	ENSG00000078237	ENSG00000078237	3.1.3.46		1185	protein-coding gene	gene with protein product	"""TP53-induced glycolysis and apoptosis regulator"""	610775				16140933, 16839880, 18945750, 19713938	Standard	NM_020375		Approved	TIGAR	uc001qmp.3	Q9NQ88		ENST00000179259.4:c.342C>T	12.37:g.4460504C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4330765	NM_020375	B2R840	Silent	SNP	ENST00000179259.4	37	CCDS8525.1																																																																																				0.493	C12orf5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398290.1	NM_020375	
KCNA1	3736	broad.mit.edu	37	12	5020638	5020638	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:5020638G>C	ENST00000382545.3	+	2	1201	c.94G>C	c.(94-96)Gac>Cac	p.D32H	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	32					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)	p.D32H(1)		NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	CGACCACGACGACCACGAGTG	0.672																																					p.D32H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G94C	12						.						34.0	35.0	35.0					12																	5020638		2203	4300	6503	4890899	SO:0001583	missense	3736	exon2			L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.94G>C	12.37:g.5020638G>C	ENSP00000371985:p.Asp32His	Somatic		Capture	Illumina HiSeq	Phase_I	4890899	NM_000217	A6NM83|Q3MIQ9	Missense_Mutation	SNP	ENST00000382545.3	37	CCDS8535.1	.	.	.	.	.	.	.	.	.	.	G	12.51	1.960808	0.34565	.	.	ENSG00000111262	ENST00000382545;ENST00000228858	D	0.96427	-4.01	3.93	3.93	0.45458	.	0.166924	0.50627	D	0.000105	D	0.94394	0.8197	M	0.61703	1.905	0.80722	D	1	B	0.13145	0.007	B	0.16722	0.016	D	0.92205	0.5771	10	0.21014	T	0.42	.	15.4851	0.75560	0.0:0.0:1.0:0.0	.	32	Q09470	KCNA1_HUMAN	H	32	ENSP00000371985:D32H	ENSP00000228858:D32H	D	+	1	0	KCNA1	4890899	.	.	0.996000	0.52242	0.744000	0.42396	.	.	2.201000	0.70794	0.555000	0.69702	GAC		0.672	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217	
KCNA5	3741	broad.mit.edu	37	12	5154179	5154179	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:5154179A>G	ENST00000252321.3	+	1	1095	c.866A>G	c.(865-867)cAc>cGc	p.H289R		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	289					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)	p.H289R(1)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	CCGGCGCCCCACCAGCCTCCC	0.692																																					p.H289R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A866G	12						.						35.0	40.0	38.0					12																	5154179		2201	4297	6498	5024440	SO:0001583	missense	3741	exon1			M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.866A>G	12.37:g.5154179A>G	ENSP00000252321:p.His289Arg	Somatic		Capture	Illumina HiSeq	Phase_I	5024440	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	37	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.829761	0.00584	.	.	ENSG00000130037	ENST00000252321	D	0.97404	-4.37	4.77	-1.09	0.09904	.	615.620000	0.00166	N	0.000000	D	0.91405	0.7288	N	0.08118	0	0.09310	N	1	B	0.19706	0.038	B	0.18263	0.021	D	0.85494	0.1187	10	0.11485	T	0.65	.	10.7518	0.46213	0.353:0.5763:0.0706:0.0	.	289	P22460	KCNA5_HUMAN	R	289	ENSP00000252321:H289R	ENSP00000252321:H289R	H	+	2	0	KCNA5	5024440	0.000000	0.05858	0.035000	0.18076	0.062000	0.15995	0.039000	0.13884	-0.355000	0.08199	-0.396000	0.06452	CAC		0.692	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234	
NTF3	4908	broad.mit.edu	37	12	5603417	5603417	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:5603417C>A	ENST00000331010.6	+	1	120	c.37C>A	c.(37-39)Ctc>Atc	p.L13I	NTF3_ENST00000535299.1_Intron|NTF3_ENST00000423158.3_Missense_Mutation_p.L26I	NM_002527.4	NP_002518.1	P20783	NTF3_HUMAN	neurotrophin 3	13					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell-cell signaling (GO:0007267)|enteric nervous system development (GO:0048484)|epidermis development (GO:0008544)|glial cell fate determination (GO:0007403)|induction of positive chemotaxis (GO:0050930)|mechanoreceptor differentiation (GO:0042490)|myelination (GO:0042552)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|peripheral nervous system development (GO:0007422)|positive chemotaxis (GO:0050918)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of synaptic transmission (GO:0050804)|signal transduction (GO:0007165)|smooth muscle cell differentiation (GO:0051145)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular region (GO:0005576)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)	p.L13I(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(3)|upper_aerodigestive_tract(1)	22						TCTCGCTTATCTCCGTGGCAT	0.423																																					p.L26I	GBM(194;1104 2182 8339 9578 18493)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C76A	12						.						117.0	111.0	113.0					12																	5603417		2203	4300	6503	5473678	SO:0001583	missense	4908	exon2				CCDS8538.1, CCDS44806.1	12p13	2014-01-30			ENSG00000185652	ENSG00000185652		"""Endogenous ligands"""	8023	protein-coding gene	gene with protein product		162660				1889806	Standard	NM_002527		Approved	NGF2	uc001qnk.4	P20783	OTTHUMG00000168649	ENST00000331010.6:c.37C>A	12.37:g.5603417C>A	ENSP00000328738:p.Leu13Ile	Somatic		Capture	Illumina HiSeq	Phase_I	5473678	NM_001102654	B7Z1T5|Q6FH50	Missense_Mutation	SNP	ENST00000331010.6	37	CCDS8538.1	.	.	.	.	.	.	.	.	.	.	C	19.99	3.928316	0.73327	.	.	ENSG00000185652	ENST00000423158;ENST00000331010	T;T	0.45276	0.9;0.9	4.79	4.79	0.61399	.	0.000000	0.64402	D	0.000001	T	0.65984	0.2744	M	0.78456	2.415	0.58432	D	0.999998	D;D	0.63880	0.993;0.993	D;D	0.73708	0.981;0.981	T	0.70985	-0.4723	10	0.87932	D	0	-27.0615	17.0016	0.86382	0.0:1.0:0.0:0.0	.	13;26	P20783;B7Z1T5	NTF3_HUMAN;.	I	26;13	ENSP00000397297:L26I;ENSP00000328738:L13I	ENSP00000328738:L13I	L	+	1	0	NTF3	5473678	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.127000	0.77210	2.504000	0.84457	0.591000	0.81541	CTC		0.423	NTF3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400486.1		
VWF	7450	broad.mit.edu	37	12	6085396	6085396	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:6085396C>T	ENST00000261405.5	-	43	7572	c.7318G>A	c.(7318-7320)Gtg>Atg	p.V2440M		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2440	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.V2440M(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	AACTGGCCCACAGGGTAGATG	0.557																																					p.V2440M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G7318A	12						.						90.0	72.0	78.0					12																	6085396		2203	4300	6503	5955657	SO:0001583	missense	7450	exon43				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.7318G>A	12.37:g.6085396C>T	ENSP00000261405:p.Val2440Met	Somatic		Capture	Illumina HiSeq	Phase_I	5955657	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.140365	0.56936	.	.	ENSG00000110799	ENST00000261405	T	0.65732	-0.17	5.38	3.57	0.40892	von Willebrand factor, type C (3);	0.000000	0.37623	N	0.002006	T	0.62380	0.2423	M	0.77103	2.36	0.80722	D	1	B	0.19200	0.034	B	0.26416	0.069	T	0.60979	-0.7155	10	0.66056	D	0.02	.	9.0426	0.36327	0.0:0.7628:0.0:0.2372	.	2440	P04275	VWF_HUMAN	M	2440	ENSP00000261405:V2440M	ENSP00000261405:V2440M	V	-	1	0	VWF	5955657	0.148000	0.22702	0.624000	0.29186	0.832000	0.47134	0.596000	0.24044	0.661000	0.30985	-0.191000	0.12829	GTG		0.557	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
CD27	939	broad.mit.edu	37	12	6560460	6560460	+	Missense_Mutation	SNP	G	G	A	rs144240256		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:6560460G>A	ENST00000266557.3	+	6	914	c.685G>A	c.(685-687)Gca>Aca	p.A229T	TAPBPL_ENST00000266556.7_5'Flank|CD27-AS1_ENST00000545339.1_RNA|TAPBPL_ENST00000544021.1_5'Flank|CD27_ENST00000541233.1_3'UTR|CD27-AS1_ENST00000399492.2_RNA	NM_001242.4	NP_001233	P26842	CD27_HUMAN	CD27 molecule	229					cell surface receptor signaling pathway (GO:0007166)|extrinsic apoptotic signaling pathway (GO:0097191)|immunoglobulin mediated immune response (GO:0016064)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of JNK cascade (GO:0046330)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|response to ethanol (GO:0045471)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|transmembrane signaling receptor activity (GO:0004888)	p.A229T(1)		kidney(1)|large_intestine(5)|lung(1)|urinary_tract(3)	10						TGTGGAGCCTGCAGAGCCTTG	0.612																																					p.A229T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G685A	12						.	G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	50.0	50.0	50.0		685	3.2	0.0	12	dbSNP_134	50	0,8600		0,0,4300	yes	missense	CD27	NM_001242.4	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	229/261	6560460	1,13005	2203	4300	6503	6430721	SO:0001583	missense	939	exon6			M63928	CCDS8545.1	12p13	2014-09-17	2006-10-27	2006-10-27	ENSG00000139193	ENSG00000139193		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11922	protein-coding gene	gene with protein product		186711	"""tumor necrosis factor receptor superfamily, member 7"""	TNFRSF7		2442250, 8530100	Standard	NM_001242		Approved	S152, Tp55	uc001qod.3	P26842	OTTHUMG00000168316	ENST00000266557.3:c.685G>A	12.37:g.6560460G>A	ENSP00000266557:p.Ala229Thr	Somatic		Capture	Illumina HiSeq	Phase_I	6430721	NM_001242	B2RDZ0	Missense_Mutation	SNP	ENST00000266557.3	37	CCDS8545.1	.	.	.	.	.	.	.	.	.	.	G	14.44	2.536273	0.45176	2.27E-4	0.0	ENSG00000139193	ENST00000266557	D	0.94723	-3.5	4.07	3.18	0.36537	.	2.578740	0.01225	N	0.008209	D	0.92691	0.7677	L	0.53249	1.67	0.09310	N	1	B	0.20550	0.046	B	0.21917	0.037	T	0.77943	-0.2398	10	0.28530	T	0.3	-0.5271	7.3578	0.26729	0.1187:0.0:0.8813:0.0	.	229	P26842	CD27_HUMAN	T	229	ENSP00000266557:A229T	ENSP00000266557:A229T	A	+	1	0	CD27	6430721	0.008000	0.16893	0.029000	0.17559	0.254000	0.26022	1.330000	0.33781	0.942000	0.37525	0.561000	0.74099	GCA		0.612	CD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399258.1		
ACRBP	84519	broad.mit.edu	37	12	6753415	6753415	+	Missense_Mutation	SNP	T	T	C	rs192361841	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:6753415T>C	ENST00000229243.2	-	5	925	c.832A>G	c.(832-834)Act>Gct	p.T278A	ACRBP_ENST00000536350.1_Missense_Mutation_p.T278A|ACRBP_ENST00000542357.1_5'Flank|ACRBP_ENST00000414226.2_Missense_Mutation_p.T245A	NM_032489.2	NP_115878.2			acrosin binding protein									p.T278A(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(8)|lung(5)|ovary(1)	17						ATCATAGGAGTAGACTCTACT	0.443																																					p.T278A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A832G	12						.						122.0	119.0	120.0					12																	6753415		2203	4300	6503	6623676	SO:0001583	missense	84519	exon5			AB051833	CCDS8554.1	12p13.31	2009-03-12			ENSG00000111644	ENSG00000111644			17195	protein-coding gene	gene with protein product	"""proacrosin binding protein sp32"", ""cancer/testis antigen 23"""	608352				11248070	Standard	NM_032489		Approved	SP32, OY-TES-1, CT23	uc001qpu.1	Q8NEB7	OTTHUMG00000168715	ENST00000229243.2:c.832A>G	12.37:g.6753415T>C	ENSP00000229243:p.Thr278Ala	Somatic		Capture	Illumina HiSeq	Phase_I	6623676	NM_032489		Missense_Mutation	SNP	ENST00000229243.2	37	CCDS8554.1	.	.	.	.	.	.	.	.	.	.	T	0.028	-1.358090	0.01245	.	.	ENSG00000111644	ENST00000229243;ENST00000414226;ENST00000536350	T;T	0.42900	0.98;0.96	4.55	0.534	0.17127	.	0.857814	0.10211	N	0.702112	T	0.20618	0.0496	N	0.19112	0.55	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.23404	-1.0189	10	0.20046	T	0.44	1.1263	0.4034	0.00429	0.2133:0.1445:0.2193:0.4229	.	245;278	E7EP66;Q8NEB7	.;ACRBP_HUMAN	A	278;245;278	ENSP00000229243:T278A;ENSP00000402725:T245A	ENSP00000229243:T278A	T	-	1	0	ACRBP	6623676	0.000000	0.05858	0.001000	0.08648	0.052000	0.14988	-1.274000	0.02820	-0.062000	0.13088	0.459000	0.35465	ACT		0.443	ACRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400703.1	NM_032489	
CD4	920	broad.mit.edu	37	12	6925170	6925170	+	Intron	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:6925170C>T	ENST00000011653.4	+	6	865				CD4_ENST00000541982.1_3'UTR|CD4_ENST00000538827.1_Intron	NM_000616.4|NM_001195015.2|NM_001195016.2|NM_001195017.2	NP_000607.1|NP_001181944.1|NP_001181945.1|NP_001181946.1	P01730	CD4_HUMAN	CD4 molecule						cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cytokine production (GO:0001816)|defense response to Gram-negative bacterium (GO:0050829)|entry into host cell (GO:0030260)|enzyme linked receptor protein signaling pathway (GO:0007167)|immune response (GO:0006955)|induction by virus of host cell-cell fusion (GO:0006948)|innate immune response (GO:0045087)|maintenance of protein location in cell (GO:0032507)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase activity (GO:0045860)|protein palmitoleylation (GO:0045234)|regulation of defense response to virus by virus (GO:0050690)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|T cell selection (GO:0045058)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|enzyme binding (GO:0019899)|extracellular matrix structural constituent (GO:0005201)|glycoprotein binding (GO:0001948)|MHC class II protein binding (GO:0042289)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	23		Myeloproliferative disorder(1001;0.0122)			Antithymocyte globulin(DB00098)	CCCACTCGTGCACCCTCATCT	0.557																																					p.H7Y												.	.	0			c.C19T	12						.						30.0	24.0	26.0					12																	6925170		876	1991	2867	6795431	SO:0001627	intron_variant	920	exon4			M35160	CCDS8562.1	12p13.31	2013-01-11	2006-03-28		ENSG00000010610	ENSG00000010610		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	1678	protein-coding gene	gene with protein product		186940	"""CD4 antigen (p55)"", ""T-cell surface glycoprotein CD4"""				Standard	NM_000616		Approved		uc001qqv.2	P01730	OTTHUMG00000168514	ENST00000011653.4:c.608-52C>T	12.37:g.6925170C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6795431	NM_001195014	B2R737|D3DUS5|Q4ZGK2|Q5U066|Q9UDE5	Missense_Mutation	SNP	ENST00000011653.4	37	CCDS8562.1																																																																																				0.557	CD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399978.1	NM_000616	
GPR162	27239	broad.mit.edu	37	12	6933483	6933483	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:6933483G>A	ENST00000311268.3	+	2	1206	c.419G>A	c.(418-420)gGc>gAc	p.G140D	GPR162_ENST00000541431.1_3'UTR|GPR162_ENST00000382315.3_Intron|GPR162_ENST00000428545.2_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	140						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.G140D(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						GCCGTCATGGGCATCTGGATG	0.612																																					p.G140D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G419A	12						.						90.0	77.0	81.0					12																	6933483		2203	4300	6503	6803744	SO:0001583	missense	27239	exon2			U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"""GPCR / Class A : Orphans"""	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.419G>A	12.37:g.6933483G>A	ENSP00000311528:p.Gly140Asp	Somatic		Capture	Illumina HiSeq	Phase_I	6803744	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	37	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.716065	0.89205	.	.	ENSG00000250510	ENST00000311268	T	0.39787	1.06	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.54271	0.1848	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.58335	-0.7654	9	0.56958	D	0.05	.	16.9233	0.86168	0.0:0.0:1.0:0.0	.	140;140	B7Z3U3;Q16538	.;GP162_HUMAN	D	140	ENSP00000311528:G140D	ENSP00000311528:G140D	G	+	2	0	GPR162	6803744	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	9.644000	0.98468	2.229000	0.72834	0.491000	0.48974	GGC		0.612	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858	
LPCAT3	10162	broad.mit.edu	37	12	7084398	7084398	+	IGR	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:7084398A>G	ENST00000261407.4	-	0	2268				EMG1_ENST00000546220.1_3'UTR|LPCAT3_ENST00000535021.1_5'Flank|EMG1_ENST00000261406.6_Missense_Mutation_p.K159R	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3						glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	17						TAGGTAATTAAGAATCCAGTA	0.433																																					p.R160G												.	.	0			c.A478G	12						.						89.0	84.0	85.0					12																	7084398		1893	4115	6008	6954659	SO:0001628	intergenic_variant	10436	exon5			U72515	CCDS8572.1	12p13.31	2010-05-12	2008-06-24	2008-06-24	ENSG00000111684	ENSG00000111684			30244	protein-coding gene	gene with protein product		611950	"""O-acyltransferase (membrane bound) domain containing 5"", ""membrane bound O-acyltransferase domain containing 5"""	OACT5, MBOAT5		8723724, 9074930, 18195019	Standard	NM_005768		Approved	C3F, nessy	uc001qsi.3	Q6P1A2	OTTHUMG00000168970		12.37:g.7084398A>G		Somatic		Capture	Illumina HiSeq	Phase_I	6954659	NM_006331	B2RDH0|B7Z3N3|Q7KZS1|Q92980|Q9BW40	Missense_Mutation	SNP	ENST00000261407.4	37	CCDS8572.1																																																																																				0.433	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401812.1	NM_005768	
CD163L1	283316	broad.mit.edu	37	12	7551110	7551110	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:7551110G>A	ENST00000313599.3	-	7	1536	c.1479C>T	c.(1477-1479)taC>taT	p.Y493Y	CD163L1_ENST00000416109.2_Silent_p.Y503Y|CD163L1_ENST00000396630.1_Silent_p.Y493Y			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	493	SRCR 5. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.Y493Y(1)		breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						ACTCTCCTTGGTATTTCACCT	0.473																																					p.Y493Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1479T	12						.						123.0	104.0	110.0					12																	7551110		2203	4300	6503	7442377	SO:0001819	synonymous_variant	283316	exon7			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.1479C>T	12.37:g.7551110G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7442377	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																				0.473	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
SLC2A14	144195	broad.mit.edu	37	12	7967096	7967096	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:7967096G>A	ENST00000543909.1	-	16	2138	c.1379C>T	c.(1378-1380)aCc>aTc	p.T460I	SLC2A14_ENST00000535295.1_Missense_Mutation_p.T351I|SLC2A14_ENST00000542505.1_Missense_Mutation_p.T101I|SLC2A14_ENST00000431042.2_Missense_Mutation_p.T437I|SLC2A14_ENST00000340749.5_Missense_Mutation_p.T437I|SLC2A14_ENST00000539924.1_Missense_Mutation_p.T475I|SLC2A14_ENST00000542546.1_Missense_Mutation_p.T351I|SLC2A14_ENST00000396589.2_Missense_Mutation_p.T460I			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	460					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)	p.T460I(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		GAGGAAGCCGGTGAAGATAAT	0.423																																					p.T460I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1379T	12						.						51.0	52.0	52.0					12																	7967096		2203	4300	6503	7858363	SO:0001583	missense	144195	exon12			AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"""Solute carriers"""	18301	protein-coding gene	gene with protein product		611039	"""solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"""	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.1379C>T	12.37:g.7967096G>A	ENSP00000440480:p.Thr460Ile	Somatic		Capture	Illumina HiSeq	Phase_I	7858363	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Missense_Mutation	SNP	ENST00000543909.1	37	CCDS8585.1	.	.	.	.	.	.	.	.	.	.	G	9.028	0.986641	0.18889	.	.	ENSG00000173262	ENST00000340749;ENST00000543909;ENST00000431042;ENST00000542505;ENST00000396589;ENST00000535295;ENST00000542546;ENST00000539924	T;T;T;T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37	3.71	1.81	0.25067	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.471893	0.22534	N	0.058801	T	0.66799	0.2826	L	0.34521	1.04	0.20196	N	0.999929	B;B;B;B	0.19445	0.036;0.011;0.009;0.0	B;B;B;B	0.21546	0.035;0.024;0.013;0.014	T	0.55159	-0.8184	10	0.40728	T	0.16	.	5.3744	0.16156	0.3645:0.0:0.6355:0.0	.	475;351;437;460	B7ZAC3;B7Z844;Q8TDB8-2;Q8TDB8	.;.;.;GTR14_HUMAN	I	437;460;437;101;460;351;351;475	ENSP00000340450:T437I;ENSP00000440480:T460I;ENSP00000407287:T437I;ENSP00000438484:T101I;ENSP00000379834:T460I;ENSP00000440492:T351I;ENSP00000443903:T351I;ENSP00000445929:T475I	ENSP00000340450:T437I	T	-	2	0	SLC2A14	7858363	0.562000	0.26586	0.029000	0.17559	0.028000	0.11728	1.381000	0.34362	0.661000	0.30985	-0.459000	0.05422	ACC		0.423	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449	
PHC1	1911	broad.mit.edu	37	12	9083166	9083166	+	Missense_Mutation	SNP	G	G	T	rs201153867		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:9083166G>T	ENST00000543824.1	+	8	1080	c.748G>T	c.(748-750)Gtg>Ttg	p.V250L	PHC1_ENST00000536844.1_Missense_Mutation_p.V29L|PHC1_ENST00000433847.2_3'UTR|PHC1_ENST00000433083.2_Missense_Mutation_p.V205L|PHC1_ENST00000544916.1_Missense_Mutation_p.V250L			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	250					cellular response to retinoic acid (GO:0071300)|histone ubiquitination (GO:0016574)|multicellular organismal development (GO:0007275)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.V250L(3)		breast(2)|cervix(1)|endometrium(5)|large_intestine(8)|liver(2)|lung(3)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	27						GGCCCTAGCGGTGGCACAGGC	0.612																																					p.V250L												.	.	3	Substitution - Missense(3)	endometrium(3)	c.G748T	12						.						6.0	6.0	6.0					12																	9083166		2152	4199	6351	8974433	SO:0001583	missense	1911	exon7			U89277	CCDS8597.1	12p13	2013-01-10	2006-09-12	2002-11-15	ENSG00000111752	ENSG00000111752		"""Sterile alpha motif (SAM) domain containing"""	3182	protein-coding gene	gene with protein product		602978	"""early development regulator 1 (homolog of polyhomeotic 1)"", ""polyhomeotic-like 1 (Drosophila)"""	EDR1		9121482	Standard	XM_005253334		Approved	HPH1, RAE28	uc001qvd.3	P78364	OTTHUMG00000168275	ENST00000543824.1:c.748G>T	12.37:g.9083166G>T	ENSP00000440674:p.Val250Leu	None		Capture	Illumina HiSeq	Phase_I	8974433	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Missense_Mutation	SNP	ENST00000543824.1	37	CCDS8597.1	.	.	.	.	.	.	.	.	.	.	G	14.32	2.501020	0.44455	.	.	ENSG00000111752	ENST00000543824;ENST00000251757;ENST00000433083;ENST00000544916;ENST00000536844;ENST00000542346	T;T;T;T;T	0.53206	1.93;1.93;1.92;1.93;0.63	5.92	5.92	0.95590	.	0.077602	0.53938	D	0.000055	T	0.26810	0.0656	N	0.12569	0.235	0.27409	N	0.954622	P;B;B	0.37101	0.582;0.447;0.447	B;B;B	0.32393	0.134;0.145;0.145	T	0.16689	-1.0394	10	0.21540	T	0.41	-16.9954	12.4189	0.55510	0.0776:0.0:0.9224:0.0	.	250;250;250	B4DF21;P78364;B2RXH1	.;PHC1_HUMAN;.	L	250;250;205;250;29;61	ENSP00000440674:V250L;ENSP00000251757:V250L;ENSP00000399194:V205L;ENSP00000437659:V250L;ENSP00000440488:V29L	ENSP00000251757:V250L	V	+	1	0	PHC1	8974433	1.000000	0.71417	0.981000	0.43875	0.886000	0.51366	3.678000	0.54627	2.813000	0.96785	0.561000	0.74099	GTG		0.612	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426	
M6PR	4074	broad.mit.edu	37	12	9094482	9094482	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:9094482G>A	ENST00000000412.3	-	7	1234	c.766C>T	c.(766-768)Cgt>Tgt	p.R256C		NM_002355.3	NP_002346.1	P20645	MPRD_HUMAN	mannose-6-phosphate receptor (cation dependent)	256					endosome to lysosome transport (GO:0008333)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	mannose binding (GO:0005537)|mannose transmembrane transporter activity (GO:0015578)|transmembrane signaling receptor activity (GO:0004888)	p.R256C(1)		cervix(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(1)	11		Hepatocellular(102;0.137)		BRCA - Breast invasive adenocarcinoma(232;0.0146)	Alglucosidase alfa(DB01272)	CCCACACCACGATATGCTGCA	0.463																																					p.R256C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C766T	12						.						127.0	117.0	121.0					12																	9094482		2203	4300	6503	8985749	SO:0001583	missense	4074	exon7				CCDS8598.1, CCDS73440.1	12p13.31	2013-09-20			ENSG00000003056	ENSG00000003056			6752	protein-coding gene	gene with protein product		154540					Standard	NM_002355		Approved		uc001qvf.3	P20645	OTTHUMG00000168276	ENST00000000412.3:c.766C>T	12.37:g.9094482G>A	ENSP00000000412:p.Arg256Cys	Somatic		Capture	Illumina HiSeq	Phase_I	8985749	NM_002355	A8K528|D3DUV5	Missense_Mutation	SNP	ENST00000000412.3	37	CCDS8598.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.131684	0.77662	.	.	ENSG00000003056	ENST00000000412;ENST00000543704	T	0.32272	1.46	5.82	3.88	0.44766	.	0.051668	0.85682	D	0.000000	T	0.52224	0.1721	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.57522	-0.7797	10	0.72032	D	0.01	-10.0137	14.7098	0.69222	0.0:0.0:0.7367:0.2633	.	256	P20645	MPRD_HUMAN	C	256;127	ENSP00000000412:R256C	ENSP00000000412:R256C	R	-	1	0	M6PR	8985749	1.000000	0.71417	0.953000	0.39169	0.998000	0.95712	3.014000	0.49590	1.412000	0.46977	0.655000	0.94253	CGT		0.463	M6PR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399130.1		
A2M	2	broad.mit.edu	37	12	9230366	9230366	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:9230366C>T	ENST00000318602.7	-	26	3514	c.3207G>A	c.(3205-3207)tgG>tgA	p.W1069*	A2M_ENST00000542567.1_5'UTR	NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	1069					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)	p.W1069*(1)		breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	TCTGGGAGAGCCATATGAGGG	0.493																																					p.W1069X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G3207A	12						.						118.0	121.0	120.0					12																	9230366		2203	4300	6503	9121633	SO:0001587	stop_gained	2	exon26			BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.3207G>A	12.37:g.9230366C>T	ENSP00000323929:p.Trp1069*	Somatic		Capture	Illumina HiSeq	Phase_I	9121633	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Nonsense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	C	42	9.579971	0.99210	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	.	.	.	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.0838	0.93194	0.0:1.0:0.0:0.0	.	.	.	.	X	1069;1084	.	ENSP00000323929:W1069X	W	-	3	0	A2M	9121633	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.750000	0.85110	2.607000	0.88179	0.585000	0.79938	TGG		0.493	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	
A2M	2	broad.mit.edu	37	12	9246171	9246171	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:9246171T>C	ENST00000318602.7	-	18	2437	c.2130A>G	c.(2128-2130)tcA>tcG	p.S710S		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	710	Bait region.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)	p.S710S(1)		breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	CCATTACATCTGACTCTATGG	0.418																																					p.S710S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2130G	12						.						68.0	62.0	64.0					12																	9246171		1894	4118	6012	9137438	SO:0001819	synonymous_variant	2	exon18			BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.2130A>G	12.37:g.9246171T>C		Somatic		Capture	Illumina HiSeq	Phase_I	9137438	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Silent	SNP	ENST00000318602.7	37	CCDS44827.1																																																																																				0.418	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	
PLBD1	79887	broad.mit.edu	37	12	14706285	14706285	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:14706285T>C	ENST00000240617.5	-	2	829	c.177A>G	c.(175-177)gtA>gtG	p.V59V	RN7SKP134_ENST00000363960.1_RNA	NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	59					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)	p.V59V(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						TCTTGTCCATTACATTTTTGA	0.443																																					p.V59V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A177G	12						.						118.0	112.0	114.0					12																	14706285		2203	4300	6503	14597552	SO:0001819	synonymous_variant	79887	exon2			BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316			26215	protein-coding gene	gene with protein product	"""PLB homolog 1 (Dictyostelium)"""					15193148, 19019078	Standard	NM_024829		Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.177A>G	12.37:g.14706285T>C		Somatic		Capture	Illumina HiSeq	Phase_I	14597552	NM_024829	A8K4E9|Q9BVV3|Q9H625	Silent	SNP	ENST00000240617.5	37	CCDS31751.1																																																																																				0.443	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829	
RERG	85004	broad.mit.edu	37	12	15262081	15262081	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:15262081T>C	ENST00000256953.2	-	5	899	c.563A>G	c.(562-564)cAa>cGa	p.Q188R	RERG_ENST00000536465.1_Missense_Mutation_p.Q188R|RERG_ENST00000538313.1_Missense_Mutation_p.Q188R|RERG_ENST00000546331.1_Missense_Mutation_p.Q169R	NM_032918.2	NP_116307.1	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor	188					negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to hormone (GO:0009725)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	estrogen receptor binding (GO:0030331)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.Q188R(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16						GTTAATGGCTTGCTTGACATG	0.507																																					p.Q188R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A563G	12						.						138.0	130.0	133.0					12																	15262081		2203	4300	6503	15153348	SO:0001583	missense	85004	exon5			AF339750	CCDS8673.1, CCDS53753.1	12p13.1	2014-05-09			ENSG00000134533	ENSG00000134533			15980	protein-coding gene	gene with protein product		612664				11533059	Standard	NM_032918		Approved	MGC15754	uc001rct.3	Q96A58	OTTHUMG00000168745	ENST00000256953.2:c.563A>G	12.37:g.15262081T>C	ENSP00000256953:p.Gln188Arg	Somatic		Capture	Illumina HiSeq	Phase_I	15153348	NM_032918	B2R9R0|B4DI02	Missense_Mutation	SNP	ENST00000256953.2	37	CCDS8673.1	.	.	.	.	.	.	.	.	.	.	T	17.75	3.465313	0.63513	.	.	ENSG00000134533	ENST00000256953;ENST00000538313;ENST00000536465;ENST00000546331	T;T;T;T	0.66995	-0.24;-0.24;-0.24;0.31	4.56	4.56	0.56223	.	0.054600	0.85682	D	0.000000	T	0.45975	0.1369	N	0.08118	0	0.80722	D	1	B;B	0.21753	0.042;0.06	B;B	0.16289	0.013;0.015	T	0.44050	-0.9353	10	0.42905	T	0.14	.	13.1662	0.59573	0.0:0.0:0.0:1.0	.	169;188	B4DI02;Q96A58	.;RERG_HUMAN	R	188;188;188;169	ENSP00000256953:Q188R;ENSP00000441505:Q188R;ENSP00000438280:Q188R;ENSP00000444485:Q169R	ENSP00000256953:Q188R	Q	-	2	0	RERG	15153348	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.820000	0.86633	2.043000	0.60533	0.533000	0.62120	CAA		0.507	RERG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400882.1	NM_032918	
PTPRO	5800	broad.mit.edu	37	12	15636961	15636961	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:15636961A>G	ENST00000281171.4	+	2	459	c.129A>G	c.(127-129)tcA>tcG	p.S43S	PTPRO_ENST00000348962.2_Silent_p.S43S|PTPRO_ENST00000543886.1_Silent_p.S43S	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	43					axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)	p.S43S(1)		NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				TCGTTGTCTCATTAGAAGCTT	0.353																																					p.S43S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A129G	12						.						94.0	94.0	94.0					12																	15636961		2203	4300	6503	15528228	SO:0001819	synonymous_variant	5800	exon2			U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9678	protein-coding gene	gene with protein product	"""osteoclastic transmembrane protein-tyrosine phosphatase"""	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.129A>G	12.37:g.15636961A>G		Somatic		Capture	Illumina HiSeq	Phase_I	15528228	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Silent	SNP	ENST00000281171.4	37	CCDS8675.1																																																																																				0.353	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1		
PYROXD1	79912	broad.mit.edu	37	12	21621444	21621444	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:21621444T>C	ENST00000240651.9	+	12	1313	c.1259T>C	c.(1258-1260)gTa>gCa	p.V420A	PYROXD1_ENST00000538582.1_Missense_Mutation_p.V349A	NM_024854.3	NP_079130.2	Q8WU10	PYRD1_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 1	420							oxidoreductase activity (GO:0016491)	p.V420A(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|soft_tissue(1)	18						ATATAGGTTGTACTGCTGGGA	0.348																																					p.V420A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1259C	12						.						63.0	64.0	64.0					12																	21621444		2203	4299	6502	21512711	SO:0001583	missense	79912	exon12			AL832441	CCDS31755.1	12p12.1	2014-02-12			ENSG00000121350	ENSG00000121350			26162	protein-coding gene	gene with protein product						12477932	Standard	NM_024854		Approved	DKFZp762G094, FLJ22028	uc001rew.3	Q8WU10	OTTHUMG00000169129	ENST00000240651.9:c.1259T>C	12.37:g.21621444T>C	ENSP00000240651:p.Val420Ala	Somatic		Capture	Illumina HiSeq	Phase_I	21512711	NM_024854	A6NKI6|B3KWN8|Q9H6P1	Missense_Mutation	SNP	ENST00000240651.9	37	CCDS31755.1	.	.	.	.	.	.	.	.	.	.	T	16.57	3.159603	0.57368	.	.	ENSG00000121350	ENST00000536935;ENST00000240651;ENST00000538582	.	.	.	5.02	5.02	0.67125	.	0.060415	0.64402	D	0.000003	T	0.53190	0.1781	M	0.71871	2.18	0.80722	D	1	P	0.42518	0.782	B	0.38921	0.285	T	0.54886	-0.8226	9	0.09084	T	0.74	.	14.2294	0.65882	0.0:0.0:0.0:1.0	.	420	Q8WU10	PYRD1_HUMAN	A	126;420;349	.	ENSP00000240651:V420A	V	+	2	0	PYROXD1	21512711	1.000000	0.71417	0.992000	0.48379	0.713000	0.41058	7.754000	0.85163	2.005000	0.58758	0.460000	0.39030	GTA		0.348	PYROXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402363.1	NM_024854	
CMAS	55907	broad.mit.edu	37	12	22213832	22213832	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:22213832T>C	ENST00000229329.2	+	5	890	c.760T>C	c.(760-762)Tgg>Cgg	p.W254R		NM_018686.4	NP_061156.1	Q8NFW8	NEUA_HUMAN	cytidine monophosphate N-acetylneuraminic acid synthetase	254					lipopolysaccharide biosynthetic process (GO:0009103)|N-acetylneuraminate metabolic process (GO:0006054)	membrane (GO:0016020)|nucleus (GO:0005634)	N-acylneuraminate cytidylyltransferase activity (GO:0008781)	p.W254R(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24						GGATATTGATTGGCCTATTGC	0.308																																					p.W254R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T760C	12						.						118.0	125.0	122.0					12																	22213832		2203	4299	6502	22105099	SO:0001583	missense	55907	exon5			AF271388	CCDS8696.1	12p12.1	2008-08-04			ENSG00000111726	ENSG00000111726			18290	protein-coding gene	gene with protein product	"""CMP-Neu5Ac synthetase"""	603316				8889549, 7566098	Standard	NM_018686		Approved		uc001rfm.4	Q8NFW8	OTTHUMG00000169097	ENST00000229329.2:c.760T>C	12.37:g.22213832T>C	ENSP00000229329:p.Trp254Arg	Somatic		Capture	Illumina HiSeq	Phase_I	22105099	NM_018686	Q96AX5|Q9NQZ0	Missense_Mutation	SNP	ENST00000229329.2	37	CCDS8696.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.958915	0.74016	.	.	ENSG00000111726	ENST00000229329;ENST00000538498	.	.	.	5.84	4.69	0.59074	.	0.000000	0.85682	D	0.000000	D	0.84566	0.5500	M	0.92367	3.3	0.50313	D	0.999867	D	0.89917	1.0	D	0.87578	0.998	D	0.87839	0.2650	9	0.87932	D	0	-3.1709	12.1633	0.54115	0.0:0.0681:0.0:0.9319	.	254	Q8NFW8	NEUA_HUMAN	R	254;95	.	ENSP00000229329:W254R	W	+	1	0	CMAS	22105099	1.000000	0.71417	0.979000	0.43373	0.990000	0.78478	5.113000	0.64640	2.238000	0.73509	0.482000	0.46254	TGG		0.308	CMAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402235.1	NM_018686	
KRAS	3845	broad.mit.edu	37	12	25380277	25380278	+	Missense_Mutation	DNP	GA	GA	TT	rs121913238|rs397517037		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	GA	GA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:25380277_25380278GA>TT	ENST00000256078.4	-	3	243_244	c.180_181TC>AA	c.(178-183)ggTCaa>ggAAaa	p.Q61K	KRAS_ENST00000311936.3_Missense_Mutation_p.Q61K|KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	61			Q -> H (in lung carcinoma; dbSNP:rs17851045). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16533793, ECO:0000269|Ref.7}.|Q -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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.Q61K(32)|p.Q61E(10)|p.G60G(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)			TACTCCTCTTGACCTGCTGTGT	0.411	Q61K(CALU6_LUNG)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											.	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,thyroid,NS,Substitution - Missense,+1 	.	43	Substitution - Missense(42)|Substitution - coding silent(1)	large_intestine(13)|lung(11)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(3)|urinary_tract(3)|prostate(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)|kidney(1)|pancreas(1)	c.180_181AA	12						.																																			25271545	SO:0001583	missense	3845	exon3	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.180_181delinsTT	12.37:g.25380277_25380278delinsTT	ENSP00000256078:p.Gln61Lys	Somatic		Capture	Illumina HiSeq	Phase_I	25271544	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	DNP	ENST00000256078.4	37	CCDS8703.1																																																																																				0.411	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
PPFIBP1	8496	broad.mit.edu	37	12	27826713	27826713	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:27826713C>T	ENST00000318304.8	+	16	1667	c.1384C>T	c.(1384-1386)Cag>Tag	p.Q462*	PPFIBP1_ENST00000542629.1_Nonsense_Mutation_p.Q431*|PPFIBP1_ENST00000228425.6_Nonsense_Mutation_p.Q445*|PPFIBP1_ENST00000537927.1_Nonsense_Mutation_p.Q309*	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	462					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)		p.Q445*(1)|p.Q462*(1)	PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					TTCAAGTCTGCAGAAGTCCAG	0.353																																					p.Q309X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C925T	12						.						65.0	69.0	67.0					12																	27826713		2203	4300	6503	27717980	SO:0001587	stop_gained	8496	exon14			AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.1384C>T	12.37:g.27826713C>T	ENSP00000314724:p.Gln462*	Somatic		Capture	Illumina HiSeq	Phase_I	27717980	NM_001198915	O75336|Q86X70|Q9NY03|Q9ULJ0	Nonsense_Mutation	SNP	ENST00000318304.8	37	CCDS55812.1	.	.	.	.	.	.	.	.	.	.	C	39	7.793945	0.98492	.	.	ENSG00000110841	ENST00000540114;ENST00000537927;ENST00000318304;ENST00000542629;ENST00000228425;ENST00000537261	.	.	.	5.81	5.81	0.92471	.	0.000000	0.32753	U	0.005684	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-11.5984	12.9565	0.58430	0.0:0.9257:0.0:0.0743	.	.	.	.	X	293;309;462;431;445;147	.	ENSP00000228425:Q445X	Q	+	1	0	PPFIBP1	27717980	1.000000	0.71417	0.982000	0.44146	0.919000	0.55068	5.011000	0.64011	2.736000	0.93811	0.655000	0.94253	CAG		0.353	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	
FGD4	121512	broad.mit.edu	37	12	32735176	32735176	+	Silent	SNP	G	G	A	rs374075663		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:32735176G>A	ENST00000427716.2	+	4	799	c.375G>A	c.(373-375)acG>acA	p.T125T	FGD4_ENST00000266482.3_5'UTR|FGD4_ENST00000546442.1_Silent_p.T32T|FGD4_ENST00000525053.1_Silent_p.T237T|FGD4_ENST00000472289.1_Silent_p.T125T|FGD4_ENST00000534526.2_Silent_p.T262T|FGD4_ENST00000531134.1_Silent_p.T210T	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	125	Actin filament-binding. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.T125T(1)		breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					TGCTTGATACGCACATAGTGA	0.468																																					p.T125T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G375A	12						.	G		0,4406		0,0,2203	146.0	123.0	131.0		375	-9.8	0.0	12		131	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FGD4	NM_139241.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		125/767	32735176	1,13005	2203	4300	6503	32626443	SO:0001819	synonymous_variant	121512	exon4			AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19125	protein-coding gene	gene with protein product		611104	"""FGD1 family, member 4"""			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.375G>A	12.37:g.32735176G>A		Somatic		Capture	Illumina HiSeq	Phase_I	32626443	NM_139241	Q6ULS2|Q8TCP6	Silent	SNP	ENST00000427716.2	37	CCDS8727.1																																																																																				0.468	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241	
PKP2	5318	broad.mit.edu	37	12	32955384	32955384	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:32955384G>A	ENST00000070846.6	-	11	2276	c.2252C>T	c.(2251-2253)tCg>tTg	p.S751L	PKP2_ENST00000340811.4_Missense_Mutation_p.S707L	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	751					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)	p.S751L(1)		NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					CCTCAGCAGCGAGATGGCTGT	0.463																																					p.S751L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2252T	12						.						170.0	162.0	165.0					12																	32955384		2203	4300	6503	32846651	SO:0001583	missense	5318	exon11			X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.2252C>T	12.37:g.32955384G>A	ENSP00000070846:p.Ser751Leu	Somatic		Capture	Illumina HiSeq	Phase_I	32846651	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730371	0.48939	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.48836	0.8;0.8	4.65	3.75	0.43078	Armadillo-like helical (1);Armadillo-type fold (1);	0.301306	0.33023	N	0.005375	T	0.67277	0.2876	M	0.78801	2.425	0.52501	D	0.999955	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.981;0.983	T	0.71490	-0.4577	10	0.87932	D	0	-14.3947	12.4174	0.55502	0.0831:0.0:0.9169:0.0	.	707;707;751	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	L	707;751;751	ENSP00000342800:S707L;ENSP00000070846:S751L	ENSP00000070846:S751L	S	-	2	0	PKP2	32846651	1.000000	0.71417	0.271000	0.24616	0.075000	0.17131	4.792000	0.62467	1.073000	0.40885	0.643000	0.83706	TCG		0.463	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572	
ALG10B	144245	broad.mit.edu	37	12	38714399	38714399	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:38714399T>C	ENST00000308742.4	+	3	1122	c.806T>C	c.(805-807)gTa>gCa	p.V269A	ALG10B_ENST00000551464.1_Intron|AC117372.1_ENST00000401168.2_RNA	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	269					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)	p.V269A(1)		breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				GCTTTTGTAGTAGTTAATGGT	0.353																																					p.V269A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T806C	12						.						179.0	184.0	182.0					12																	38714399		2203	4297	6500	37000666	SO:0001583	missense	144245	exon3			AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"""potassium channel regulator 1"", ""dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"""		"""asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"""				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.806T>C	12.37:g.38714399T>C	ENSP00000310120:p.Val269Ala	Somatic		Capture	Illumina HiSeq	Phase_I	37000666	NM_001013620	B2RPF4	Missense_Mutation	SNP	ENST00000308742.4	37	CCDS31772.1	.	.	.	.	.	.	.	.	.	.	t	4.349	0.064305	0.08388	.	.	ENSG00000175548	ENST00000308742	T	0.57107	0.42	3.23	-1.9	0.07665	.	0.566837	0.19233	N	0.119358	T	0.29093	0.0723	N	0.20530	0.585	0.09310	N	0.999996	B	0.09022	0.002	B	0.13407	0.009	T	0.26677	-1.0096	10	0.10377	T	0.69	.	9.6735	0.40026	0.0:0.6492:0.0:0.3508	.	269	Q5I7T1	AG10B_HUMAN	A	269	ENSP00000310120:V269A	ENSP00000310120:V269A	V	+	2	0	ALG10B	37000666	0.029000	0.19370	0.000000	0.03702	0.638000	0.38207	0.753000	0.26376	-0.399000	0.07668	0.523000	0.50628	GTA		0.353	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620	
CNTN1	1272	broad.mit.edu	37	12	41337804	41337804	+	Silent	SNP	G	G	A	rs148905523	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:41337804G>A	ENST00000551295.2	+	14	1632	c.1515G>A	c.(1513-1515)acG>acA	p.T505T	CNTN1_ENST00000348761.2_Silent_p.T494T|CNTN1_ENST00000360099.3_Silent_p.T505T|CNTN1_ENST00000547702.1_Silent_p.T505T|CNTN1_ENST00000347616.1_Silent_p.T505T|CNTN1_ENST00000547849.1_Silent_p.T505T	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	505	Ig-like C2-type 6.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.T505T(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TAGATCCTACGCGAATTATAT	0.338													G|||	4	0.000798722	0.0	0.0	5008	,	,		16171	0.004		0.0	False		,,,				2504	0.0				p.T494T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1482A	12						.						88.0	77.0	81.0					12																	41337804		2203	4299	6502	39624071	SO:0001819	synonymous_variant	1272	exon13			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"", ""Endogenous ligands"""	2171	protein-coding gene	gene with protein product	"""glycoprotein gP135"""	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.1515G>A	12.37:g.41337804G>A		Somatic		Capture	Illumina HiSeq	Phase_I	39624071	NM_175038	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Silent	SNP	ENST00000551295.2	37	CCDS8737.1																																																																																				0.338	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843	
PDZRN4	29951	broad.mit.edu	37	12	41967550	41967550	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:41967550T>G	ENST00000402685.2	+	10	2977	c.2969T>G	c.(2968-2970)cTg>cGg	p.L990R	PDZRN4_ENST00000539469.2_Missense_Mutation_p.L732R|PDZRN4_ENST00000298919.7_Missense_Mutation_p.L730R	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	990							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L990R(1)|p.L732R(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				ATCATTGAACTGAGTCACAAA	0.478																																					p.L990R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T2969G	12						.						52.0	49.0	50.0					12																	41967550		2203	4300	6503	40253817	SO:0001583	missense	29951	exon10			AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2969T>G	12.37:g.41967550T>G	ENSP00000384197:p.Leu990Arg	Somatic		Capture	Illumina HiSeq	Phase_I	40253817	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	37	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.530305	0.64860	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.79352	-1.26;-1.26;-1.26	4.9	4.9	0.64082	.	0.218604	0.31624	N	0.007335	D	0.88164	0.6363	M	0.82056	2.57	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.972;0.998;0.998	D	0.89976	0.4097	10	0.87932	D	0	-20.226	15.2422	0.73480	0.0:0.0:0.0:1.0	.	990;730;732	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	R	990;732;730	ENSP00000384197:L990R;ENSP00000439990:L732R;ENSP00000298919:L730R	ENSP00000298919:L730R	L	+	2	0	PDZRN4	40253817	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.997000	0.88414	2.145000	0.66743	0.455000	0.32223	CTG		0.478	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
GXYLT1	283464	broad.mit.edu	37	12	42491370	42491370	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:42491370A>G	ENST00000398675.3	-	7	1267	c.1035T>C	c.(1033-1035)caT>caC	p.H345H	GXYLT1_ENST00000280876.6_Silent_p.H314H	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	345					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)	p.H345H(1)|p.H314H(1)		kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						CATATATACAATGATCTGGTC	0.373																																					p.H345H												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1035C	12						.						136.0	130.0	132.0					12																	42491370		1851	4100	5951	40777637	SO:0001819	synonymous_variant	283464	exon7			BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"""Glycosyltransferase family 8 domain containing"""	27482	protein-coding gene	gene with protein product		613321	"""glycosyltransferase 8 domain containing 3"""	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.1035T>C	12.37:g.42491370A>G		Somatic		Capture	Illumina HiSeq	Phase_I	40777637	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Silent	SNP	ENST00000398675.3	37	CCDS41772.1																																																																																				0.373	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597	
NELL2	4753	broad.mit.edu	37	12	45059271	45059271	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:45059271A>G	ENST00000429094.2	-	13	1944	c.1440T>C	c.(1438-1440)tgT>tgC	p.C480C	NELL2_ENST00000333837.4_Silent_p.C503C|NELL2_ENST00000437801.2_Silent_p.C530C|NELL2_ENST00000551601.1_Silent_p.C479C|NELL2_ENST00000549027.1_Silent_p.C479C|NELL2_ENST00000395487.2_Silent_p.C479C|NELL2_ENST00000452445.2_Silent_p.C480C	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	480	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.C480C(1)|p.C530C(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		GTTTACCTGTACATGAATAAT	0.323																																					p.C480C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1440C	12						.						61.0	58.0	59.0					12																	45059271		2203	4300	6503	43345538	SO:0001819	synonymous_variant	4753	exon13			D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"""nel (chicken)-like 2"""			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.1440T>C	12.37:g.45059271A>G		Somatic		Capture	Illumina HiSeq	Phase_I	43345538	NM_001145108	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000429094.2	37	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	A	9.744	1.165760	0.21538	.	.	ENSG00000184613	ENST00000550313	.	.	.	5.28	2.74	0.32292	.	.	.	.	.	T	0.57740	0.2074	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52275	-0.8597	4	.	.	.	-9.5453	8.3452	0.32268	0.7637:0.0:0.2363:0.0	.	.	.	.	A	224	.	.	V	-	2	0	NELL2	43345538	0.997000	0.39634	1.000000	0.80357	0.976000	0.68499	0.541000	0.23207	0.762000	0.33152	0.528000	0.53228	GTA		0.323	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159	
ARID2	196528	broad.mit.edu	37	12	46230676	46230676	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:46230676A>G	ENST00000334344.6	+	8	1097	c.925A>G	c.(925-927)Aat>Gat	p.N309D	ARID2_ENST00000444670.1_5'Flank|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Missense_Mutation_p.N160D	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	309					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N309D(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CTTGGCAGCTAATCGTACCTG	0.408			"""N, S, F"""		hepatocellular carcinoma																																p.N309D			Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A925G	12						.						188.0	176.0	180.0					12																	46230676		2203	4300	6503	44516943	SO:0001583	missense	196528	exon8				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.925A>G	12.37:g.46230676A>G	ENSP00000335044:p.Asn309Asp	Somatic		Capture	Illumina HiSeq	Phase_I	44516943	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.260786	0.80246	.	.	ENSG00000189079	ENST00000334344;ENST00000422737	T;T	0.44881	0.91;0.91	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.63593	0.2524	M	0.65975	2.015	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.66400	-0.5933	10	0.72032	D	0.01	-13.958	16.2628	0.82557	1.0:0.0:0.0:0.0	.	309	Q68CP9	ARID2_HUMAN	D	309;160	ENSP00000335044:N309D;ENSP00000415650:N160D	ENSP00000335044:N309D	N	+	1	0	ARID2	44516943	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.265000	0.78442	2.233000	0.73108	0.482000	0.46254	AAT		0.408	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	
SLC38A2	54407	broad.mit.edu	37	12	46754963	46754963	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:46754963C>T	ENST00000256689.5	-	16	1896	c.1452G>A	c.(1450-1452)ctG>ctA	p.L484L	SLC38A2_ENST00000551374.1_Silent_p.L322L	NM_018976.4	NP_061849.2	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	484					amino acid transport (GO:0006865)|glutamate secretion (GO:0014047)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|sodium ion transport (GO:0006814)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)	p.L484L(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	18	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		CGGTCATCACCAGTACACCAC	0.398																																					p.L484L	Ovarian(9;448 492 8335 28722 40361)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1452A	12						.						93.0	80.0	85.0					12																	46754963		2203	4299	6502	45041230	SO:0001819	synonymous_variant	54407	exon16			AB037803	CCDS8749.1	12q13.11	2014-08-12			ENSG00000134294	ENSG00000134294		"""Solute carriers"""	13448	protein-coding gene	gene with protein product		605180				10747860, 17237199	Standard	NM_018976		Approved	SAT2, ATA2, KIAA1382, SNAT2	uc001rpg.3	Q96QD8	OTTHUMG00000169471	ENST00000256689.5:c.1452G>A	12.37:g.46754963C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45041230	NM_018976	Q6IA88|Q6ZMG2|Q9HAV3|Q9NVA8|Q9P2G5	Silent	SNP	ENST00000256689.5	37	CCDS8749.1																																																																																				0.398	SLC38A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404226.1		
PCED1B	91523	broad.mit.edu	37	12	47471241	47471241	+	5'Flank	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:47471241G>A	ENST00000546455.1	+	0	0				AMIGO2_ENST00000429635.1_Silent_p.D515D|AMIGO2_ENST00000266581.4_Silent_p.D515D|AMIGO2_ENST00000550413.1_Silent_p.D515D|AMIGO2_ENST00000321382.3_Silent_p.D515D			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B								hydrolase activity (GO:0016787)	p.D515D(1)									CAAAAGGTGTGTCAGAAAACA	0.408																																					p.D515D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1545T	12						.						65.0	63.0	64.0					12																	47471241		2203	4300	6503	45757508	SO:0001631	upstream_gene_variant	347902	exon2			BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"""family with sequence similarity 113, member B"""	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617		12.37:g.47471241G>A	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	45757508	NM_181847	Q96B20	Silent	SNP	ENST00000546455.1	37	CCDS8752.1																																																																																				0.408	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
PCED1B	91523	broad.mit.edu	37	12	47629954	47629954	+	Nonsense_Mutation	SNP	G	G	T	rs267603480		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:47629954G>T	ENST00000546455.1	+	4	1839	c.1108G>T	c.(1108-1110)Gaa>Taa	p.E370*	PCED1B_ENST00000432328.1_Nonsense_Mutation_p.E370*|RP11-493L12.3_ENST00000547748.1_RNA			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	370	Pro-rich.						hydrolase activity (GO:0016787)	p.E370*(1)									TTTCTTCGTCGAAGACAATTT	0.517																																					p.E370X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1108T	12						.						154.0	150.0	152.0					12																	47629954		2203	4300	6503	45916221	SO:0001587	stop_gained	91523	exon2			BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"""family with sequence similarity 113, member B"""	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.1108G>T	12.37:g.47629954G>T	ENSP00000446688:p.Glu370*	Somatic		Capture	Illumina HiSeq	Phase_I	45916221	NM_138371	Q96B20	Nonsense_Mutation	SNP	ENST00000546455.1	37	CCDS8752.1	.	.	.	.	.	.	.	.	.	.	G	34	5.309838	0.95629	.	.	ENSG00000179715	ENST00000546455;ENST00000432328	.	.	.	4.04	0.0106	0.14083	.	0.794299	0.10735	N	0.640108	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	-5.5517	15.5827	0.76459	0.0:0.5361:0.4639:0.0	.	.	.	.	X	370	.	ENSP00000396040:E370X	E	+	1	0	FAM113B	45916221	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.205000	0.17356	-0.213000	0.10094	-2.241000	0.00287	GAA		0.517	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
RPAP3	79657	broad.mit.edu	37	12	48073292	48073292	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:48073292G>A	ENST00000005386.3	-	12	1386	c.1271C>T	c.(1270-1272)cCg>cTg	p.P424L	RPAP3_ENST00000380650.4_Intron|RPAP3_ENST00000432584.3_Missense_Mutation_p.P265L	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3	424								p.P424L(1)		endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Lung SC(27;0.192)					TCCAGGATGCGGTGGATTATC	0.323																																					p.P265L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C794T	12						.						100.0	91.0	94.0					12																	48073292		2203	4300	6503	46359559	SO:0001583	missense	79657	exon11			AK025561	CCDS8753.1, CCDS53782.1, CCDS53783.1	12q13.11	2013-01-10				ENSG00000005175		"""Tetratricopeptide (TTC) repeat domain containing"""	26151	protein-coding gene	gene with protein product		611477				17643375	Standard	NM_024604		Approved	FLJ21908, spag	uc001rpr.3	Q9H6T3	OTTHUMG00000169668	ENST00000005386.3:c.1271C>T	12.37:g.48073292G>A	ENSP00000005386:p.Pro424Leu	Somatic		Capture	Illumina HiSeq	Phase_I	46359559	NM_001146076	B4DRW9|Q6PHR5	Missense_Mutation	SNP	ENST00000005386.3	37	CCDS8753.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.616553	0.00828	.	.	ENSG00000005175	ENST00000005386;ENST00000432584	T;T	0.14893	2.95;2.47	5.15	2.29	0.28610	.	2.528170	0.01367	N	0.012425	T	0.14614	0.0353	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.21655	-1.0239	10	0.22109	T	0.4	.	4.6233	0.12465	0.2342:0.0:0.5954:0.1704	.	424	Q9H6T3	RPAP3_HUMAN	L	424;265	ENSP00000005386:P424L;ENSP00000401823:P265L	ENSP00000005386:P424L	P	-	2	0	RPAP3	46359559	0.627000	0.27129	0.001000	0.08648	0.081000	0.17604	0.895000	0.28363	0.696000	0.31696	-0.784000	0.03344	CCG		0.323	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	NM_024604	
ENDOU	8909	broad.mit.edu	37	12	48119148	48119148	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:48119148A>T	ENST00000422538.3	-	1	171	c.49T>A	c.(49-51)Tgg>Agg	p.W17R	ENDOU_ENST00000229003.3_Missense_Mutation_p.W17R|RP1-197B17.3_ENST00000547799.1_lincRNA|ENDOU_ENST00000545824.2_Missense_Mutation_p.W17R	NM_001172439.1	NP_001165910.1	P21128	ENDOU_HUMAN	endonuclease, polyU-specific	17					female pregnancy (GO:0007565)|immune response (GO:0006955)|proteolysis (GO:0006508)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endoribonuclease activity (GO:0004521)|growth factor activity (GO:0008083)|manganese ion binding (GO:0030145)|polysaccharide binding (GO:0030247)|RNA binding (GO:0003723)|scavenger receptor activity (GO:0005044)|serine-type peptidase activity (GO:0008236)	p.W17R(1)		autonomic_ganglia(1)|endometrium(2)|large_intestine(4)|lung(2)|ovary(3)|pancreas(1)|stomach(1)	14						TTACCAGCCCAGGCCAGGCCA	0.587																																					p.W17R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T49A	12						.						89.0	79.0	82.0					12																	48119148		2203	4300	6503	46405415	SO:0001583	missense	8909	exon1			M32402	CCDS8754.1, CCDS53784.1, CCDS53785.1	12q13.1	2011-08-31			ENSG00000111405	ENSG00000111405		"""Serine peptidases / Serine peptidases"""	14369	protein-coding gene	gene with protein product		606720				2350438, 1710108, 15755742, 18936097	Standard	NM_006025		Approved	PP11, P11, PRSS26	uc001rpu.2	P21128	OTTHUMG00000169670	ENST00000422538.3:c.49T>A	12.37:g.48119148A>T	ENSP00000397679:p.Trp17Arg	Somatic		Capture	Illumina HiSeq	Phase_I	46405415	NM_001172439	B2RBJ3|B3KQS7|B7Z6E1|Q2NKJ4	Missense_Mutation	SNP	ENST00000422538.3	37	CCDS53785.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.749270	0.69533	.	.	ENSG00000111405	ENST00000229003;ENST00000422538;ENST00000545824	T;T	0.50277	0.75;1.58	6.17	6.17	0.99709	.	0.478277	0.20888	N	0.083874	T	0.60792	0.2296	L	0.51422	1.61	0.80722	D	1	D;D;D	0.60575	0.978;0.987;0.988	P;P;D	0.63192	0.714;0.735;0.912	T	0.62358	-0.6871	10	0.72032	D	0.01	-7.911	13.214	0.59844	1.0:0.0:0.0:0.0	.	17;17;17	P21128-3;P21128;P21128-2	.;ENDOU_HUMAN;.	R	17	ENSP00000229003:W17R;ENSP00000397679:W17R	ENSP00000229003:W17R	W	-	1	0	ENDOU	46405415	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	4.187000	0.58344	2.371000	0.80710	0.533000	0.62120	TGG		0.587	ENDOU-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000405352.1	NM_006025.2	
OR8S1	341568	broad.mit.edu	37	12	48919888	48919888	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:48919888C>A	ENST00000310194.1	+	1	474	c.474C>A	c.(472-474)atC>atA	p.I158I	OR8S1_ENST00000551654.1_Intron	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	158						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I158I(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|skin(4)	22						ACGCACTCATCAATGTCCTCC	0.498																																					p.I158I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C474A	12						.						178.0	162.0	167.0					12																	48919888		2203	4300	6503	47206155	SO:0001819	synonymous_variant	341568	exon1				CCDS31789.1	12q13.2	2012-08-09				ENSG00000197376		"""GPCR / Class A : Olfactory receptors"""	19628	protein-coding gene	gene with protein product							Standard	NM_001005203		Approved		uc010slu.2	Q8NH09		ENST00000310194.1:c.474C>A	12.37:g.48919888C>A		Somatic		Capture	Illumina HiSeq	Phase_I	47206155	NM_001005203		Silent	SNP	ENST00000310194.1	37	CCDS31789.1																																																																																				0.498	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406881.1		
RND1	27289	broad.mit.edu	37	12	49254798	49254798	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:49254798C>T	ENST00000309739.5	-	4	565	c.435G>A	c.(433-435)gcG>gcA	p.A145A		NM_014470.3	NP_055285.1	Q92730	RND1_HUMAN	Rho family GTPase 1	145					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|GTP catabolic process (GO:0006184)|negative regulation of cell adhesion (GO:0007162)|neuron remodeling (GO:0016322)|small GTPase mediated signal transduction (GO:0007264)	adherens junction (GO:0005912)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|receptor binding (GO:0005102)	p.A145A(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(2)|skin(1)|urinary_tract(1)	10						AGGAGATGGGCGCCTGCTTCT	0.552																																					p.A145A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G435A	12						.						103.0	95.0	98.0					12																	49254798		2203	4300	6503	47541065	SO:0001819	synonymous_variant	27289	exon4			Y07923	CCDS8771.1	12q12	2008-01-23				ENSG00000172602			18314	protein-coding gene	gene with protein product	"""ras homolog gene family, member S"""	609038				9531558	Standard	NM_014470		Approved	Rho6, ARHS, RHOS	uc001rsn.3	Q92730	OTTHUMG00000170400	ENST00000309739.5:c.435G>A	12.37:g.49254798C>T		Somatic		Capture	Illumina HiSeq	Phase_I	47541065	NM_014470	A8K9P7	Silent	SNP	ENST00000309739.5	37	CCDS8771.1																																																																																				0.552	RND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408915.1	NM_014470	
KMT2D	8085	broad.mit.edu	37	12	49435048	49435048	+	Missense_Mutation	SNP	C	C	T	rs369501280		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:49435048C>T	ENST00000301067.7	-	31	6504	c.6505G>A	c.(6505-6507)Gcc>Acc	p.A2169T		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2169	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.A1899T(1)|p.A2169T(1)									GGCACTTGGGCGGGCACCTGG	0.692																																					p.A2169T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G6505A	12						.						6.0	9.0	8.0					12																	49435048		1848	3971	5819	47721315	SO:0001583	missense	8085	exon31			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.6505G>A	12.37:g.49435048C>T	ENSP00000301067:p.Ala2169Thr	Somatic		Capture	Illumina HiSeq	Phase_I	47721315	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.377779	0.24944	.	.	ENSG00000167548	ENST00000301067	T	0.81078	-1.45	4.09	4.09	0.47781	.	0.000000	0.32769	N	0.005666	T	0.62551	0.2437	N	0.08118	0	0.25682	N	0.985789	B	0.30439	0.279	B	0.20577	0.03	T	0.63175	-0.6696	10	0.87932	D	0	.	14.0517	0.64742	0.0:1.0:0.0:0.0	.	2169	O14686	MLL2_HUMAN	T	2169	ENSP00000301067:A2169T	ENSP00000301067:A2169T	A	-	1	0	MLL2	47721315	0.999000	0.42202	1.000000	0.80357	0.990000	0.78478	1.747000	0.38298	2.210000	0.71456	0.561000	0.74099	GCC		0.692	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
KMT2D	8085	broad.mit.edu	37	12	49439940	49439940	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:49439940C>T	ENST00000301067.7	-	17	4600	c.4601G>A	c.(4600-4602)tGt>tAt	p.C1534Y		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1534					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.C1261Y(1)|p.C1534Y(1)									GAGGCTCTCACAGCCTGCATG	0.557																																					p.C1534Y												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4601A	12						.						43.0	49.0	47.0					12																	49439940		2118	4238	6356	47726207	SO:0001583	missense	8085	exon17			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.4601G>A	12.37:g.49439940C>T	ENSP00000301067:p.Cys1534Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	47726207	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.395162	0.42512	.	.	ENSG00000167548	ENST00000301067	D	0.86297	-2.1	5.28	5.28	0.74379	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.41605	D	0.000847	D	0.94165	0.8128	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94923	0.8075	10	0.87932	D	0	.	17.6914	0.88269	0.0:1.0:0.0:0.0	.	1534	O14686	MLL2_HUMAN	Y	1534	ENSP00000301067:C1534Y	ENSP00000301067:C1534Y	C	-	2	0	MLL2	47726207	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.818000	0.86416	2.470000	0.83445	0.655000	0.94253	TGT		0.557	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
KMT2D	8085	broad.mit.edu	37	12	49443937	49443937	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:49443937G>T	ENST00000301067.7	-	11	3433	c.3434C>A	c.(3433-3435)gCt>gAt	p.A1145D		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1145	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.A872D(1)|p.A1145D(1)									AAGTTCACTAGCCAAACTGCC	0.607																																					p.A1145D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3434A	12						.						29.0	32.0	31.0					12																	49443937		1910	4107	6017	47730204	SO:0001583	missense	8085	exon11			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.3434C>A	12.37:g.49443937G>T	ENSP00000301067:p.Ala1145Asp	Somatic		Capture	Illumina HiSeq	Phase_I	47730204	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	9.009	0.981968	0.18812	.	.	ENSG00000167548	ENST00000301067	D	0.81579	-1.51	4.99	4.04	0.47022	.	0.267871	0.20001	N	0.101323	T	0.66684	0.2814	N	0.08118	0	0.20196	N	0.999927	P	0.40476	0.718	B	0.39299	0.296	T	0.66650	-0.5870	10	0.87932	D	0	.	15.9757	0.80063	0.0:0.1474:0.8526:0.0	.	1145	O14686	MLL2_HUMAN	D	1145	ENSP00000301067:A1145D	ENSP00000301067:A1145D	A	-	2	0	MLL2	47730204	0.820000	0.29190	0.936000	0.37596	0.861000	0.49209	1.141000	0.31528	2.310000	0.77875	0.563000	0.77884	GCT		0.607	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
RHEBL1	121268	broad.mit.edu	37	12	49458905	49458905	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:49458905C>T	ENST00000301068.6	-	8	772	c.533G>A	c.(532-534)cGt>cAt	p.R178H		NM_144593.1	NP_653194.1	Q8TAI7	REBL1_HUMAN	Ras homolog enriched in brain like 1	178					GTP catabolic process (GO:0006184)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|small GTPase mediated signal transduction (GO:0007264)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.R178H(1)		breast(2)|large_intestine(2)|lung(5)	9						ATGGCAGCGACGCTCTTGCCC	0.552																																					p.R178H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G533A	12						.						103.0	85.0	91.0					12																	49458905		2203	4300	6503	47745172	SO:0001583	missense	121268	exon8			AK098663	CCDS8778.1	12q13.12	2014-05-09				ENSG00000167550			21166	protein-coding gene	gene with protein product						12477932	Standard	NM_144593		Approved	MGC34869, FLJ25797	uc001rtc.1	Q8TAI7	OTTHUMG00000170407	ENST00000301068.6:c.533G>A	12.37:g.49458905C>T	ENSP00000301068:p.Arg178His	Somatic		Capture	Illumina HiSeq	Phase_I	47745172	NM_144593	Q56VH8	Missense_Mutation	SNP	ENST00000301068.6	37	CCDS8778.1	.	.	.	.	.	.	.	.	.	.	C	10.84	1.463924	0.26335	.	.	ENSG00000167550	ENST00000301068	T	0.69435	-0.4	5.5	0.351	0.16042	.	0.202696	0.41396	N	0.000887	T	0.47563	0.1452	L	0.33485	1.01	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.31336	-0.9947	10	0.48119	T	0.1	.	4.3258	0.11039	0.2754:0.5099:0.0:0.2147	.	178	Q8TAI7	REBL1_HUMAN	H	178	ENSP00000301068:R178H	ENSP00000301068:R178H	R	-	2	0	RHEBL1	47745172	0.292000	0.24362	0.068000	0.19968	0.575000	0.36095	0.764000	0.26532	-0.126000	0.11682	-0.181000	0.13052	CGT		0.552	RHEBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408969.1	NM_144593	
KCNH3	23416	broad.mit.edu	37	12	49951334	49951334	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:49951334G>A	ENST00000257981.6	+	15	3110	c.2850G>A	c.(2848-2850)caG>caA	p.Q950Q	MCRS1_ENST00000547182.1_5'Flank	NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	950					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.Q950Q(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						ACTGCCTGCAGCCCCCAGCTG	0.701																																					p.Q950Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2850A	12						.						53.0	51.0	52.0					12																	49951334		2203	4300	6503	48237601	SO:0001819	synonymous_variant	23416	exon15			AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.2850G>A	12.37:g.49951334G>A		Somatic		Capture	Illumina HiSeq	Phase_I	48237601	NM_012284	Q9UQ06	Silent	SNP	ENST00000257981.6	37	CCDS8786.1																																																																																				0.701	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284	
SMARCD1	6602	broad.mit.edu	37	12	50484178	50484178	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:50484178T>C	ENST00000394963.4	+	8	1426	c.1028T>C	c.(1027-1029)cTg>cCg	p.L343P	SMARCD1_ENST00000548573.1_Missense_Mutation_p.L141P|SMARCD1_ENST00000381513.4_Missense_Mutation_p.L343P	NM_003076.4	NP_003067.3			SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1									p.L304P(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	18						GACAAGTACCTGCAGCAGGTA	0.463																																					p.L343P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1028C	12						.						130.0	120.0	123.0					12																	50484178		2203	4300	6503	48770445	SO:0001583	missense	6602	exon8			U66617	CCDS8797.2, CCDS8798.2	12q13-q14	2008-08-05			ENSG00000066117	ENSG00000066117			11106	protein-coding gene	gene with protein product		601735				8804307, 9693044, 12917342	Standard	NM_003076		Approved	BAF60A, Rsc6p, CRACD1	uc001rvx.4	Q96GM5	OTTHUMG00000150194	ENST00000394963.4:c.1028T>C	12.37:g.50484178T>C	ENSP00000378414:p.Leu343Pro	Somatic		Capture	Illumina HiSeq	Phase_I	48770445	NM_139071		Missense_Mutation	SNP	ENST00000394963.4	37	CCDS8797.2	.	.	.	.	.	.	.	.	.	.	T	21.1	4.103621	0.76983	.	.	ENSG00000066117	ENST00000394963;ENST00000381513;ENST00000550477;ENST00000542914;ENST00000548573	T;T	0.73575	-0.76;-0.76	5.17	5.17	0.71159	SWIB domain (1);SWIB/MDM2 domain (2);	0.131248	0.52532	D	0.000063	D	0.89389	0.6701	M	0.93898	3.47	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.986;0.986;0.994	D	0.92136	0.5716	10	0.87932	D	0	-11.1439	15.4976	0.75666	0.0:0.0:0.0:1.0	.	141;343;343	F8VRQ4;Q96GM5-2;Q96GM5	.;.;SMRD1_HUMAN	P	343;343;263;119;141	ENSP00000378414:L343P;ENSP00000370924:L343P	ENSP00000370924:L343P	L	+	2	0	SMARCD1	48770445	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.819000	0.86621	2.308000	0.77769	0.533000	0.62120	CTG		0.463	SMARCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316759.2	NM_003076	
LIMA1	51474	broad.mit.edu	37	12	50571361	50571361	+	Missense_Mutation	SNP	C	C	T	rs564473856		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:50571361C>T	ENST00000341247.4	-	11	1915	c.1766G>A	c.(1765-1767)cGc>cAc	p.R589H	LIMA1_ENST00000394943.3_Missense_Mutation_p.R590H|LIMA1_ENST00000552909.1_Missense_Mutation_p.R428H|LIMA1_ENST00000552491.1_Missense_Mutation_p.R286H|LIMA1_ENST00000547825.1_Missense_Mutation_p.R287H|LIMA1_ENST00000552783.1_Missense_Mutation_p.R430H|LIMA1_ENST00000552823.1_Missense_Mutation_p.R429H	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	589					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)	p.R589H(1)		NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						AGTGAATGGGCGGCTTCTTTC	0.493																																					p.R590H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1769A	12						.						136.0	139.0	138.0					12																	50571361		2203	4300	6503	48857628	SO:0001583	missense	51474	exon11			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.1766G>A	12.37:g.50571361C>T	ENSP00000340184:p.Arg589His	Somatic		Capture	Illumina HiSeq	Phase_I	48857628	NM_001113546	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.142133	0.77775	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	T;T;D;D;T;D;D	0.86297	-1.33;-1.32;-1.69;-2.1;-1.36;-1.69;-1.69	5.49	4.6	0.57074	.	0.235149	0.43260	D	0.000593	D	0.92280	0.7551	M	0.66939	2.045	0.48762	D	0.999709	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.987;0.998;0.982	D	0.92932	0.6364	10	0.66056	D	0.02	.	14.7104	0.69225	0.0:0.9301:0.0:0.0699	.	599;589;428	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	H	286;287;429;590;589;430;428;508	ENSP00000448463:R286H;ENSP00000448706:R287H;ENSP00000450266:R429H;ENSP00000378400:R590H;ENSP00000340184:R589H;ENSP00000448779:R430H;ENSP00000450087:R428H	ENSP00000340184:R589H	R	-	2	0	LIMA1	48857628	0.997000	0.39634	0.992000	0.48379	0.992000	0.81027	2.875000	0.48491	1.457000	0.47850	0.655000	0.94253	CGC		0.493	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357	
DIP2B	57609	broad.mit.edu	37	12	51108259	51108259	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:51108259G>T	ENST00000301180.5	+	23	2765	c.2731G>T	c.(2731-2733)Gga>Tga	p.G911*		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	911						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.G911*(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						TCCACTAGGAGGAATCCATAT	0.438																																					p.G911X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G2731T	12						.						130.0	119.0	123.0					12																	51108259		2203	4300	6503	49394526	SO:0001587	stop_gained	57609	exon23			AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.2731G>T	12.37:g.51108259G>T	ENSP00000301180:p.Gly911*	Somatic		Capture	Illumina HiSeq	Phase_I	49394526	NM_173602	Q6B011|Q8N1L5|Q8NB38	Nonsense_Mutation	SNP	ENST00000301180.5	37	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	G	41	8.618356	0.98888	.	.	ENSG00000066084	ENST00000301180	.	.	.	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-17.4669	18.3337	0.90280	0.0:0.0:1.0:0.0	.	.	.	.	X	911	.	ENSP00000301180:G911X	G	+	1	0	DIP2B	49394526	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.657000	0.98554	2.885000	0.99019	0.655000	0.94253	GGA		0.438	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602	
SLC4A8	9498	broad.mit.edu	37	12	51853879	51853879	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:51853879C>T	ENST00000453097.2	+	8	1217	c.1000C>T	c.(1000-1002)Cca>Tca	p.P334S	SLC4A8_ENST00000514353.3_Missense_Mutation_p.P281S|SLC4A8_ENST00000358657.3_Missense_Mutation_p.P361S|SLC4A8_ENST00000535225.2_Missense_Mutation_p.P281S|SLC4A8_ENST00000394856.1_Missense_Mutation_p.P281S	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8									p.P281S(1)|p.P334S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		AACAGAAGTGCCAATCCCAAC	0.418																																					p.P334S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1000T	12						.						166.0	161.0	163.0					12																	51853879		2203	4300	6503	50140146	SO:0001583	missense	9498	exon8			AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"""Solute carriers"""	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1000C>T	12.37:g.51853879C>T	ENSP00000405812:p.Pro334Ser	Somatic		Capture	Illumina HiSeq	Phase_I	50140146	NM_001039960		Missense_Mutation	SNP	ENST00000453097.2	37	CCDS44890.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.861652	0.91433	.	.	ENSG00000050438	ENST00000535225;ENST00000358657;ENST00000453097;ENST00000394856;ENST00000319957;ENST00000514353;ENST00000547697;ENST00000551071	T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37	5.38	5.38	0.77491	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.000000	0.85682	D	0.000000	D	0.91503	0.7317	M	0.88241	2.94	0.80722	D	1	D;P;D;P;P;P;D	0.89917	1.0;0.889;0.983;0.457;0.826;0.826;0.997	D;P;D;P;D;D;D	0.91635	0.999;0.72;0.935;0.845;0.913;0.959;0.972	D	0.92691	0.6166	10	0.87932	D	0	.	18.2902	0.90127	0.0:1.0:0.0:0.0	.	281;361;281;334;334;334;281	E7EML0;Q2Y0W8-2;F5GZ31;Q2Y0W8;Q2Y0W8-3;Q2Y0W8-6;F8VSA8	.;.;.;S4A8_HUMAN;.;.;.	S	281;361;334;281;334;281;281;281	ENSP00000441520:P281S;ENSP00000351483:P361S;ENSP00000405812:P334S;ENSP00000378325:P281S;ENSP00000442561:P281S	ENSP00000315789:P334S	P	+	1	0	SLC4A8	50140146	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.773000	0.85462	2.704000	0.92352	0.655000	0.94253	CCA		0.418	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858	
KRT83	3889	broad.mit.edu	37	12	52713069	52713069	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:52713069T>C	ENST00000293670.3	-	2	526	c.464A>G	c.(463-465)aAc>aGc	p.N155S		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	155	Linker 1.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.N155S(1)		NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GGGCTCCAGGTTACTCTGGCA	0.622																																					p.N155S	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A464G	12						.						88.0	96.0	93.0					12																	52713069		2203	4300	6503	50999336	SO:0001583	missense	3889	exon2			X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.464A>G	12.37:g.52713069T>C	ENSP00000293670:p.Asn155Ser	Somatic		Capture	Illumina HiSeq	Phase_I	50999336	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Missense_Mutation	SNP	ENST00000293670.3	37	CCDS8823.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420491	0.83559	.	.	ENSG00000170523	ENST00000293670	T	0.75154	-0.91	4.39	4.39	0.52855	Filament (1);	0.000000	0.44285	U	0.000465	D	0.83083	0.5177	M	0.69248	2.105	0.41368	D	0.987471	D	0.59357	0.985	D	0.64687	0.928	D	0.85254	0.1046	10	0.62326	D	0.03	.	13.9276	0.63972	0.0:0.0:0.0:1.0	.	155	P78385	KRT83_HUMAN	S	155	ENSP00000293670:N155S	ENSP00000293670:N155S	N	-	2	0	KRT83	50999336	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.033000	0.49743	1.753000	0.51906	0.460000	0.39030	AAC		0.622	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
KRT83	3889	broad.mit.edu	37	12	52714940	52714940	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:52714940G>A	ENST00000293670.3	-	1	242	c.180C>T	c.(178-180)cgC>cgT	p.R60R		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	60	Head.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R60R(1)		NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		AGGAGCCGGCGCGGAAGCCCC	0.721																																					p.R60R	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C180T	12						.						20.0	26.0	24.0					12																	52714940		2190	4280	6470	51001207	SO:0001819	synonymous_variant	3889	exon1			X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.180C>T	12.37:g.52714940G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51001207	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent	SNP	ENST00000293670.3	37	CCDS8823.1																																																																																				0.721	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
KRT85	3891	broad.mit.edu	37	12	52754795	52754795	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:52754795C>T	ENST00000257901.3	-	9	1441	c.1366G>A	c.(1366-1368)Ggc>Agc	p.G456S	KRT85_ENST00000544265.1_Missense_Mutation_p.G244S	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	456	Tail.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.G456S(1)		NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TAGGAGAGGCCCCCACAGGAG	0.652																																					p.G456S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1366A	12						.						25.0	26.0	26.0					12																	52754795		2202	4299	6501	51041062	SO:0001583	missense	3891	exon9			X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6462	protein-coding gene	gene with protein product	"""hard keratin type II"""	602767	"""keratin, hair, basic, 5"""	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.1366G>A	12.37:g.52754795C>T	ENSP00000257901:p.Gly456Ser	Somatic		Capture	Illumina HiSeq	Phase_I	51041062	NM_002283	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	37	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	C	9.570	1.120745	0.20877	.	.	ENSG00000135443	ENST00000257901;ENST00000544265	D;D	0.83673	-1.75;-1.62	5.01	2.97	0.34412	.	0.298157	0.29205	N	0.012833	T	0.75598	0.3871	L	0.49350	1.555	0.24681	N	0.99336	B	0.06786	0.001	B	0.06405	0.002	T	0.65150	-0.6238	10	0.48119	T	0.1	.	7.5193	0.27618	0.0:0.786:0.0:0.214	.	456	P78386	KRT85_HUMAN	S	456;244	ENSP00000257901:G456S;ENSP00000440240:G244S	ENSP00000257901:G456S	G	-	1	0	KRT85	51041062	0.115000	0.22152	0.958000	0.39756	0.335000	0.28730	1.094000	0.30951	0.563000	0.29222	0.655000	0.94253	GGC		0.652	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283	
KRT84	3890	broad.mit.edu	37	12	52774243	52774243	+	Missense_Mutation	SNP	C	C	A	rs372984157		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:52774243C>A	ENST00000257951.3	-	7	1394	c.1328G>T	c.(1327-1329)cGg>cTg	p.R443L	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	443	Coil 2.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)	p.R443L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GCACAGCTGCCGCGCCATGTC	0.652											OREG0021848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R443L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1328T	12						.						58.0	51.0	54.0					12																	52774243		2203	4300	6503	51060510	SO:0001583	missense	3890	exon7			Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.1328G>T	12.37:g.52774243C>A	ENSP00000257951:p.Arg443Leu	Somatic	987	Capture	Illumina HiSeq	Phase_I	51060510	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	.	.	.	.	.	.	.	.	.	.	C	17.22	3.333559	0.60853	.	.	ENSG00000161849	ENST00000257951	T	0.76839	-1.05	4.94	4.05	0.47172	Filament (1);	0.000000	0.41938	D	0.000791	T	0.77253	0.4103	L	0.61218	1.895	0.41034	D	0.985171	P	0.40794	0.729	B	0.42916	0.402	T	0.79142	-0.1925	10	0.52906	T	0.07	.	13.57	0.61841	0.0:0.9251:0.0:0.0749	.	443	Q9NSB2	KRT84_HUMAN	L	443	ENSP00000257951:R443L	ENSP00000257951:R443L	R	-	2	0	KRT84	51060510	0.980000	0.34600	0.757000	0.31301	0.843000	0.47879	5.911000	0.69939	1.313000	0.45069	0.591000	0.81541	CGG		0.652	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
KRT6B	3854	broad.mit.edu	37	12	52842673	52842673	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:52842673G>A	ENST00000252252.3	-	6	1203	c.1156C>T	c.(1156-1158)Cgc>Tgc	p.R386C		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	386	Coil 2.|Rod.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)	p.R386C(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		TGGATCATGCGGTTGATCTCA	0.522																																					p.R386C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1156T	12						.						126.0	101.0	110.0					12																	52842673		2203	4297	6500	51128940	SO:0001583	missense	3854	exon6			BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6444	protein-coding gene	gene with protein product		148042	"""keratin-like 1 (a type II keratin sequence)"""	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.1156C>T	12.37:g.52842673G>A	ENSP00000252252:p.Arg386Cys	Somatic		Capture	Illumina HiSeq	Phase_I	51128940	NM_005555	P48669	Missense_Mutation	SNP	ENST00000252252.3	37	CCDS8828.1	.	.	.	.	.	.	.	.	.	.	G	19.38	3.817011	0.70912	.	.	ENSG00000185479	ENST00000252252;ENST00000544607	D	0.90732	-2.72	2.81	2.81	0.32909	Filament (1);	0.097447	0.45867	D	0.000333	D	0.96682	0.8917	H	0.96691	3.865	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	D	0.97801	1.0244	10	0.87932	D	0	.	14.411	0.67115	0.0:0.0:1.0:0.0	.	386	P04259	K2C6B_HUMAN	C	386;346	ENSP00000252252:R386C	ENSP00000252252:R386C	R	-	1	0	KRT6B	51128940	1.000000	0.71417	0.977000	0.42913	0.708000	0.40852	5.262000	0.65501	1.901000	0.55032	0.305000	0.20034	CGC		0.522	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
AMHR2	269	broad.mit.edu	37	12	53819644	53819644	+	Missense_Mutation	SNP	C	C	T	rs369599312		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:53819644C>T	ENST00000257863.4	+	6	873	c.793C>T	c.(793-795)Cgg>Tgg	p.R265W	AMHR2_ENST00000550311.1_Missense_Mutation_p.R265W|AMHR2_ENST00000379791.3_Missense_Mutation_p.R265W	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	265	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)	p.R265W(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	CACTGCCAGCCGGGGGGGTCC	0.582																																					p.R265W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C793T	12						.	C	TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	45.0	45.0	45.0		793,793,793	0.9	0.9	12		45	0,8600		0,0,4300	no	missense,missense,missense	AMHR2	NM_001164690.1,NM_001164691.1,NM_020547.2	101,101,101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	265/479,265/479,265/574	53819644	1,13005	2203	4300	6503	52105911	SO:0001583	missense	269	exon6			AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"""Muellerian inhibiting substance type II receptor"""	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.793C>T	12.37:g.53819644C>T	ENSP00000257863:p.Arg265Trp	Somatic		Capture	Illumina HiSeq	Phase_I	52105911	NM_001164691	A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Missense_Mutation	SNP	ENST00000257863.4	37	CCDS8858.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.630008	0.46944	2.27E-4	0.0	ENSG00000135409	ENST00000257863;ENST00000550311;ENST00000379791	T;T;T	0.66815	-0.23;-0.23;-0.23	5.66	0.871	0.19107	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.421951	0.17349	N	0.177453	T	0.58722	0.2142	N	0.21448	0.665	0.27685	N	0.946323	D;D	0.67145	0.995;0.996	P;P	0.54210	0.528;0.745	T	0.53892	-0.8374	10	0.66056	D	0.02	.	7.1983	0.25866	0.226:0.57:0.0:0.204	.	265;265	F8W1D2;Q16671	.;AMHR2_HUMAN	W	265	ENSP00000257863:R265W;ENSP00000446661:R265W;ENSP00000369117:R265W	ENSP00000257863:R265W	R	+	1	2	AMHR2	52105911	0.958000	0.32768	0.891000	0.34965	0.147000	0.21601	-0.192000	0.09587	0.029000	0.15352	-0.797000	0.03246	CGG		0.582	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407048.1	NM_020547	
SMUG1	23583	broad.mit.edu	37	12	54577723	54577723	+	Start_Codon_SNP	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:54577723A>G	ENST00000508394.2	-	2	64	c.2T>C	c.(1-3)aTg>aCg	p.M1T	SMUG1_ENST00000505128.1_Start_Codon_SNP_p.M1T|SMUG1_ENST00000514196.1_Start_Codon_SNP_p.M1T|SMUG1_ENST00000337581.3_Start_Codon_SNP_p.M1T|SMUG1_ENST00000506595.1_Start_Codon_SNP_p.M1T|SMUG1_ENST00000514685.1_Start_Codon_SNP_p.M1T|SMUG1_ENST00000505662.1_5'UTR|SMUG1_ENST00000401977.2_Start_Codon_SNP_p.M1T|SMUG1_ENST00000513838.1_Start_Codon_SNP_p.M1T|SMUG1_ENST00000243112.5_Start_Codon_SNP_p.M1T	NM_001243787.1|NM_001243788.1|NM_014311.2	NP_001230716.1|NP_001230717.1|NP_055126.1	Q53HV7	SMUG1_HUMAN	single-strand-selective monofunctional uracil-DNA glycosylase 1	1					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA repair (GO:0006281)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA N-glycosylase activity (GO:0019104)|oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity (GO:0000703)|single-strand selective uracil DNA N-glycosylase activity (GO:0017065)|uracil DNA N-glycosylase activity (GO:0004844)	p.M1T(1)		kidney(1)|large_intestine(4)|lung(1)	6						AGCCTGGGGCATATGTCCATG	0.617								Base excision repair (BER), DNA glycosylases																													p.M1T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2C	12						.						13.0	14.0	13.0					12																	54577723		2202	4296	6498	52863990	SO:0001582	initiator_codon_variant	23583	exon3			AF125182	CCDS8874.1, CCDS58239.1	12q13.13	2013-10-28			ENSG00000123415	ENSG00000123415			17148	protein-coding gene	gene with protein product		607753				10074426, 11526119	Standard	NM_014311		Approved	UNG3, FDG, HMUDG	uc009znf.2	Q53HV7	OTTHUMG00000160068	ENST00000508394.2:c.2T>C	12.37:g.54577723A>G	ENSP00000424191:p.Met1Thr	Somatic		Capture	Illumina HiSeq	Phase_I	52863990	NM_014311	A8K2K9|O95862|Q0D2M0|Q8NB71|Q9BWC8	Missense_Mutation	SNP	ENST00000508394.2	37	CCDS8874.1	.	.	.	.	.	.	.	.	.	.	A	8.312	0.822234	0.16678	.	.	ENSG00000123415	ENST00000506595;ENST00000514685;ENST00000505128;ENST00000337581;ENST00000508394;ENST00000513838;ENST00000243112;ENST00000401977;ENST00000514196;ENST00000504338;ENST00000507904;ENST00000503447;ENST00000504797;ENST00000506169;ENST00000503306	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.44482	1.48;1.48;0.92;1.59;1.59;1.48;1.48;1.59;1.58;1.58;1.58;0.99;0.98;0.96	4.85	2.24	0.28232	.	1.808910	0.02986	N	0.146280	T	0.36110	0.0955	.	.	.	0.80722	D	1	B;B;B	0.16396	0.001;0.003;0.017	B;B;B	0.16722	0.002;0.009;0.016	T	0.41928	-0.9481	9	0.72032	D	0.01	.	5.608	0.17391	0.7601:0.0:0.0881:0.1518	.	1;1;1	Q53HV7;D6RAI1;Q53HV7-2	SMUG1_HUMAN;.;.	T	1	ENSP00000421206:M1T;ENSP00000421139:M1T;ENSP00000421894:M1T;ENSP00000338606:M1T;ENSP00000424191:M1T;ENSP00000423629:M1T;ENSP00000243112:M1T;ENSP00000384828:M1T;ENSP00000425974:M1T;ENSP00000423083:M1T;ENSP00000423457:M1T;ENSP00000421790:M1T;ENSP00000427547:M1T;ENSP00000425426:M1T	ENSP00000243112:M1T	M	-	2	0	SMUG1	52863990	0.243000	0.23878	0.931000	0.37212	0.780000	0.44128	1.102000	0.31050	0.934000	0.37316	0.482000	0.46254	ATG		0.617	SMUG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359074.3	NM_014311	Missense_Mutation
ITGA7	3679	broad.mit.edu	37	12	56094068	56094068	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:56094068C>T	ENST00000555728.1	-	5	808	c.780G>A	c.(778-780)ccG>ccA	p.P260P	ITGA7_ENST00000257880.7_Silent_p.P260P|ITGA7_ENST00000553804.1_Silent_p.P260P|ITGA7_ENST00000394230.2_Silent_p.P260P|ITGA7_ENST00000452168.2_Silent_p.P163P|ITGA7_ENST00000394229.2_Intron|ITGA7_ENST00000347027.6_Intron|ITGA7_ENST00000257879.6_Intron			Q13683	ITA7_HUMAN	integrin, alpha 7	260					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)	p.P260P(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						TGGCAGGGACCGGGATGAGGC	0.647																																					p.P163P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G489A	12						.						32.0	35.0	34.0					12																	56094068		1568	3582	5150	54380335	SO:0001819	synonymous_variant	3679	exon5				CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"""Integrins"""	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.780G>A	12.37:g.56094068C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54380335	NM_001144997	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Silent	SNP	ENST00000555728.1	37																																																																																					0.647	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206	
GDF11	10220	broad.mit.edu	37	12	56142573	56142573	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:56142573C>T	ENST00000257868.5	+	2	686	c.649C>T	c.(649-651)Cgt>Tgt	p.R217C		NM_005811.3	NP_005802.1	O95390	GDF11_HUMAN	growth differentiation factor 11	217					camera-type eye morphogenesis (GO:0048593)|cell maturation (GO:0048469)|growth (GO:0040007)|mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|palate development (GO:0060021)|pancreas development (GO:0031016)|skeletal system development (GO:0001501)|spinal cord anterior/posterior patterning (GO:0021512)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)|protein complex (GO:0043234)		p.R217C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|urinary_tract(1)	12						CGGAGGCCGGCGTCACATCCG	0.612																																					p.R217C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C649T	12						.						46.0	39.0	41.0					12																	56142573		2203	4300	6503	54428840	SO:0001583	missense	10220	exon2			AF100907	CCDS8891.1	12q13.13	2008-08-01							4216	protein-coding gene	gene with protein product		603936				15988002	Standard	NM_005811		Approved	BMP-11	uc001shq.3	O95390		ENST00000257868.5:c.649C>T	12.37:g.56142573C>T	ENSP00000257868:p.Arg217Cys	Somatic		Capture	Illumina HiSeq	Phase_I	54428840	NM_005811	Q9UID1|Q9UID2	Missense_Mutation	SNP	ENST00000257868.5	37	CCDS8891.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698548	0.68386	.	.	ENSG00000135414	ENST00000257868	T	0.70749	-0.51	4.22	4.22	0.49857	Transforming growth factor-beta, N-terminal (1);	0.066092	0.64402	D	0.000019	T	0.78842	0.4347	L	0.59436	1.845	0.58432	D	0.999999	D	0.71674	0.998	D	0.64877	0.93	T	0.80876	-0.1186	10	0.87932	D	0	-4.6699	12.2975	0.54857	0.0:1.0:0.0:0.0	.	217	O95390	GDF11_HUMAN	C	217	ENSP00000257868:R217C	ENSP00000257868:R217C	R	+	1	0	GDF11	54428840	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.254000	0.43214	2.380000	0.81148	0.555000	0.69702	CGT		0.612	GDF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407842.3		
ERBB3	2065	broad.mit.edu	37	12	56481845	56481845	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:56481845G>A	ENST00000267101.3	+	7	1213	c.773G>A	c.(772-774)cGc>cAc	p.R258H	ERBB3_ENST00000415288.2_Missense_Mutation_p.R199H|ERBB3_ENST00000450146.2_Intron	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	258					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)	p.R258H(1)		central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			TGTGTACCTCGCTGTCCACAG	0.517																																					p.R258H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G773A	12						.						91.0	85.0	87.0					12																	56481845		2203	4300	6503	54768112	SO:0001583	missense	2065	exon7			M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"""lethal congenital contracture syndrome 2"""	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.773G>A	12.37:g.56481845G>A	ENSP00000267101:p.Arg258His	Somatic		Capture	Illumina HiSeq	Phase_I	54768112	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	37	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	G	9.277	1.047223	0.19827	.	.	ENSG00000065361	ENST00000267101;ENST00000394099;ENST00000415288	D;D	0.84146	-1.81;-1.81	4.78	-1.95	0.07548	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	0.487240	0.18598	N	0.136533	T	0.59649	0.2209	N	0.04063	-0.285	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27468	-1.0073	10	0.18276	T	0.48	.	4.0232	0.09675	0.4646:0.0:0.2022:0.3333	.	258	P21860	ERBB3_HUMAN	H	258;258;199	ENSP00000267101:R258H;ENSP00000408340:R199H	ENSP00000267101:R258H	R	+	2	0	ERBB3	54768112	0.843000	0.29541	0.942000	0.38095	0.710000	0.40934	0.776000	0.26704	-0.134000	0.11516	-0.251000	0.11542	CGC		0.517	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3		
TIMELESS	8914	broad.mit.edu	37	12	56826266	56826266	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:56826266C>A	ENST00000553532.1	-	7	724	c.574G>T	c.(574-576)Gcg>Tcg	p.A192S	TIMELESS_ENST00000554616.1_Missense_Mutation_p.A192S|TIMELESS_ENST00000229201.4_Missense_Mutation_p.A191S					timeless circadian clock									p.A192S(1)		NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						AGGTGAATCGCCCAGAGGAGC	0.547																																					p.A192S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G574T	12						.						109.0	105.0	106.0					12																	56826266		2203	4300	6503	55112533	SO:0001583	missense	8914	exon7			AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.574G>T	12.37:g.56826266C>A	ENSP00000450607:p.Ala192Ser	Somatic		Capture	Illumina HiSeq	Phase_I	55112533	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.835441	0.71373	.	.	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.54866	0.55;0.55;0.55	5.21	4.31	0.51392	Timeless protein (1);	0.112294	0.64402	D	0.000017	T	0.46405	0.1391	L	0.41824	1.3	0.80722	D	1	P;B	0.35656	0.514;0.426	B;B	0.39339	0.297;0.246	T	0.46048	-0.9219	10	0.44086	T	0.13	-15.8089	12.4884	0.55886	0.0:0.9168:0.0:0.0832	.	191;192	Q9UNS1-2;Q9UNS1	.;TIM_HUMAN	S	191;192;192	ENSP00000229201:A191S;ENSP00000450607:A192S;ENSP00000450848:A192S	ENSP00000229201:A192S	A	-	1	0	TIMELESS	55112533	1.000000	0.71417	0.998000	0.56505	0.936000	0.57629	5.698000	0.68302	2.619000	0.88677	0.462000	0.41574	GCG		0.547	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
NACA	4666	broad.mit.edu	37	12	57106875	57106875	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:57106875T>G	ENST00000454682.1	-	7	6351	c.6070A>C	c.(6070-6072)Act>Cct	p.T2024P	NACA_ENST00000548563.1_Missense_Mutation_p.T82P|NACA_ENST00000356769.3_Missense_Mutation_p.T161P|NACA_ENST00000550952.1_Missense_Mutation_p.T871P|NACA_ENST00000552540.1_Missense_Mutation_p.T161P|NACA_ENST00000551793.1_5'Flank|NACA_ENST00000393891.4_Missense_Mutation_p.T161P|NACA_ENST00000546392.1_Missense_Mutation_p.T161P	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	2024					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T161P(1)|p.T2024P(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						TCTTGTACAGTTGGAGTCTGT	0.403			T	BCL6	NHL																																p.T2024P			Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A6070C	12						.						95.0	90.0	91.0					12																	57106875		2203	4300	6503	55393142	SO:0001583	missense	4666	exon7			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.6070A>C	12.37:g.57106875T>G	ENSP00000403817:p.Thr2024Pro	Somatic		Capture	Illumina HiSeq	Phase_I	55393142	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	37		.	.	.	.	.	.	.	.	.	.	T	18.50	3.637669	0.67130	.	.	ENSG00000196531	ENST00000550920;ENST00000454682;ENST00000550952;ENST00000356769;ENST00000552540;ENST00000393891;ENST00000548563;ENST00000546392;ENST00000549259	T;T;T;T;T;T;T;T	0.48836	0.91;0.81;0.8;0.92;0.92;0.92;0.92;0.92	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.35128	0.0921	N	0.00483	-1.445	0.52099	D	0.999942	D;D;D	0.71674	0.979;0.998;0.959	P;D;P	0.79784	0.899;0.993;0.739	T	0.59974	-0.7353	10	0.29301	T	0.29	.	14.244	0.65975	0.0:0.0:0.0:1.0	.	2024;871;161	E9PAV3;F8VU71;Q13765	.;.;NACA_HUMAN	P	159;2024;871;161;161;161;82;161;161	ENSP00000448039:T159P;ENSP00000403817:T2024P;ENSP00000448035:T871P;ENSP00000349212:T161P;ENSP00000447821:T161P;ENSP00000377469:T161P;ENSP00000446801:T161P;ENSP00000447133:T161P	ENSP00000349212:T161P	T	-	1	0	NACA	55393142	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.967000	0.70403	2.015000	0.59207	0.455000	0.32223	ACT		0.403	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
MYO1A	4640	broad.mit.edu	37	12	57432651	57432651	+	Missense_Mutation	SNP	C	C	T	rs138932052		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:57432651C>T	ENST00000442789.2	-	17	1762	c.1475G>A	c.(1474-1476)cGt>cAt	p.R492H	MYO1A_ENST00000300119.3_Missense_Mutation_p.R492H|MYO1A_ENST00000544473.1_Missense_Mutation_p.R330H|MYO1A_ENST00000476795.1_5'UTR	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	492	Myosin motor.				microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R492H(1)		breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						GTCATACTGACGCTGGGCATT	0.587																																					p.R492H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1475A	12						.	C	HIS/ARG	0,4406		0,0,2203	103.0	94.0	97.0		1475	-4.8	0.9	12	dbSNP_134	97	2,8598	2.2+/-6.3	0,2,4298	no	missense	MYO1A	NM_005379.2	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	492/1044	57432651	2,13004	2203	4300	6503	55718918	SO:0001583	missense	4640	exon16			L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"""Myosins / Myosin superfamily : Class I"""	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.1475G>A	12.37:g.57432651C>T	ENSP00000393392:p.Arg492His	Somatic		Capture	Illumina HiSeq	Phase_I	55718918	NM_005379	Q9UQD7	Missense_Mutation	SNP	ENST00000442789.2	37	CCDS8929.1	.	.	.	.	.	.	.	.	.	.	C	7.217	0.596596	0.13875	0.0	2.33E-4	ENSG00000166866	ENST00000300119;ENST00000442789;ENST00000544473	D;D;D	0.88124	-2.29;-2.29;-2.34	4.55	-4.77	0.03219	Myosin head, motor domain (2);	0.353731	0.33253	N	0.005119	T	0.70919	0.3279	N	0.17082	0.46	0.39170	D	0.962578	B	0.06786	0.001	B	0.04013	0.001	T	0.49624	-0.8920	10	0.15066	T	0.55	.	12.5009	0.55955	0.0:0.4364:0.0:0.5636	.	492	Q9UBC5	MYO1A_HUMAN	H	492;492;330	ENSP00000300119:R492H;ENSP00000393392:R492H;ENSP00000440514:R330H	ENSP00000300119:R492H	R	-	2	0	MYO1A	55718918	0.002000	0.14202	0.910000	0.35882	0.594000	0.36715	-1.293000	0.02770	-0.845000	0.04179	-0.474000	0.04947	CGT		0.587	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379	
LRP1	4035	broad.mit.edu	37	12	57570964	57570964	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:57570964C>T	ENST00000243077.3	+	25	4598	c.4132C>T	c.(4132-4134)Cgg>Tgg	p.R1378W		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1378					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.R1378W(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)	TGGGACCCTCCGGACCACCCT	0.627																																					p.R1378W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4132T	12						.						118.0	94.0	102.0					12																	57570964		2203	4300	6503	55857231	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.4132C>T	12.37:g.57570964C>T	ENSP00000243077:p.Arg1378Trp	Somatic		Capture	Illumina HiSeq	Phase_I	55857231	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	14.84	2.654044	0.47362	.	.	ENSG00000123384	ENST00000243077	D	0.97665	-4.48	5.0	3.02	0.34903	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000011	D	0.98924	0.9635	H	0.97896	4.1	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.98914	1.0781	10	0.87932	D	0	.	12.4553	0.55700	0.3882:0.6118:0.0:0.0	.	1378	Q07954	LRP1_HUMAN	W	1378	ENSP00000243077:R1378W	ENSP00000243077:R1378W	R	+	1	2	LRP1	55857231	0.945000	0.32115	0.976000	0.42696	0.971000	0.66376	0.104000	0.15313	1.333000	0.45449	0.462000	0.41574	CGG		0.627	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
LRP1	4035	broad.mit.edu	37	12	57604564	57604564	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:57604564C>T	ENST00000243077.3	+	83	13284	c.12818C>T	c.(12817-12819)gCg>gTg	p.A4273V		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	4273	EGF-like 19. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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.A4273V(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)	CAGGTGTGTGCGGGCTACTGT	0.667																																					p.A4273V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C12818T	12						.						59.0	61.0	60.0					12																	57604564		2203	4300	6503	55890831	SO:0001583	missense	4035	exon83			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.12818C>T	12.37:g.57604564C>T	ENSP00000243077:p.Ala4273Val	Somatic		Capture	Illumina HiSeq	Phase_I	55890831	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	16.06	3.016722	0.54468	.	.	ENSG00000123384	ENST00000243077	T	0.10382	2.88	4.45	4.45	0.53987	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.352157	0.24052	N	0.041998	T	0.12135	0.0295	L	0.47190	1.495	0.80722	D	1	B	0.26318	0.146	B	0.14578	0.011	T	0.05053	-1.0909	10	0.56958	D	0.05	.	16.3851	0.83502	0.0:1.0:0.0:0.0	.	4273	Q07954	LRP1_HUMAN	V	4273	ENSP00000243077:A4273V	ENSP00000243077:A4273V	A	+	2	0	LRP1	55890831	0.149000	0.22717	0.996000	0.52242	0.963000	0.63663	2.580000	0.46068	2.502000	0.84385	0.462000	0.41574	GCG		0.667	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
MARS	4141	broad.mit.edu	37	12	57906610	57906610	+	Silent	SNP	G	G	A	rs149742633		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:57906610G>A	ENST00000262027.5	+	15	1964	c.1830G>A	c.(1828-1830)acG>acA	p.T610T	MARS_ENST00000315473.5_Silent_p.T376T|RN7SL312P_ENST00000582079.1_RNA|RNU6-594P_ENST00000517056.1_RNA	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	610					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)	p.T610T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	CCCAGGACACGGGGATCCCTG	0.542																																					p.T610T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1830A	12						.	G		1,4405	2.1+/-5.4	0,1,2202	151.0	154.0	153.0		1830	-4.5	1.0	12	dbSNP_134	153	0,8600		0,0,4300	no	coding-synonymous	MARS	NM_004990.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		610/901	57906610	1,13005	2203	4300	6503	56192877	SO:0001819	synonymous_variant	4141	exon15			X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"""Aminoacyl tRNA synthetases / Class I"""	6898	protein-coding gene	gene with protein product	"""methionine tRNA ligase 1, cytoplasmic"""	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.1830G>A	12.37:g.57906610G>A		Somatic		Capture	Illumina HiSeq	Phase_I	56192877	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Silent	SNP	ENST00000262027.5	37	CCDS8942.1																																																																																				0.542	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990	
SRGAP1	57522	broad.mit.edu	37	12	64377841	64377841	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:64377841C>T	ENST00000355086.3	+	2	706	c.182C>T	c.(181-183)aCg>aTg	p.T61M	SRGAP1_ENST00000543397.1_Missense_Mutation_p.T21M|SRGAP1_ENST00000357825.3_Missense_Mutation_p.T61M	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	61	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.T61M(1)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		GAAATTGAGACGGAATATTCC	0.403																																					p.T61M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C182T	12						.						115.0	117.0	116.0					12																	64377841		2203	4300	6503	62664108	SO:0001583	missense	57522	exon2			AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"""Rho GTPase activating proteins"""	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.182C>T	12.37:g.64377841C>T	ENSP00000347198:p.Thr61Met	Somatic		Capture	Illumina HiSeq	Phase_I	62664108	NM_020762	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	37	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	C	9.879	1.201164	0.22121	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.17370	2.28;2.28;2.56	5.13	4.24	0.50183	Fps/Fes/Fer/CIP4 homology (3);	0.197894	0.23793	U	0.044509	T	0.06280	0.0162	N	0.01705	-0.755	0.34572	D	0.713549	B;B;B	0.20988	0.004;0.021;0.05	B;B;B	0.19666	0.009;0.026;0.026	T	0.25847	-1.0120	9	.	.	.	.	10.7929	0.46443	0.0:0.8326:0.0:0.1674	.	61;21;61	Q7Z6B7;G5EA48;Q7Z6B7-2	SRGP1_HUMAN;.;.	M	61;61;21	ENSP00000347198:T61M;ENSP00000350480:T61M;ENSP00000437948:T21M	.	T	+	2	0	SRGAP1	62664108	0.868000	0.29978	0.926000	0.36857	0.988000	0.76386	1.495000	0.35627	1.290000	0.44636	0.585000	0.79938	ACG		0.403	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1		
HELB	92797	broad.mit.edu	37	12	66724979	66724979	+	Missense_Mutation	SNP	C	C	T	rs139082430		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:66724979C>T	ENST00000247815.4	+	12	2775	c.2716C>T	c.(2716-2718)Cgc>Tgc	p.R906C		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	906					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)	p.R906C(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		GAAGGCGGGCCGCCAGCACTG	0.527													C|||	1	0.000199681	0.0	0.0	5008	,	,		15682	0.0		0.0	False		,,,				2504	0.001				p.R906C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2716T	12						.						50.0	57.0	55.0					12																	66724979		2203	4300	6503	65011246	SO:0001583	missense	92797	exon12			AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.2716C>T	12.37:g.66724979C>T	ENSP00000247815:p.Arg906Cys	Somatic		Capture	Illumina HiSeq	Phase_I	65011246	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	37	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	C	19.69	3.874447	0.72180	.	.	ENSG00000127311	ENST00000247815	T	0.14640	2.49	5.21	4.31	0.51392	.	0.167110	0.40469	N	0.001097	T	0.41419	0.1158	M	0.89904	3.07	0.44719	D	0.997712	D	0.89917	1.0	D	0.67231	0.95	T	0.48115	-0.9063	9	.	.	.	-13.675	12.4815	0.55844	0.0:0.9205:0.0:0.0795	.	906	Q8NG08	HELB_HUMAN	C	906	ENSP00000247815:R906C	.	R	+	1	0	HELB	65011246	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	1.406000	0.34646	2.430000	0.82344	0.561000	0.74099	CGC		0.527	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
DYRK2	8445	broad.mit.edu	37	12	68051110	68051110	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:68051110G>A	ENST00000344096.3	+	3	836	c.423G>A	c.(421-423)aaG>aaA	p.K141K	DYRK2_ENST00000393555.3_Silent_p.K68K|RP11-335O4.3_ENST00000425371.2_RNA	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	141					cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)	p.K141K(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		CCTCTCTAAAGTCCATGGAAG	0.532																																					p.K68K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G204A	12						.						59.0	54.0	56.0					12																	68051110		2203	4300	6503	66337377	SO:0001819	synonymous_variant	8445	exon2			Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.423G>A	12.37:g.68051110G>A		Somatic		Capture	Illumina HiSeq	Phase_I	66337377	NM_003583	B2R9V9|Q9BRB5	Silent	SNP	ENST00000344096.3	37	CCDS8978.1																																																																																				0.532	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1		
CPSF6	11052	broad.mit.edu	37	12	69656328	69656328	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:69656328C>T	ENST00000435070.2	+	9	1755	c.1645C>T	c.(1645-1647)Cgt>Tgt	p.R549C	CPSF6_ENST00000551516.1_Silent_p.I51I|CPSF6_ENST00000456847.3_Missense_Mutation_p.R476C|CPSF6_ENST00000266679.8_Missense_Mutation_p.R586C	NM_007007.2	NP_008938.2	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6, 68kDa	549	Arg-rich.|Sufficient for nuclear targeting.				mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R549C(2)		endometrium(1)|large_intestine(7)|lung(8)	16	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			gcgCGAATATCGTCATCGTTA	0.468																																					p.R549C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1645T	12						.						201.0	137.0	158.0					12																	69656328		2203	4300	6503	67942595	SO:0001583	missense	11052	exon9			X67336	CCDS8988.1, CCDS73494.1	12q15	2013-06-18	2002-08-29			ENSG00000111605		"""RNA binding motif (RRM) containing"""	13871	protein-coding gene	gene with protein product	"""cleavage factor Im complex 68 kDa subunit"""	604979	"""cleavage and polyadenylation specific factor 6, 68kD subunit"""			9659921, 17267687	Standard	NM_007007		Approved	CFIM, HPBRII-4, HPBRII-7, CFIM68	uc001sut.4	Q16630		ENST00000435070.2:c.1645C>T	12.37:g.69656328C>T	ENSP00000391774:p.Arg549Cys	Somatic		Capture	Illumina HiSeq	Phase_I	67942595	NM_007007	A8K7K9|Q53ES1|Q9BSJ7|Q9BW18	Missense_Mutation	SNP	ENST00000435070.2	37	CCDS8988.1	.	.	.	.	.	.	.	.	.	.	C	18.45	3.626944	0.66901	.	.	ENSG00000111605	ENST00000435070;ENST00000456847;ENST00000266679	T;T;T	0.72394	-0.65;-0.65;-0.65	5.75	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.64283	0.2584	L	0.52573	1.65	0.80722	D	1	B;B;B	0.17465	0.001;0.022;0.013	B;B;B	0.08055	0.001;0.003;0.001	T	0.57894	-0.7732	9	.	.	.	-9.6562	15.5295	0.75942	0.0:0.9294:0.0:0.0706	.	298;586;549	B4DSU9;Q16630-2;Q16630	.;.;CPSF6_HUMAN	C	549;476;586	ENSP00000391774:R549C;ENSP00000391437:R476C;ENSP00000266679:R586C	.	R	+	1	0	CPSF6	67942595	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.885000	0.99019	0.655000	0.94253	CGT		0.468	CPSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403609.1	NM_007007	
TRHDE	29953	broad.mit.edu	37	12	72863631	72863631	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:72863631T>C	ENST00000261180.4	+	4	1370	c.1274T>C	c.(1273-1275)gTt>gCt	p.V425A		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	425					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.V425A(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						GATCCCAGTGTTTCATCTATT	0.388																																					p.V425A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1274C	12						.						156.0	158.0	157.0					12																	72863631		2203	4300	6503	71149898	SO:0001583	missense	29953	exon4			AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"""pyroglutamyl-peptidase II"", ""pyroglutamyl aminopeptidase II"", ""TRH-specific aminopeptidase"""	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.1274T>C	12.37:g.72863631T>C	ENSP00000261180:p.Val425Ala	Somatic		Capture	Illumina HiSeq	Phase_I	71149898	NM_013381	A5PL19|Q6UWJ4	Missense_Mutation	SNP	ENST00000261180.4	37	CCDS9004.1	.	.	.	.	.	.	.	.	.	.	T	18.85	3.711456	0.68730	.	.	ENSG00000072657	ENST00000261180	T	0.02525	4.26	5.87	5.87	0.94306	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.205916	0.43416	D	0.000570	T	0.03608	0.0103	L	0.33093	0.98	0.53005	D	0.999961	B	0.13594	0.008	B	0.16289	0.015	T	0.53606	-0.8415	10	0.25106	T	0.35	.	16.2662	0.82581	0.0:0.0:0.0:1.0	.	425	Q9UKU6	TRHDE_HUMAN	A	425	ENSP00000261180:V425A	ENSP00000261180:V425A	V	+	2	0	TRHDE	71149898	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.145000	0.71769	2.247000	0.74100	0.528000	0.53228	GTT		0.388	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381	
ZDHHC17	23390	broad.mit.edu	37	12	77199147	77199147	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:77199147T>C	ENST00000426126.2	+	3	897	c.248T>C	c.(247-249)gTa>gCa	p.V83A	ZDHHC17_ENST00000359019.4_Missense_Mutation_p.V33A|ZDHHC17_ENST00000334822.5_Missense_Mutation_p.V83A	NM_015336.2	NP_056151.2	Q8IUH5	ZDH17_HUMAN	zinc finger, DHHC-type containing 17	83					lipoprotein transport (GO:0042953)|magnesium ion transport (GO:0015693)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein palmitoylation (GO:0018345)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.V83A(1)		breast(2)|endometrium(2)|large_intestine(3)|liver(2)|lung(14)	23						GGTTATGATGTACGGCAACCG	0.328																																					p.V83A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T248C	12						.						61.0	59.0	60.0					12																	77199147		1839	4093	5932	75723278	SO:0001583	missense	23390	exon3			AB023163	CCDS44946.1	12q21.2	2013-01-10				ENSG00000186908		"""Zinc fingers, DHHC-type"", ""Ankyrin repeat domain containing"""	18412	protein-coding gene	gene with protein product		607799				9700202, 18794299	Standard	NM_015336		Approved	HIP14, HYPH, KIAA0946	uc001syk.1	Q8IUH5	OTTHUMG00000169917	ENST00000426126.2:c.248T>C	12.37:g.77199147T>C	ENSP00000403397:p.Val83Ala	Somatic		Capture	Illumina HiSeq	Phase_I	75723278	NM_015336	B4DR39|O75407|Q7Z2I0|Q86W89|Q86YK0|Q9P088|Q9UPZ8	Missense_Mutation	SNP	ENST00000426126.2	37	CCDS44946.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.878556	0.91740	.	.	ENSG00000186908	ENST00000426126;ENST00000334822;ENST00000359019;ENST00000549682	T;T;T;T	0.73047	0.45;0.45;0.45;-0.71	4.9	4.9	0.64082	Ankyrin repeat-containing domain (4);	0.060667	0.64402	D	0.000004	T	0.80003	0.4544	L	0.59436	1.845	0.80722	D	1	D	0.53312	0.959	D	0.66847	0.947	T	0.78175	-0.2306	10	0.33141	T	0.24	-13.7777	14.9694	0.71220	0.0:0.0:0.0:1.0	.	83	Q8IUH5	ZDH17_HUMAN	A	83;83;33;60	ENSP00000403397:V83A;ENSP00000334868:V83A;ENSP00000351913:V33A;ENSP00000450295:V60A	ENSP00000334868:V83A	V	+	2	0	ZDHHC17	75723278	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.825000	0.86693	2.183000	0.69458	0.533000	0.62120	GTA		0.328	ZDHHC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406555.1	NM_015336	
E2F7	144455	broad.mit.edu	37	12	77436898	77436898	+	Missense_Mutation	SNP	C	C	T	rs377645692		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:77436898C>T	ENST00000322886.7	-	7	1305	c.1070G>A	c.(1069-1071)cGa>cAa	p.R357Q	E2F7_ENST00000416496.2_Missense_Mutation_p.R357Q	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	357					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.R357Q(2)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						TTTACGACCTCGCTCTTCTGT	0.463																																					p.R357Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1070A	12						.	C	GLN/ARG	0,4406		0,0,2203	207.0	178.0	188.0		1070	5.9	1.0	12		188	1,8599	1.2+/-3.3	0,1,4299	no	missense	E2F7	NM_203394.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	357/912	77436898	1,13005	2203	4300	6503	75961029	SO:0001583	missense	144455	exon7			BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.1070G>A	12.37:g.77436898C>T	ENSP00000323246:p.Arg357Gln	Somatic		Capture	Illumina HiSeq	Phase_I	75961029	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	37	CCDS9016.1	.	.	.	.	.	.	.	.	.	.	C	35	5.497122	0.96355	0.0	1.16E-4	ENSG00000165891	ENST00000322886;ENST00000416496;ENST00000550669	T;T;T	0.20738	2.3;2.05;2.06	5.95	5.95	0.96441	Transcription factor E2F/dimerisation partner (TDP) (1);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.054138	0.64402	D	0.000001	T	0.44074	0.1276	L	0.49350	1.555	0.58432	D	0.999998	D	0.89917	1.0	D	0.79784	0.993	T	0.11717	-1.0576	10	0.66056	D	0.02	-13.2017	19.3671	0.94468	0.0:1.0:0.0:0.0	.	357	Q96AV8	E2F7_HUMAN	Q	357	ENSP00000323246:R357Q;ENSP00000393639:R357Q;ENSP00000448245:R357Q	ENSP00000323246:R357Q	R	-	2	0	E2F7	75961029	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	6.002000	0.70693	2.826000	0.97356	0.563000	0.77884	CGA		0.463	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871	
MYF6	4618	broad.mit.edu	37	12	81101645	81101645	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:81101645C>T	ENST00000228641.3	+	1	369	c.147C>T	c.(145-147)ccC>ccT	p.P49P		NM_002469.2	NP_002460.1	P23409	MYF6_HUMAN	myogenic factor 6 (herculin)	49					muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P49P(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|skin(1)	26						ACCAAATGCCCCCGGAAGCGG	0.612																																					p.P49P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C147T	12						.						59.0	64.0	62.0					12																	81101645		2203	4300	6503	79625776	SO:0001819	synonymous_variant	4618	exon1				CCDS9019.1	12q21	2013-05-21				ENSG00000111046		"""Basic helix-loop-helix proteins"""	7566	protein-coding gene	gene with protein product	"""muscle-specific regulatory factor 4"""	159991				8978788	Standard	NM_002469		Approved	MRF4, bHLHc4	uc001szf.2	P23409		ENST00000228641.3:c.147C>T	12.37:g.81101645C>T		Somatic		Capture	Illumina HiSeq	Phase_I	79625776	NM_002469	B2R898|Q53X80|Q6FHI9	Silent	SNP	ENST00000228641.3	37	CCDS9019.1																																																																																				0.612	MYF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407756.1	NM_002469	
MYF5	4617	broad.mit.edu	37	12	81111075	81111075	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:81111075A>G	ENST00000228644.3	+	1	385	c.233A>G	c.(232-234)aAg>aGg	p.K78R		NM_005593.2	NP_005584.2	P13349	MYF5_HUMAN	myogenic factor 5	78					camera-type eye development (GO:0043010)|cartilage condensation (GO:0001502)|embryonic skeletal system morphogenesis (GO:0048704)|extracellular matrix organization (GO:0030198)|muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle tissue morphogenesis (GO:0060415)|ossification (GO:0001503)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)	protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)	p.K78R(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(8)|lung(15)|ovary(2)|pancreas(1)	30						TGCAAGAGGAAGTCCACCACC	0.627																																					p.K78R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A233G	12						.						41.0	37.0	38.0					12																	81111075		2203	4300	6503	79635206	SO:0001583	missense	4617	exon1				CCDS9020.1	12q21	2013-05-21			ENSG00000111049	ENSG00000111049		"""Basic helix-loop-helix proteins"""	7565	protein-coding gene	gene with protein product		159990				8978788, 12105204	Standard	NM_005593		Approved	bHLHc2	uc001szg.2	P13349	OTTHUMG00000170166	ENST00000228644.3:c.233A>G	12.37:g.81111075A>G	ENSP00000228644:p.Lys78Arg	Somatic		Capture	Illumina HiSeq	Phase_I	79635206	NM_005593	Q6ISR9	Missense_Mutation	SNP	ENST00000228644.3	37	CCDS9020.1	.	.	.	.	.	.	.	.	.	.	A	32	5.138506	0.94560	.	.	ENSG00000111049	ENST00000228644	D	0.85702	-2.02	6.17	6.17	0.99709	Myogenic basic muscle-specific protein (2);Helix-loop-helix DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.92835	0.7721	M	0.83603	2.65	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.92765	0.6227	10	0.48119	T	0.1	-3.2409	16.8222	0.85835	1.0:0.0:0.0:0.0	.	78	P13349	MYF5_HUMAN	R	78	ENSP00000228644:K78R	ENSP00000228644:K78R	K	+	2	0	MYF5	79635206	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.371000	0.80710	0.533000	0.62120	AAG		0.627	MYF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407757.1	NM_005593	
TSPAN19	144448	broad.mit.edu	37	12	85417129	85417129	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:85417129G>A	ENST00000532498.2	-	5	394	c.314C>T	c.(313-315)gCa>gTa	p.A105V	TSPAN19_ENST00000547403.2_5'UTR	NM_001100917.1	NP_001094387.1	P0C672	TSN19_HUMAN	tetraspanin 19	105						integral component of membrane (GO:0016021)		p.A105V(1)		ovary(1)	1						GATGATGAATGCTGAAAGTAC	0.313																																					p.A105V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C314T	12						.						78.0	69.0	72.0					12																	85417129		1852	4091	5943	83941260	SO:0001583	missense	144448	exon5				CCDS44949.1	12q21.31	2013-02-14			ENSG00000231738	ENSG00000231738		"""Tetraspanins"""	31886	protein-coding gene	gene with protein product							Standard	NM_001100917		Approved		uc009zsj.3	P0C672	OTTHUMG00000166181	ENST00000532498.2:c.314C>T	12.37:g.85417129G>A	ENSP00000433816:p.Ala105Val	Somatic		Capture	Illumina HiSeq	Phase_I	83941260	NM_001100917		Missense_Mutation	SNP	ENST00000532498.2	37	CCDS44949.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.462147	0.00171	.	.	ENSG00000231738	ENST00000532498	T	0.77098	-1.07	3.82	-0.633	0.11519	.	.	.	.	.	T	0.47451	0.1446	N	0.04508	-0.205	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.32428	-0.9907	9	0.10377	T	0.69	.	3.3683	0.07211	0.3702:0.2052:0.4246:0.0	.	105	P0C672	TSN19_HUMAN	V	105	ENSP00000433816:A105V	ENSP00000433816:A105V	A	-	2	0	TSPAN19	83941260	0.003000	0.15002	0.002000	0.10522	0.009000	0.06853	-0.717000	0.04986	0.046000	0.15833	0.609000	0.83330	GCA		0.313	TSPAN19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388240.2	NM_001100917	
CEP290	80184	broad.mit.edu	37	12	88478411	88478411	+	Frame_Shift_Del	DEL	T	T	-	rs62640572		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:88478411delT	ENST00000552810.1	-	35	4999	c.4656delA	c.(4654-4656)aaafs	p.K1552fs	CEP290_ENST00000397838.3_Frame_Shift_Del_p.K612fs|CEP290_ENST00000547691.2_Frame_Shift_Del_p.K612fs|CEP290_ENST00000309041.7_Frame_Shift_Del_p.K1554fs	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1552					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)		p.E1555fs*4(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						ATACTTCTTCTTTTTGATTTA	0.328																																					p.K1552fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.4656delA	12	GRCh37	CD062131	CEP290	D	rs62640572	.						174.0	161.0	165.0					12																	88478411		1808	4076	5884	87002542	SO:0001589	frameshift_variant	80184	exon35			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.4656delA	12.37:g.88478411delT	ENSP00000448012:p.Lys1552fs	Somatic		Capture	Illumina HiSeq	Phase_I	87002542	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Frame_Shift_Del	DEL	ENST00000552810.1	37	CCDS55858.1																																																																																				0.328	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
NDUFA12	55967	broad.mit.edu	37	12	95365364	95365364	+	Missense_Mutation	SNP	G	G	T	rs145916701		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:95365364G>T	ENST00000327772.2	-	4	379	c.290C>A	c.(289-291)cCt>cAt	p.P97H	NDUFA12_ENST00000547157.1_Intron|NDUFA12_ENST00000550187.1_5'UTR|NDUFA12_ENST00000547986.1_3'UTR	NM_018838.4	NP_061326.1	Q9UI09	NDUAC_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12	97					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.P97H(1)		endometrium(1)|large_intestine(2)|lung(3)	6						TGTTGTTGGAGGATCATCAGT	0.418																																					p.P97H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C290A	12						.						135.0	120.0	125.0					12																	95365364		2203	4300	6503	93889495	SO:0001583	missense	55967	exon4			BC005936	CCDS9050.1, CCDS58263.1	12q22	2011-07-04			ENSG00000184752	ENSG00000184752		"""Mitochondrial respiratory chain complex / Complex I"""	23987	protein-coding gene	gene with protein product	"""complex I B17.2 subunit"""	614530				10830904, 9827566	Standard	NM_018838		Approved	DAP13, B17.2	uc001tdl.4	Q9UI09		ENST00000327772.2:c.290C>A	12.37:g.95365364G>T	ENSP00000330737:p.Pro97His	Somatic		Capture	Illumina HiSeq	Phase_I	93889495	NM_018838	F8VQS7|Q53XX0|Q9BRV6	Missense_Mutation	SNP	ENST00000327772.2	37	CCDS9050.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.960836	0.92791	.	.	ENSG00000184752	ENST00000327772	T	0.49139	0.79	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.73745	0.3626	M	0.91038	3.17	0.80722	D	1	D	0.56287	0.975	P	0.59221	0.854	T	0.80500	-0.1355	10	0.87932	D	0	-13.5885	19.3015	0.94145	0.0:0.0:1.0:0.0	.	97	Q9UI09	NDUAC_HUMAN	H	97	ENSP00000330737:P97H	ENSP00000330737:P97H	P	-	2	0	NDUFA12	93889495	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	8.709000	0.91379	2.552000	0.86080	0.561000	0.74099	CCT		0.418	NDUFA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407245.2	NM_018838	
USP44	84101	broad.mit.edu	37	12	95927206	95927206	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:95927206C>T	ENST00000258499.3	-	2	1115	c.827G>A	c.(826-828)aGa>aAa	p.R276K	USP44_ENST00000537435.2_Missense_Mutation_p.R276K|USP44_ENST00000552440.1_Missense_Mutation_p.R276K|USP44_ENST00000393091.2_Missense_Mutation_p.R276K	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	276	USP.				mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.R276K(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						TCCCAAATTTCTCAATCCTGT	0.348																																					p.R276K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G827A	12						.						96.0	97.0	96.0					12																	95927206		2203	4300	6503	94451337	SO:0001583	missense	84101	exon2			AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"""Ubiquitin-specific peptidases"""	20064	protein-coding gene	gene with protein product		610993	"""ubiquitin specific protease 44"""			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.827G>A	12.37:g.95927206C>T	ENSP00000258499:p.Arg276Lys	Somatic		Capture	Illumina HiSeq	Phase_I	94451337	NM_001042403	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	37	CCDS9053.1	.	.	.	.	.	.	.	.	.	.	C	19.60	3.858734	0.71834	.	.	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000552440;ENST00000537435	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	4.87	3.98	0.46160	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.37625	0.1010	L	0.52126	1.63	0.46416	D	0.999039	P	0.50156	0.932	P	0.51453	0.67	T	0.07558	-1.0766	10	0.27785	T	0.31	.	13.5225	0.61576	0.0:0.9236:0.0:0.0763	.	276	Q9H0E7	UBP44_HUMAN	K	276	ENSP00000258499:R276K;ENSP00000376806:R276K;ENSP00000448670:R276K;ENSP00000442629:R276K	ENSP00000258499:R276K	R	-	2	0	USP44	94451337	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	7.252000	0.78309	1.179000	0.42884	0.491000	0.48974	AGA		0.348	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147	
AMDHD1	144193	broad.mit.edu	37	12	96350611	96350611	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:96350611T>C	ENST00000266736.2	+	4	564	c.458T>C	c.(457-459)gTg>gCg	p.V153A		NM_152435.2	NP_689648.2	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	153					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	imidazolonepropionase activity (GO:0050480)|metal ion binding (GO:0046872)	p.V153A(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|skin(1)	22						ACCACGCTGGTGGAGTGCAAG	0.637																																					p.V153A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T458C	12						.						91.0	80.0	84.0					12																	96350611		2203	4300	6503	94874742	SO:0001583	missense	144193	exon4			AB075878	CCDS9057.1	12q23.1	2006-02-02				ENSG00000139344			28577	protein-coding gene	gene with protein product							Standard	NM_152435		Approved	MGC35366	uc001tel.2	Q96NU7	OTTHUMG00000170353	ENST00000266736.2:c.458T>C	12.37:g.96350611T>C	ENSP00000266736:p.Val153Ala	Somatic		Capture	Illumina HiSeq	Phase_I	94874742	NM_152435	A8K463|Q68CI8	Missense_Mutation	SNP	ENST00000266736.2	37	CCDS9057.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.123559	0.56613	.	.	ENSG00000139344	ENST00000266736	T	0.49432	0.78	5.57	3.22	0.36961	Metal-dependent hydrolase, composite domain (1);	0.109186	0.64402	N	0.000008	T	0.44371	0.1290	L	0.61218	1.895	0.58432	D	0.99999	B	0.15141	0.012	B	0.20955	0.032	T	0.34079	-0.9843	10	0.54805	T	0.06	-15.5681	9.8928	0.41300	0.0:0.1387:0.0:0.8612	.	153	Q96NU7	HUTI_HUMAN	A	153	ENSP00000266736:V153A	ENSP00000266736:V153A	V	+	2	0	AMDHD1	94874742	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.926000	0.56491	0.410000	0.25675	0.402000	0.26972	GTG		0.637	AMDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408640.1	NM_152435	
PWP1	11137	broad.mit.edu	37	12	108086790	108086790	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:108086790delG	ENST00000412830.3	+	5	587	c.419delG	c.(418-420)cgtfs	p.R140fs	PWP1_ENST00000541166.1_Frame_Shift_Del_p.R78fs	NM_007062.1	NP_008993.1	Q13610	PWP1_HUMAN	PWP1 homolog (S. cerevisiae)	140					transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.R140fs*5(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(8)|lung(6)|urinary_tract(1)	23						CAATATGAACGTGAAGATTTC	0.373																																					p.R140fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.419delG	12						.						108.0	109.0	109.0					12																	108086790		2203	4300	6503	106610920	SO:0001589	frameshift_variant	11137	exon5			BC000067	CCDS9114.1	12q23.3	2013-06-10				ENSG00000136045		"""WD repeat domain containing"""	17015	protein-coding gene	gene with protein product	"""endonuclein"""					7828893, 11850830	Standard	NM_007062		Approved	IEF-SSP-9502	uc001tmo.1	Q13610	OTTHUMG00000169913	ENST00000412830.3:c.419delG	12.37:g.108086790delG	ENSP00000387365:p.Arg140fs	Somatic		Capture	Illumina HiSeq	Phase_I	106610920	NM_007062	A8K3R6|Q7Z3X9	Frame_Shift_Del	DEL	ENST00000412830.3	37	CCDS9114.1																																																																																				0.373	PWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406539.1	NM_007062	
SSH1	54434	broad.mit.edu	37	12	109194657	109194657	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:109194657delA	ENST00000326495.5	-	12	1140	c.1047delT	c.(1045-1047)tttfs	p.F349fs	SSH1_ENST00000551165.1_Frame_Shift_Del_p.F349fs|SSH1_ENST00000360239.3_Frame_Shift_Del_p.F37fs|SSH1_ENST00000326470.5_Frame_Shift_Del_p.F360fs	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	349	Tyrosine-protein phosphatase.				actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.P350fs*30(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ATAAGCCAGGAAAAAAATTAT	0.348																																					p.F360fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1080delT	12						.						87.0	96.0	93.0					12																	109194657		2203	4300	6503	107718786	SO:0001589	frameshift_variant	54434	exon11			BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30579	protein-coding gene	gene with protein product		606778	"""slingshot homolog 1 (Drosophila)"""			10718198, 11832213	Standard	NM_018984		Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.1047delT	12.37:g.109194657delA	ENSP00000315713:p.Phe349fs	Somatic		Capture	Illumina HiSeq	Phase_I	107718786	NM_001161331	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Frame_Shift_Del	DEL	ENST00000326495.5	37	CCDS9121.1																																																																																				0.348	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984	
FBXO21	23014	broad.mit.edu	37	12	117624320	117624320	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:117624320delA	ENST00000330622.5	-	3	431	c.432delT	c.(430-432)tttfs	p.F144fs	FBXO21_ENST00000549689.1_5'UTR|FBXO21_ENST00000427718.2_Frame_Shift_Del_p.F144fs			O94952	FBX21_HUMAN	F-box protein 21	144					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	ubiquitin ligase complex (GO:0000151)	DNA binding (GO:0003677)|ubiquitin-protein transferase activity (GO:0004842)	p.F144fs*9(1)		breast(4)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|pancreas(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	29	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)		GTTCATCCTCAAAAAAAATCT	0.373																																					p.F144fs	GBM(168;452 2038 13535 17701 43680)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.432delT	12						.						98.0	97.0	97.0					12																	117624320		2203	4300	6503	116108703	SO:0001589	frameshift_variant	23014	exon3			AB020682	CCDS9184.1, CCDS44989.1	12q24.23	2004-06-15	2004-06-15					"""F-boxes /  ""other"""""	13592	protein-coding gene	gene with protein product		609095	"""F-box only protein 21"""			10048485, 10531035	Standard	NM_033624		Approved	FBX21, KIAA0875	uc001twk.3	O94952	OTTHUMG00000169495	ENST00000330622.5:c.432delT	12.37:g.117624320delA	ENSP00000328187:p.Phe144fs	Somatic		Capture	Illumina HiSeq	Phase_I	116108703	NM_015002	B3KMF0|Q5BJG0|Q9H087	Frame_Shift_Del	DEL	ENST00000330622.5	37	CCDS9184.1																																																																																				0.373	FBXO21-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404409.1	NM_033624	
MLXIP	22877	broad.mit.edu	37	12	122618185	122618185	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:122618185delC	ENST00000319080.7	+	9	1515	c.1383delC	c.(1381-1383)aacfs	p.N461fs	MLXIP_ENST00000538698.1_Frame_Shift_Del_p.N68fs|MLXIP_ENST00000377037.2_Frame_Shift_Del_p.N51fs					MLX interacting protein									p.P463fs*46(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		CTGCCCTGAACCCCCCGGCTC	0.637																																					p.N461fs	Esophageal Squamous(105;787 1493 16200 18566 52466)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1383delC	12						.						24.0	29.0	27.0					12																	122618185		2125	4228	6353	121184138	SO:0001589	frameshift_variant	22877	exon9			AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"""Basic helix-loop-helix proteins"""	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.1383delC	12.37:g.122618185delC	ENSP00000312834:p.Asn461fs	Somatic		Capture	Illumina HiSeq	Phase_I	121184138	NM_014938		Frame_Shift_Del	DEL	ENST00000319080.7	37																																																																																					0.637	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938	
DNAH10	196385	broad.mit.edu	37	12	124379234	124379234	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:124379234delC	ENST00000409039.3	+	53	8915	c.8890delC	c.(8890-8892)cccfs	p.P2964fs		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2964	AAA 4. {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.Q2965fs*11(1)|p.Q1557fs*11(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GCCCTGGCCTCCCCAAGCCCT	0.448																																					p.P2964fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.8890delC	12						.						105.0	109.0	108.0					12																	124379234		1920	4131	6051	122945187	SO:0001589	frameshift_variant	196385	exon53			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.8890delC	12.37:g.124379234delC	ENSP00000386770:p.Pro2964fs	Somatic		Capture	Illumina HiSeq	Phase_I	122945187	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Frame_Shift_Del	DEL	ENST00000409039.3	37	CCDS9255.2																																																																																				0.448	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
RIMBP2	23504	broad.mit.edu	37	12	130912764	130912764	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:130912764delC	ENST00000261655.4	-	12	2484	c.2321delG	c.(2320-2322)ggafs	p.G774fs		NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	774					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.G774fs*16(1)		NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CCGCCTCCTTCCCCCATCTTC	0.622																																					p.G774fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2321delG	12						.						81.0	63.0	69.0					12																	130912764		2203	4300	6503	129478717	SO:0001589	frameshift_variant	23504	exon12			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.2321delG	12.37:g.130912764delC	ENSP00000261655:p.Gly774fs	Somatic		Capture	Illumina HiSeq	Phase_I	129478717	NM_015347	Q96ID2	Frame_Shift_Del	DEL	ENST00000261655.4	37	CCDS31925.1																																																																																				0.622	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	
EP400	57634	broad.mit.edu	37	12	132530095	132530095	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr12:132530095C>T	ENST00000333577.4	+	39	7233	c.7124C>T	c.(7123-7125)gCg>gTg	p.A2375V	EP400_ENST00000332482.4_Missense_Mutation_p.A2302V|EP400_ENST00000389562.2_Missense_Mutation_p.A2338V|EP400_ENST00000389561.2_Missense_Mutation_p.A2339V|EP400_ENST00000330386.6_Missense_Mutation_p.A2258V			Q96L91	EP400_HUMAN	E1A binding protein p400	2375	Myb-like. {ECO:0000255|PROSITE- ProRule:PRU00133}.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.A2338V(1)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		GAGGACTGGGCGCTGCTGCAG	0.577																																					p.A2338V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C7013T	12						.						70.0	68.0	69.0					12																	132530095		2203	4300	6503	131096048	SO:0001583	missense	57634	exon38			U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.7124C>T	12.37:g.132530095C>T	ENSP00000333602:p.Ala2375Val	Somatic		Capture	Illumina HiSeq	Phase_I	131096048	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	C	15.96	2.987435	0.53934	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.68641	0.3023	M	0.86178	2.8	0.49299	D	0.999772	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.64506	0.926;0.926;0.926	T	0.71859	-0.4465	10	0.54805	T	0.06	.	19.6322	0.95713	0.0:1.0:0.0:0.0	.	2339;2258;2338	Q96L91-2;Q96L91-4;Q96L91-5	.;.;.	V	2375;2339;2338;2302;2258;2339	ENSP00000333602:A2375V;ENSP00000374212:A2339V;ENSP00000374213:A2338V;ENSP00000331737:A2302V;ENSP00000330620:A2258V	ENSP00000330620:A2258V	A	+	2	0	EP400	131096048	1.000000	0.71417	0.997000	0.53966	0.611000	0.37282	7.476000	0.81055	2.652000	0.90054	0.655000	0.94253	GCG		0.577	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
MYO16	23026	broad.mit.edu	37	13	109779804	109779804	+	Silent	SNP	G	G	A	rs151007439	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:109779804G>A	ENST00000357550.2	+	30	3932	c.3891G>A	c.(3889-3891)ccG>ccA	p.P1297P	MYO16_ENST00000457511.2_Silent_p.P809P|MYO16_ENST00000356711.2_Silent_p.P1297P	NM_001198950.1	NP_001185879.1			myosin XVI									p.P1297P(2)		NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			AACAGCCCCCGCCCAAGCCAA	0.652													G|||	2	0.000399361	0.0008	0.0	5008	,	,		12247	0.0		0.001	False		,,,				2504	0.0				p.P1319P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G3957A	13						.	G	,	1,4405	2.1+/-5.4	0,1,2202	32.0	34.0	34.0		3957,3891	-7.2	0.9	13	dbSNP_134	34	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MYO16	NM_001198950.1,NM_015011.1	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	1319/1881,1297/1859	109779804	1,13005	2203	4300	6503	108577805	SO:0001819	synonymous_variant	23026	exon31				CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.3891G>A	13.37:g.109779804G>A		Somatic		Capture	Illumina HiSeq	Phase_I	108577805	NM_001198950		Silent	SNP	ENST00000357550.2	37	CCDS32008.1																																																																																				0.652	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
COL4A1	1282	broad.mit.edu	37	13	110818594	110818594	+	Missense_Mutation	SNP	C	C	T	rs202209298		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:110818594C>T	ENST00000375820.4	-	45	4127	c.4006G>A	c.(4006-4008)Gtc>Atc	p.V1336I	COL4A1_ENST00000467182.1_5'Flank	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1336	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)	p.V1336I(2)|p.V979I(2)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			GCTCCCGGGACGCCTTGATCG	0.478													c|||	1	0.000199681	0.0	0.0	5008	,	,		18953	0.001		0.0	False		,,,				2504	0.0				p.V1336I												.	.	4	Substitution - Missense(4)	large_intestine(2)|endometrium(2)	c.G4006A	13						.	T	ILE/VAL	0,4406		0,0,2203	186.0	170.0	175.0		4006	-8.8	0.0	13		175	1,8599	1.2+/-3.3	0,1,4299	no	missense	COL4A1	NM_001845.4	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	1336/1670	110818594	1,13005	2203	4300	6503	109616595	SO:0001583	missense	1282	exon45			J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.4006G>A	13.37:g.110818594C>T	ENSP00000364979:p.Val1336Ile	Somatic		Capture	Illumina HiSeq	Phase_I	109616595	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	37	CCDS9511.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	c	0.427	-0.905261	0.02453	0.0	1.16E-4	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198	D	0.93547	-3.24	4.68	-8.81	0.00813	.	0.660183	0.14714	N	0.302736	T	0.75421	0.3847	N	0.17631	0.505	0.80722	D	1	P	0.37824	0.609	B	0.25506	0.061	T	0.68409	-0.5416	10	0.18710	T	0.47	.	1.7632	0.02996	0.2823:0.1196:0.1317:0.4663	.	1336	P02462	CO4A1_HUMAN	I	979;1336;985	ENSP00000364979:V1336I	ENSP00000364973:V979I	V	-	1	0	COL4A1	109616595	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-0.744000	0.04839	-1.899000	0.01098	-2.030000	0.00424	GTC		0.478	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
COL4A2	1284	broad.mit.edu	37	13	111156251	111156251	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:111156251T>C	ENST00000360467.5	+	44	4502	c.4196T>C	c.(4195-4197)gTc>gCc	p.V1399A	COL4A2-AS1_ENST00000417970.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1399	Triple-helical region.		V -> I (in dbSNP:rs45520539). {ECO:0000269|PubMed:22209247, ECO:0000269|PubMed:3582677}.		angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)	p.V1399A(1)		NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			AAGATTGCCGTCCAACCAGGG	0.682																																					p.V1399A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T4196C	13						.						47.0	49.0	49.0					13																	111156251		1814	4064	5878	109954252	SO:0001583	missense	1284	exon44			AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.4196T>C	13.37:g.111156251T>C	ENSP00000353654:p.Val1399Ala	Somatic		Capture	Illumina HiSeq	Phase_I	109954252	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	37	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	T	5.715	0.316503	0.10845	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.92911	-3.13	5.2	-2.52	0.06346	.	1.658900	0.03478	N	0.214603	D	0.82825	0.5121	N	0.19112	0.55	0.09310	N	1	B	0.18741	0.03	B	0.28139	0.086	T	0.73867	-0.3847	10	0.02654	T	1	.	5.5612	0.17144	0.1375:0.4697:0.0:0.3927	.	1399	P08572	CO4A2_HUMAN	A	1399	ENSP00000353654:V1399A	ENSP00000257309:V1399A	V	+	2	0	COL4A2	109954252	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.098000	0.11024	-0.540000	0.06265	-0.411000	0.06167	GTC		0.682	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
CARS2	79587	broad.mit.edu	37	13	111357871	111357871	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:111357871G>T	ENST00000257347.4	-	2	335	c.272C>A	c.(271-273)gCt>gAt	p.A91D	CARS2_ENST00000535398.1_Intron	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	91					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)	p.A91D(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	AACTCACCAAGCATGGCCAAG	0.383																																					p.A91D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C272A	13						.						86.0	79.0	81.0					13																	111357871		2203	4300	6503	110155872	SO:0001583	missense	79587	exon2			BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	25695	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 2, mitochondrial (putative)"""	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.272C>A	13.37:g.111357871G>T	ENSP00000257347:p.Ala91Asp	Somatic		Capture	Illumina HiSeq	Phase_I	110155872	NM_024537	Q8NI84|Q96IV4	Missense_Mutation	SNP	ENST00000257347.4	37	CCDS9514.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.448562	0.84101	.	.	ENSG00000134905	ENST00000257347;ENST00000542709	T	0.40756	1.02	4.94	4.08	0.47627	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.78496	0.4292	H	0.99261	4.49	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86629	0.1884	10	0.87932	D	0	.	13.4483	0.61155	0.0:0.0:0.8415:0.1585	.	91	Q9HA77	SYCM_HUMAN	D	91;82	ENSP00000257347:A91D	ENSP00000257347:A91D	A	-	2	0	CARS2	110155872	1.000000	0.71417	0.991000	0.47740	0.898000	0.52572	8.045000	0.89436	1.050000	0.40346	0.455000	0.32223	GCT		0.383	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537	
SPATA13	221178	broad.mit.edu	37	13	24863160	24863160	+	Silent	SNP	G	G	A	rs188597102	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:24863160G>A	ENST00000382095.4	+	7	1223	c.816G>A	c.(814-816)aaG>aaA	p.K272K	SPATA13_ENST00000409126.1_Silent_p.K132K|SPATA13_ENST00000424834.2_Silent_p.K897K|RP11-307N16.6_ENST00000382141.4_Silent_p.K775K|SPATA13_ENST00000343003.6_Silent_p.K216K|SPATA13_ENST00000382108.3_Silent_p.K897K|SPATA13_ENST00000399949.2_Silent_p.K194K	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	272	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.K272K(1)		breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		AGTGCCGCAAGCACACAGGAA	0.363													G|||	4	0.000798722	0.003	0.0	5008	,	,		17353	0.0		0.0	False		,,,				2504	0.0				p.K897K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2691A	13						.						58.0	58.0	58.0					13																	24863160		2203	4300	6503	23761160	SO:0001819	synonymous_variant	221178	exon8			AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.816G>A	13.37:g.24863160G>A		Somatic		Capture	Illumina HiSeq	Phase_I	23761160	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	37	CCDS9305.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	8.475	0.858480	0.17178	.	.	ENSG00000182957	ENST00000424834	.	.	.	5.54	1.15	0.20763	.	.	.	.	.	T	0.46054	0.1373	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37776	-0.9691	4	.	.	.	.	6.9591	0.24587	0.644:0.0:0.356:0.0	.	.	.	.	T	935	.	.	A	+	1	0	SPATA13	23761160	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	1.705000	0.37867	0.263000	0.21812	0.462000	0.41574	GCA		0.363	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023	
ATP12A	479	broad.mit.edu	37	13	25272901	25272901	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:25272901G>A	ENST00000381946.3	+	12	1785	c.1618G>A	c.(1618-1620)Ggc>Agc	p.G540S	ATP12A_ENST00000218548.6_Missense_Mutation_p.G546S			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	540					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.G540S(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)		CATGATCAACGGCGAGGAGCA	0.617																																					p.G546S	Pancreas(156;1582 1935 18898 22665 26498)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1636A	13						.						130.0	121.0	124.0					13																	25272901		2203	4300	6503	24170901	SO:0001583	missense	479	exon12			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.1618G>A	13.37:g.25272901G>A	ENSP00000371372:p.Gly540Ser	Somatic		Capture	Illumina HiSeq	Phase_I	24170901	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.432387	0.62844	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.82711	-1.64;-1.64	5.89	5.05	0.67936	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.90096	0.6906	M	0.76002	2.32	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.985;1.0	D	0.91021	0.4857	10	0.87932	D	0	.	12.8143	0.57657	0.0787:0.0:0.9213:0.0	.	546;540	P54707-2;P54707	.;AT12A_HUMAN	S	546;540	ENSP00000218548:G546S;ENSP00000371372:G540S	ENSP00000218548:G546S	G	+	1	0	ATP12A	24170901	1.000000	0.71417	0.651000	0.29564	0.001000	0.01503	9.695000	0.98691	1.508000	0.48769	-0.136000	0.14681	GGC		0.617	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
CENPJ	55835	broad.mit.edu	37	13	25457330	25457330	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:25457330C>A	ENST00000381884.4	-	17	4187	c.4002G>T	c.(4000-4002)atG>atT	p.M1334I	CENPJ_ENST00000545981.1_3'UTR|CENPJ_ENST00000493190.1_5'Flank	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	1334					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)	p.M1334I(1)		endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		GCTCCGTGTCCATTAGCACAT	0.383																																					p.M1334I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4002T	13						.						328.0	270.0	290.0					13																	25457330		2203	4300	6503	24355330	SO:0001583	missense	55835	exon17			AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"""centrosomal P4.1-associated protein"""	609279	"""microcephaly, primary autosomal recessive 6"""	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.4002G>T	13.37:g.25457330C>A	ENSP00000371308:p.Met1334Ile	Somatic		Capture	Illumina HiSeq	Phase_I	24355330	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Missense_Mutation	SNP	ENST00000381884.4	37	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.998682	0.54147	.	.	ENSG00000151849	ENST00000381884	T	0.76709	-1.04	5.89	5.05	0.67936	.	0.149650	0.64402	N	0.000001	T	0.74397	0.3711	L	0.56124	1.755	0.80722	D	1	B	0.14012	0.009	B	0.18561	0.022	T	0.72077	-0.4399	10	0.72032	D	0.01	.	13.9778	0.64284	0.0:0.926:0.0:0.074	.	1334	Q9HC77	CENPJ_HUMAN	I	1334	ENSP00000371308:M1334I	ENSP00000371308:M1334I	M	-	3	0	CENPJ	24355330	1.000000	0.71417	0.994000	0.49952	0.680000	0.39746	5.399000	0.66314	1.497000	0.48584	0.591000	0.81541	ATG		0.383	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451	
AMER2	219287	broad.mit.edu	37	13	25744073	25744073	+	Missense_Mutation	SNP	G	G	A	rs201439289		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:25744073G>A	ENST00000515384.1	-	1	2352	c.1685C>T	c.(1684-1686)cCg>cTg	p.P562L	AMER2_ENST00000381853.3_Missense_Mutation_p.P443L|AMER2_ENST00000357816.2_Missense_Mutation_p.P443L|AMER2-AS1_ENST00000413501.1_lincRNA			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	562					ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.P443L(1)|p.P562L(1)									ACTTCCGTCCGGGTCAGCATA	0.622													G|||	1	0.000199681	0.0	0.0	5008	,	,		18490	0.001		0.0	False		,,,				2504	0.0				p.P562L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1685T	13						.						76.0	72.0	73.0					13																	25744073		2203	4300	6503	24642073	SO:0001583	missense	219287	exon1			AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"""-"""	26360	protein-coding gene	gene with protein product		614659	"""family with sequence similarity 123A"""	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.1685C>T	13.37:g.25744073G>A	ENSP00000426528:p.Pro562Leu	Somatic		Capture	Illumina HiSeq	Phase_I	24642073	NM_152704	Q5RL80|Q5VX56|Q8N593|Q96NN5	Missense_Mutation	SNP	ENST00000515384.1	37	CCDS53859.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	18.84	3.710302	0.68730	.	.	ENSG00000165566	ENST00000357816;ENST00000381853;ENST00000515384	T;T;T	0.62232	0.04;0.04;0.04	5.47	5.47	0.80525	.	0.058466	0.64402	D	0.000001	T	0.75110	0.3805	M	0.80616	2.505	0.80722	D	1	D;D	0.57571	0.98;0.975	P;P	0.52031	0.688;0.561	T	0.79715	-0.1687	10	0.87932	D	0	-15.0612	18.3069	0.90185	0.0:0.0:1.0:0.0	.	562;443	Q8N7J2;Q8N7J2-2	F123A_HUMAN;.	L	443;443;562	ENSP00000350469:P443L;ENSP00000371277:P443L;ENSP00000426528:P562L	ENSP00000350469:P443L	P	-	2	0	FAM123A	24642073	1.000000	0.71417	0.104000	0.21259	0.617000	0.37484	6.083000	0.71326	2.560000	0.86352	0.561000	0.74099	CCG		0.622	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704	
ATP8A2	51761	broad.mit.edu	37	13	26273408	26273408	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:26273408A>C	ENST00000381655.2	+	25	2451	c.2309A>C	c.(2308-2310)aAg>aCg	p.K770T	ATP8A2_ENST00000255283.8_Missense_Mutation_p.K730T|ATP8A2_ENST00000491840.1_3'UTR	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	730					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.K770T(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		CACACCCTGAAGTACGCGCTC	0.562																																					p.K770T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2309C	13						.						88.0	84.0	85.0					13																	26273408		1988	4161	6149	25171408	SO:0001583	missense	51761	exon25			AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"""ATPases / P-type"""	13533	protein-coding gene	gene with protein product		605870	"""ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2"", ""ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"""			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.2309A>C	13.37:g.26273408A>C	ENSP00000371070:p.Lys770Thr	Somatic		Capture	Illumina HiSeq	Phase_I	25171408	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	37	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.222345	0.58560	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	T;T	0.52754	0.65;0.65	5.88	5.88	0.94601	HAD-like domain (1);	0.000000	0.85682	D	0.000000	T	0.54532	0.1864	L	0.28740	0.885	0.80722	D	1	D;D;D	0.67145	0.996;0.995;0.996	D;D;D	0.74023	0.978;0.962;0.982	T	0.46484	-0.9188	10	0.12430	T	0.62	.	16.2824	0.82697	1.0:0.0:0.0:0.0	.	730;550;730	B7Z880;F5GZN5;Q9NTI2	.;.;AT8A2_HUMAN	T	770;730;550	ENSP00000371070:K770T;ENSP00000255283:K730T	ENSP00000255283:K730T	K	+	2	0	ATP8A2	25171408	1.000000	0.71417	0.996000	0.52242	0.922000	0.55478	9.334000	0.96470	2.250000	0.74265	0.533000	0.62120	AAG		0.562	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529	
ATP8A2	51761	broad.mit.edu	37	13	26349060	26349060	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:26349060A>G	ENST00000381655.2	+	27	2784	c.2642A>G	c.(2641-2643)tAc>tGc	p.Y881C	ATP8A2_ENST00000255283.8_Missense_Mutation_p.Y841C|ATP8A2_ENST00000491840.1_3'UTR	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	841					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.Y881C(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		TGCATCTTGTACTGCTTCTAT	0.388																																					p.Y881C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2642G	13						.						152.0	131.0	138.0					13																	26349060		1857	4099	5956	25247060	SO:0001583	missense	51761	exon27			AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"""ATPases / P-type"""	13533	protein-coding gene	gene with protein product		605870	"""ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2"", ""ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"""			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.2642A>G	13.37:g.26349060A>G	ENSP00000371070:p.Tyr881Cys	Somatic		Capture	Illumina HiSeq	Phase_I	25247060	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	37	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.248200	0.80024	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	D;D	0.91068	-2.78;-2.78	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.95661	0.8589	M	0.85542	2.76	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.995;0.999;0.992	D	0.96251	0.9183	10	0.87932	D	0	.	15.8331	0.78773	1.0:0.0:0.0:0.0	.	841;661;841	B7Z880;F5GZN5;Q9NTI2	.;.;AT8A2_HUMAN	C	881;841;661	ENSP00000371070:Y881C;ENSP00000255283:Y841C	ENSP00000255283:Y841C	Y	+	2	0	ATP8A2	25247060	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	9.085000	0.94083	2.315000	0.78130	0.533000	0.62120	TAC		0.388	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529	
GPR12	2835	broad.mit.edu	37	13	27333613	27333613	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:27333613C>T	ENST00000381436.2	-	1	814	c.352G>A	c.(352-354)Ggc>Agc	p.G118S	GPR12_ENST00000405846.3_Missense_Mutation_p.G118S			P47775	GPR12_HUMAN	G protein-coupled receptor 12	118					cellular calcium ion homeostasis (GO:0006874)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)	p.G118S(1)		endometrium(7)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)		ACAATGAGGCCGATCGTGACC	0.542																																					p.G118S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G352A	13						.						117.0	107.0	110.0					13																	27333613		2203	4300	6503	26231613	SO:0001583	missense	2835	exon2			U18548	CCDS9319.1	13q12	2014-06-12			ENSG00000132975	ENSG00000132975		"""GPCR / Class A : Orphans"""	4466	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 84"""	600752				8262253, 8530049	Standard	NM_005288		Approved	GPCR21, PPP1R84	uc010aal.3	P47775	OTTHUMG00000016620	ENST00000381436.2:c.352G>A	13.37:g.27333613C>T	ENSP00000370844:p.Gly118Ser	Somatic		Capture	Illumina HiSeq	Phase_I	26231613	NM_005288	Q5T8P3	Missense_Mutation	SNP	ENST00000381436.2	37	CCDS9319.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.933290	0.92458	.	.	ENSG00000132975	ENST00000405846;ENST00000381436	T;T	0.35789	1.29;1.29	5.36	5.36	0.76844	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.55433	0.1920	L	0.47078	1.49	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.51608	-0.8684	10	0.44086	T	0.13	.	19.0843	0.93196	0.0:1.0:0.0:0.0	.	118	P47775	GPR12_HUMAN	S	118	ENSP00000384932:G118S;ENSP00000370844:G118S	ENSP00000370844:G118S	G	-	1	0	GPR12	26231613	1.000000	0.71417	0.303000	0.25071	0.978000	0.69477	7.685000	0.84117	2.532000	0.85374	0.561000	0.74099	GGC		0.542	GPR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044257.2		
PDS5B	23047	broad.mit.edu	37	13	33327626	33327626	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:33327626A>G	ENST00000315596.10	+	25	3079	c.2893A>G	c.(2893-2895)Aat>Gat	p.N965D		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	965					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.N965D(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		TTTGGTGAAAAATATAAATGT	0.418																																					p.N965D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2893G	13						.						88.0	83.0	85.0					13																	33327626		1870	4111	5981	32225626	SO:0001583	missense	23047	exon25			AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.2893A>G	13.37:g.33327626A>G	ENSP00000313851:p.Asn965Asp	Somatic		Capture	Illumina HiSeq	Phase_I	32225626	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	37	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	A	17.09	3.299980	0.60195	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	T	0.67698	-0.28	5.02	5.02	0.67125	Armadillo-like helical (1);Armadillo-type fold (1);	0.045716	0.85682	D	0.000000	T	0.68796	0.3040	N	0.19112	0.55	0.58432	D	0.999999	D	0.69078	0.997	D	0.81914	0.995	T	0.66929	-0.5799	10	0.25106	T	0.35	-4.3917	14.7197	0.69297	1.0:0.0:0.0:0.0	.	965	Q9NTI5	PDS5B_HUMAN	D	965	ENSP00000313851:N965D	ENSP00000313851:N965D	N	+	1	0	PDS5B	32225626	1.000000	0.71417	0.987000	0.45799	0.990000	0.78478	9.233000	0.95337	1.872000	0.54250	0.397000	0.26171	AAT		0.418	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032	
KL	9365	broad.mit.edu	37	13	33635103	33635103	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:33635103C>T	ENST00000380099.3	+	4	1895	c.1887C>T	c.(1885-1887)gtC>gtT	p.V629V	KL_ENST00000487852.1_3'UTR|KL_ENST00000426690.2_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	629	Glycosyl hydrolase-1 2.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)	p.V629V(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		TTGTCCGTGTCAACATCACCC	0.642																																					p.V629V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1887T	13						.						78.0	75.0	76.0					13																	33635103		2203	4300	6503	32533103	SO:0001819	synonymous_variant	9365	exon4			AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.1887C>T	13.37:g.33635103C>T		Somatic		Capture	Illumina HiSeq	Phase_I	32533103	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	37	CCDS9347.1																																																																																				0.642	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
SOHLH2	54937	broad.mit.edu	37	13	36748935	36748935	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:36748935G>A	ENST00000379881.3	-	7	801	c.713C>T	c.(712-714)gCg>gTg	p.A238V	SOHLH2_ENST00000554962.1_Missense_Mutation_p.A315V|CCDC169-SOHLH2_ENST00000511166.1_Missense_Mutation_p.A315V	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	238	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A238V(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		AACTGAAGCCGCATCATTCTT	0.423																																					p.A238V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C713T	13						.						87.0	85.0	86.0					13																	36748935		2203	4300	6503	35646935	SO:0001583	missense	54937	exon7			AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"""Basic helix-loop-helix proteins"""	26026	protein-coding gene	gene with protein product	"""spermatogenesis associated 28"""					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.713C>T	13.37:g.36748935G>A	ENSP00000369210:p.Ala238Val	Somatic		Capture	Illumina HiSeq	Phase_I	35646935	NM_017826	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Missense_Mutation	SNP	ENST00000379881.3	37	CCDS9355.1	.	.	.	.	.	.	.	.	.	.	G	2.989	-0.208647	0.06140	.	.	ENSG00000120669;ENSG00000120669;ENSG00000250709	ENST00000379881;ENST00000554962;ENST00000511166	D;D;D	0.97870	-4.58;-4.58;-4.58	5.11	1.36	0.22044	Helix-loop-helix DNA-binding (5);	0.805136	0.11273	N	0.581183	D	0.88130	0.6354	N	0.00926	-1.1	0.09310	N	1	B;B	0.18863	0.031;0.031	B;B	0.17722	0.019;0.019	T	0.81865	-0.0736	10	0.15952	T	0.53	-0.4171	6.2825	0.21015	0.4319:0.0:0.5681:0.0	.	315;238	B4DX90;Q9NX45	.;SOLH2_HUMAN	V	238;315;315	ENSP00000369210:A238V;ENSP00000451542:A315V;ENSP00000421868:A315V	ENSP00000421868:A315V	A	-	2	0	CCDC169-SOHLH2;SOHLH2	35646935	0.001000	0.12720	0.000000	0.03702	0.095000	0.18619	0.841000	0.27613	0.177000	0.19895	0.650000	0.86243	GCG		0.423	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826	
TRPC4	7223	broad.mit.edu	37	13	38320306	38320306	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:38320306T>C	ENST00000379705.3	-	3	1522	c.665A>G	c.(664-666)cAg>cGg	p.Q222R	TRPC4_ENST00000355779.2_Missense_Mutation_p.Q222R|TRPC4_ENST00000379681.3_Missense_Mutation_p.Q222R|TRPC4_ENST00000338947.5_Intron|TRPC4_ENST00000447043.1_Missense_Mutation_p.Q222R|TRPC4_ENST00000379679.1_Intron|TRPC4_ENST00000426868.2_Missense_Mutation_p.Q222R|TRPC4_ENST00000379673.2_Missense_Mutation_p.Q222R|TRPC4_ENST00000358477.2_Missense_Mutation_p.Q222R			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	222					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.Q222R(2)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		CCAACTTAACTGAAAGGCTGT	0.483																																					p.Q222R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A665G	13						.						113.0	100.0	105.0					13																	38320306		2203	4300	6503	37218306	SO:0001583	missense	7223	exon3			U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.665A>G	13.37:g.38320306T>C	ENSP00000369027:p.Gln222Arg	Somatic		Capture	Illumina HiSeq	Phase_I	37218306	NM_001135957	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	T	11.68	1.711487	0.30322	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000426868;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	T;T;T;T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04;-1.04;-1.04;-1.04	5.98	5.98	0.97165	Transient receptor potential II (1);	0.052428	0.85682	D	0.000000	T	0.61060	0.2317	N	0.04959	-0.14	0.36653	D	0.8775	B;B;B;B;B	0.11235	0.001;0.003;0.004;0.001;0.001	B;B;B;B;B	0.14578	0.005;0.011;0.004;0.005;0.009	T	0.61212	-0.7108	10	0.29301	T	0.29	-24.3065	16.4696	0.84102	0.0:0.0:0.0:1.0	.	222;222;222;222;222	Q9UBN4-3;Q9UBN4-4;Q9UBN4-5;Q9UBN4-2;Q9UBN4	.;.;.;.;TRPC4_HUMAN	R	222	ENSP00000369027:Q222R;ENSP00000369003:Q222R;ENSP00000410133:Q222R;ENSP00000348025:Q222R;ENSP00000351264:Q222R;ENSP00000368995:Q222R;ENSP00000414316:Q222R	ENSP00000348025:Q222R	Q	-	2	0	TRPC4	37218306	1.000000	0.71417	0.964000	0.40570	0.996000	0.88848	3.363000	0.52321	2.289000	0.77006	0.482000	0.46254	CAG		0.483	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
FREM2	341640	broad.mit.edu	37	13	39263381	39263381	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:39263381G>A	ENST00000280481.7	+	1	2116	c.1900G>A	c.(1900-1902)Gca>Aca	p.A634T		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	634					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A634T(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GAAGGAGGGGGCATTTTATGA	0.557																																					p.A634T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1900A	13						.						77.0	74.0	75.0					13																	39263381		2203	4300	6503	38161381	SO:0001583	missense	341640	exon1			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.1900G>A	13.37:g.39263381G>A	ENSP00000280481:p.Ala634Thr	Somatic		Capture	Illumina HiSeq	Phase_I	38161381	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	1.728	-0.494928	0.04322	.	.	ENSG00000150893	ENST00000280481	T	0.18810	2.19	5.94	-2.03	0.07365	.	1.132450	0.06236	N	0.689592	T	0.07728	0.0194	N	0.03115	-0.41	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32587	-0.9901	10	0.29301	T	0.29	.	2.7943	0.05397	0.4151:0.1076:0.3621:0.1151	.	634	Q5SZK8	FREM2_HUMAN	T	634	ENSP00000280481:A634T	ENSP00000280481:A634T	A	+	1	0	FREM2	38161381	0.000000	0.05858	0.000000	0.03702	0.550000	0.35303	-0.525000	0.06214	-0.091000	0.12440	0.561000	0.74099	GCA		0.557	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
MED4	29079	broad.mit.edu	37	13	48655810	48655810	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:48655810G>T	ENST00000258648.2	-	5	504	c.479C>A	c.(478-480)gCt>gAt	p.A160D	MED4_ENST00000378586.1_Missense_Mutation_p.A114D|MED4_ENST00000495013.1_5'Flank|MED4-AS1_ENST00000422483.1_RNA	NM_014166.3	NP_054885.1	Q9NPJ6	MED4_HUMAN	mediator complex subunit 4	160					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.A160D(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)	8		all_cancers(8;2.93e-25)|all_epithelial(8;4.38e-13)|all_lung(13;7.37e-06)|all_hematologic(8;8.61e-05)|Breast(56;0.000141)|Lung NSC(96;0.000518)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.00559)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;5.18e-07)		AGCACATACAGCATTACTTGC	0.373																																					p.A160D	Pancreas(38;399 1016 9170 13426 20145)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C479A	13						.						116.0	107.0	110.0					13																	48655810		2203	4300	6503	47553811	SO:0001583	missense	29079	exon5			AF161475	CCDS9408.1, CCDS59241.1	13q14.12	2008-02-05	2007-07-30	2004-11-09	ENSG00000136146	ENSG00000136146			17903	protein-coding gene	gene with protein product		605718	"""vitamin D receptor interacting protein"", ""mediator of RNA polymerase II transcription, subunit 4 homolog (S. cerevisiae)"""	VDRIP		10235266, 11042152	Standard	NM_014166		Approved	HSPC126, DRIP36, TRAP36	uc001vby.2	Q9NPJ6	OTTHUMG00000016891	ENST00000258648.2:c.479C>A	13.37:g.48655810G>T	ENSP00000258648:p.Ala160Asp	Somatic		Capture	Illumina HiSeq	Phase_I	47553811	NM_014166	B4DX67|Q53GB4|Q53H68|Q5T912|Q6FHC4|Q6IA79|Q9BS95|Q9NYR5	Missense_Mutation	SNP	ENST00000258648.2	37	CCDS9408.1	.	.	.	.	.	.	.	.	.	.	G	31	5.077545	0.94000	.	.	ENSG00000136146	ENST00000258648;ENST00000378594;ENST00000378586;ENST00000417167	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.80025	0.4548	M	0.75615	2.305	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.954	T	0.81870	-0.0734	9	0.87932	D	0	-15.2005	18.4476	0.90690	0.0:0.0:1.0:0.0	.	138;160	E9PDW1;Q9NPJ6	.;MED4_HUMAN	D	160;138;114;138	.	ENSP00000258648:A160D	A	-	2	0	MED4	47553811	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.756000	0.98918	2.610000	0.88304	0.449000	0.29647	GCT		0.373	MED4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044863.1	NM_014166	
CDADC1	81602	broad.mit.edu	37	13	49848470	49848470	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:49848470G>A	ENST00000251108.6	+	6	1157	c.1044G>A	c.(1042-1044)ggG>ggA	p.G348G	CDADC1_ENST00000444959.1_Silent_p.G150G	NM_001193478.1|NM_030911.3	NP_001180407.1|NP_112173.1	Q9BWV3	CDAC1_HUMAN	cytidine and dCMP deaminase domain containing 1	348							hydrolase activity (GO:0016787)|zinc ion binding (GO:0008270)	p.G348G(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	16		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)		GGGCAGAAGGGAAATCTGTAA	0.338																																					p.G348G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1044A	13						.						104.0	116.0	112.0					13																	49848470		2203	4300	6503	48746471	SO:0001819	synonymous_variant	81602	exon6			AY027525	CCDS9415.1	13q14.11	2008-02-05			ENSG00000102543	ENSG00000102543			20299	protein-coding gene	gene with protein product							Standard	NM_001193478		Approved	NYD-SP15	uc001vcu.3	Q9BWV3	OTTHUMG00000016913	ENST00000251108.6:c.1044G>A	13.37:g.49848470G>A		Somatic		Capture	Illumina HiSeq	Phase_I	48746471	NM_030911	Q49A08|Q4G119|Q5TAW9|Q7Z764|Q9NT36	Silent	SNP	ENST00000251108.6	37	CCDS9415.1																																																																																				0.338	CDADC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044902.2	NM_030911	
FAM124A	220108	broad.mit.edu	37	13	51854854	51854854	+	Missense_Mutation	SNP	C	C	T	rs143623611	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:51854854C>T	ENST00000322475.8	+	4	1238	c.1103C>T	c.(1102-1104)aCg>aTg	p.T368M	FAM124A_ENST00000280057.6_Missense_Mutation_p.T404M	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	368								p.T404M(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		TGTTTGCCCACGGGAGGCCCC	0.612																																					p.T404M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1211T	13						.	C	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	83.0	98.0	93.0		1103,1211	3.3	0.3	13	dbSNP_134	93	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	FAM124A	NM_001242312.1,NM_145019.3	81,81	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	probably-damaging,probably-damaging	368/547,404/583	51854854	4,13002	2203	4300	6503	50752855	SO:0001583	missense	220108	exon5			AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.1103C>T	13.37:g.51854854C>T	ENSP00000324625:p.Thr368Met	Somatic		Capture	Illumina HiSeq	Phase_I	50752855	NM_145019	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	37	CCDS55900.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.831325	0.32329	2.27E-4	3.49E-4	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.50277	0.75;0.75	5.12	3.33	0.38152	.	0.417810	0.22078	N	0.064938	T	0.60104	0.2243	L	0.58101	1.795	0.27655	N	0.947251	D;D	0.89917	1.0;1.0	D;D	0.69307	0.963;0.917	T	0.53683	-0.8404	10	0.66056	D	0.02	3.2834	9.3323	0.38030	0.0:0.7742:0.1458:0.08	.	368;404	Q86V42;Q86V42-2	F124A_HUMAN;.	M	368;404	ENSP00000324625:T368M;ENSP00000280057:T404M	ENSP00000280057:T404M	T	+	2	0	FAM124A	50752855	0.921000	0.31238	0.343000	0.25615	0.066000	0.16364	1.765000	0.38481	0.506000	0.28125	0.655000	0.94253	ACG		0.612	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019	
CKAP2	26586	broad.mit.edu	37	13	53049042	53049042	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:53049042G>A	ENST00000378037.5	+	9	1908	c.1818G>A	c.(1816-1818)aaG>aaA	p.K606K	CKAP2_ENST00000258607.5_Silent_p.K605K|CKAP2_ENST00000490903.1_Silent_p.K557K	NM_001098525.1|NM_018204.3	NP_001091995.1|NP_060674.3			cytoskeleton associated protein 2									p.K605K(1)		breast(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(3)|skin(1)|urinary_tract(1)	20		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.6e-08)		TGAAAAAAAAGGTGCAGTTTG	0.328																																					p.K606K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1818A	13						.						42.0	42.0	42.0					13																	53049042		2203	4300	6503	51947043	SO:0001819	synonymous_variant	26586	exon9			AF177227	CCDS9435.1, CCDS41893.1, CCDS66557.1, CCDS73578.1	13q14	2014-03-21			ENSG00000136108	ENSG00000136108			1990	protein-coding gene	gene with protein product		611569				9771967	Standard	XM_005266343		Approved	LB1, FLJ10749, se20-10, TMAP	uc001vgv.2	Q8WWK9	OTTHUMG00000016967	ENST00000378037.5:c.1818G>A	13.37:g.53049042G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51947043	NM_001098525		Silent	SNP	ENST00000378037.5	37	CCDS41893.1																																																																																				0.328	CKAP2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355010.2		
PCDH17	27253	broad.mit.edu	37	13	58207250	58207250	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:58207250C>A	ENST00000377918.3	+	1	596	c.570C>A	c.(568-570)acC>acA	p.T190T		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	190	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T190T(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		GCGACGGCACCAAGTTCCCAG	0.632																																					p.T190T	Melanoma(72;952 1291 1619 12849 33676)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C570A	13						.						32.0	33.0	33.0					13																	58207250		2203	4300	6503	57105251	SO:0001819	synonymous_variant	27253	exon1			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.570C>A	13.37:g.58207250C>A		Somatic		Capture	Illumina HiSeq	Phase_I	57105251	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	37	CCDS31986.1																																																																																				0.632	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429	
PCDH20	64881	broad.mit.edu	37	13	61986525	61986525	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:61986525T>G	ENST00000409186.1	-	5	3812	c.1707A>C	c.(1705-1707)caA>caC	p.Q569H	PCDH20_ENST00000409204.4_Missense_Mutation_p.Q569H			Q8N6Y1	PCD20_HUMAN	protocadherin 20	569	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.Q542H(1)|p.Q569H(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		AATATGAAACTTGGCCTCTCT	0.438																																					p.Q569H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A1707C	13						.						107.0	111.0	109.0					13																	61986525		2203	4300	6503	60884526	SO:0001583	missense	64881	exon2			AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"""Cadherins / Protocadherins : Non-clustered"""	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.1707A>C	13.37:g.61986525T>G	ENSP00000386653:p.Gln569His	Somatic		Capture	Illumina HiSeq	Phase_I	60884526	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	37	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	T	11.61	1.689381	0.29962	.	.	ENSG00000197991	ENST00000409204;ENST00000409186;ENST00000358674	T;T	0.53206	0.63;0.63	6.0	3.64	0.41730	.	0.700523	0.13076	N	0.415683	T	0.44393	0.1291	L	0.46947	1.48	0.44289	D	0.997154	B	0.30793	0.295	B	0.37508	0.252	T	0.28744	-1.0034	10	0.54805	T	0.06	.	7.7668	0.28984	0.0:0.2411:0.0:0.7589	.	569	A8K1K9	.	H	569;569;315	ENSP00000387250:Q569H;ENSP00000386653:Q569H	ENSP00000351500:Q315H	Q	-	3	2	PCDH20	60884526	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	0.590000	0.23954	0.528000	0.28580	-0.256000	0.11100	CAA		0.438	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843	
PCDH9	5101	broad.mit.edu	37	13	67205436	67205436	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:67205436G>A	ENST00000377865.2	-	3	3380	c.3246C>T	c.(3244-3246)caC>caT	p.H1082H	PCDH9_ENST00000456367.1_Silent_p.H1048H|RNU7-87P_ENST00000459343.1_RNA|PCDH9_ENST00000328454.5_Silent_p.H1048H|PCDH9_ENST00000544246.1_Silent_p.H1082H			Q9HC56	PCDH9_HUMAN	protocadherin 9	1082					forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.H1082H(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GAGGAAGAGGGTGTGAGATCA	0.552																																					p.H1048H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3144T	13						.						138.0	120.0	127.0					13																	67205436		2203	4300	6503	66103437	SO:0001819	synonymous_variant	5101	exon3			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.3246C>T	13.37:g.67205436G>A		Somatic		Capture	Illumina HiSeq	Phase_I	66103437	NM_020403	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Silent	SNP	ENST00000377865.2	37	CCDS9444.1																																																																																				0.552	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487	
TBC1D4	9882	broad.mit.edu	37	13	75873655	75873655	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:75873655C>A	ENST00000377636.3	-	17	3313	c.2967G>T	c.(2965-2967)ctG>ctT	p.L989L	TBC1D4_ENST00000478591.1_5'UTR|TBC1D4_ENST00000425511.1_Silent_p.L153L|TBC1D4_ENST00000431480.2_Silent_p.L981L|TBC1D4_ENST00000377625.2_Silent_p.L926L	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	989	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)	p.L989L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		TAAACAGTGACAGCTGTCCTG	0.463																																					p.L989L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2967T	13						.						53.0	55.0	54.0					13																	75873655		1894	4128	6022	74771656	SO:0001819	synonymous_variant	9882	exon17			AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.2967G>T	13.37:g.75873655C>A		Somatic		Capture	Illumina HiSeq	Phase_I	74771656	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	37	CCDS41901.1																																																																																				0.463	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
LMO7	4008	broad.mit.edu	37	13	76408487	76408487	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:76408487C>T	ENST00000321797.8	+	15	3212	c.2491C>T	c.(2491-2493)Cac>Tac	p.H831Y	LMO7_ENST00000377534.3_Missense_Mutation_p.H1116Y|LMO7_ENST00000341547.4_Missense_Mutation_p.H782Y|LMO7_ENST00000526202.1_Missense_Mutation_p.H681Y|LMO7_ENST00000357063.3_Missense_Mutation_p.H1116Y|LMO7_ENST00000465261.2_Missense_Mutation_p.H831Y			Q8WWI1	LMO7_HUMAN	LIM domain 7	1116					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.H1116Y(1)|p.H782Y(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		AGAAACTGGACACCTAGTGAT	0.448																																					p.H831Y												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2491T	13						.						141.0	127.0	132.0					13																	76408487		2203	4300	6503	75306488	SO:0001583	missense	4008	exon14			AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.2491C>T	13.37:g.76408487C>T	ENSP00000317802:p.His831Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	75306488	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.64|14.64	2.596963|2.596963	0.46318|0.46318	.|.	.|.	ENSG00000136153|ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000321797;ENST00000526202;ENST00000465261|ENST00000447038;ENST00000525914	T;T;T;T;T;T;T|.	0.46063|.	1.5;1.49;1.5;0.88;0.93;0.97;0.94|.	5.57|5.57	3.05|3.05	0.35203|0.35203	PDZ/DHR/GLGF (3);|.	0.210301|.	0.56097|.	D|.	0.000021|.	T|T	0.18551|0.18551	0.0445|0.0445	N|N	0.08118|0.08118	0|0	0.25309|0.25309	N|N	0.989213|0.989213	B;B;P;B;B|.	0.42357|.	0.274;0.032;0.777;0.039;0.205|.	B;B;B;B;B|.	0.39465|.	0.207;0.052;0.207;0.086;0.3|.	T|T	0.25363|0.25363	-1.0134|-1.0134	10|5	0.72032|.	D|.	0.01|.	-6.1414|-6.1414	8.3977|8.3977	0.32568|0.32568	0.6186:0.2606:0.0:0.1208|0.6186:0.2606:0.0:0.1208	.|.	681;782;1116;831;1064|.	E9PMS6;Q8WWI1-3;Q8WWI1;E9PLH4;F8J2B5|.	.;.;LMO7_HUMAN;.;.|.	Y|I	782;1116;1116;730;831;681;831|739;18	ENSP00000342112:H782Y;ENSP00000349571:H1116Y;ENSP00000366757:H1116Y;ENSP00000366719:H730Y;ENSP00000317802:H831Y;ENSP00000431129:H681Y;ENSP00000433352:H831Y|.	ENSP00000317802:H831Y|.	H|T	+|+	1|2	0|0	LMO7|LMO7	75306488|75306488	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.691000|0.691000	0.40173|0.40173	2.941000|2.941000	0.49011|0.49011	0.455000|0.455000	0.26910|0.26910	-0.266000|-0.266000	0.10368|0.10368	CAC|ACA		0.448	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
LMO7	4008	broad.mit.edu	37	13	76415258	76415258	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:76415258G>A	ENST00000321797.8	+	21	3618	c.2897G>A	c.(2896-2898)cGt>cAt	p.R966H	LMO7_ENST00000377534.3_Missense_Mutation_p.R1251H|LMO7_ENST00000341547.4_Missense_Mutation_p.R917H|LMO7_ENST00000526202.1_Missense_Mutation_p.R843H|LMO7_ENST00000357063.3_Missense_Mutation_p.R1251H|LMO7_ENST00000465261.2_Missense_Mutation_p.R966H			Q8WWI1	LMO7_HUMAN	LIM domain 7	1251					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R1251H(1)|p.R917H(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		AAATATCAACGTGAGCAGGAG	0.363																																					p.R966H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2897A	13						.						106.0	105.0	105.0					13																	76415258		2203	4300	6503	75313259	SO:0001583	missense	4008	exon20			AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.2897G>A	13.37:g.76415258G>A	ENSP00000317802:p.Arg966His	Somatic		Capture	Illumina HiSeq	Phase_I	75313259	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.412363|5.412363	0.96072|0.96072	.|.	.|.	ENSG00000136153|ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000321797;ENST00000526202;ENST00000465261|ENST00000524651	T;T;T;T;T;T;T|.	0.49432|.	0.78;0.78;0.78;0.78;0.78;0.78;0.78|.	5.61|5.61	5.61|5.61	0.85477|0.85477	.|.	0.049976|.	0.85682|.	D|.	0.000000|.	T|T	0.77498|0.77498	0.4139|0.4139	M|M	0.74881|0.74881	2.28|2.28	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.91635|.	0.998;0.999;0.991;0.998;0.999|.	T|T	0.76222|0.76222	-0.3038|-0.3038	10|5	0.87932|.	D|.	0|.	-10.9795|-10.9795	19.6471|19.6471	0.95779|0.95779	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	843;917;1251;966;1199|.	E9PMS6;Q8WWI1-3;Q8WWI1;E9PLH4;F8J2B5|.	.;.;LMO7_HUMAN;.;.|.	H|M	917;1251;1251;865;966;843;966|279	ENSP00000342112:R917H;ENSP00000349571:R1251H;ENSP00000366757:R1251H;ENSP00000366719:R865H;ENSP00000317802:R966H;ENSP00000431129:R843H;ENSP00000433352:R966H|.	ENSP00000317802:R966H|.	R|V	+|+	2|1	0|0	LMO7|LMO7	75313259|75313259	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.956000|0.956000	0.61745|0.61745	5.879000|5.879000	0.69690|0.69690	2.629000|2.629000	0.89072|0.89072	0.655000|0.655000	0.94253|0.94253	CGT|GTG		0.363	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
STK24	8428	broad.mit.edu	37	13	99118654	99118654	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:99118654G>T	ENST00000376547.3	-	6	940	c.795C>A	c.(793-795)gcC>gcA	p.A265A	STK24_ENST00000539966.1_Silent_p.A234A|STK24_ENST00000397517.2_Silent_p.A253A	NM_003576.3	NP_003567.2	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24	265	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of cell migration (GO:0030336)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of axon regeneration (GO:0048679)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.A265A(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			TATTCAAACAGGCCTCCACAA	0.488																																					p.A265A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C795A	13						.						77.0	74.0	75.0					13																	99118654		2203	4300	6503	97916655	SO:0001819	synonymous_variant	8428	exon6			AF024636	CCDS9488.1, CCDS32001.1, CCDS66573.1	13q31.2-q32.3	2010-06-25	2010-06-25		ENSG00000102572	ENSG00000102572			11403	protein-coding gene	gene with protein product	"""STE20-like kinase 3"", ""sterile 20-like kinase 3"""	604984	"""serine/threonine kinase 24 (Ste20, yeast homolog)"""			9353338, 10644707	Standard	NM_003576		Approved	MST-3, MST3, MST3B, STK3, STE20	uc001vnn.1	Q9Y6E0	OTTHUMG00000017250	ENST00000376547.3:c.795C>A	13.37:g.99118654G>T		Somatic		Capture	Illumina HiSeq	Phase_I	97916655	NM_003576	O14840|Q5JV92	Silent	SNP	ENST00000376547.3	37	CCDS9488.1	.	.	.	.	.	.	.	.	.	.	G	10.88	1.475767	0.26511	.	.	ENSG00000102572	ENST00000444574	.	.	.	5.16	5.16	0.70880	.	.	.	.	.	T	0.74650	0.3744	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73959	-0.3818	4	.	.	.	.	18.6716	0.91513	0.0:0.0:1.0:0.0	.	.	.	.	M	171	.	.	L	-	1	2	STK24	97916655	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.489000	0.66875	2.389000	0.81357	0.563000	0.77884	CTG		0.488	STK24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045549.2	NM_003576	
GPR183	1880	broad.mit.edu	37	13	99948041	99948041	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:99948041T>C	ENST00000376414.4	-	2	442	c.359A>G	c.(358-360)aAc>aGc	p.N120S	UBAC2_ENST00000403766.3_Intron|UBAC2_ENST00000376440.2_Intron	NM_004951.4	NP_004942.1	P32249	GP183_HUMAN	G protein-coupled receptor 183	120					G-protein coupled receptor signaling pathway (GO:0007186)|humoral immune response (GO:0006959)|immune response (GO:0006955)|mature B cell differentiation involved in immune response (GO:0002313)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|oxysterol binding (GO:0008142)	p.N120S(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	23						GGTCATAAAGTTCACACCTGC	0.448																																					p.N120S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A359G	13						.						154.0	126.0	135.0					13																	99948041		2203	4300	6503	98746042	SO:0001583	missense	1880	exon2			L08177	CCDS9492.1	13q32.3	2012-08-21	2008-07-21	2008-07-21	ENSG00000169508	ENSG00000169508		"""GPCR / Class A : Orphans"""	3128	protein-coding gene	gene with protein product	"""EBV-induced G-protein coupled receptor 2"""	605741	"""Epstein-Barr virus induced gene 2 (lymphocyte-specific G protein-coupled receptor)"""	EBI2		8383238	Standard	NM_004951		Approved		uc001vog.3	P32249	OTTHUMG00000017263	ENST00000376414.4:c.359A>G	13.37:g.99948041T>C	ENSP00000365596:p.Asn120Ser	Somatic		Capture	Illumina HiSeq	Phase_I	98746042	NM_004951	B2R8N5|Q53F99|Q5JUH7	Missense_Mutation	SNP	ENST00000376414.4	37	CCDS9492.1	.	.	.	.	.	.	.	.	.	.	T	16.59	3.166177	0.57476	.	.	ENSG00000169508	ENST00000376414	T	0.35973	1.28	5.81	5.81	0.92471	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.53174	0.1780	L	0.54965	1.715	0.49051	D	0.999745	D	0.60160	0.987	P	0.62649	0.905	T	0.48906	-0.8993	9	.	.	.	.	16.1668	0.81768	0.0:0.0:0.0:1.0	.	120	P32249	GP183_HUMAN	S	120	ENSP00000365596:N120S	.	N	-	2	0	GPR183	98746042	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.139000	0.71728	2.210000	0.71456	0.533000	0.62120	AAC		0.448	GPR183-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045582.2	NM_004951	
CLYBL	171425	broad.mit.edu	37	13	100543590	100543590	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:100543590G>T	ENST00000376360.1	+	8	973	c.946G>T	c.(946-948)Ggg>Tgg	p.G316W	CLYBL_ENST00000339105.4_Missense_Mutation_p.G316W|CLYBL_ENST00000376355.3_Missense_Mutation_p.G282W|CLYBL_ENST00000376354.1_Missense_Mutation_p.G282W			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	316						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|metal ion binding (GO:0046872)	p.G316W(1)|p.G316R(1)		NS(1)|kidney(6)|large_intestine(6)|lung(10)|skin(2)	25	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TACTTTCCAAGGGAGTATGAT	0.423																																					p.G316W												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G946T	13						.						115.0	109.0	111.0					13																	100543590		2203	4300	6503	99341591	SO:0001583	missense	171425	exon8			AF428253	CCDS32002.1	13q32.3	2011-04-08			ENSG00000125246	ENSG00000125246			18355	protein-coding gene	gene with protein product		609686					Standard	XM_005254030		Approved	CLB	uc001vok.3	Q8N0X4	OTTHUMG00000017278	ENST00000376360.1:c.946G>T	13.37:g.100543590G>T	ENSP00000365538:p.Gly316Trp	Somatic		Capture	Illumina HiSeq	Phase_I	99341591	NM_206808	Q5W0F7|Q8TDH8	Missense_Mutation	SNP	ENST00000376360.1	37	CCDS32002.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.760813	0.69763	.	.	ENSG00000125246	ENST00000376355;ENST00000376360;ENST00000376354;ENST00000339105;ENST00000419700;ENST00000425186	T;T;T;T;T	0.61859	0.75;0.72;0.75;0.72;0.07	5.03	5.03	0.67393	.	0.047314	0.85682	D	0.000000	D	0.85191	0.5640	H	0.97315	3.98	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90737	0.4647	10	0.87932	D	0	-19.1892	18.7527	0.91821	0.0:0.0:1.0:0.0	.	316	Q8N0X4	CLYBL_HUMAN	W	282;316;282;316;79;65	ENSP00000365533:G282W;ENSP00000365538:G316W;ENSP00000365532:G282W;ENSP00000342991:G316W;ENSP00000396574:G79W	ENSP00000342991:G316W	G	+	1	0	CLYBL	99341591	1.000000	0.71417	0.992000	0.48379	0.999000	0.98932	9.248000	0.95456	2.490000	0.84030	0.655000	0.94253	GGG		0.423	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045611.1		
MCF2L	23263	broad.mit.edu	37	13	113744040	113744040	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr13:113744040A>G	ENST00000375608.3	+	27	3099	c.3041A>G	c.(3040-3042)aAa>aGa	p.K1014R	MCF2L_ENST00000535094.2_Missense_Mutation_p.K984R|MCF2L_ENST00000375597.4_Missense_Mutation_p.K982R|MCF2L_ENST00000397030.1_Missense_Mutation_p.K1017R|MCF2L_ENST00000442652.2_Missense_Mutation_p.K1014R|MCF2L_ENST00000434480.2_Missense_Mutation_p.K990R|MCF2L_ENST00000375601.3_Missense_Mutation_p.K988R|MCF2L_ENST00000375604.2_Missense_Mutation_p.K1041R|MCF2L_ENST00000421756.1_Missense_Mutation_p.K988R|MCF2L_ENST00000423482.2_Missense_Mutation_p.K982R			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	1014					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.K988R(1)		kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				GAAAAGGGCAAAGGTGGGTAT	0.582																																					p.K988R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2963G	13						.						84.0	72.0	76.0					13																	113744040		2203	4300	6503	112792041	SO:0001583	missense	23263	exon26			AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.3041A>G	13.37:g.113744040A>G	ENSP00000364758:p.Lys1014Arg	Somatic		Capture	Illumina HiSeq	Phase_I	112792041	NM_024979	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.223|9.223	1.033970|1.033970	0.19590|0.19590	.|.	.|.	ENSG00000126217|ENSG00000126217	ENST00000413354;ENST00000261963;ENST00000420013|ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000375597;ENST00000440749	T;T;T|T;T;T;T;T;T;T;T;T;T	0.67171|0.36699	2.87;2.08;-0.25|1.34;1.34;1.3;1.36;1.32;1.36;1.31;1.35;1.32;1.24	4.7|4.7	-1.94|-1.94	0.07571|0.07571	.|.	0.451388|0.451388	0.21238|0.21238	N|N	0.077862|0.077862	T|T	0.22166|0.22166	0.0534|0.0534	L|L	0.29908|0.29908	0.895|0.895	0.35979|0.35979	D|D	0.835869|0.835869	.|B;B;B;B;B	.|0.12630	.|0.002;0.002;0.006;0.005;0.003	.|B;B;B;B;B	.|0.20384	.|0.018;0.018;0.029;0.019;0.013	T|T	0.11941|0.11941	-1.0567|-1.0567	8|10	0.25751|0.26408	T|T	0.34|0.33	.|.	9.821|9.821	0.40883|0.40883	0.7071:0.0:0.2929:0.0|0.7071:0.0:0.2929:0.0	.|.	.|982;984;1041;982;1014	.|E9PDN8;O15068-9;G5E9A1;O15068-4;O15068	.|.;.;.;.;MCF2L_HUMAN	E|R	214;155;31|1014;1014;1041;1017;984;988;988;990;982;982;825	ENSP00000407392:K214E;ENSP00000261963:K155E;ENSP00000404422:K31E|ENSP00000364758:K1014R;ENSP00000401422:K1014R;ENSP00000364754:K1041R;ENSP00000380225:K1017R;ENSP00000440374:K984R;ENSP00000397285:K988R;ENSP00000364751:K988R;ENSP00000407722:K990R;ENSP00000405639:K982R;ENSP00000364747:K982R	ENSP00000261963:K155E|ENSP00000364747:K982R	K|K	+|+	1|2	0|0	MCF2L|MCF2L	112792041|112792041	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.462000|0.462000	0.32619|0.32619	0.888000|0.888000	0.28268|0.28268	-0.650000|-0.650000	0.05423|0.05423	-0.376000|-0.376000	0.06991|0.06991	AAG|AAA		0.582	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
KHNYN	23351	broad.mit.edu	37	14	24909676	24909677	+	3'UTR	INS	-	-	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:24909676_24909677insC	ENST00000251343.5	+	0	5361_5362				SDR39U1_ENST00000555561.1_Intron|SDR39U1_ENST00000399390.1_Frame_Shift_Ins_p.G70fs|SDR39U1_ENST00000399395.3_Frame_Shift_Ins_p.G165fs|SDR39U1_ENST00000554698.1_Frame_Shift_Ins_p.G57fs|SDR39U1_ENST00000555365.1_5'UTR|SDR39U1_ENST00000553930.1_Frame_Shift_Ins_p.G40fs|SDR39U1_ENST00000538105.2_Frame_Shift_Ins_p.G83fs			O15037	KHNYN_HUMAN	KH and NYN domain containing								RNA binding (GO:0003723)	p.G191fs*42(1)		kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						CCATGGCACCACCCCCACGGCC	0.639																																					p.G165fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.495_496insG	14						.																																			23979517	SO:0001624	3_prime_UTR_variant	56948	exon6			AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"""KIAA0323"""	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037		ENST00000251343.5:c.*3186->C	14.37:g.24909681_24909681dupC		Somatic		Capture	Illumina HiSeq	Phase_I	23979516	NM_020195	Q86TZ6|Q8IUQ2|Q96BA9	Frame_Shift_Ins	INS	ENST00000251343.5	37	CCDS32058.1																																																																																				0.639	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1		
AHNAK2	113146	broad.mit.edu	37	14	105408618	105408618	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:105408618C>A	ENST00000333244.5	-	7	13289	c.13170G>T	c.(13168-13170)aaG>aaT	p.K4390N	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4390						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.K4390N(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CTTTGGGTACCTTGAAACTGG	0.602																																					p.K4390N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G13170T	14						.						88.0	94.0	92.0					14																	105408618		1910	4114	6024	104479663	SO:0001583	missense	113146	exon7			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.13170G>T	14.37:g.105408618C>A	ENSP00000353114:p.Lys4390Asn	Somatic		Capture	Illumina HiSeq	Phase_I	104479663	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	8.004	0.756043	0.15846	.	.	ENSG00000185567	ENST00000333244	T	0.00882	5.58	3.15	1.84	0.25277	.	0.678548	0.10642	U	0.650857	T	0.04679	0.0127	M	0.87269	2.87	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.38824	-0.9643	10	0.22109	T	0.4	.	5.6679	0.17704	0.0:0.5934:0.1837:0.2229	.	4390	Q8IVF2	AHNK2_HUMAN	N	4390	ENSP00000353114:K4390N	ENSP00000353114:K4390N	K	-	3	2	AHNAK2	104479663	0.432000	0.25554	0.064000	0.19789	0.013000	0.08279	0.157000	0.16402	1.461000	0.47929	0.306000	0.20318	AAG		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
AHNAK2	113146	broad.mit.edu	37	14	105418913	105418913	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:105418913C>G	ENST00000333244.5	-	7	2994	c.2875G>C	c.(2875-2877)Gtg>Ctg	p.V959L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	959						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.V959L(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGCAGAGACACCTCGCCATCG	0.637																																					p.V959L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2875C	14						.						154.0	179.0	171.0					14																	105418913		2003	4167	6170	104489958	SO:0001583	missense	113146	exon7			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.2875G>C	14.37:g.105418913C>G	ENSP00000353114:p.Val959Leu	Somatic		Capture	Illumina HiSeq	Phase_I	104489958	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	10.07	1.250819	0.22880	.	.	ENSG00000185567	ENST00000333244	T	0.00691	5.84	3.26	2.33	0.28932	.	.	.	.	.	T	0.03053	0.0090	M	0.79693	2.465	0.09310	N	1	P	0.50528	0.936	P	0.62740	0.906	T	0.39663	-0.9603	9	0.23302	T	0.38	.	8.4483	0.32856	0.0:0.7938:0.0:0.2062	.	959	Q8IVF2	AHNK2_HUMAN	L	959	ENSP00000353114:V959L	ENSP00000353114:V959L	V	-	1	0	AHNAK2	104489958	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-0.050000	0.11904	1.350000	0.45770	0.313000	0.20887	GTG		0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
POTEG	404785	broad.mit.edu	37	14	19563532	19563532	+	Missense_Mutation	SNP	A	A	G	rs199732644		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:19563532A>G	ENST00000409832.3	+	5	1098	c.1046A>G	c.(1045-1047)cAt>cGt	p.H349R	CTD-2311B13.5_ENST00000548748.1_lincRNA|RNU6-1239P_ENST00000391310.1_RNA	NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	349				H -> R (in Ref. 1; AAS58868/AAS58871). {ECO:0000305}.						cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						GTTTCTAGTCATCATAATGTG	0.353																																					p.H349R												.	.	0			c.A1046G	14						.	A	ARG/HIS	52,2240		0,52,1094	61.0	98.0	86.0		1046	-1.0	0.0	14	dbSNP_134	86	3,4981		0,3,2489	no	missense	POTEG	NM_001005356.2	29	0,55,3583	GG,GA,AA		0.0602,2.2688,0.7559	benign	349/509	19563532	55,7221	1146	2492	3638	18633532	SO:0001583	missense	404785	exon5				CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33896	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 4"""	608916	"""ANKRD26-like family C, member 2"""	A26C2			Standard	NR_027480		Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.1046A>G	14.37:g.19563532A>G	ENSP00000386971:p.His349Arg	None		Capture	Illumina HiSeq	Phase_I	18633532	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Missense_Mutation	SNP	ENST00000409832.3	37	CCDS32018.1	.	.	.	.	.	.	.	.	.	.	N	0.424	-0.906853	0.02434	0.022688	6.02E-4	ENSG00000222036	ENST00000409832	T	0.62941	-0.01	1.09	-1.03	0.10102	Ankyrin repeat-containing domain (4);	3.636160	0.02887	N	0.133696	T	0.28928	0.0718	N	0.17248	0.465	0.80722	P	0.0	B	0.16802	0.019	B	0.20955	0.032	T	0.16217	-1.0410	9	0.34782	T	0.22	.	5.8199	0.18522	0.235:0.0:0.765:0.0	.	349	Q6S5H5	POTEG_HUMAN	R	349	ENSP00000386971:H349R	ENSP00000386971:H349R	H	+	2	0	POTEG	18633532	0.001000	0.12720	0.000000	0.03702	0.044000	0.14063	0.831000	0.27476	-0.390000	0.07774	-1.412000	0.01120	CAT		0.353	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356	
RNASE9	390443	broad.mit.edu	37	14	21025078	21025078	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:21025078A>T	ENST00000557068.1	-	4	1876	c.151T>A	c.(151-153)Ttt>Att	p.F51I	RNASE9_ENST00000556208.1_Missense_Mutation_p.F56I|RNASE9_ENST00000338904.3_Missense_Mutation_p.F51I|RNASE9_ENST00000553706.1_Missense_Mutation_p.F56I|RNASE9_ENST00000429244.2_Missense_Mutation_p.F51I|RNASE9_ENST00000404716.3_Missense_Mutation_p.F56I|RNASE9_ENST00000557209.1_Missense_Mutation_p.F56I|RNASE9_ENST00000553541.1_Missense_Mutation_p.F51I|RNASE9_ENST00000555230.1_Missense_Mutation_p.F51I|RNASE9_ENST00000554964.1_Missense_Mutation_p.F51I			P60153	RNAS9_HUMAN	ribonuclease, RNase A family, 9 (non-active)	51						extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)	p.F51I(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|ovary(2)|urinary_tract(1)	8	all_cancers(95;0.00238)		Epithelial(56;3.32e-06)|all cancers(55;2.46e-05)	GBM - Glioblastoma multiforme(265;0.0141)		GTACTAAAAAATTTTTCCAAA	0.403																																					p.F51I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T151A	14						.						102.0	107.0	105.0					14																	21025078		2203	4300	6503	20094918	SO:0001583	missense	390443	exon3			AY665804	CCDS32036.1, CCDS53883.1, CCDS55904.1	14q11.2	2006-10-31				ENSG00000188655		"""Ribonucleases, RNase A"""	20673	protein-coding gene	gene with protein product		614014				15676279, 12920233	Standard	NM_001001673		Approved	h461	uc010ahu.3	P60153		ENST00000557068.1:c.151T>A	14.37:g.21025078A>T	ENSP00000451565:p.Phe51Ile	Somatic		Capture	Illumina HiSeq	Phase_I	20094918	NM_001110357	A2RQR8|A8QJS1|Q5GAN7|Q6KG53	Missense_Mutation	SNP	ENST00000557068.1	37	CCDS32036.1	.	.	.	.	.	.	.	.	.	.	A	13.92	2.381867	0.42207	.	.	ENSG00000188655	ENST00000338904;ENST00000554964;ENST00000555230;ENST00000557068;ENST00000404716;ENST00000556208;ENST00000553541;ENST00000429244;ENST00000553706;ENST00000557209	T;T;T;T;T;T;T;T;T;T	0.11604	2.78;2.78;2.78;2.78;2.76;2.76;2.78;2.78;2.76;2.76	3.62	-7.24	0.01475	.	.	.	.	.	T	0.05547	0.0146	L	0.28274	0.84	0.09310	N	1	B;B	0.21905	0.062;0.05	B;B	0.23716	0.048;0.028	T	0.39292	-0.9621	9	0.52906	T	0.07	-11.853	1.6904	0.02850	0.195:0.3383:0.0882:0.3786	.	51;56	P60153;P60153-2	RNAS9_HUMAN;.	I	51;51;51;51;56;56;51;51;56;56	ENSP00000340162:F51I;ENSP00000450599:F51I;ENSP00000450800:F51I;ENSP00000451565:F51I;ENSP00000384683:F56I;ENSP00000451160:F56I;ENSP00000451285:F51I;ENSP00000409504:F51I;ENSP00000450570:F56I;ENSP00000450987:F56I	ENSP00000340162:F51I	F	-	1	0	RNASE9	20094918	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.813000	0.04491	-1.853000	0.01165	-0.452000	0.05504	TTT		0.403	RNASE9-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411094.1	NM_001001673	
RNASE4	6038	broad.mit.edu	37	14	21167921	21167921	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:21167921G>A	ENST00000555835.1	+	2	1067	c.391G>A	c.(391-393)Gtt>Att	p.V131I	AL163636.6_ENST00000553909.1_3'UTR|RNASE4_ENST00000397995.2_Missense_Mutation_p.V131I|RNASE4_ENST00000555597.1_Missense_Mutation_p.V131I|RNASE4_ENST00000304704.4_Missense_Mutation_p.V131I|RP11-903H12.3_ENST00000554286.1_RNA	NM_002937.3	NP_002928.1	P34096	RNAS4_HUMAN	ribonuclease, RNase A family, 4	131					cellular response to starvation (GO:0009267)|mRNA cleavage (GO:0006379)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)	p.V131I(1)		central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_cancers(95;0.00304)		Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	GBM - Glioblastoma multiforme(265;0.0133)		CACTAGACGTGTTGTCATTGC	0.527																																					p.V131I	Esophageal Squamous(59;1059 1362 26290 51151)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G391A	14						.						128.0	116.0	120.0					14																	21167921		2203	4299	6502	20237761	SO:0001583	missense	6038	exon2			U36775	CCDS9555.1	14q11	2014-07-16			ENSG00000258818	ENSG00000258818		"""Ribonucleases, RNase A"""	10047	protein-coding gene	gene with protein product		601030				7501448	Standard	NM_002937		Approved		uc001vxy.4	P34096	OTTHUMG00000029575	ENST00000555835.1:c.391G>A	14.37:g.21167921G>A	ENSP00000452245:p.Val131Ile	Somatic		Capture	Illumina HiSeq	Phase_I	20237761	NM_002937		Missense_Mutation	SNP	ENST00000555835.1	37	CCDS9555.1	.	.	.	.	.	.	.	.	.	.	G	12.82	2.053155	0.36181	.	.	ENSG00000258818;ENSG00000258818;ENSG00000258818;ENSG00000181784;ENSG00000181784;ENSG00000181784	ENST00000555835;ENST00000397995;ENST00000555597;ENST00000398001;ENST00000304704;ENST00000397999	T;T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53;-0.53	5.8	3.99	0.46301	Ribonuclease A, domain (4);	0.248188	0.35013	N	0.003516	T	0.45895	0.1365	N	0.11023	0.085	0.33214	D	0.553765	B	0.11235	0.004	B	0.24848	0.056	T	0.46830	-0.9163	10	0.02654	T	1	-9.5937	9.0804	0.36547	0.1678:0.0:0.8322:0.0	.	131	P34096	RNAS4_HUMAN	I	131	ENSP00000452245:V131I;ENSP00000381081:V131I;ENSP00000451624:V131I;ENSP00000381087:V131I;ENSP00000307096:V131I;ENSP00000381085:V131I	ENSP00000307096:V131I	V	+	1	0	AL163636.2;RNASE4	20237761	0.668000	0.27493	0.545000	0.28153	0.782000	0.44232	0.717000	0.25851	0.924000	0.37069	-0.145000	0.13849	GTT		0.527	RNASE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073729.3		
NDRG2	57447	broad.mit.edu	37	14	21490567	21490567	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:21490567G>A	ENST00000556147.1	-	4	1147	c.207C>T	c.(205-207)caC>caT	p.H69H	NDRG2_ENST00000360463.3_Silent_p.H55H|NDRG2_ENST00000397844.2_Silent_p.H55H|NDRG2_ENST00000397853.3_Silent_p.H69H|NDRG2_ENST00000555158.1_Silent_p.H55H|NDRG2_ENST00000554143.1_Silent_p.H55H|NDRG2_ENST00000554104.1_De_novo_Start_OutOfFrame|NDRG2_ENST00000397847.2_Silent_p.H69H|NDRG2_ENST00000298687.5_Silent_p.H69H|NDRG2_ENST00000350792.3_Silent_p.H55H|NDRG2_ENST00000397856.3_Silent_p.H55H|NDRG2_ENST00000298684.5_Silent_p.H55H|NDRG2_ENST00000553503.1_Silent_p.H55H|AL161668.5_ENST00000533984.1_lincRNA|NDRG2_ENST00000397858.1_Silent_p.H69H|NDRG2_ENST00000403829.3_Silent_p.H65H|NDRG2_ENST00000397851.2_Silent_p.H69H|NDRG2_ENST00000554277.1_5'Flank|NDRG2_ENST00000397855.3_Silent_p.H55H			Q9UN36	NDRG2_HUMAN	NDRG family member 2	69					cell differentiation (GO:0030154)|negative regulation of cytokine production (GO:0001818)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of platelet-derived growth factor production (GO:0090361)|regulation of vascular endothelial growth factor production (GO:0010574)|substantia nigra development (GO:0021762)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)		p.H69H(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	23	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		GTCCCACATCGTGGTAGGTAA	0.542																																					p.H55H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C165T	14						.						129.0	117.0	121.0					14																	21490567		2203	4300	6503	20560407	SO:0001819	synonymous_variant	57447	exon4			AB033074	CCDS9564.1, CCDS9565.1, CCDS61384.1, CCDS61386.1, CCDS73613.1	14q11.2	2008-07-09			ENSG00000165795	ENSG00000165795			14460	protein-coding gene	gene with protein product		605272				10831399	Standard	NM_201535		Approved	KIAA1248, SYLD	uc001vyx.3	Q9UN36	OTTHUMG00000029619	ENST00000556147.1:c.207C>T	14.37:g.21490567G>A		Somatic		Capture	Illumina HiSeq	Phase_I	20560407	NM_016250	B3KUE3|B4DE86|B7WP11|B7WPD5|D3DS07|D3DS10|Q567T1|Q68DW2|Q86U08|Q86U46|Q96FD3|Q96FT0|Q96JU0|Q96PN0|Q9BQH5|Q9ULH2	De_novo_Start_OutOfFrame	SNP	ENST00000556147.1	37	CCDS9565.1																																																																																				0.542	NDRG2-013	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411717.1		
ARHGEF40	55701	broad.mit.edu	37	14	21543595	21543595	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:21543595T>C	ENST00000298694.4	+	4	1682	c.1555T>C	c.(1555-1557)Tcc>Ccc	p.S519P	ARHGEF40_ENST00000298693.3_Missense_Mutation_p.S519P			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	519						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S519P(1)		large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						CCTTGCAGTCTCCGTCTCTGA	0.567																																					p.S519P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1555C	14						.						129.0	123.0	125.0					14																	21543595		2203	4300	6503	20613435	SO:0001583	missense	55701	exon4				CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.1555T>C	14.37:g.21543595T>C	ENSP00000298694:p.Ser519Pro	Somatic		Capture	Illumina HiSeq	Phase_I	20613435	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	37	CCDS32041.1	.	.	.	.	.	.	.	.	.	.	T	5.144	0.212227	0.09757	.	.	ENSG00000165801	ENST00000298694;ENST00000555038;ENST00000298693	T;T	0.02498	4.34;4.27	5.12	2.7	0.31948	.	0.147991	0.33040	N	0.005358	T	0.06917	0.0176	L	0.46157	1.445	0.09310	N	1	D;D	0.67145	0.996;0.992	P;D	0.73708	0.806;0.981	T	0.30268	-0.9984	10	0.26408	T	0.33	.	4.5324	0.12011	0.17:0.0929:0.0:0.7371	.	519;519	Q8TER5;G3V3N2	ARH40_HUMAN;.	P	519	ENSP00000298694:S519P;ENSP00000298693:S519P	ENSP00000298693:S519P	S	+	1	0	ARHGEF40	20613435	0.003000	0.15002	0.016000	0.15963	0.080000	0.17528	1.261000	0.32980	0.347000	0.23924	0.459000	0.35465	TCC		0.567	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
RPGRIP1	57096	broad.mit.edu	37	14	21796655	21796655	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:21796655G>A	ENST00000400017.2	+	18	2968	c.2968G>A	c.(2968-2970)Gga>Aga	p.G990R	RPGRIP1_ENST00000382933.4_Missense_Mutation_p.G316R|RPGRIP1_ENST00000307974.4_Missense_Mutation_p.G349R|RPGRIP1_ENST00000556336.1_Missense_Mutation_p.G647R|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.G990R|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.G952R	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	990					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)		p.G606R(1)|p.G990R(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		TCCTCATGGGGGAGAAAGAAA	0.428																																					p.G990R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2968A	14						.						84.0	80.0	81.0					14																	21796655		1853	4104	5957	20866495	SO:0001583	missense	57096	exon18			AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.2968G>A	14.37:g.21796655G>A	ENSP00000382895:p.Gly990Arg	Somatic		Capture	Illumina HiSeq	Phase_I	20866495	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.570734	0.28003	.	.	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660;ENST00000382933;ENST00000555587;ENST00000307974	T;T;T;T;T;T;T	0.78595	-0.02;-0.82;-0.85;-0.85;-0.43;-1.19;-1.19	4.65	3.71	0.42584	.	0.550760	0.18313	N	0.145036	T	0.81716	0.4881	L	0.57536	1.79	0.09310	N	1	D;D;D;D;D;D	0.71674	0.989;0.991;0.989;0.994;0.997;0.998	P;D;P;P;D;P	0.66602	0.847;0.914;0.847;0.907;0.945;0.905	T	0.69483	-0.5133	10	0.18710	T	0.47	-9.2294	10.1462	0.42764	0.0:0.0:0.8022:0.1978	.	373;349;465;316;606;990	Q96KN7-2;Q96KN7-3;G3V3I7;Q96KN7-4;Q96KN7-5;Q96KN7	.;.;.;.;.;RPGR1_HUMAN	R	647;952;990;990;316;465;349	ENSP00000450445:G647R;ENSP00000451219:G952R;ENSP00000382895:G990R;ENSP00000206660:G990R;ENSP00000372391:G316R;ENSP00000451262:G465R;ENSP00000309721:G349R	ENSP00000206660:G990R	G	+	1	0	RPGRIP1	20866495	0.988000	0.35896	0.911000	0.35937	0.455000	0.32408	2.341000	0.43983	2.430000	0.82344	0.585000	0.79938	GGA		0.428	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
CDH24	64403	broad.mit.edu	37	14	23524562	23524562	+	Splice_Site	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:23524562G>A	ENST00000267383.5	-	2	294	c.202C>T	c.(202-204)Ctg>Ttg	p.L68L	CDH24_ENST00000397359.3_Splice_Site_p.L68L|CDH24_ENST00000554034.1_Splice_Site_p.L68L|CDH24_ENST00000487137.2_Splice_Site_p.L68L			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	68	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)	p.L68L(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		TCCGAGTGCAGCTGCAGGGGT	0.572											OREG0022594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L68L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C202T	14						.						41.0	45.0	44.0					14																	23524562		2203	4300	6503	22594402	SO:0001630	splice_region_variant	64403	exon3			AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880		"""Cadherins / Major cadherins"""	14265	protein-coding gene	gene with protein product			"""cadherin-like 24"""			12734196	Standard	NM_022478		Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000267383.5:c.202-1C>T	14.37:g.23524562G>A		Somatic	764	Capture	Illumina HiSeq	Phase_I	22594402	NM_022478	D3DS44|Q86UP1|Q9NT84	Silent	SNP	ENST00000267383.5	37	CCDS9585.1																																																																																				0.572	CDH24-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257241.2	NM_022478	Silent
AP1G2	8906	broad.mit.edu	37	14	24030825	24030825	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:24030825delT	ENST00000308724.5	-	17	2508	c.1753delA	c.(1753-1755)atgfs	p.M585fs	RP11-66N24.4_ENST00000553985.1_RNA|RP11-66N24.3_ENST00000555968.1_RNA|AP1G2_ENST00000397120.3_Frame_Shift_Del_p.M585fs|RP11-66N24.4_ENST00000556354.1_RNA|AP1G2_ENST00000556277.1_5'Flank|RP11-66N24.4_ENST00000555446.1_RNA	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	585					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)	p.M585fs*43(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		ACAAGAGGCATTTTTTCCAGG	0.542																																					p.M585fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1753delA	14						.						56.0	47.0	50.0					14																	24030825		2203	4300	6503	23100665	SO:0001589	frameshift_variant	8906	exon18			AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.1753delA	14.37:g.24030825delT	ENSP00000312442:p.Met585fs	Somatic		Capture	Illumina HiSeq	Phase_I	23100665	NM_003917	D3DS51|O75504	Frame_Shift_Del	DEL	ENST00000308724.5	37	CCDS9602.1																																																																																				0.542	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917	
RNF31	55072	broad.mit.edu	37	14	24621025	24621025	+	Missense_Mutation	SNP	G	G	A	rs201544567		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:24621025G>A	ENST00000324103.6	+	11	2274	c.1954G>A	c.(1954-1956)Gca>Aca	p.A652T	RP11-468E2.4_ENST00000558468.1_Missense_Mutation_p.A127T|RNF31_ENST00000382687.3_Missense_Mutation_p.A501T|RNF31_ENST00000559275.1_Missense_Mutation_p.A501T	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	652					CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A652T(1)		breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		GGCAGTCTACGCACTCCCCAG	0.607																																					p.A652T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1954A	14						.	G	THR/ALA	0,3936		0,0,1968	59.0	66.0	64.0		1954	0.9	0.2	14		64	2,8336		0,2,4167	yes	missense	RNF31	NM_017999.4	58	0,2,6135	AA,AG,GG		0.024,0.0,0.0163	benign	652/1073	24621025	2,12272	1968	4169	6137	23690865	SO:0001583	missense	55072	exon11			AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"""RING-type (C3HC4) zinc fingers"""	16031	protein-coding gene	gene with protein product	"""HOIL-1-interacting protein"""	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.1954G>A	14.37:g.24621025G>A	ENSP00000315112:p.Ala652Thr	Somatic		Capture	Illumina HiSeq	Phase_I	23690865	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	37	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	G	5.592	0.293957	0.10567	0.0	2.4E-4	ENSG00000092098	ENST00000382682;ENST00000324103;ENST00000382687	T;T	0.42900	0.96;0.96	5.83	0.867	0.19085	.	0.310015	0.30620	N	0.009236	T	0.20941	0.0504	N	0.22421	0.69	0.09310	N	0.999998	B;B;B	0.10296	0.001;0.002;0.003	B;B;B	0.04013	0.0;0.001;0.001	T	0.14531	-1.0469	10	0.17832	T	0.49	-0.1801	3.789	0.08712	0.3653:0.0:0.3755:0.2591	.	411;652;501	B3KV71;Q96EP0;Q96EP0-3	.;RNF31_HUMAN;.	T	94;652;501	ENSP00000315112:A652T;ENSP00000372134:A501T	ENSP00000315112:A652T	A	+	1	0	RNF31	23690865	0.079000	0.21365	0.215000	0.23724	0.962000	0.63368	1.248000	0.32827	-0.100000	0.12241	-0.137000	0.14449	GCA		0.607	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999	
TINF2	26277	broad.mit.edu	37	14	24709895	24709895	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:24709895C>T	ENST00000267415.7	-	6	1132	c.791G>A	c.(790-792)gGc>gAc	p.G264D	TINF2_ENST00000559019.1_3'UTR|TINF2_ENST00000540705.1_Missense_Mutation_p.G229D|TINF2_ENST00000399423.4_Missense_Mutation_p.G264D|TINF2_ENST00000538777.1_Missense_Mutation_p.G50D|TINF2_ENST00000558510.1_5'Flank|TINF2_ENST00000558566.1_3'UTR	NM_001099274.1	NP_001092744.1	Q9BSI4	TINF2_HUMAN	TERF1 (TRF1)-interacting nuclear factor 2	264					negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of protein ADP-ribosylation (GO:0010836)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of telomere maintenance (GO:0032206)|protein localization to chromosome (GO:0034502)|protein localization to chromosome, telomeric region (GO:0070198)|telomere assembly (GO:0032202)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)	chromosome, telomeric region (GO:0000781)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinucleolar chromocenter (GO:0010370)	telomeric DNA binding (GO:0042162)	p.G264D(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|prostate(1)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0185)		TCTTCGTCGGCCTAGAGGGGC	0.577									Congenital Dyskeratosis;Ataxia Pancytopenia syndrome																												p.G264D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G791A	14						.						88.0	83.0	85.0					14																	24709895		1918	4119	6037	23779735	SO:0001583	missense	26277	exon6	Familial Cancer Database	Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita;Myelocerebellar disorder	AF195512	CCDS41936.1, CCDS41937.1	14q12	2008-07-29				ENSG00000092330			11824	protein-coding gene	gene with protein product		604319				10581025, 18252230	Standard	NM_012461		Approved	TIN2	uc001woa.4	Q9BSI4		ENST00000267415.7:c.791G>A	14.37:g.24709895C>T	ENSP00000267415:p.Gly264Asp	Somatic		Capture	Illumina HiSeq	Phase_I	23779735	NM_012461	B3W5Q7|Q9H904|Q9UHC2	Missense_Mutation	SNP	ENST00000267415.7	37	CCDS41936.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.160218	0.57368	.	.	ENSG00000092330	ENST00000267415;ENST00000540705;ENST00000399423;ENST00000538777	D;D;D;D	0.96011	-3.48;-3.49;-3.46;-3.88	5.16	5.16	0.70880	.	0.164640	0.38217	N	0.001761	D	0.97074	0.9044	M	0.66939	2.045	0.43787	D	0.996322	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97431	1.0015	10	0.72032	D	0.01	-4.844	14.1675	0.65488	0.0:1.0:0.0:0.0	.	229;264	B4DFJ1;Q9BSI4	.;TINF2_HUMAN	D	264;229;264;50	ENSP00000267415:G264D;ENSP00000442154:G229D;ENSP00000382350:G264D;ENSP00000437495:G50D	ENSP00000267415:G264D	G	-	2	0	TINF2	23779735	0.999000	0.42202	0.823000	0.32752	0.409000	0.31022	3.482000	0.53186	2.404000	0.81709	0.462000	0.41574	GGC		0.577	TINF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415406.2		
FOXG1	2290	broad.mit.edu	37	14	29237305	29237305	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:29237305C>T	ENST00000313071.4	+	1	1019	c.820C>T	c.(820-822)Cgg>Tgg	p.R274W	RP11-966I7.1_ENST00000549487.1_RNA|FOXG1_ENST00000382535.3_Missense_Mutation_p.R274W|RP11-966I7.1_ENST00000546560.1_RNA|RP11-966I7.1_ENST00000551395.1_RNA	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	274				Missing (in Ref. 1; CAA52240 and 2; CAA55038). {ECO:0000305}.	aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R274W(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		GGGCAAGCTGCGGCGCCGCTC	0.701																																					p.R274W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C820T	14						.						28.0	32.0	31.0					14																	29237305		2203	4299	6502	28307056	SO:0001583	missense	2290	exon1				CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"""Forkhead boxes"""	3811	protein-coding gene	gene with protein product		164874	"""forkhead box G1B"", ""forkhead box G1C"", ""forkhead box G1A"""	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.820C>T	14.37:g.29237305C>T	ENSP00000339004:p.Arg274Trp	Somatic		Capture	Illumina HiSeq	Phase_I	28307056	NM_005249	A6NFY2|P55315|Q14488|Q86XT7	Missense_Mutation	SNP	ENST00000313071.4	37	CCDS9636.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.611514	0.87258	.	.	ENSG00000176165	ENST00000382535;ENST00000313071	D;D	0.96011	-3.88;-3.88	4.05	3.11	0.35812	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (2);	0.000000	0.85682	U	0.000000	D	0.97770	0.9268	M	0.90309	3.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97760	1.0220	10	0.87932	D	0	.	12.1905	0.54268	0.1728:0.8272:0.0:0.0	.	274	P55316	FOXG1_HUMAN	W	274	ENSP00000371975:R274W;ENSP00000339004:R274W	ENSP00000339004:R274W	R	+	1	2	FOXG1	28307056	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.887000	0.69751	0.608000	0.30000	0.313000	0.20887	CGG		0.701	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3		
STRN3	29966	broad.mit.edu	37	14	31381263	31381263	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:31381263C>A	ENST00000357479.5	-	11	1696	c.1500G>T	c.(1498-1500)gaG>gaT	p.E500D	STRN3_ENST00000355683.5_Missense_Mutation_p.E416D|STRN3_ENST00000366206.2_5'Flank	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	500					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E416D(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		GGGTATGGTCCTCAGAAGCAG	0.408																																					p.E416D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1248T	14						.						117.0	113.0	115.0					14																	31381263		2203	4300	6503	30451014	SO:0001583	missense	29966	exon9				CCDS9641.1, CCDS41938.1	14q13-q21	2013-01-10			ENSG00000196792	ENSG00000196792		"""WD repeat domain containing"""	15720	protein-coding gene	gene with protein product	"""cell cycle S/G2 nuclear autoantigen"""	614766				7864889, 10681496	Standard	NM_014574		Approved	SG2NA	uc001wqu.2	Q13033	OTTHUMG00000140201	ENST00000357479.5:c.1500G>T	14.37:g.31381263C>A	ENSP00000350071:p.Glu500Asp	Somatic		Capture	Illumina HiSeq	Phase_I	30451014	NM_014574	A2RTX7|A6NHZ7|Q9NRA5	Missense_Mutation	SNP	ENST00000357479.5	37	CCDS41938.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.535912	0.85812	.	.	ENSG00000196792	ENST00000355683;ENST00000357479	T;T	0.59502	0.26;0.26	5.63	4.72	0.59763	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.044446	0.85682	D	0.000000	T	0.49762	0.1576	N	0.01640	-0.785	0.80722	D	1	P;D	0.63046	0.837;0.992	P;D	0.77004	0.635;0.989	T	0.62525	-0.6836	10	0.35671	T	0.21	-11.9255	15.466	0.75400	0.0:0.9302:0.0:0.0698	.	416;500	Q13033-2;Q13033	.;STRN3_HUMAN	D	416;500	ENSP00000347909:E416D;ENSP00000350071:E500D	ENSP00000347909:E416D	E	-	3	2	STRN3	30451014	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.391000	0.44424	2.797000	0.96272	0.655000	0.94253	GAG		0.408	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574	
RALGAPA1	253959	broad.mit.edu	37	14	36230044	36230044	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:36230044G>T	ENST00000389698.3	-	6	928	c.538C>A	c.(538-540)Ctt>Att	p.L180I	RALGAPA1_ENST00000382366.3_Missense_Mutation_p.L180I|RALGAPA1_ENST00000258840.6_Missense_Mutation_p.L180I|RALGAPA1_ENST00000554704.1_5'UTR|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.L180I	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	180					activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.L180I(2)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CTTTCTTGAAGGTTGAGTGGA	0.383																																					p.L180I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C538A	14						.						86.0	77.0	80.0					14																	36230044		2203	4300	6503	35299795	SO:0001583	missense	253959	exon6			AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"""tuberin-like protein 1"", ""GAP-related interacting protein to E12"""	608884	"""GTPase activating RANGAP domain-like 1"", ""GTPase activating Rap/RanGAP domain-like 1"""	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.538C>A	14.37:g.36230044G>T	ENSP00000374348:p.Leu180Ile	Somatic		Capture	Illumina HiSeq	Phase_I	35299795	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	37	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.863051	0.32884	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000382366;ENST00000553892	D;D;D;D;D	0.94537	-3.45;-3.45;-3.45;-3.45;-3.45	5.4	5.4	0.78164	.	0.064020	0.64402	D	0.000013	D	0.93015	0.7777	L	0.57536	1.79	0.48135	D	0.999594	B;B;B;B;B	0.28801	0.223;0.085;0.125;0.004;0.094	B;B;B;B;B	0.36289	0.221;0.062;0.126;0.023;0.067	D	0.89713	0.3913	10	0.14656	T	0.56	-16.8864	15.4168	0.74977	0.0:0.178:0.822:0.0	.	180;180;180;180;180	Q6GYQ0-6;B9EK38;Q6GYQ0-3;Q6GYQ0-2;Q6GYQ0	.;.;.;.;RGPA1_HUMAN	I	180	ENSP00000374348:L180I;ENSP00000302647:L180I;ENSP00000258840:L180I;ENSP00000371803:L180I;ENSP00000451877:L180I	ENSP00000258840:L180I	L	-	1	0	RALGAPA1	35299795	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.591000	0.46163	2.695000	0.91970	0.462000	0.41574	CTT		0.383	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	
CTAGE5	4253	broad.mit.edu	37	14	39815181	39815181	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:39815181T>C	ENST00000280083.3	+	21	2219	c.1905T>C	c.(1903-1905)tcT>tcC	p.S635S	CTAGE5_ENST00000556148.1_Silent_p.S560S|CTAGE5_ENST00000553352.1_Silent_p.S606S|CTAGE5_ENST00000348007.3_Silent_p.S592S|RP11-407N17.3_ENST00000603904.1_Silent_p.S606S|CTAGE5_ENST00000396165.4_Silent_p.S606S|CTAGE5_ENST00000396158.2_Silent_p.S640S|CTAGE5_ENST00000341502.5_Silent_p.S635S|RP11-407N17.3_ENST00000553728.1_Silent_p.S1170S|CTAGE5_ENST00000557038.1_Silent_p.S555S|CTAGE5_ENST00000341749.3_Silent_p.S623S			O15320	CTGE5_HUMAN	CTAGE family, member 5	635	Pro-rich.				positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)	p.S635S(1)	CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		GTAGACTGTCTGGACCAGCAG	0.353																																					p.S623S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1869C	14						.						80.0	80.0	80.0					14																	39815181		2203	4300	6503	38884932	SO:0001819	synonymous_variant	4253	exon21			U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.1905T>C	14.37:g.39815181T>C		Somatic		Capture	Illumina HiSeq	Phase_I	38884932	NM_203354	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Silent	SNP	ENST00000280083.3	37	CCDS9674.1																																																																																				0.353	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
FAM179B	23116	broad.mit.edu	37	14	45481236	45481236	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:45481236A>G	ENST00000361577.3	+	7	3410	c.3196A>G	c.(3196-3198)Aag>Gag	p.K1066E	FAM179B_ENST00000361462.2_Missense_Mutation_p.K1066E|FAM179B_ENST00000382233.2_Missense_Mutation_p.K988R|KLHL28_ENST00000553817.1_Intron	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1066	Ser-rich.							p.K1066E(1)		endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TTCTTCTGCAAAGAAAAAAAT	0.289																																					p.K1066E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3196G	14						.						54.0	57.0	56.0					14																	45481236		2201	4299	6500	44550986	SO:0001583	missense	23116	exon7			AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"""KIAA0423"""	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.3196A>G	14.37:g.45481236A>G	ENSP00000355045:p.Lys1066Glu	Somatic		Capture	Illumina HiSeq	Phase_I	44550986	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	37	CCDS9681.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.68|11.68	1.709772|1.709772	0.30322|0.30322	.|.	.|.	ENSG00000198718|ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462|ENST00000382233	T;T|T	0.03441|0.32515	3.93;3.93|1.45	5.92|5.92	5.92|5.92	0.95590|0.95590	Armadillo-type fold (1);|.	0.213911|0.213911	0.39615|0.39615	N|N	0.001309|0.001309	T|T	0.30541|0.30541	0.0768|0.0768	L|L	0.29908|0.29908	0.895|0.895	0.18873|0.18873	N|N	0.999985|0.999985	D;D|.	0.60575|.	0.988;0.988|.	P;P|.	0.55545|.	0.778;0.778|.	T|T	0.30446|0.30446	-0.9978|-0.9978	10|8	0.46703|0.87932	T|D	0.11|0	-16.9715|-16.9715	11.2957|11.2957	0.49277|0.49277	0.848:0.152:0.0:0.0|0.848:0.152:0.0:0.0	.|.	1066;1066|.	G3XAE9;Q9Y4F4|.	.;F179B_HUMAN|.	E|R	1066|988	ENSP00000355045:K1066E;ENSP00000354917:K1066E|ENSP00000371668:K988R	ENSP00000354917:K1066E|ENSP00000371668:K988R	K|K	+|+	1|2	0|0	FAM179B|FAM179B	44550986|44550986	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.323000|0.323000	0.28346|0.28346	3.637000|3.637000	0.54324|0.54324	2.254000|2.254000	0.74563|0.74563	0.528000|0.528000	0.53228|0.53228	AAG|AAA		0.289	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781	
SOS2	6655	broad.mit.edu	37	14	50605450	50605450	+	Missense_Mutation	SNP	T	T	A	rs532833599		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:50605450T>A	ENST00000216373.5	-	18	3112	c.2838A>T	c.(2836-2838)ttA>ttT	p.L946F	SOS2_ENST00000543680.1_Missense_Mutation_p.L913F	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	946	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L946F(2)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					CTTTCTTTTTTAAAAAATCAT	0.264													T|||	1	0.000199681	0.0	0.0	5008	,	,		13030	0.001		0.0	False		,,,				2504	0.0				p.L946F												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A2838T	14						.						42.0	41.0	41.0					14																	50605450		2199	4296	6495	49675200	SO:0001583	missense	6655	exon18			L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11188	protein-coding gene	gene with protein product		601247	"""son of sevenless (Drosophilia) homolog 2"""			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.2838A>T	14.37:g.50605450T>A	ENSP00000216373:p.Leu946Phe	Somatic		Capture	Illumina HiSeq	Phase_I	49675200	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	37	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.618782	0.66787	.	.	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.35605	1.3;1.3	5.6	3.14	0.36123	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine-nucleotide exchange factor, conserved site (1);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.51787	0.1695	M	0.84846	2.72	0.58432	D	0.999994	P;P	0.50272	0.933;0.86	P;P	0.57548	0.823;0.583	T	0.53809	-0.8386	10	0.87932	D	0	.	3.6215	0.08097	0.2755:0.1915:0.0:0.533	.	913;946	B7ZKT6;Q07890	.;SOS2_HUMAN	F	946;913	ENSP00000216373:L946F;ENSP00000445328:L913F	ENSP00000216373:L946F	L	-	3	2	SOS2	49675200	0.981000	0.34729	1.000000	0.80357	0.997000	0.91878	0.134000	0.15932	0.969000	0.38237	0.533000	0.62120	TTA		0.264	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
ATL1	51062	broad.mit.edu	37	14	51087337	51087337	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:51087337delA	ENST00000358385.6	+	9	1124	c.883delA	c.(883-885)aaafs	p.K295fs	ATL1_ENST00000441560.2_Frame_Shift_Del_p.K295fs|ATL1_ENST00000357032.3_Frame_Shift_Del_p.K295fs|ATL1_ENST00000354525.4_Frame_Shift_Del_p.K295fs	NM_015915.4	NP_056999.2	Q8WXF7	ATLA1_HUMAN	atlastin GTPase 1	295	GB1/RHD3-type G.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.N296fs*2(1)|p.K295*(1)		central_nervous_system(1)|cervix(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(3)	18						TGAATTCATCAAAAACTTGAA	0.378																																					p.K295fs												.	.	2	Substitution - Nonsense(1)|Deletion - Frameshift(1)	large_intestine(1)|lung(1)	c.883delA	14						.						73.0	75.0	74.0					14																	51087337		2203	4300	6503	50157087	SO:0001589	frameshift_variant	51062	exon9			AF131801	CCDS9700.1, CCDS32077.1	14q21.3	2014-09-17	2008-09-17	2008-09-17	ENSG00000198513	ENSG00000198513			11231	protein-coding gene	gene with protein product	"""atlastin"""	606439	"""spastic paraplegia 3A (autosomal dominant)"""	SPG3, SPG3A		8252041, 7825576	Standard	NM_015915		Approved	FSP1, AD-FSP	uc001wyd.4	Q8WXF7	OTTHUMG00000140297	ENST00000358385.6:c.883delA	14.37:g.51087337delA	ENSP00000351155:p.Lys295fs	Somatic		Capture	Illumina HiSeq	Phase_I	50157087	NM_181598	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Frame_Shift_Del	DEL	ENST00000358385.6	37	CCDS9700.1																																																																																				0.378	ATL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276884.2		
NIN	51199	broad.mit.edu	37	14	51259467	51259467	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:51259467G>A	ENST00000382041.3	-	5	588	c.398C>T	c.(397-399)gCg>gTg	p.A133V	NIN_ENST00000530997.2_Missense_Mutation_p.A133V|NIN_ENST00000486200.1_5'UTR|NIN_ENST00000453196.1_Missense_Mutation_p.A133V|NIN_ENST00000389868.3_Missense_Mutation_p.A133V|NIN_ENST00000324330.9_Missense_Mutation_p.A133V|NIN_ENST00000382043.4_Missense_Mutation_p.A133V|NIN_ENST00000245441.5_Missense_Mutation_p.A133V	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	133					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)	p.A139V(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					TGAAGGCCGCGCTTCTTCATC	0.572			T	PDGFRB	MPD																																p.A133V			Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C398T	14						.						109.0	86.0	94.0					14																	51259467		2203	4300	6503	50329217	SO:0001583	missense	51199	exon5			AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"""EF-hand domain containing"""	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.398C>T	14.37:g.51259467G>A	ENSP00000371472:p.Ala133Val	Somatic		Capture	Illumina HiSeq	Phase_I	50329217	NM_182944	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	37	CCDS32079.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.782071	0.70222	.	.	ENSG00000100503	ENST00000245441;ENST00000311149;ENST00000389868;ENST00000382043;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196;ENST00000453401	T;T;T;T;T;T;T	0.25414	1.8;1.8;1.8;1.8;1.8;1.8;1.8	6.07	5.18	0.71444	.	0.390341	0.29646	N	0.011577	T	0.32704	0.0838	L	0.27053	0.805	0.35329	D	0.785431	B;B;B;B;D	0.89917	0.082;0.134;0.178;0.036;1.0	B;B;B;B;D	0.80764	0.024;0.021;0.025;0.008;0.994	T	0.27872	-1.0061	10	0.12103	T	0.63	-7.5976	11.5129	0.50504	0.1465:0.0:0.8535:0.0	.	139;133;133;133;133	Q8N4C6-5;C9J066;Q8N4C6;Q5BKU3;Q8N4C6-7	.;.;NIN_HUMAN;.;.	V	133;133;133;133;139;133;133;133;95	ENSP00000245441:A133V;ENSP00000374518:A133V;ENSP00000371474:A133V;ENSP00000371472:A133V;ENSP00000324210:A133V;ENSP00000412391:A133V;ENSP00000398641:A95V	ENSP00000245441:A133V	A	-	2	0	NIN	50329217	0.997000	0.39634	0.904000	0.35570	0.528000	0.34623	2.749000	0.47492	1.554000	0.49487	0.655000	0.94253	GCG		0.572	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
FBXO34	55030	broad.mit.edu	37	14	55818067	55818067	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:55818067G>A	ENST00000313833.4	+	2	1204	c.959G>A	c.(958-960)aGc>aAc	p.S320N	FBXO34_ENST00000440021.1_Missense_Mutation_p.S320N	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	320								p.S320N(1)		breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						CTTGCAAATAGCACTCAGGCT	0.537																																					p.S320N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G959A	14						.						116.0	112.0	113.0					14																	55818067		2203	4300	6503	54887820	SO:0001583	missense	55030	exon2			AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.959G>A	14.37:g.55818067G>A	ENSP00000313159:p.Ser320Asn	Somatic		Capture	Illumina HiSeq	Phase_I	54887820	NM_152231	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	.	.	.	.	.	.	.	.	.	.	G	6.209	0.406800	0.11754	.	.	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.19250	2.16;2.16	5.21	4.29	0.51040	.	0.557387	0.14604	N	0.309460	T	0.16342	0.0393	N	0.22421	0.69	0.09310	N	0.999999	B	0.23249	0.082	B	0.21708	0.036	T	0.17107	-1.0380	10	0.49607	T	0.09	-28.9283	13.07	0.59055	0.0802:0.0:0.9198:0.0	.	320	Q9NWN3	FBX34_HUMAN	N	320	ENSP00000313159:S320N;ENSP00000394117:S320N	ENSP00000313159:S320N	S	+	2	0	FBXO34	54887820	1.000000	0.71417	0.007000	0.13788	0.036000	0.12997	7.946000	0.87746	1.358000	0.45922	0.555000	0.69702	AGC		0.537	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
TOMM20L	387990	broad.mit.edu	37	14	58874140	58874140	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:58874140C>A	ENST00000360945.2	+	4	401	c.359C>A	c.(358-360)cCc>cAc	p.P120H	TIMM9_ENST00000216463.4_5'Flank|RP11-517O13.1_ENST00000556734.1_RNA	NM_207377.2	NP_997260.1	Q6UXN7	TO20L_HUMAN	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	120					protein targeting (GO:0006605)	integral component of membrane (GO:0016021)|mitochondrial outer membrane translocase complex (GO:0005742)		p.P120H(1)		large_intestine(2)|lung(2)	4						ACTCTCCCTCCCAAGGTATTT	0.423																																					p.P120H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C359A	14						.						86.0	81.0	82.0					14																	58874140		2203	4300	6503	57943893	SO:0001583	missense	387990	exon4				CCDS9734.1	14q23.1	2009-01-14			ENSG00000196860	ENSG00000196860			33752	protein-coding gene	gene with protein product	"""translocase of outer mitochondrial membrane 20 homolog type I"""					15733919	Standard	NM_207377		Approved	UNQ9438	uc001xdr.1	Q6UXN7	OTTHUMG00000140323	ENST00000360945.2:c.359C>A	14.37:g.58874140C>A	ENSP00000354204:p.Pro120His	Somatic		Capture	Illumina HiSeq	Phase_I	57943893	NM_207377	B2RPR0	Missense_Mutation	SNP	ENST00000360945.2	37	CCDS9734.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.185897	0.78789	.	.	ENSG00000196860	ENST00000360945	T	0.34072	1.38	4.96	4.96	0.65561	Mitochondrial outer membrane translocase complex, subunit Tom20 domain (2);	0.141093	0.33127	N	0.005251	T	0.62109	0.2401	M	0.83953	2.67	0.36213	D	0.851498	D	0.89917	1.0	D	0.68765	0.96	T	0.73553	-0.3946	10	0.72032	D	0.01	-6.679	15.229	0.73372	0.0:1.0:0.0:0.0	.	120	Q6UXN7	TO20L_HUMAN	H	120	ENSP00000354204:P120H	ENSP00000354204:P120H	P	+	2	0	TOMM20L	57943893	0.984000	0.35163	1.000000	0.80357	0.992000	0.81027	2.917000	0.48821	2.577000	0.86979	0.650000	0.86243	CCC		0.423	TOMM20L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276937.1	NM_207377	
SLC38A6	145389	broad.mit.edu	37	14	61451471	61451471	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:61451471T>C	ENST00000267488.4	+	3	376	c.260T>C	c.(259-261)cTc>cCc	p.L87P	SLC38A6_ENST00000554304.1_3'UTR|RP11-193F5.1_ENST00000553946.1_RNA|SLC38A6_ENST00000354886.2_Missense_Mutation_p.L87P|SLC38A6_ENST00000456840.2_Missense_Mutation_p.L64P	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	87					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)		p.L87P(2)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		ACAGTTGCTCTCCTGGCTTCT	0.373																																					p.L87P												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T260C	14						.						202.0	186.0	191.0					14																	61451471		2203	4300	6503	60521224	SO:0001583	missense	145389	exon3			AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"""Solute carriers"""	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000267488.4:c.260T>C	14.37:g.61451471T>C	ENSP00000267488:p.Leu87Pro	Somatic		Capture	Illumina HiSeq	Phase_I	60521224	NM_153811	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000267488.4	37	CCDS9751.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.06|19.06	3.753814|3.753814	0.69648|0.69648	.|.	.|.	ENSG00000139974|ENSG00000139974	ENST00000354886;ENST00000267488;ENST00000451406;ENST00000456840;ENST00000526105|ENST00000533744	T;T;T;T;T|.	0.02974|.	4.09;4.09;4.09;4.09;4.09|.	6.15|6.15	6.15|6.15	0.99193|0.99193	.|.	0.373559|.	0.31082|.	N|.	0.008289|.	T|T	0.71558|0.71558	0.3354|0.3354	M|M	0.67397|0.67397	2.05|2.05	0.54753|0.54753	D|D	0.999981|0.999981	P;P;P|.	0.51057|.	0.855;0.941;0.915|.	P;P;P|.	0.50708|.	0.544;0.648;0.567|.	T|T	0.71097|0.71097	-0.4691|-0.4691	10|5	0.72032|.	D|.	0.01|.	-0.2293|-0.2293	13.4067|13.4067	0.60917|0.60917	0.0:0.0:0.1391:0.8609|0.0:0.0:0.1391:0.8609	.|.	64;87;87|.	E7ETF2;Q8IZM9-2;Q8IZM9|.	.;.;S38A6_HUMAN|.	P|P	87;87;82;64;33|36	ENSP00000346959:L87P;ENSP00000267488:L87P;ENSP00000395851:L82P;ENSP00000413863:L64P;ENSP00000451244:L33P|.	ENSP00000267488:L87P|.	L|S	+|+	2|1	0|0	SLC38A6|SLC38A6	60521224|60521224	0.823000|0.823000	0.29233|0.29233	0.993000|0.993000	0.49108|0.49108	0.996000|0.996000	0.88848|0.88848	3.648000|3.648000	0.54410|0.54410	2.363000|2.363000	0.80096|0.80096	0.523000|0.523000	0.50628|0.50628	CTC|TCC		0.373	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1		
TMEM30B	161291	broad.mit.edu	37	14	61746973	61746973	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:61746973C>T	ENST00000555868.1	-	1	1585	c.893G>A	c.(892-894)gGc>gAc	p.G298D	TMEM30B_ENST00000557163.1_5'UTR|TMEM30B_ENST00000355702.2_Missense_Mutation_p.G298D	NM_001017970.2	NP_001017970.1	Q3MIR4	CC50B_HUMAN	transmembrane protein 30B	298					lipid transport (GO:0006869)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G298D(1)		breast(2)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.107)|BRCA - Breast invasive adenocarcinoma(234;0.181)		GAGCTTGTGGCCGCCGAACGC	0.662																																					p.G298D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G893A	14						.						58.0	54.0	55.0					14																	61746973		2203	4300	6503	60816726	SO:0001583	missense	161291	exon1			AK091169	CCDS32093.1	14q23.1	2006-09-20				ENSG00000182107			27254	protein-coding gene	gene with protein product		611029				15375526	Standard	NM_001017970		Approved	CDC50B	uc001xfl.3	Q3MIR4		ENST00000555868.1:c.893G>A	14.37:g.61746973C>T	ENSP00000450842:p.Gly298Asp	Somatic		Capture	Illumina HiSeq	Phase_I	60816726	NM_001017970	B3KR84|Q14D00	Missense_Mutation	SNP	ENST00000555868.1	37	CCDS32093.1	.	.	.	.	.	.	.	.	.	.	C	31	5.071135	0.93950	.	.	ENSG00000182107	ENST00000555868;ENST00000355702	.	.	.	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	D	0.90086	0.6903	H	0.98525	4.255	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93685	0.7002	9	0.87932	D	0	-17.4879	15.1605	0.72782	0.0:1.0:0.0:0.0	.	298	Q3MIR4	CC50B_HUMAN	D	298	.	ENSP00000347930:G298D	G	-	2	0	TMEM30B	60816726	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.265000	0.78442	2.420000	0.82092	0.650000	0.86243	GGC		0.662	TMEM30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413358.1	XM_090844	
RHOJ	57381	broad.mit.edu	37	14	63757654	63757654	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:63757654delT	ENST00000316754.3	+	5	1019	c.557delT	c.(556-558)gttfs	p.V186fs		NM_020663.4	NP_065714.1	Q9H4E5	RHOJ_HUMAN	ras homolog family member J	186					actin cytoskeleton organization (GO:0030036)|GTP catabolic process (GO:0006184)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.F187fs*>28(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.00326)|all cancers(60;0.031)|BRCA - Breast invasive adenocarcinoma(234;0.119)		CTCAAAGCGGTTTTTGATGAA	0.433																																					p.V186fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.557delT	14						.						130.0	129.0	129.0					14																	63757654		2203	4300	6503	62827407	SO:0001589	frameshift_variant	57381	exon5			AK027351	CCDS9757.1	14q23.1	2012-02-27	2012-02-27	2004-03-24	ENSG00000126785	ENSG00000126785			688	protein-coding gene	gene with protein product		607653	"""RAS-like, family 7, member B"", ""ras homolog gene family, member J"""	RASL7B, ARHJ		10967094	Standard	NM_020663		Approved	FLJ14445, TCL	uc001xgb.2	Q9H4E5	OTTHUMG00000140342	ENST00000316754.3:c.557delT	14.37:g.63757654delT	ENSP00000316729:p.Val186fs	Somatic		Capture	Illumina HiSeq	Phase_I	62827407	NM_020663	Q96KC1	Frame_Shift_Del	DEL	ENST00000316754.3	37	CCDS9757.1																																																																																				0.433	RHOJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276975.3		
HSPA2	3306	broad.mit.edu	37	14	65008378	65008378	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:65008378G>A	ENST00000394709.1	+	2	887	c.811G>A	c.(811-813)Gag>Aag	p.E271K	RP11-973N13.4_ENST00000554918.1_RNA|HSPA2_ENST00000247207.6_Missense_Mutation_p.E271K			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	271					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)	p.E271K(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		CACCGCTTGCGAGCGCGCCAA	0.657																																					p.E271K	Pancreas(136;1211 1835 24894 31984 38227)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G811A	14						.						21.0	22.0	22.0					14																	65008378		2200	4299	6499	64078131	SO:0001583	missense	3306	exon1			L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"""Heat shock proteins / HSP70"""	5235	protein-coding gene	gene with protein product		140560	"""heat shock 70kD protein 2"""				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.811G>A	14.37:g.65008378G>A	ENSP00000378199:p.Glu271Lys	Somatic		Capture	Illumina HiSeq	Phase_I	64078131	NM_021979	Q15508|Q53XM3|Q9UE78	Missense_Mutation	SNP	ENST00000394709.1	37	CCDS9766.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.830860	0.91036	.	.	ENSG00000126803	ENST00000394709;ENST00000247207	T;T	0.17528	2.27;2.27	4.94	4.94	0.65067	.	0.000000	0.56097	U	0.000040	T	0.61578	0.2358	H	0.98769	4.325	0.58432	D	0.99999	D	0.76494	0.999	D	0.70016	0.967	T	0.80261	-0.1456	10	0.87932	D	0	-3.5289	18.1451	0.89652	0.0:0.0:1.0:0.0	.	271	P54652	HSP72_HUMAN	K	271	ENSP00000378199:E271K;ENSP00000247207:E271K	ENSP00000247207:E271K	E	+	1	0	HSPA2	64078131	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.869000	0.99810	2.287000	0.76781	0.563000	0.77884	GAG		0.657	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1		
SLC10A1	6554	broad.mit.edu	37	14	70263789	70263789	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:70263789G>A	ENST00000216540.4	-	1	217	c.84C>T	c.(82-84)agC>agT	p.S28S		NM_003049.3	NP_003040.1	Q14973	NTCP_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 1	28					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)	p.S28S(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)	14				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)	Bumetanide(DB00887)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Ethinyl Estradiol(DB00977)|Indomethacin(DB00328)|Liothyronine(DB00279)|Liotrix(DB01583)|Pitavastatin(DB08860)|Probenecid(DB01032)|Progesterone(DB00396)|Testosterone(DB00624)|Ursodeoxycholic acid(DB01586)	CCAGGATGACGCTCAGTGCCA	0.567																																					p.S28S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C84T	14						.						103.0	99.0	100.0					14																	70263789		2203	4300	6503	69333542	SO:0001819	synonymous_variant	6554	exon1			L21893	CCDS9797.1	14q24.2	2013-07-18	2013-07-18		ENSG00000100652	ENSG00000100652		"""Solute carriers"""	10905	protein-coding gene	gene with protein product		182396				8132774	Standard	NM_003049		Approved	NTCP	uc001xlr.2	Q14973	OTTHUMG00000171236	ENST00000216540.4:c.84C>T	14.37:g.70263789G>A		Somatic		Capture	Illumina HiSeq	Phase_I	69333542	NM_003049	B9EGB6|Q2TU29	Silent	SNP	ENST00000216540.4	37	CCDS9797.1																																																																																				0.567	SLC10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412464.1		
SIPA1L1	26037	broad.mit.edu	37	14	72196975	72196975	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:72196975G>A	ENST00000555818.1	+	18	5229	c.4881G>A	c.(4879-4881)ccG>ccA	p.P1627P	SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000358550.2_Silent_p.P1606P|SIPA1L1_ENST00000381232.3_Silent_p.P1606P|SIPA1L1_ENST00000537413.1_Silent_p.P1081P	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1627					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.P1627P(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		AGTCGCTCCCGTTGAGGAGGC	0.562																																					p.P1627P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4881A	14						.						110.0	99.0	102.0					14																	72196975		2203	4300	6503	71266728	SO:0001819	synonymous_variant	26037	exon18			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.4881G>A	14.37:g.72196975G>A		Somatic		Capture	Illumina HiSeq	Phase_I	71266728	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	37	CCDS9807.1																																																																																				0.562	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	
HEATR4	399671	broad.mit.edu	37	14	73987658	73987658	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:73987658G>T	ENST00000553558.1	-	4	1288	c.967C>A	c.(967-969)Ctc>Atc	p.L323I	RP3-414A15.11_ENST00000553394.1_RNA|HEATR4_ENST00000334988.2_Missense_Mutation_p.L323I|HEATR4_ENST00000560393.1_Missense_Mutation_p.L276I|RP3-414A15.2_ENST00000555972.2_RNA	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	323								p.L276I(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		GGCTGGGAGAGGCTCGTCTTT	0.512																																					p.L276I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C826A	14						.						159.0	145.0	150.0					14																	73987658		2203	4300	6503	73057411	SO:0001583	missense	399671	exon3			BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.967C>A	14.37:g.73987658G>T	ENSP00000450444:p.Leu323Ile	Somatic		Capture	Illumina HiSeq	Phase_I	73057411	NM_203309	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2	.	.	.	.	.	.	.	.	.	.	G	5.216	0.225316	0.09916	.	.	ENSG00000187105	ENST00000553558;ENST00000334988	T	0.47177	0.85	4.57	-9.14	0.00701	.	1.883610	0.02501	N	0.090510	T	0.20861	0.0502	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08146	-1.0736	10	0.25106	T	0.35	2.0938	4.5141	0.11926	0.1035:0.31:0.4312:0.1552	.	323	Q86WZ0	HEAT4_HUMAN	I	323;276	ENSP00000450444:L323I	ENSP00000335447:L276I	L	-	1	0	HEATR4	73057411	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.545000	0.06069	-1.593000	0.01617	-1.063000	0.02288	CTC		0.512	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309	
ABCD4	5826	broad.mit.edu	37	14	74762570	74762570	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:74762570C>A	ENST00000356924.4	-	6	798	c.655G>T	c.(655-657)Gag>Tag	p.E219*	ABCD4_ENST00000557554.1_Intron|AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000298816.7_Nonsense_Mutation_p.E132*|ABCD4_ENST00000557588.1_Intron	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	219	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.E219*(1)		cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		AAATCTCCCTCCAGCTTCTCC	0.502																																					p.E219X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G655T	14						.						90.0	83.0	85.0					14																	74762570		2203	4300	6503	73832323	SO:0001587	stop_gained	5826	exon6			AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"""ATP binding cassette transporters / subfamily D"""	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.655G>T	14.37:g.74762570C>A	ENSP00000349396:p.Glu219*	Somatic		Capture	Illumina HiSeq	Phase_I	73832323	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Nonsense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	7.011144|7.011144	0.98002|0.98002	.|.	.|.	ENSG00000119688|ENSG00000119688	ENST00000356924;ENST00000298816|ENST00000556971	.|.	.|.	.|.	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.76271	.|0.3964	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.75059	.|-0.3451	.|3	0.56958|.	D|.	0.05|.	.|.	19.3245|19.3245	0.94256|0.94256	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|C	219;132|178	.|.	ENSP00000298816:E132X|.	E|W	-|-	1|3	0|0	ABCD4|ABCD4	73832323|73832323	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.704000|7.704000	0.84595|0.84595	2.549000|2.549000	0.85964|0.85964	0.655000|0.655000	0.94253|0.94253	GAG|TGG		0.502	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
YLPM1	56252	broad.mit.edu	37	14	75276205	75276205	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:75276205A>G	ENST00000552421.1	+	6	2650	c.2526A>G	c.(2524-2526)ccA>ccG	p.P842P	YLPM1_ENST00000238571.3_Silent_p.P1353P|YLPM1_ENST00000325680.7_Silent_p.P1548P			P49750	YLPM1_HUMAN	YLP motif containing 1	1353	Arg-rich.				regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.P1353P(1)|p.P1548P(1)		breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		CAATACCACCAcctccacctc	0.527																																					p.P1548P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A4644G	14						.						94.0	91.0	92.0					14																	75276205		2033	4211	6244	74345958	SO:0001819	synonymous_variant	56252	exon7			AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 169"""		"""chromosome 14 open reading frame 170"""	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.2526A>G	14.37:g.75276205A>G		Somatic		Capture	Illumina HiSeq	Phase_I	74345958	NM_019589	P49752|Q96I64|Q9P1V7	Silent	SNP	ENST00000552421.1	37																																																																																					0.527	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589	
ZC2HC1C	79696	broad.mit.edu	37	14	75538332	75538332	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:75538332G>A	ENST00000524913.1	+	2	1545	c.1056G>A	c.(1054-1056)ccG>ccA	p.P352P	ZC2HC1C_ENST00000439583.2_Intron|ZC2HC1C_ENST00000238686.8_Silent_p.P352P|ZC2HC1C_ENST00000526748.1_Intron|ACYP1_ENST00000555463.1_5'Flank	NM_024643.2	NP_078919.2	Q53FD0	ZC21C_HUMAN	zinc finger, C2HC-type containing 1C	352							metal ion binding (GO:0046872)	p.P352P(1)									AATTCTCCCCGCCTTCAGAAA	0.517																																					p.P352P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1056A	14						.						44.0	43.0	44.0					14																	75538332		1895	4115	6010	74608085	SO:0001819	synonymous_variant	79696	exon2			AK026746	CCDS41972.1, CCDS45138.1	14q24.3	2013-01-10	2012-02-03	2012-02-03	ENSG00000119703	ENSG00000119703		"""Zinc fingers, C2HC-type containing"""	20354	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 140"", ""family with sequence similarity 164, member C"""	C14orf140, FAM164C			Standard	XM_005268062		Approved		uc001xrh.3	Q53FD0	OTTHUMG00000167439	ENST00000524913.1:c.1056G>A	14.37:g.75538332G>A		Somatic		Capture	Illumina HiSeq	Phase_I	74608085	NM_024643	E9PJQ0|Q9BTA8|Q9H5S9	Silent	SNP	ENST00000524913.1	37	CCDS41972.1																																																																																				0.517	ZC2HC1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394616.4	NM_001042430	
IFT43	112752	broad.mit.edu	37	14	76542976	76542976	+	Intron	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:76542976C>T	ENST00000314067.6	+	6	329				IFT43_ENST00000238628.6_Silent_p.N84N	NM_001102564.1	NP_001096034.1	Q96FT9	IFT43_HUMAN	intraflagellar transport 43						cilium morphogenesis (GO:0060271)|intraciliary retrograde transport (GO:0035721)	cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)		p.N84N(1)		endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						TGGATCTGAACGCATGCTATC	0.478																																					p.N84N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C252T	14						.						142.0	119.0	126.0					14																	76542976		2203	4300	6503	75612729	SO:0001627	intron_variant	112752	exon4			BC010436	CCDS9847.1, CCDS41973.1, CCDS58330.1	14q24.3	2014-07-03	2014-07-03	2011-06-09				"""Intraflagellar transport homologs"""	29669	protein-coding gene	gene with protein product		614068	"""chromosome 14 open reading frame 179"", ""intraflagellar transport 43 homolog (Chlamydomonas)"""	C14orf179		21378380	Standard	NM_052873		Approved	FLJ32173, MGC16028	uc010asm.1	Q96FT9		ENST00000314067.6:c.296-5662C>T	14.37:g.76542976C>T		Somatic		Capture	Illumina HiSeq	Phase_I	75612729	NM_052873	B3KPT6|B4DZI9|G3V385|O95418|Q9ULA9	Silent	SNP	ENST00000314067.6	37	CCDS41973.1																																																																																				0.478	IFT43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_052873	
SPTLC2	9517	broad.mit.edu	37	14	78021798	78021798	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:78021798A>G	ENST00000216484.2	-	8	1214	c.1021T>C	c.(1021-1023)Ttg>Ctg	p.L341L	SPTLC2_ENST00000556264.1_5'Flank	NM_004863.3	NP_004854.1	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base subunit 2	341					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)	p.L341L(1)		kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(5)	19			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)	TCCAGATACAAGTATGCCTTG	0.473																																					p.L341L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1021C	14						.						74.0	77.0	76.0					14																	78021798		2203	4300	6503	77091551	SO:0001819	synonymous_variant	9517	exon8			AB011098	CCDS9865.1	14q24.3	2014-09-17			ENSG00000100596	ENSG00000100596	2.3.1.50		11278	protein-coding gene	gene with protein product		605713				8921873, 9363775	Standard	NM_004863		Approved	KIAA0526, LCB2, LCB2A, hLCB2a	uc001xub.3	O15270		ENST00000216484.2:c.1021T>C	14.37:g.78021798A>G		Somatic		Capture	Illumina HiSeq	Phase_I	77091551	NM_004863	Q16685	Silent	SNP	ENST00000216484.2	37	CCDS9865.1	.	.	.	.	.	.	.	.	.	.	A	9.826	1.187081	0.21870	.	.	ENSG00000100596	ENST00000554901	.	.	.	4.89	1.38	0.22167	.	0.136541	0.51477	D	0.000095	T	0.54598	0.1868	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46373	-0.9196	5	.	.	.	-7.3866	7.5064	0.27547	0.5942:0.0:0.4058:0.0	.	.	.	.	P	277	.	.	L	-	2	0	SPTLC2	77091551	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	3.709000	0.54853	0.459000	0.27016	0.528000	0.53228	CTT		0.473	SPTLC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414030.1	NM_004863	
SNW1	22938	broad.mit.edu	37	14	78189602	78189602	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:78189602T>G	ENST00000261531.7	-	11	1114	c.1052A>C	c.(1051-1053)gAg>gCg	p.E351A	SNW1_ENST00000554775.1_Missense_Mutation_p.E189A|SNW1_ENST00000555761.1_Missense_Mutation_p.E351A|SLIRP_ENST00000557431.1_Intron	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	351					cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin D receptor signaling pathway (GO:0070562)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|chromatin (GO:0000785)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	Notch binding (GO:0005112)|nuclear hormone receptor binding (GO:0035257)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)|SMAD binding (GO:0046332)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|vitamin D receptor binding (GO:0042809)	p.E351A(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		TTCATCCCTCTCACGTGCCTC	0.423																																					p.E351A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1052C	14						.						145.0	116.0	125.0					14																	78189602		2203	4300	6503	77259355	SO:0001583	missense	22938	exon11			AF045184	CCDS9867.1	14q22.1-q22.3	2005-09-13	2005-09-13	2005-09-13		ENSG00000100603			16696	protein-coding gene	gene with protein product		603055	"""SKI interacting protein"""	SKIIP		8973337, 9632709	Standard	NM_012245		Approved	NCoA-62, SKIP, Prp45, PRPF45, Bx42	uc001xuf.3	Q13573		ENST00000261531.7:c.1052A>C	14.37:g.78189602T>G	ENSP00000261531:p.Glu351Ala	Somatic		Capture	Illumina HiSeq	Phase_I	77259355	NM_012245	A8K8A9|Q13483|Q32N03|Q5D0D6	Missense_Mutation	SNP	ENST00000261531.7	37	CCDS9867.1	.	.	.	.	.	.	.	.	.	.	T	16.30	3.085585	0.55861	.	.	ENSG00000100603	ENST00000261531;ENST00000554775;ENST00000555761	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.67373	0.2886	M	0.73372	2.23	0.80722	D	1	B;B	0.30793	0.245;0.295	B;B	0.38378	0.272;0.099	T	0.67440	-0.5670	9	0.45353	T	0.12	.	15.7631	0.78103	0.0:0.0:0.0:1.0	.	351;351	G3V3A4;Q13573	.;SNW1_HUMAN	A	351;189;351	.	ENSP00000261531:E351A	E	-	2	0	SNW1	77259355	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	7.774000	0.85478	2.126000	0.65437	0.377000	0.23210	GAG		0.423	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1	NM_012245	
FLRT2	23768	broad.mit.edu	37	14	86088401	86088401	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:86088401C>A	ENST00000330753.4	+	2	1310	c.543C>A	c.(541-543)gaC>gaA	p.D181E	FLRT2_ENST00000554746.1_Missense_Mutation_p.D181E	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	181					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.D181E(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		TTCCTGTGGACTTGCAAGAGC	0.512																																					p.D181E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C543A	14						.						78.0	80.0	79.0					14																	86088401		2203	4300	6503	85158154	SO:0001583	missense	23768	exon2			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.543C>A	14.37:g.86088401C>A	ENSP00000332879:p.Asp181Glu	Somatic		Capture	Illumina HiSeq	Phase_I	85158154	NM_013231	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	C	9.203	1.029002	0.19512	.	.	ENSG00000185070	ENST00000330753;ENST00000554746	T;T	0.02323	4.34;4.34	5.42	1.34	0.21922	.	0.215729	0.46758	D	0.000264	T	0.01592	0.0051	N	0.12471	0.22	0.44424	D	0.99734	B	0.20261	0.043	B	0.19946	0.027	T	0.55379	-0.8150	10	0.16896	T	0.51	-23.1491	6.3835	0.21548	0.0:0.5897:0.123:0.2873	.	181	O43155	FLRT2_HUMAN	E	181	ENSP00000332879:D181E;ENSP00000451050:D181E	ENSP00000332879:D181E	D	+	3	2	FLRT2	85158154	1.000000	0.71417	0.983000	0.44433	0.985000	0.73830	0.884000	0.28214	0.302000	0.22762	-0.142000	0.14014	GAC		0.512	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1		
FLRT2	23768	broad.mit.edu	37	14	86089367	86089367	+	Silent	SNP	G	G	A	rs147101710		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:86089367G>A	ENST00000330753.4	+	2	2276	c.1509G>A	c.(1507-1509)gcG>gcA	p.A503A	FLRT2_ENST00000554746.1_Silent_p.A503A	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	503	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.A503A(2)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		ACTACCGCGCGGTAGAAGACA	0.537													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16112	0.0		0.0	False		,,,				2504	0.0				p.A503A												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G1509A	14						.	G		1,4405	2.1+/-5.4	0,1,2202	131.0	119.0	123.0		1509	-12.3	0.0	14	dbSNP_134	123	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	FLRT2	NM_013231.4		0,5,6498	AA,AG,GG		0.0465,0.0227,0.0384		503/661	86089367	5,13001	2203	4300	6503	85159120	SO:0001819	synonymous_variant	23768	exon2			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1509G>A	14.37:g.86089367G>A		Somatic		Capture	Illumina HiSeq	Phase_I	85159120	NM_013231	A0AV84|B7ZLP3	Silent	SNP	ENST00000330753.4	37	CCDS9877.1																																																																																				0.537	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1		
NDUFB1	4707	broad.mit.edu	37	14	92588045	92588045	+	5'UTR	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:92588045G>A	ENST00000553514.1	-	0	23				CPSF2_ENST00000298875.4_5'Flank|NDUFB1_ENST00000555441.1_5'Flank|NDUFB1_ENST00000556555.1_5'Flank|NDUFB1_ENST00000329559.3_Missense_Mutation_p.A26V|NDUFB1_ENST00000605997.1_5'UTR			O75438	NDUB1_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.A26V(1)		large_intestine(1)|lung(1)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.205)		CTCAACCCGCGCCAGTGGAAG	0.662																																					p.A26V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C77T	14						.						43.0	48.0	46.0					14																	92588045		2203	4299	6502	91657798	SO:0001623	5_prime_UTR_variant	4707	exon1			BC104672	CCDS9901.1	14q31.3	2011-07-04	2002-08-29		ENSG00000183648	ENSG00000183648		"""Mitochondrial respiratory chain complex / Complex I"""	7695	protein-coding gene	gene with protein product	"""complex I MNLL subunit"""	603837	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1 (7kD, MNLL)"""			9763677	Standard	NM_004545		Approved	MNLL, CI-MNLL	uc001yaf.3	O75438		ENST00000553514.1:c.-183C>T	14.37:g.92588045G>A		Somatic		Capture	Illumina HiSeq	Phase_I	91657798	NM_004545	A0AV68	Missense_Mutation	SNP	ENST00000553514.1	37		.	.	.	.	.	.	.	.	.	.	G	13.03	2.114949	0.37339	.	.	ENSG00000183648	ENST00000329559	.	.	.	5.02	1.97	0.26223	.	.	.	.	.	T	0.36580	0.0972	.	.	.	0.80722	D	1	P	0.34462	0.454	B	0.26614	0.071	T	0.21143	-1.0254	7	0.59425	D	0.04	.	6.8017	0.23754	0.095:0.3432:0.5618:0.0	.	26	O75438-2	.	V	26	.	ENSP00000330787:A26V	A	-	2	0	NDUFB1	91657798	0.749000	0.28305	0.975000	0.42487	0.030000	0.12068	0.281000	0.18810	0.621000	0.30232	-0.273000	0.10243	GCG		0.662	NDUFB1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412116.2	NM_004545	
LGMN	5641	broad.mit.edu	37	14	93178266	93178266	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:93178266C>T	ENST00000393218.2	-	10	982	c.645G>A	c.(643-645)tcG>tcA	p.S215S	LGMN_ENST00000334869.4_Silent_p.S215S|LGMN_ENST00000555699.1_Silent_p.S215S|LGMN_ENST00000557434.1_Silent_p.S215S	NM_001008530.2	NP_001008530.1	Q99538	LGMN_HUMAN	legumain	215					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|innate immune response (GO:0045087)|negative regulation of ERBB signaling pathway (GO:1901185)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of neuron apoptotic process (GO:0043524)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|receptor catabolic process (GO:0032801)|renal system process (GO:0003014)|response to acidic pH (GO:0010447)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|toll-like receptor signaling pathway (GO:0002224)|vitamin D metabolic process (GO:0042359)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)	p.S215S(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|skin(2)	18		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		AGGCGTAGGACGACTCTCTGG	0.488																																					p.S215S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G645A	14						.						80.0	76.0	77.0					14																	93178266		2203	4300	6503	92248019	SO:0001819	synonymous_variant	5641	exon10			D55696	CCDS9904.1	14q32.12	2011-04-08		2002-01-18	ENSG00000100600	ENSG00000100600			9472	protein-coding gene	gene with protein product		602620	"""protease, cysteine, 1 (legumain)"""	PRSC1		8893817, 9065484	Standard	NM_001008530		Approved	LGMN1	uc001yaw.3	Q99538		ENST00000393218.2:c.645G>A	14.37:g.93178266C>T		Somatic		Capture	Illumina HiSeq	Phase_I	92248019	NM_001008530	O00123|Q86TV2|Q86TV3|Q9BTY1	Silent	SNP	ENST00000393218.2	37	CCDS9904.1																																																																																				0.488	LGMN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412288.1	NM_005606	
UBR7	55148	broad.mit.edu	37	14	93685585	93685585	+	Missense_Mutation	SNP	G	G	A	rs568426322		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:93685585G>A	ENST00000013070.6	+	8	1074	c.838G>A	c.(838-840)Gca>Aca	p.A280T	UBR7_ENST00000416753.1_Missense_Mutation_p.A204T	NM_175748.3	NP_786924.2	Q8N806	UBR7_HUMAN	ubiquitin protein ligase E3 component n-recognin 7 (putative)	280							ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A280T(1)		breast(2)|endometrium(2)|large_intestine(2)|lung(12)|urinary_tract(1)	19						AAGCCTCAACGCAGAATCAAA	0.363																																					p.A204T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G610A	14						.						52.0	52.0	52.0					14																	93685585		2203	4300	6503	92755338	SO:0001583	missense	55148	exon7			AK001345	CCDS9909.1	14q32.12	2008-06-23	2008-06-23	2008-06-23		ENSG00000012963		"""Ubiquitin protein ligase E3 component n-recognins"""	20344	protein-coding gene	gene with protein product		613816	"""chromosome 14 open reading frame 130"""	C14orf130		18162545	Standard	NM_175748		Approved		uc001ybm.4	Q8N806		ENST00000013070.6:c.838G>A	14.37:g.93685585G>A	ENSP00000013070:p.Ala280Thr	Somatic		Capture	Illumina HiSeq	Phase_I	92755338	NM_001100417	Q86U21|Q86UA9|Q96BY0|Q9NVV6	Missense_Mutation	SNP	ENST00000013070.6	37	CCDS9909.1	.	.	.	.	.	.	.	.	.	.	G	2.507	-0.313817	0.05422	.	.	ENSG00000012963	ENST00000013070;ENST00000535646;ENST00000416753	T;T	0.76968	-1.05;-1.06	5.56	-2.05	0.07321	.	0.530351	0.17860	N	0.159557	T	0.41949	0.1181	N	0.02539	-0.55	0.09310	N	1	B;B	0.14012	0.009;0.001	B;B	0.06405	0.002;0.0	T	0.35500	-0.9786	10	0.12430	T	0.62	-7.4434	3.3742	0.07232	0.4016:0.0:0.1985:0.3999	.	204;280	E9PCJ7;Q8N806	.;UBR7_HUMAN	T	280;204;204	ENSP00000013070:A280T;ENSP00000391706:A204T	ENSP00000013070:A280T	A	+	1	0	UBR7	92755338	0.000000	0.05858	0.001000	0.08648	0.192000	0.23643	-0.719000	0.04974	-0.248000	0.09583	-0.312000	0.09012	GCA		0.363	UBR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412693.1	NM_175748	
UNC79	57578	broad.mit.edu	37	14	94139793	94139793	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:94139793C>T	ENST00000393151.2	+	42	6850	c.6850C>T	c.(6850-6852)Ctt>Ttt	p.L2284F	UNC79_ENST00000555664.1_Missense_Mutation_p.L2245F|UNC79_ENST00000256339.4_Missense_Mutation_p.L2107F|UNC79_ENST00000553484.1_Missense_Mutation_p.L2306F			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2284					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L2306F(1)|p.L2107F(1)		breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						CCTTCTTCTGCTTGTTCAGGT	0.378																																					p.L2107F												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C6319T	14						.						139.0	132.0	135.0					14																	94139793		2203	4300	6503	93209546	SO:0001583	missense	57578	exon42			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.6850C>T	14.37:g.94139793C>T	ENSP00000376858:p.Leu2284Phe	Somatic		Capture	Illumina HiSeq	Phase_I	93209546	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	C	18.38	3.610588	0.66558	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.30182	1.54;1.58;1.54;1.54	5.9	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.49457	0.1558	M	0.68593	2.085	0.47374	D	0.999405	D	0.69078	0.997	D	0.74674	0.984	T	0.48714	-0.9011	10	0.72032	D	0.01	-19.8882	9.0243	0.36220	0.0:0.8399:0.0:0.1601	.	2306	C9JQL1	.	F	2107;2245;2306;2284;2306	ENSP00000256339:L2107F;ENSP00000450868:L2245F;ENSP00000451360:L2306F;ENSP00000376858:L2284F	ENSP00000256339:L2107F	L	+	1	0	KIAA1409	93209546	1.000000	0.71417	1.000000	0.80357	0.649000	0.38597	3.019000	0.49635	2.788000	0.95919	0.650000	0.86243	CTT		0.378	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
UNC79	57578	broad.mit.edu	37	14	94155037	94155037	+	Silent	SNP	T	T	G	rs199612305		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:94155037T>G	ENST00000393151.2	+	45	7053	c.7053T>G	c.(7051-7053)ccT>ccG	p.P2351P	UNC79_ENST00000555664.1_Silent_p.P2312P|UNC79_ENST00000256339.4_Silent_p.P2174P|UNC79_ENST00000553484.1_Silent_p.P2373P			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2351					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P2174P(1)|p.P2373P(1)		breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						GTTCCCAGCCTCTGCATGAAG	0.483																																					p.P2174P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T6522G	14						.						81.0	78.0	79.0					14																	94155037		2203	4300	6503	93224790	SO:0001819	synonymous_variant	57578	exon45			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.7053T>G	14.37:g.94155037T>G		Somatic		Capture	Illumina HiSeq	Phase_I	93224790	NM_020818	B5MDL6|Q6ZUT7	Silent	SNP	ENST00000393151.2	37																																																																																					0.483	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
SERPINA6	866	broad.mit.edu	37	14	94776112	94776112	+	Missense_Mutation	SNP	C	C	T	rs267604111		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:94776112C>T	ENST00000341584.3	-	3	991	c.845G>A	c.(844-846)cGg>cAg	p.R282Q		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	282					glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)	p.R282L(2)|p.R282Q(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	AATCGTGTCCCGGCTCAGTGC	0.562																																					p.R282Q												SERPINA6,skin,NS,Substitution - Missense,0 	.	3	Substitution - Missense(3)	skin(2)|large_intestine(1)	c.G845A	14						.						155.0	107.0	123.0					14																	94776112		2203	4300	6503	93845865	SO:0001583	missense	866	exon3			J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"""Serine (or cysteine) peptidase inhibitors"""	1540	protein-coding gene	gene with protein product	"""corticosteroid binding globulin"", ""transcortin"""	122500	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"""	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.845G>A	14.37:g.94776112C>T	ENSP00000342850:p.Arg282Gln	Somatic		Capture	Illumina HiSeq	Phase_I	93845865	NM_001756	A8K456|Q7Z2Q9	Missense_Mutation	SNP	ENST00000341584.3	37	CCDS9924.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.432604	0.25813	.	.	ENSG00000170099	ENST00000341584	D	0.83992	-1.79	5.43	3.48	0.39840	Serpin domain (3);	0.267525	0.25607	N	0.029520	T	0.70911	0.3278	L	0.59967	1.855	0.21984	N	0.999439	P	0.37015	0.578	B	0.21360	0.034	T	0.63028	-0.6728	10	0.35671	T	0.21	.	4.7077	0.12858	0.1611:0.5973:0.0:0.2415	.	282	P08185	CBG_HUMAN	Q	282	ENSP00000342850:R282Q	ENSP00000342850:R282Q	R	-	2	0	SERPINA6	93845865	0.263000	0.24083	0.913000	0.36048	0.145000	0.21501	1.000000	0.29770	1.428000	0.47296	0.563000	0.77884	CGG		0.562	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756	
SERPINA5	5104	broad.mit.edu	37	14	95053780	95053780	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:95053780G>T	ENST00000554866.1	+	2	195	c.81G>T	c.(79-81)atG>atT	p.M27I	SERPINA5_ENST00000329597.7_Missense_Mutation_p.M27I|SERPINA5_ENST00000554276.1_Missense_Mutation_p.M27I|SERPINA5_ENST00000553780.1_Missense_Mutation_p.M27I			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	27					fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.M27I(1)		endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	CCCGGGAGATGAAGAAGAGAG	0.612																																					p.M27I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G81T	14						.						60.0	63.0	62.0					14																	95053780		2203	4300	6503	94123533	SO:0001583	missense	5104	exon3			M68516	CCDS9928.1	14q32.1	2014-02-18	2005-08-18		ENSG00000188488	ENSG00000188488		"""Serine (or cysteine) peptidase inhibitors"""	8723	protein-coding gene	gene with protein product		601841	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5"""	PLANH3, PCI		1714450, 8381582, 24172014	Standard	NM_000624		Approved	PAI3, PROCI	uc001ydm.3	P05154	OTTHUMG00000170860	ENST00000554866.1:c.81G>T	14.37:g.95053780G>T	ENSP00000451126:p.Met27Ile	Somatic		Capture	Illumina HiSeq	Phase_I	94123533	NM_000624	Q07616|Q9UG30	Missense_Mutation	SNP	ENST00000554866.1	37	CCDS9928.1	.	.	.	.	.	.	.	.	.	.	G	10.25	1.297128	0.23650	.	.	ENSG00000188488	ENST00000554220;ENST00000553780;ENST00000554760;ENST00000554866;ENST00000329597;ENST00000556775;ENST00000553511;ENST00000554506;ENST00000554633;ENST00000555681;ENST00000438291;ENST00000554276;ENST00000557598	D;D;D;D;D;T;T;T;T;D;T	0.87103	-1.55;-1.55;-2.21;-1.55;-1.55;-0.76;-0.76;-0.76;-0.76;-1.55;-0.76	3.59	-4.21	0.03812	Serpin domain (1);	7.205980	0.00496	N	0.000156	T	0.73434	0.3586	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.62618	-0.6816	10	0.38643	T	0.18	.	7.5119	0.27579	0.5756:0.1218:0.3026:0.0	.	27;27	G3V5Q9;P05154	.;IPSP_HUMAN	I	27	ENSP00000450484:M27I;ENSP00000450837:M27I;ENSP00000452469:M27I;ENSP00000451126:M27I;ENSP00000333203:M27I;ENSP00000450745:M27I;ENSP00000451215:M27I;ENSP00000451697:M27I;ENSP00000451650:M27I;ENSP00000451610:M27I;ENSP00000450485:M27I	ENSP00000333203:M27I	M	+	3	0	SERPINA5	94123533	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.536000	0.06135	-0.920000	0.03799	0.561000	0.74099	ATG		0.612	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
CLMN	79789	broad.mit.edu	37	14	95662949	95662949	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:95662949delT	ENST00000298912.4	-	10	2707	c.2594delA	c.(2593-2595)aagfs	p.K865fs	CLMN_ENST00000556441.1_5'Flank|CLMN_ENST00000557215.1_5'Flank	NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	865					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.K865fs*10(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		CCTTTTTTCCTTTTTTTTACT	0.408																																					p.K865fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2594delA	14						.						152.0	132.0	139.0					14																	95662949		2203	4300	6503	94732702	SO:0001589	frameshift_variant	79789	exon10			AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.2594delA	14.37:g.95662949delT	ENSP00000298912:p.Lys865fs	Somatic		Capture	Illumina HiSeq	Phase_I	94732702	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Frame_Shift_Del	DEL	ENST00000298912.4	37	CCDS9933.1																																																																																				0.408	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2		
BDKRB2	624	broad.mit.edu	37	14	96706906	96706906	+	Missense_Mutation	SNP	G	G	A	rs200683377		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:96706906G>A	ENST00000306005.3	+	3	437	c.241G>A	c.(241-243)Gtc>Atc	p.V81I	BDKRB2_ENST00000539359.1_Missense_Mutation_p.V54I|BDKRB2_ENST00000554311.1_Missense_Mutation_p.V81I|BDKRB2_ENST00000542454.2_Missense_Mutation_p.V54I|RP11-404P21.8_ENST00000553811.1_Intron	NM_000623.3	NP_000614.1	P30411	BKRB2_HUMAN	bradykinin receptor B2	81					arachidonic acid secretion (GO:0050482)|blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator (GO:1902239)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of vascular permeability (GO:0043114)|regulation of vasoconstriction (GO:0019229)|response to salt stress (GO:0009651)|smooth muscle contraction (GO:0006939)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|phosphatidylinositol phospholipase C activity (GO:0004435)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|type 1 angiotensin receptor binding (GO:0031702)	p.V81I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|lung(7)|ovary(3)|skin(1)	24		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)	Icatibant(DB06196)	TGTCCTCAGCGTCTTCTGCCT	0.637													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18868	0.0		0.0	False		,,,				2504	0.0				p.V81I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G241A	14						.	G	ILE/VAL	0,4406		0,0,2203	99.0	100.0	100.0		241	3.8	1.0	14		100	1,8599	1.2+/-3.3	0,1,4299	no	missense	BDKRB2	NM_000623.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	81/392	96706906	1,13005	2203	4300	6503	95776659	SO:0001583	missense	624	exon3			S56772	CCDS9942.1	14q32.1-q32.2	2012-08-08				ENSG00000168398		"""GPCR / Class A : Bradykinin receptors"""	1030	protein-coding gene	gene with protein product		113503				7916737	Standard	NM_000623		Approved	BK-2	uc010avm.1	P30411		ENST00000306005.3:c.241G>A	14.37:g.96706906G>A	ENSP00000307713:p.Val81Ile	Somatic		Capture	Illumina HiSeq	Phase_I	95776659	NM_000623		Missense_Mutation	SNP	ENST00000306005.3	37	CCDS9942.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	19.65	3.867704	0.72065	0.0	1.16E-4	ENSG00000168398	ENST00000542454;ENST00000554311;ENST00000306005;ENST00000539359	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	4.68	3.78	0.43462	GPCR, rhodopsin-like superfamily (1);	0.063724	0.64402	N	0.000008	T	0.33904	0.0879	L	0.42245	1.32	0.48830	D	0.999713	P	0.46621	0.881	P	0.44477	0.451	T	0.21999	-1.0229	10	0.02654	T	1	-37.6504	13.1932	0.59723	0.0782:0.0:0.9218:0.0	.	81	P30411	BKRB2_HUMAN	I	54;81;81;54	ENSP00000439459:V54I;ENSP00000450482:V81I;ENSP00000307713:V81I;ENSP00000438376:V54I	ENSP00000307713:V81I	V	+	1	0	BDKRB2	95776659	1.000000	0.71417	0.990000	0.47175	0.964000	0.63967	4.700000	0.61803	1.100000	0.41517	0.561000	0.74099	GTC		0.637	BDKRB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413294.1		
MIR380	494329	broad.mit.edu	37	14	101492138	101492138	+	RNA	SNP	C	C	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:101492138C>G	ENST00000362112.2	-	0	0				MIR758_ENST00000390227.1_RNA|MIR411_ENST00000362239.2_RNA|MIR329-1_ENST00000385028.1_RNA|MIR323A_ENST00000362199.1_RNA|MIR329-2_ENST00000385029.1_RNA|MIR1197_ENST00000408818.1_RNA|MIR299_ENST00000385016.2_RNA	NR_029872.1				microRNA 380																		CGGTCGACCTCTTTGCAGTAT	0.577																																					.												.	.	0			.	14						.						125.0	117.0	120.0					14																	101492138		1568	3582	5150	100561891			442897	.					14q32.31	2013-02-12		2008-12-18		ENSG00000198982		"""ncRNAs / Micro RNAs"""	31873	non-coding RNA	RNA, micro		613654		MIRN380			Standard	NR_029872		Approved	hsa-mir-380	uc010awb.1				14.37:g.101492138C>G		Somatic		Capture	Illumina HiSeq	Phase_I	100561891	.		RNA	SNP	ENST00000362112.2	37																																																																																					0.577	MIR380-201	KNOWN	basic	miRNA	miRNA		NR_029872	
BRF1	2972	broad.mit.edu	37	14	105752656	105752656	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr14:105752656G>A	ENST00000546474.1	-	2	15201	c.242C>T	c.(241-243)tCg>tTg	p.S81L	BRF1_ENST00000327359.3_5'UTR|BRF1_ENST00000548421.1_Missense_Mutation_p.S81L|BRF1_ENST00000440513.3_5'UTR|BRF1_ENST00000379937.2_Intron	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	81					gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)	p.S81L(1)		NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		CTGCGCTCTCGACTCCTTCCC	0.587																																					p.S81L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C242T	14						.						53.0	47.0	49.0					14																	105752656		2203	4300	6503	104823701	SO:0001583	missense	2972	exon2			U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024		"""General transcription factors"""	11551	protein-coding gene	gene with protein product		604902	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2"", ""BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"""	TAF3B2, TAF3C, GTF3B		7624363, 8943358	Standard	NM_145685		Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.242C>T	14.37:g.105752656G>A	ENSP00000448323:p.Ser81Leu	Somatic		Capture	Illumina HiSeq	Phase_I	104823701	NM_001519	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Missense_Mutation	SNP	ENST00000546474.1	37	CCDS10001.1	.	.	.	.	.	.	.	.	.	.	G	8.858	0.946220	0.18356	.	.	ENSG00000185024	ENST00000546474;ENST00000548421;ENST00000345053	.	.	.	4.22	4.22	0.49857	Cyclin-like (1);	0.133715	0.52532	D	0.000079	T	0.79143	0.4396	M	0.84948	2.725	0.80722	D	1	D;D	0.89917	1.0;0.998	D;P	0.74023	0.982;0.893	T	0.82581	-0.0386	9	0.87932	D	0	.	11.9652	0.53031	0.0:0.0:1.0:0.0	.	81;81	Q96KX3;Q92994	.;TF3B_HUMAN	L	81	.	ENSP00000339442:S81L	S	-	2	0	BRF1	104823701	1.000000	0.71417	0.957000	0.39632	0.918000	0.54935	4.147000	0.58078	2.163000	0.67991	0.563000	0.77884	TCG		0.587	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519	
CYFIP1	23191	broad.mit.edu	37	15	22954272	22954272	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:22954272C>T	ENST00000313077.7	+	14	1547	c.1422C>T	c.(1420-1422)caC>caT	p.H474H	CYFIP1_ENST00000435939.2_5'Flank|CYFIP1_ENST00000560848.1_Silent_p.H474H	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1									p.H474H(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		TGTTCAACCACGCCATCCGGC	0.607																																					p.H474H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1422T	15						.						85.0	72.0	76.0					15																	22954272		2203	4300	6503	20505713	SO:0001819	synonymous_variant	23191	exon14			D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.1422C>T	15.37:g.22954272C>T		Somatic		Capture	Illumina HiSeq	Phase_I	20505713	NM_014608		Silent	SNP	ENST00000313077.7	37	CCDS10009.1																																																																																				0.607	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608	
MAGEL2	54551	broad.mit.edu	37	15	23890016	23890016	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:23890016C>A	ENST00000532292.1	-	1	1159	c.1065G>T	c.(1063-1065)tgG>tgT	p.W355C		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	238	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)	p.W387L(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		TGGGCCCTTCCCAGCCACTCA	0.672																																					p.W958C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2874T	15						.						23.0	25.0	24.0					15																	23890016		1848	4092	5940	21441109	SO:0001583	missense	54551	exon1			AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.1065G>T	15.37:g.23890016C>A	ENSP00000433433:p.Trp355Cys	Somatic		Capture	Illumina HiSeq	Phase_I	21441109	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	37		.	.	.	.	.	.	.	.	.	.	C	14.94	2.684950	0.47991	.	.	ENSG00000254585	ENST00000532292	.	.	.	3.57	3.57	0.40892	.	.	.	.	.	T	0.62454	0.2429	L	0.59436	1.845	0.40608	D	0.98164	.	.	.	.	.	.	T	0.61950	-0.6957	5	.	.	.	.	10.9872	0.47528	0.0:1.0:0.0:0.0	.	.	.	.	V	387	.	.	G	-	2	0	MAGEL2	21441109	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	2.549000	0.45803	2.290000	0.77057	0.655000	0.94253	GGG		0.672	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066	
UBE3A	7337	broad.mit.edu	37	15	25601841	25601841	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:25601841G>A	ENST00000397954.2	-	6	1964	c.1965C>T	c.(1963-1965)caC>caT	p.H655H	UBE3A_ENST00000232165.3_Silent_p.H652H|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000428984.2_Silent_p.H632H|UBE3A_ENST00000566215.1_Silent_p.H632H|UBE3A_ENST00000438097.1_Silent_p.H632H			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	655					androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)	p.H655H(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		AACTTACTGGGTGAGAGTCTC	0.299																																					p.H652H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1956T	15						.						98.0	107.0	104.0					15																	25601841		2203	4300	6503	23152934	SO:0001819	synonymous_variant	7337	exon8			AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"""Angelman syndrome"""	601623	"""human papilloma virus E6-associated protein"""	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.1965C>T	15.37:g.25601841G>A		Somatic		Capture	Illumina HiSeq	Phase_I	23152934	NM_130839	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Silent	SNP	ENST00000397954.2	37	CCDS45192.1																																																																																				0.299	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462	
UBE3A	7337	broad.mit.edu	37	15	25616673	25616673	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:25616673C>T	ENST00000397954.2	-	4	656	c.657G>A	c.(655-657)caG>caA	p.Q219Q	UBE3A_ENST00000232165.3_Silent_p.Q216Q|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000428984.2_Silent_p.Q196Q|UBE3A_ENST00000566215.1_Silent_p.Q196Q|UBE3A_ENST00000438097.1_Silent_p.Q196Q			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	219					androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)	p.Q219Q(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		TGTTGTCTCCCTGTGAGCTAT	0.408																																					p.Q216Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G648A	15						.						197.0	190.0	193.0					15																	25616673		2203	4300	6503	23167766	SO:0001819	synonymous_variant	7337	exon6			AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"""Angelman syndrome"""	601623	"""human papilloma virus E6-associated protein"""	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.657G>A	15.37:g.25616673C>T		Somatic		Capture	Illumina HiSeq	Phase_I	23167766	NM_130839	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Silent	SNP	ENST00000397954.2	37	CCDS45192.1																																																																																				0.408	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462	
ATP10A	57194	broad.mit.edu	37	15	25959364	25959364	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:25959364A>C	ENST00000356865.6	-	10	1912	c.1801T>G	c.(1801-1803)Tcc>Gcc	p.S601A		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	601					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.S601A(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TTCACCGGGGACTTCAGCTCA	0.602																																					p.S601A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1801G	15						.						36.0	41.0	39.0					15																	25959364		2197	4290	6487	23510457	SO:0001583	missense	57194	exon10			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1801T>G	15.37:g.25959364A>C	ENSP00000349325:p.Ser601Ala	Somatic		Capture	Illumina HiSeq	Phase_I	23510457	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.907826	0.52333	.	.	ENSG00000206190	ENST00000356865	T	0.10573	2.86	4.62	4.62	0.57501	HAD-like domain (1);	0.178051	0.50627	D	0.000102	T	0.13372	0.0324	L	0.58428	1.81	0.50313	D	0.999867	B	0.28470	0.213	B	0.30401	0.115	T	0.06409	-1.0828	10	0.21014	T	0.42	-32.0787	14.1846	0.65598	1.0:0.0:0.0:0.0	.	601	O60312	AT10A_HUMAN	A	601	ENSP00000349325:S601A	ENSP00000349325:S601A	S	-	1	0	ATP10A	23510457	1.000000	0.71417	0.994000	0.49952	0.767000	0.43475	8.301000	0.89951	1.953000	0.56701	0.533000	0.62120	TCC		0.602	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
GABRB3	2562	broad.mit.edu	37	15	26812863	26812863	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:26812863A>T	ENST00000311550.5	-	7	811	c.700T>A	c.(700-702)Tca>Aca	p.S234T	GABRB3_ENST00000299267.4_Missense_Mutation_p.S234T|GABRB3_ENST00000545868.1_Missense_Mutation_p.S149T|GABRB3_ENST00000541819.2_Missense_Mutation_p.S290T|GABRB3_ENST00000400188.3_Missense_Mutation_p.S163T	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	234					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)	p.S234T(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AAGCTCAGTGACAGTCGAGGA	0.428																																					p.S234T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T700A	15						.						115.0	99.0	104.0					15																	26812863		2203	4300	6503	24363956	SO:0001583	missense	2562	exon7				CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.700T>A	15.37:g.26812863A>T	ENSP00000308725:p.Ser234Thr	Somatic		Capture	Illumina HiSeq	Phase_I	24363956	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	37	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	A	19.15	3.771920	0.69992	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	T;T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93;-0.93	6.06	6.06	0.98353	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.76492	0.3995	L	0.41632	1.29	0.80722	D	1	P;P;D	0.59767	0.928;0.928;0.986	P;P;P	0.58391	0.729;0.666;0.838	T	0.71374	-0.4612	10	0.11485	T	0.65	.	15.7938	0.78394	1.0:0.0:0.0:0.0	.	290;234;234	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	T	234;290;234;163;149	ENSP00000308725:S234T;ENSP00000442408:S290T;ENSP00000299267:S234T;ENSP00000383049:S163T;ENSP00000439169:S149T	ENSP00000299267:S234T	S	-	1	0	GABRB3	24363956	1.000000	0.71417	0.993000	0.49108	0.919000	0.55068	9.204000	0.95041	2.322000	0.78497	0.528000	0.53228	TCA		0.428	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
GABRA5	2558	broad.mit.edu	37	15	27128584	27128584	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:27128584G>A	ENST00000335625.5	+	6	1265	c.377G>A	c.(376-378)aGc>aAc	p.S126N	GABRA5_ENST00000400081.3_Missense_Mutation_p.S126N|GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000557449.1_Intron|GABRA5_ENST00000355395.5_Missense_Mutation_p.S126N	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	126					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.S126N(2)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	CTCCTTGCCAGCAAGATCTGG	0.557																																					p.S126N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G377A	15						.						88.0	98.0	95.0					15																	27128584		2199	4296	6495	24679677	SO:0001583	missense	2558	exon6				CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4079	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 5"""	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.377G>A	15.37:g.27128584G>A	ENSP00000335592:p.Ser126Asn	Somatic		Capture	Illumina HiSeq	Phase_I	24679677	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	37	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.627328	0.66901	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000555182;ENST00000400081;ENST00000554596;ENST00000554599	T;T;T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17;-1.17;-1.17	5.4	5.4	0.78164	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.75867	0.3908	L	0.50919	1.6	0.58432	D	0.999996	B	0.20550	0.046	B	0.28991	0.097	T	0.69837	-0.5037	10	0.30078	T	0.28	.	18.53	0.90987	0.0:0.0:1.0:0.0	.	126	P31644	GBRA5_HUMAN	N	126;126;94;126;126;126	ENSP00000335592:S126N;ENSP00000347557:S126N;ENSP00000450653:S94N;ENSP00000382953:S126N;ENSP00000450806:S126N;ENSP00000450717:S126N	ENSP00000335592:S126N	S	+	2	0	GABRA5	24679677	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.801000	0.85960	2.695000	0.91970	0.561000	0.74099	AGC		0.557	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1		
RYR3	6263	broad.mit.edu	37	15	34023735	34023735	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:34023735C>T	ENST00000389232.4	+	48	7334	c.7264C>T	c.(7264-7266)Ctc>Ttc	p.L2422F	RYR3_ENST00000415757.3_Missense_Mutation_p.L2422F	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2422	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.L2422F(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TTCTGCTGTGCTCCCGCTCCT	0.493																																					p.L2422F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C7264T	15						.						75.0	70.0	72.0					15																	34023735		2014	4192	6206	31811027	SO:0001583	missense	6263	exon48				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.7264C>T	15.37:g.34023735C>T	ENSP00000373884:p.Leu2422Phe	Somatic		Capture	Illumina HiSeq	Phase_I	31811027	NM_001036	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.330964	0.60853	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.90955	-2.76;-2.76	5.38	5.38	0.77491	.	0.082357	0.51477	D	0.000100	D	0.90625	0.7060	M	0.85197	2.74	0.51233	D	0.999916	B;B	0.22414	0.069;0.064	B;B	0.23716	0.039;0.048	D	0.88163	0.2859	10	0.66056	D	0.02	.	10.1181	0.42603	0.0:0.883:0.0:0.117	.	2422;2422	Q15413-2;Q15413	.;RYR3_HUMAN	F	2422	ENSP00000373884:L2422F;ENSP00000399610:L2422F	ENSP00000354735:L2422F	L	+	1	0	RYR3	31811027	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.700000	0.54786	2.793000	0.96121	0.655000	0.94253	CTC		0.493	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
RYR3	6263	broad.mit.edu	37	15	34146637	34146637	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:34146637T>C	ENST00000389232.4	+	97	13917	c.13847T>C	c.(13846-13848)gTt>gCt	p.V4616A	RYR3_ENST00000559917.1_3'UTR|RP11-3D4.3_ENST00000560404.1_RNA|RYR3_ENST00000415757.3_Missense_Mutation_p.V4611A	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4616					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.V4615A(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CTTGGAGTTGTTTTTACTGAC	0.398																																					p.V4616A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T13847C	15						.						80.0	68.0	72.0					15																	34146637		1863	4099	5962	31933929	SO:0001583	missense	6263	exon97				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.13847T>C	15.37:g.34146637T>C	ENSP00000373884:p.Val4616Ala	Somatic		Capture	Illumina HiSeq	Phase_I	31933929	NM_001036	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.661617	0.88154	.	.	ENSG00000198838	ENST00000389232;ENST00000361728	D	0.91011	-2.77	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	D	0.94503	0.8230	M	0.76002	2.32	0.52099	D	0.999946	D;P	0.54047	0.964;0.923	D;P	0.66084	0.941;0.792	D	0.94896	0.8052	10	0.62326	D	0.03	.	15.1032	0.72299	0.0:0.0:0.0:1.0	.	4611;4616	Q15413-2;Q15413	.;RYR3_HUMAN	A	4616;4612	ENSP00000373884:V4616A	ENSP00000354735:V4612A	V	+	2	0	RYR3	31933929	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.637000	0.83313	2.207000	0.71202	0.533000	0.62120	GTT		0.398	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
THBS1	7057	broad.mit.edu	37	15	39876295	39876295	+	Silent	SNP	C	C	T	rs554987285		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:39876295C>T	ENST00000260356.5	+	5	975	c.810C>T	c.(808-810)tgC>tgT	p.C270C		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	270	Laminin G-like.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.C270C(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		AAGCCATCTGCGGCATCTCCT	0.567													C|||	1	0.000199681	0.0	0.0	5008	,	,		20724	0.0		0.0	False		,,,				2504	0.001				p.C270C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C810T	15						.						66.0	62.0	63.0					15																	39876295		2200	4297	6497	37663587	SO:0001819	synonymous_variant	7057	exon5				CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.810C>T	15.37:g.39876295C>T		Somatic		Capture	Illumina HiSeq	Phase_I	37663587	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																				0.567	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
THBS1	7057	broad.mit.edu	37	15	39886303	39886303	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:39886303C>T	ENST00000260356.5	+	20	3436	c.3271C>T	c.(3271-3273)Cgc>Tgc	p.R1091C	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1091	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.R1091C(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CCTTCAGGTGCGCACCCTGTG	0.473																																					p.R1091C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3271T	15						.						54.0	52.0	53.0					15																	39886303		2200	4297	6497	37673595	SO:0001583	missense	7057	exon20				CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.3271C>T	15.37:g.39886303C>T	ENSP00000260356:p.Arg1091Cys	Somatic		Capture	Illumina HiSeq	Phase_I	37673595	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.533047	0.85812	.	.	ENSG00000137801	ENST00000260356	D	0.91686	-2.89	5.83	4.91	0.64330	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.36665	N	0.002477	D	0.95937	0.8677	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.994;0.999	D	0.96399	0.9295	10	0.87932	D	0	-24.3674	14.9289	0.70900	0.2731:0.7269:0.0:0.0	.	1006;1091	B4E3J7;P07996	.;TSP1_HUMAN	C	1091	ENSP00000260356:R1091C	ENSP00000260356:R1091C	R	+	1	0	THBS1	37673595	1.000000	0.71417	0.998000	0.56505	0.949000	0.60115	4.913000	0.63341	1.452000	0.47756	0.655000	0.94253	CGC		0.473	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
PLCB2	5330	broad.mit.edu	37	15	40582991	40582991	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:40582991C>A	ENST00000260402.3	-	28	3333	c.3084G>T	c.(3082-3084)gaG>gaT	p.E1028D	PLCB2_ENST00000557821.1_Missense_Mutation_p.E1024D|PLCB2_ENST00000456256.2_Missense_Mutation_p.E1013D	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	1028					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.E1028D(1)|p.E1024D(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		GGGCCTTCAGCTCTGCCGCCT	0.572																																					p.E1028D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3084T	15						.						66.0	72.0	70.0					15																	40582991		2014	4164	6178	38370283	SO:0001583	missense	5330	exon28				CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.3084G>T	15.37:g.40582991C>A	ENSP00000260402:p.Glu1028Asp	Somatic		Capture	Illumina HiSeq	Phase_I	38370283	NM_004573	A8K6J2|B9EGH5	Missense_Mutation	SNP	ENST00000260402.3	37	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.008960	0.54361	.	.	ENSG00000137841	ENST00000260402;ENST00000456256	T;T	0.48522	0.81;0.81	4.42	0.275	0.15659	PLC-beta, C-terminal (1);	0.620687	0.15789	N	0.244530	T	0.56093	0.1962	L	0.46157	1.445	0.80722	D	1	D;B;P	0.61080	0.989;0.001;0.944	D;B;P	0.76071	0.987;0.01;0.858	T	0.54510	-0.8283	10	0.72032	D	0.01	.	8.2304	0.31595	0.0:0.5894:0.0:0.4106	.	1013;1024;1028	B9EGH5;Q00722-2;Q00722	.;.;PLCB2_HUMAN	D	1028;1013	ENSP00000260402:E1028D;ENSP00000411991:E1013D	ENSP00000260402:E1028D	E	-	3	2	PLCB2	38370283	0.981000	0.34729	0.569000	0.28460	0.953000	0.61014	0.177000	0.16801	0.114000	0.18032	0.561000	0.74099	GAG		0.572	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1		
C15orf52	388115	broad.mit.edu	37	15	40630983	40630983	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:40630983A>G	ENST00000559313.1	-	4	500	c.485T>C	c.(484-486)gTg>gCg	p.V162A	C15orf52_ENST00000397536.2_5'Flank|C15orf52_ENST00000557973.1_5'Flank	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	162							poly(A) RNA binding (GO:0044822)	p.V162A(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	19		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		AGCCAGCTCCACCAGCTCCCC	0.602																																					p.V162A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T485C	15						.						186.0	210.0	202.0					15																	40630983		2167	4259	6426	38418275	SO:0001583	missense	388115	exon4			AK124643	CCDS10055.2	15q15.1	2007-06-14			ENSG00000188549	ENSG00000188549			33488	protein-coding gene	gene with protein product							Standard	NM_207380		Approved	FLJ43339	uc001zlh.4	Q6ZUT6	OTTHUMG00000129981	ENST00000559313.1:c.485T>C	15.37:g.40630983A>G	ENSP00000453969:p.Val162Ala	Somatic		Capture	Illumina HiSeq	Phase_I	38418275	NM_207380	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Missense_Mutation	SNP	ENST00000559313.1	37	CCDS10055.2	.	.	.	.	.	.	.	.	.	.	A	13.67	2.306102	0.40795	.	.	ENSG00000188549	ENST00000382688;ENST00000397535	.	.	.	4.96	3.82	0.43975	.	0.135101	0.33023	N	0.005379	T	0.64461	0.2600	M	0.65975	2.015	0.32970	D	0.522188	D;D	0.67145	0.99;0.996	D;D	0.75484	0.98;0.986	T	0.68273	-0.5452	9	0.25106	T	0.35	-17.2716	7.9146	0.29810	0.8165:0.0:0.0:0.1835	.	94;162	Q6ZUT6-3;Q6ZUT6	.;CO052_HUMAN	A	162;94	.	ENSP00000372135:V162A	V	-	2	0	C15orf52	38418275	1.000000	0.71417	0.953000	0.39169	0.085000	0.17905	4.922000	0.63404	0.713000	0.32060	-0.490000	0.04691	GTG		0.602	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380	
CHAC1	79094	broad.mit.edu	37	15	41247850	41247850	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:41247850G>A	ENST00000446533.3	+	3	982	c.673G>A	c.(673-675)Gca>Aca	p.A225T	CHAC1_ENST00000487220.1_5'UTR|CHAC1_ENST00000444189.2_Missense_Mutation_p.A180T	NM_001142776.1|NM_024111.3	NP_001136248.1|NP_077016.2	Q9BUX1	CHAC1_HUMAN	ChaC, cation transport regulator homolog 1 (E. coli)	225					intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein processing (GO:0010955)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|trans-Golgi network (GO:0005802)	Notch binding (GO:0005112)	p.A183T(1)		endometrium(1)|large_intestine(1)|skin(1)	3		all_cancers(109;1.42e-13)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.66e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.163)		GCTGCGTCTGGCAGACTTCAT	0.647																																					p.A180T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G538A	15						.						57.0	57.0	57.0					15																	41247850		2203	4300	6503	39035142	SO:0001583	missense	79094	exon4			BC019625	CCDS10070.2, CCDS45233.1	15q15.1	2013-09-12	2006-09-12		ENSG00000128965	ENSG00000128965			28680	protein-coding gene	gene with protein product	"""gamma-GCT acting on glutathione homolog 1"""	614587	"""ChaC, cation transport regulator-like 1 (E. coli)"""			23070364	Standard	NM_024111		Approved	MGC4504	uc001znh.2	Q9BUX1	OTTHUMG00000130208	ENST00000446533.3:c.673G>A	15.37:g.41247850G>A	ENSP00000398105:p.Ala225Thr	Somatic		Capture	Illumina HiSeq	Phase_I	39035142	NM_001142776	Q0VIA0	Missense_Mutation	SNP	ENST00000446533.3	37	CCDS10070.2	.	.	.	.	.	.	.	.	.	.	G	21.4	4.146901	0.77888	.	.	ENSG00000128965	ENST00000446533;ENST00000444189	T	0.46451	0.87	5.66	4.74	0.60224	Butirosin biosynthesis, BtrG-like (1);	0.048572	0.85682	D	0.000000	T	0.67543	0.2904	M	0.88031	2.925	0.80722	D	1	B;P	0.50943	0.145;0.94	B;P	0.62014	0.13;0.897	T	0.73726	-0.3892	10	0.52906	T	0.07	-19.7021	14.9815	0.71313	0.0691:0.0:0.9309:0.0	.	180;225	Q9BUX1-2;Q9BUX1	.;CHAC1_HUMAN	T	225;180	ENSP00000398105:A225T	ENSP00000395466:A180T	A	+	1	0	CHAC1	39035142	1.000000	0.71417	0.963000	0.40424	0.122000	0.20287	9.781000	0.99029	1.377000	0.46286	0.462000	0.41574	GCA		0.647	CHAC1-001	KNOWN	downstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252526.3	NM_024111	
MGA	23269	broad.mit.edu	37	15	41989089	41989089	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:41989089A>G	ENST00000570161.1	+	2	1881	c.1881A>G	c.(1879-1881)cgA>cgG	p.R627R	MGA_ENST00000545763.1_Silent_p.R627R|MGA_ENST00000566586.1_Silent_p.R627R|MGA_ENST00000389936.4_Silent_p.R627R|MGA_ENST00000219905.7_Silent_p.R627R			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.R627R(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGGCAGGACGACCACCTAAGA	0.453																																					p.R627R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1881G	15						.						23.0	21.0	21.0					15																	41989089		1870	4102	5972	39776381	SO:0001819	synonymous_variant	23269	exon3			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1881A>G	15.37:g.41989089A>G		Somatic		Capture	Illumina HiSeq	Phase_I	39776381	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	37	CCDS55959.1																																																																																				0.453	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
MGA	23269	broad.mit.edu	37	15	42046752	42046752	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:42046752T>C	ENST00000570161.1	+	17	7126	c.7126T>C	c.(7126-7128)Tca>Cca	p.S2376P	MGA_ENST00000545763.1_Missense_Mutation_p.S2167P|MGA_ENST00000566586.1_Missense_Mutation_p.S2167P|MGA_ENST00000389936.4_Missense_Mutation_p.S2337P|MGA_ENST00000219905.7_Missense_Mutation_p.S2376P			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.S2425P(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CCACACACAGTCATTCAAACA	0.428																																					p.S2376P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T7126C	15						.						67.0	71.0	70.0					15																	42046752		1958	4139	6097	39834044	SO:0001583	missense	23269	exon18			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7126T>C	15.37:g.42046752T>C	ENSP00000457035:p.Ser2376Pro	Somatic		Capture	Illumina HiSeq	Phase_I	39834044	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	T	8.896	0.955256	0.18507	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.84589	-1.85;-1.87;-1.86	5.04	3.91	0.45181	.	0.997188	0.08119	N	0.995043	T	0.73289	0.3568	N	0.19112	0.55	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.59182	-0.7502	10	0.34782	T	0.22	.	3.9461	0.09349	0.2605:0.1455:0.0:0.594	.	992;2167;2376	B4DVS1;F5H7K2;E7ENI0	.;.;.	P	2376;2337;2167	ENSP00000219905:S2376P;ENSP00000374586:S2337P;ENSP00000442467:S2167P	ENSP00000219905:S2376P	S	+	1	0	MGA	39834044	0.279000	0.24239	0.103000	0.21229	0.744000	0.42396	1.197000	0.32211	0.865000	0.35603	0.397000	0.26171	TCA		0.428	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
TTBK2	146057	broad.mit.edu	37	15	43067378	43067378	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:43067378C>T	ENST00000267890.6	-	13	2061	c.1953G>A	c.(1951-1953)acG>acA	p.T651T		NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	651					cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.T651T(1)		NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		GACTTGTGGGCGTCGCTGCAA	0.463																																					p.T651T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1953A	15						.						83.0	80.0	81.0					15																	43067378		1852	4095	5947	40854670	SO:0001819	synonymous_variant	146057	exon13			AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"""spinocerebellar ataxia 11"""	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.1953G>A	15.37:g.43067378C>T		Somatic		Capture	Illumina HiSeq	Phase_I	40854670	NM_173500	O94932|Q6ZN52|Q8IVV1	Silent	SNP	ENST00000267890.6	37	CCDS42029.1																																																																																				0.463	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500	
TP53BP1	7158	broad.mit.edu	37	15	43724446	43724446	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:43724446A>G	ENST00000263801.3	-	17	3858	c.3606T>C	c.(3604-3606)agT>agC	p.S1202S	TP53BP1_ENST00000450115.2_Silent_p.S1207S|TP53BP1_ENST00000382039.3_Silent_p.S1207S|TP53BP1_ENST00000382044.4_Silent_p.S1207S	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1202					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|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)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)	p.S1202S(1)		breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GTTTCTCACCACTCCCCCTCT	0.498								Other conserved DNA damage response genes																													p.S1202S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3606C	15						.						152.0	117.0	129.0					15																	43724446		2201	4298	6499	41511738	SO:0001819	synonymous_variant	7158	exon17			U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"""tumor protein p53-binding protein, 1"""			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.3606T>C	15.37:g.43724446A>G		Somatic		Capture	Illumina HiSeq	Phase_I	41511738	NM_005657	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Silent	SNP	ENST00000263801.3	37	CCDS10096.1																																																																																				0.498	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
WDR76	79968	broad.mit.edu	37	15	44143409	44143409	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:44143409G>A	ENST00000263795.6	+	9	1227	c.1157G>A	c.(1156-1158)cGc>cAc	p.R386H	WDR76_ENST00000381246.2_Missense_Mutation_p.R322H	NM_001167941.1|NM_024908.3	NP_001161413.1|NP_079184.2	Q9H967	WDR76_HUMAN	WD repeat domain 76	386								p.R386H(1)		breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)	20		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		all cancers(107;3.78e-21)|GBM - Glioblastoma multiforme(94;5.04e-07)		GGCACGTTACGCTGTGGGGAT	0.428																																					p.R322H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G965A	15						.						187.0	173.0	178.0					15																	44143409		2198	4298	6496	41930701	SO:0001583	missense	79968	exon9			AK023035	CCDS10106.1, CCDS53938.1	15q15.3	2013-01-09			ENSG00000092470	ENSG00000092470		"""WD repeat domain containing"""	25773	protein-coding gene	gene with protein product						12860291	Standard	NM_024908		Approved	FLJ12973	uc001zti.2	Q9H967	OTTHUMG00000060143	ENST00000263795.6:c.1157G>A	15.37:g.44143409G>A	ENSP00000263795:p.Arg386His	Somatic		Capture	Illumina HiSeq	Phase_I	41930701	NM_001167941	A0MNP5|Q05CI4	Missense_Mutation	SNP	ENST00000263795.6	37	CCDS10106.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.995696	0.93167	.	.	ENSG00000092470	ENST00000263795;ENST00000381246	T;T	0.67523	-0.27;-0.27	5.93	5.93	0.95920	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.107865	0.64402	D	0.000005	D	0.84669	0.5523	M	0.86573	2.825	0.49798	D	0.999824	D	0.89917	1.0	D	0.91635	0.999	D	0.86321	0.1692	10	0.72032	D	0.01	-7.4155	17.8445	0.88725	0.0:0.0:1.0:0.0	.	386	Q9H967	WDR76_HUMAN	H	386;322	ENSP00000263795:R386H;ENSP00000370645:R322H	ENSP00000263795:R386H	R	+	2	0	WDR76	41930701	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.194000	0.72082	2.808000	0.96608	0.655000	0.94253	CGC		0.428	WDR76-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133482.2	NM_024908	
SLC28A2	9153	broad.mit.edu	37	15	45560576	45560576	+	Splice_Site	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:45560576G>T	ENST00000347644.3	+	13	1433	c.1368G>T	c.(1366-1368)caG>caT	p.Q456H	CTD-2651B20.3_ENST00000561404.1_RNA|CTD-2651B20.3_ENST00000560344.1_RNA	NM_004212.3	NP_004203.2	O43868	S28A2_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 2	456					nucleobase-containing compound metabolic process (GO:0006139)|purine nucleoside transmembrane transport (GO:0015860)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside:sodium symporter activity (GO:0005415)|purine nucleoside transmembrane transporter activity (GO:0015211)	p.Q456H(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(4)|skin(1)	26		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)	Mercaptopurine(DB01033)	TCACTTTCCAGGTAAAGGATT	0.493																																					p.Q456H	NSCLC(92;493 1501 26361 28917 47116)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1368T	15						.						117.0	115.0	115.0					15																	45560576		2198	4298	6496	43347868	SO:0001630	splice_region_variant	9153	exon13			U84392	CCDS10121.1	15q15	2013-07-17	2013-07-17		ENSG00000137860	ENSG00000137860		"""Solute carriers"""	11002	protein-coding gene	gene with protein product		606208	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 2"""			9435697	Standard	NM_004212		Approved	CNT2, SPNT1, HCNT2, HsT17153	uc001zva.2	O43868	OTTHUMG00000131426	ENST00000347644.3:c.1368+1G>T	15.37:g.45560576G>T		Somatic		Capture	Illumina HiSeq	Phase_I	43347868	NM_004212	A8K7F9|O43239|Q52LZ0	Missense_Mutation	SNP	ENST00000347644.3	37	CCDS10121.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.442789	0.83993	.	.	ENSG00000137860	ENST00000347644	T	0.08282	3.11	5.8	4.88	0.63580	Na dependent nucleoside transporter, C-terminal (1);	0.102292	0.64402	D	0.000002	T	0.39682	0.1087	H	0.95402	3.665	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.55121	-0.8190	10	0.87932	D	0	-9.3241	12.5278	0.56096	0.0804:0.0:0.9196:0.0	.	456	O43868	S28A2_HUMAN	H	456	ENSP00000315006:Q456H	ENSP00000315006:Q456H	Q	+	3	2	SLC28A2	43347868	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.505000	0.66981	1.459000	0.47892	0.561000	0.74099	CAG		0.493	SLC28A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254219.2	NM_004212	Missense_Mutation
MYEF2	50804	broad.mit.edu	37	15	48459562	48459562	+	Missense_Mutation	SNP	G	G	A	rs372821159		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:48459562G>A	ENST00000324324.7	-	3	686	c.407C>T	c.(406-408)gCg>gTg	p.A136V	MYEF2_ENST00000267836.6_Missense_Mutation_p.A136V	NM_016132.3	NP_057216	Q9P2K5	MYEF2_HUMAN	myelin expression factor 2	136	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				myotube differentiation (GO:0014902)|neuron differentiation (GO:0030182)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A136V(1)		endometrium(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)		TTTTCCTTCCGCATCCTTAAA	0.368																																					p.A136V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C407T	15						.	G	VAL/ALA	0,4396		0,0,2198	173.0	156.0	162.0		407	6.1	1.0	15		162	1,8593	1.2+/-3.3	0,1,4296	no	missense	MYEF2	NM_016132.3	64	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	136/601	48459562	1,12989	2198	4297	6495	46246854	SO:0001583	missense	50804	exon3			AB037762	CCDS32230.1, CCDS73722.1	15q15.1	2013-07-16				ENSG00000104177		"""RNA binding motif (RRM) containing"""	17940	protein-coding gene	gene with protein product						10718198, 2601707	Standard	XM_005254422		Approved	MEF-2, FLJ11213, KIAA1341, HsT18564	uc001zwi.4	Q9P2K5		ENST00000324324.7:c.407C>T	15.37:g.48459562G>A	ENSP00000316950:p.Ala136Val	Somatic		Capture	Illumina HiSeq	Phase_I	46246854	NM_016132	A7MCZ9|C9J921|C9K0J4|Q6NUM5|Q7L388|Q7Z4B7|Q9H922|Q9NUQ1	Missense_Mutation	SNP	ENST00000324324.7	37	CCDS32230.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.514297	0.64522	0.0	1.16E-4	ENSG00000104177	ENST00000324324;ENST00000267836	T;T	0.16457	2.34;2.34	6.05	6.05	0.98169	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.099057	0.64402	D	0.000002	T	0.23171	0.0560	N	0.25094	0.71	0.58432	D	0.999995	P;P	0.48764	0.807;0.915	P;P	0.50490	0.642;0.595	T	0.00386	-1.1772	10	0.62326	D	0.03	-5.8463	20.6013	0.99457	0.0:0.0:1.0:0.0	.	136;136	Q9P2K5-2;Q9P2K5	.;MYEF2_HUMAN	V	136	ENSP00000316950:A136V;ENSP00000267836:A136V	ENSP00000267836:A136V	A	-	2	0	MYEF2	46246854	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.512000	0.81728	2.878000	0.98634	0.650000	0.86243	GCG		0.368	MYEF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416909.2	NM_016132	
FBN1	2200	broad.mit.edu	37	15	48800881	48800881	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:48800881T>C	ENST00000316623.5	-	15	2190	c.1735A>G	c.(1735-1737)Agg>Ggg	p.R579G		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	579	EGF-like 9; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.R579G(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CACATGTTCCTTATGCTGCAT	0.358																																					p.R579G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1735G	15						.						157.0	130.0	139.0					15																	48800881		2197	4296	6493	46588173	SO:0001583	missense	2200	exon15			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.1735A>G	15.37:g.48800881T>C	ENSP00000325527:p.Arg579Gly	Somatic		Capture	Illumina HiSeq	Phase_I	46588173	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	T	18.69	3.677504	0.68042	.	.	ENSG00000166147	ENST00000316623	T	0.70869	-0.52	5.47	-5.46	0.02608	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	T	0.39410	0.1077	N	0.01493	-0.835	0.58432	D	0.999993	P	0.39480	0.675	B	0.37144	0.242	T	0.28650	-1.0037	10	0.22109	T	0.4	.	20.5193	0.99215	0.0:0.0:0.7358:0.2642	.	579	P35555	FBN1_HUMAN	G	579	ENSP00000325527:R579G	ENSP00000325527:R579G	R	-	1	2	FBN1	46588173	0.965000	0.33210	0.592000	0.28758	0.997000	0.91878	0.493000	0.22451	-0.492000	0.06687	0.533000	0.62120	AGG		0.358	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
TRPM7	54822	broad.mit.edu	37	15	50929718	50929718	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:50929718A>T	ENST00000313478.7	-	7	1014	c.733T>A	c.(733-735)Ttc>Atc	p.F245I	TRPM7_ENST00000560955.1_Missense_Mutation_p.F245I	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	245					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.F245I(1)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		ACCAATATGAAATGGGAATGC	0.378																																					p.F245I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T733A	15						.						94.0	87.0	89.0					15																	50929718		1881	4116	5997	48717010	SO:0001583	missense	54822	exon7			AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.733T>A	15.37:g.50929718A>T	ENSP00000320239:p.Phe245Ile	Somatic		Capture	Illumina HiSeq	Phase_I	48717010	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	37	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	A	32	5.134024	0.94517	.	.	ENSG00000092439	ENST00000313478	T	0.10382	2.88	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.44286	0.1286	H	0.94345	3.525	0.80722	D	1	D	0.69078	0.997	D	0.69479	0.964	T	0.60100	-0.7329	10	0.87932	D	0	-13.8773	15.5645	0.76281	1.0:0.0:0.0:0.0	.	245	Q96QT4	TRPM7_HUMAN	I	245	ENSP00000320239:F245I	ENSP00000320239:F245I	F	-	1	0	TRPM7	48717010	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.139000	0.94554	2.263000	0.75096	0.529000	0.55759	TTC		0.378	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672	
AP4E1	23431	broad.mit.edu	37	15	51289781	51289781	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:51289781T>C	ENST00000261842.5	+	18	2711	c.2605T>C	c.(2605-2607)Tat>Cat	p.Y869H	AP4E1_ENST00000560508.1_Missense_Mutation_p.Y794H	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	869					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)		p.Y869H(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		GAAATTCTCATATTGTAGTCT	0.398																																					p.Y869H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2605C	15						.						114.0	111.0	112.0					15																	51289781		2196	4294	6490	49077073	SO:0001583	missense	23431	exon18			AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2605T>C	15.37:g.51289781T>C	ENSP00000261842:p.Tyr869His	Somatic		Capture	Illumina HiSeq	Phase_I	49077073	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	T	3.392	-0.124093	0.06795	.	.	ENSG00000081014	ENST00000261842	T	0.16597	2.33	5.24	-6.66	0.01789	Coatomer, beta subunit, C-terminal (1);	1.579780	0.03507	N	0.219010	T	0.09247	0.0228	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.32161	-0.9917	10	0.45353	T	0.12	0.3458	12.035	0.53420	0.1681:0.0:0.6999:0.1319	.	869	Q9UPM8	AP4E1_HUMAN	H	869	ENSP00000261842:Y869H	ENSP00000261842:Y869H	Y	+	1	0	AP4E1	49077073	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.612000	0.05616	-1.311000	0.02309	-1.455000	0.01032	TAT		0.398	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1		
AP4E1	23431	broad.mit.edu	37	15	51291415	51291415	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:51291415T>C	ENST00000261842.5	+	19	3157	c.3051T>C	c.(3049-3051)gcT>gcC	p.A1017A	AP4E1_ENST00000560508.1_Silent_p.A942A|AP4E1_ENST00000561397.1_Intron	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	1017					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)		p.A1017A(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		CTCATTCTGCTCAGCTGGAAT	0.294																																					p.A1017A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3051C	15						.						72.0	70.0	71.0					15																	51291415		2196	4294	6490	49078707	SO:0001819	synonymous_variant	23431	exon19			AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.3051T>C	15.37:g.51291415T>C		Somatic		Capture	Illumina HiSeq	Phase_I	49078707	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Silent	SNP	ENST00000261842.5	37	CCDS32240.1																																																																																				0.294	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1		
TMOD2	29767	broad.mit.edu	37	15	52098676	52098676	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:52098676C>T	ENST00000249700.4	+	9	1200	c.979C>T	c.(979-981)Cga>Tga	p.R327*	TMOD2_ENST00000539962.2_Nonsense_Mutation_p.R283*|TMOD2_ENST00000435126.2_Nonsense_Mutation_p.R291*	NM_001142885.1|NM_014548.3	NP_001136357.1|NP_055363.1	Q9NZR1	TMOD2_HUMAN	tropomodulin 2 (neuronal)	327					learning or memory (GO:0007611)|nervous system development (GO:0007399)|neuron-neuron synaptic transmission (GO:0007270)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)	tropomyosin binding (GO:0005523)	p.R327*(2)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	16				all cancers(107;0.00435)		GCAAGGGCCACGAACAAGGGT	0.453																																					p.R327X												.	.	2	Substitution - Nonsense(2)	large_intestine(1)|kidney(1)	c.C979T	15						.						99.0	90.0	93.0					15																	52098676		2195	4293	6488	49885968	SO:0001587	stop_gained	29767	exon9			AF177169	CCDS10144.1, CCDS45260.1	15q21.2	2008-05-14			ENSG00000128872	ENSG00000128872			11872	protein-coding gene	gene with protein product		602928				10662549	Standard	NM_014548		Approved	NTMOD	uc002abk.3	Q9NZR1	OTTHUMG00000131805	ENST00000249700.4:c.979C>T	15.37:g.52098676C>T	ENSP00000249700:p.Arg327*	Somatic		Capture	Illumina HiSeq	Phase_I	49885968	NM_014548	B4DEW6	Nonsense_Mutation	SNP	ENST00000249700.4	37	CCDS10144.1	.	.	.	.	.	.	.	.	.	.	C	37	6.075348	0.97262	.	.	ENSG00000128872	ENST00000435126;ENST00000249700;ENST00000539962	.	.	.	5.34	2.1	0.27182	.	0.133842	0.49916	D	0.000129	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.9906	10.0469	0.42192	0.4153:0.4883:0.0963:0.0	.	.	.	.	X	291;327;283	.	ENSP00000249700:R327X	R	+	1	2	TMOD2	49885968	0.997000	0.39634	0.997000	0.53966	0.999000	0.98932	1.240000	0.32731	0.758000	0.33059	0.655000	0.94253	CGA		0.453	TMOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254742.2		
MAPK6	5597	broad.mit.edu	37	15	52339190	52339190	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:52339190T>C	ENST00000261845.5	+	2	1340	c.533T>C	c.(532-534)aTg>aCg	p.M178T		NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	178	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)	p.M178T(1)		breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		GCACGGATCATGGATCCTCAT	0.383																																					p.M178T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T533C	15						.						89.0	90.0	90.0					15																	52339190		2164	4270	6434	50126482	SO:0001583	missense	5597	exon2			L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"""Mitogen-activated protein kinase cascade / Kinases"""	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.533T>C	15.37:g.52339190T>C	ENSP00000261845:p.Met178Thr	Somatic		Capture	Illumina HiSeq	Phase_I	50126482	NM_002748	B2R945|B5BU65|Q68DH4|Q8IYN8	Missense_Mutation	SNP	ENST00000261845.5	37	CCDS10147.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.582766	0.28268	.	.	ENSG00000069956	ENST00000261845	T	0.64991	-0.13	5.53	5.53	0.82687	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.52757	0.1754	L	0.33624	1.015	0.80722	D	1	P	0.47409	0.895	B	0.42827	0.399	T	0.49615	-0.8921	10	0.18276	T	0.48	-11.9428	15.7177	0.77681	0.0:0.0:0.0:1.0	.	178	Q16659	MK06_HUMAN	T	178	ENSP00000261845:M178T	ENSP00000261845:M178T	M	+	2	0	MAPK6	50126482	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.037000	0.88933	2.130000	0.65690	0.529000	0.55759	ATG		0.383	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748	
UNC13C	440279	broad.mit.edu	37	15	54556460	54556460	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:54556460C>A	ENST00000260323.11	+	8	3543	c.3543C>A	c.(3541-3543)aaC>aaA	p.N1181K	UNC13C_ENST00000545554.1_Missense_Mutation_p.N1181K|UNC13C_ENST00000537900.1_Missense_Mutation_p.N1179K	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1181					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.N1181K(2)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		GGGAGAAAAACCGGCCAGAAG	0.403																																					p.N1181K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3543A	15						.						56.0	52.0	53.0					15																	54556460		1826	4071	5897	52343752	SO:0001583	missense	440279	exon7			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.3543C>A	15.37:g.54556460C>A	ENSP00000260323:p.Asn1181Lys	Somatic		Capture	Illumina HiSeq	Phase_I	52343752	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.457088	0.63401	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.79454	-1.27;-1.27;-1.27	5.54	2.48	0.30137	.	0.046667	0.85682	D	0.000000	D	0.85553	0.5723	M	0.78637	2.42	0.43863	D	0.996469	P;D	0.76494	0.864;0.999	P;D	0.80764	0.79;0.994	D	0.85139	0.0979	10	0.72032	D	0.01	.	9.3463	0.38111	0.0:0.671:0.0:0.329	.	1181;1181	F5H090;Q8NB66	.;UN13C_HUMAN	K	1181;1181;1179	ENSP00000260323:N1181K;ENSP00000438156:N1181K;ENSP00000442569:N1179K	ENSP00000260323:N1181K	N	+	3	2	UNC13C	52343752	0.281000	0.24258	1.000000	0.80357	0.958000	0.62258	-0.124000	0.10595	0.743000	0.32719	-0.345000	0.07892	AAC		0.403	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
CCPG1	9236	broad.mit.edu	37	15	55652412	55652412	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:55652412T>C	ENST00000310958.6	-	8	1857	c.1559A>G	c.(1558-1560)gAa>gGa	p.E520G	CCPG1_ENST00000425574.3_Intron|CCPG1_ENST00000569205.1_Missense_Mutation_p.E520G|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000442196.3_Missense_Mutation_p.E520G	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	520					cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)		p.E520G(1)		autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		TTTCAGATTTTCCTTCACAGC	0.333																																					p.E520G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1559G	15						.						120.0	115.0	116.0					15																	55652412		1789	4056	5845	53439704	SO:0001583	missense	9236	exon8			AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.1559A>G	15.37:g.55652412T>C	ENSP00000311656:p.Glu520Gly	Somatic		Capture	Illumina HiSeq	Phase_I	53439704	NM_004748	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Missense_Mutation	SNP	ENST00000310958.6	37	CCDS42039.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.963875	0.74131	.	.	ENSG00000256061	ENST00000310958;ENST00000442196	T;T	0.37915	1.17;1.17	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.56587	0.1995	L	0.59436	1.845	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.998;0.998	T	0.59963	-0.7355	10	0.87932	D	0	.	14.527	0.67894	0.0:0.0:0.0:1.0	.	520;520;520;376	A8K9T0;Q9ULG6-4;Q9ULG6;Q9ULG6-2	.;.;CCPG1_HUMAN;.	G	520	ENSP00000311656:E520G;ENSP00000403400:E520G	ENSP00000311656:E520G	E	-	2	0	DYX1C1	53439704	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.603000	0.82811	2.048000	0.60808	0.482000	0.46254	GAA		0.333	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748	
NEDD4	4734	broad.mit.edu	37	15	56209013	56209013	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:56209013C>T	ENST00000508342.1	-	1	316	c.17G>A	c.(16-18)cGa>cAa	p.R6Q	NEDD4_ENST00000506154.1_Missense_Mutation_p.R6Q|NEDD4_ENST00000338963.2_Missense_Mutation_p.R6Q|NEDD4_ENST00000435532.3_Intron	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	6					adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)	p.R6Q(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		AAAGTGCAATCGTAAGCTTTG	0.443																																					p.R6Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G17A	15						.						124.0	126.0	125.0					15																	56209013		2193	4290	6483	53996305	SO:0001583	missense	4734	exon1			D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"""receptor-potentiating factor 1"""	602278	"""neural precursor cell expressed, developmentally down-regulated 4"""			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.17G>A	15.37:g.56209013C>T	ENSP00000424827:p.Arg6Gln	Somatic		Capture	Illumina HiSeq	Phase_I	53996305	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	37		.	.	.	.	.	.	.	.	.	.	C	13.96	2.392795	0.42410	.	.	ENSG00000069869	ENST00000508342;ENST00000338963;ENST00000506154	T;T;T	0.21361	2.01;2.05;2.02	5.63	3.7	0.42460	.	.	.	.	.	T	0.16385	0.0394	.	.	.	0.25148	N	0.990445	P;P;P	0.39624	0.681;0.553;0.681	B;B;B	0.33960	0.173;0.084;0.173	T	0.10917	-1.0609	8	0.87932	D	0	.	10.7985	0.46474	0.1327:0.7963:0.0:0.071	.	6;6;6	P46934-2;P46934;P46934-3	.;NEDD4_HUMAN;.	Q	6	ENSP00000424827:R6Q;ENSP00000345530:R6Q;ENSP00000422705:R6Q	ENSP00000345530:R6Q	R	-	2	0	NEDD4	53996305	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.310000	0.59141	1.502000	0.48669	0.655000	0.94253	CGA		0.443	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400	
CGNL1	84952	broad.mit.edu	37	15	57743715	57743715	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:57743715T>C	ENST00000281282.5	+	5	1899	c.1821T>C	c.(1819-1821)tcT>tcC	p.S607S		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	607						myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)	p.S607S(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		ATTCCACATCTGAAGTCAAAG	0.348																																					p.S607S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1821C	15						.						79.0	87.0	85.0					15																	57743715		2192	4292	6484	55531007	SO:0001819	synonymous_variant	84952	exon5			AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.1821T>C	15.37:g.57743715T>C		Somatic		Capture	Illumina HiSeq	Phase_I	55531007	NM_032866	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Silent	SNP	ENST00000281282.5	37	CCDS10161.1																																																																																				0.348	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866	
ALDH1A2	8854	broad.mit.edu	37	15	58306416	58306416	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:58306416C>T	ENST00000249750.4	-	2	948	c.181G>A	c.(181-183)Gcc>Acc	p.A61T	ALDH1A2_ENST00000559517.1_5'Flank|ALDH1A2_ENST00000558231.1_Missense_Mutation_p.A32T|ALDH1A2_ENST00000537372.1_Missense_Mutation_p.A40T|ALDH1A2_ENST00000347587.3_Missense_Mutation_p.A61T	NM_003888.3	NP_003879.2	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1 family, member A2	61					9-cis-retinoic acid biosynthetic process (GO:0042904)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|cardiac muscle tissue development (GO:0048738)|cellular response to retinoic acid (GO:0071300)|determination of bilateral symmetry (GO:0009855)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract development (GO:0048566)|embryonic forelimb morphogenesis (GO:0035115)|face development (GO:0060324)|heart morphogenesis (GO:0003007)|hindbrain development (GO:0030902)|kidney development (GO:0001822)|liver development (GO:0001889)|lung development (GO:0030324)|midgut development (GO:0007494)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|neural crest cell development (GO:0014032)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|proximal/distal pattern formation (GO:0009954)|regulation of endothelial cell proliferation (GO:0001936)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to vitamin A (GO:0033189)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)|retinoic acid receptor signaling pathway (GO:0048384)|retinol metabolic process (GO:0042572)|ureter maturation (GO:0035799)|vitamin A metabolic process (GO:0006776)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|retinal binding (GO:0016918)|retinal dehydrogenase activity (GO:0001758)	p.A61T(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	Tretinoin(DB00755)|Vitamin A(DB00162)	TCTCCTGTGGCTGGATTATAG	0.418																																					p.A61T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G181A	15						.						118.0	114.0	115.0					15																	58306416		2192	4292	6484	56093708	SO:0001583	missense	8854	exon2			AB015228	CCDS10163.1, CCDS10164.1, CCDS45266.1, CCDS55968.1	15q21.2	2011-02-18			ENSG00000128918	ENSG00000128918		"""Aldehyde dehydrogenases"""	15472	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 2"""	603687				9819382	Standard	NM_003888		Approved	RALDH2	uc002aex.3	O94788	OTTHUMG00000132624	ENST00000249750.4:c.181G>A	15.37:g.58306416C>T	ENSP00000249750:p.Ala61Thr	Somatic		Capture	Illumina HiSeq	Phase_I	56093708	NM_003888	B3KY52|B4DZR2|F5H2Y9|H0YM00|Q2PJS6|Q8NHQ4|Q9UBR8|Q9UFY0	Missense_Mutation	SNP	ENST00000249750.4	37	CCDS10163.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.653225	0.47362	.	.	ENSG00000128918	ENST00000249750;ENST00000543386;ENST00000347587;ENST00000537372	T;T;T	0.19532	2.14;2.14;2.14	4.35	4.35	0.52113	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.30510	0.0767	L	0.61036	1.89	0.80722	D	1	B;B;P;P	0.45348	0.382;0.151;0.794;0.856	B;B;B;P	0.46172	0.076;0.046;0.444;0.506	T	0.07102	-1.0790	10	0.37606	T	0.19	.	17.0566	0.86535	0.0:1.0:0.0:0.0	.	32;40;61;61	B4DH89;F5H2Y9;O94788-2;O94788	.;.;.;AL1A2_HUMAN	T	61;32;61;40	ENSP00000249750:A61T;ENSP00000309623:A61T;ENSP00000438296:A40T	ENSP00000249750:A61T	A	-	1	0	ALDH1A2	56093708	1.000000	0.71417	1.000000	0.80357	0.299000	0.27559	3.477000	0.53151	2.252000	0.74401	0.655000	0.94253	GCC		0.418	ALDH1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255869.1		
ADAM10	102	broad.mit.edu	37	15	58919973	58919973	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:58919973T>C	ENST00000260408.3	-	10	1729	c.1286A>G	c.(1285-1287)aAc>aGc	p.N429S	ADAM10_ENST00000396140.2_Missense_Mutation_p.N128S|ADAM10_ENST00000561288.1_Intron|ADAM10_ENST00000402627.1_Intron	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	429	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)	p.N429S(1)		breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		GAATTTATTGTTGTTAAGTTT	0.348																																					p.N429S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1286G	15						.						169.0	160.0	163.0					15																	58919973		2192	4292	6484	56707265	SO:0001583	missense	102	exon10			AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	188	protein-coding gene	gene with protein product		602192	"""a disintegrin and metalloproteinase domain 10"""			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.1286A>G	15.37:g.58919973T>C	ENSP00000260408:p.Asn429Ser	Somatic		Capture	Illumina HiSeq	Phase_I	56707265	NM_001110	B4DU28|Q10742|Q92650	Missense_Mutation	SNP	ENST00000260408.3	37	CCDS10167.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.267037	0.80469	.	.	ENSG00000137845	ENST00000260408;ENST00000396136;ENST00000396140	D;D	0.86562	-2.14;-2.14	5.52	5.52	0.82312	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	D	0.89570	0.6753	L	0.35288	1.05	0.80722	D	1	D;D	0.65815	0.995;0.989	D;D	0.76575	0.988;0.951	D	0.88757	0.3254	10	0.34782	T	0.22	-19.1574	15.6398	0.76989	0.0:0.0:0.0:1.0	.	128;429	B4DU28;O14672	.;ADA10_HUMAN	S	429;248;128	ENSP00000260408:N429S;ENSP00000379444:N128S	ENSP00000260408:N429S	N	-	2	0	ADAM10	56707265	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.673000	0.83973	2.094000	0.63399	0.460000	0.39030	AAC		0.348	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110	
RBPMS2	348093	broad.mit.edu	37	15	65040723	65040723	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:65040723G>T	ENST00000300069.4	-	6	729	c.462C>A	c.(460-462)gcC>gcA	p.A154A	RBPMS2_ENST00000560606.1_Silent_p.A43A	NM_194272.1	NP_919248.1	Q6ZRY4	RBPS2_HUMAN	RNA binding protein with multiple splicing 2	154							nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)	p.A154A(1)		breast(1)|large_intestine(3)|lung(3)|prostate(1)	8						AGGGGGCCCAGGCCTCTGGGG	0.622																																					p.A154A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C462A	15						.						71.0	67.0	68.0					15																	65040723		2202	4299	6501	62827776	SO:0001819	synonymous_variant	348093	exon6			AY369207	CCDS32271.1	15q22.31	2014-05-15			ENSG00000166831	ENSG00000166831		"""RNA binding motif (RRM) containing"""	19098	protein-coding gene	gene with protein product							Standard	NM_194272		Approved		uc002anq.3	Q6ZRY4	OTTHUMG00000172423	ENST00000300069.4:c.462C>A	15.37:g.65040723G>T		Somatic		Capture	Illumina HiSeq	Phase_I	62827776	NM_194272	A2RRG0	Silent	SNP	ENST00000300069.4	37	CCDS32271.1																																																																																				0.622	RBPMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418466.1		
CLPX	10845	broad.mit.edu	37	15	65449237	65449237	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:65449237C>T	ENST00000300107.3	-	9	1279	c.1091G>A	c.(1090-1092)gGc>gAc	p.G364D		NM_006660.3	NP_006651.2	O76031	CLPX_HUMAN	caseinolytic mitochondrial matrix peptidase chaperone subunit	364					ATP catabolic process (GO:0006200)|positive regulation of peptidase activity (GO:0010952)|protein folding (GO:0006457)|proteolysis involved in cellular protein catabolic process (GO:0051603)	endopeptidase Clp complex (GO:0009368)|mitochondrial endopeptidase Clp complex (GO:0009841)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|metal ion binding (GO:0046872)|peptidase activator activity (GO:0016504)	p.G364D(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(4)|prostate(1)|skin(2)	16						TGGCACACTGCCAATCTTATC	0.378																																					p.G364D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1091A	15						.						145.0	125.0	132.0					15																	65449237		2202	4299	6501	63236290	SO:0001583	missense	10845	exon9			AJ006267	CCDS10202.1	15q22.31	2013-09-12	2013-09-12		ENSG00000166855	ENSG00000166855		"""ATPases / AAA-type"""	2088	protein-coding gene	gene with protein product		615611	"""ClpX (caseinolytic protease X, E. coli) homolog"", ""ClpX caseinolytic protease X homolog (E. coli)"", ""ClpX caseinolytic peptidase X homolog (E. coli)"""			22841477	Standard	NM_006660		Approved		uc002aom.3	O76031	OTTHUMG00000133139	ENST00000300107.3:c.1091G>A	15.37:g.65449237C>T	ENSP00000300107:p.Gly364Asp	Somatic		Capture	Illumina HiSeq	Phase_I	63236290	NM_006660	A1L428|A8K8F1|B9EGI8|Q9H4D9	Missense_Mutation	SNP	ENST00000300107.3	37	CCDS10202.1	.	.	.	.	.	.	.	.	.	.	C	35	5.419852	0.96111	.	.	ENSG00000166855	ENST00000300107;ENST00000546194	T	0.40476	1.03	5.94	5.94	0.96194	ATPase, AAA-2 (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.70885	0.3275	M	0.85462	2.755	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.79784	0.993;0.978	T	0.73613	-0.3927	10	0.72032	D	0.01	.	20.3552	0.98837	0.0:1.0:0.0:0.0	.	364;364	Q9H072;O76031	.;CLPX_HUMAN	D	364	ENSP00000300107:G364D	ENSP00000300107:G364D	G	-	2	0	CLPX	63236290	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.812000	0.96745	0.557000	0.71058	GGC		0.378	CLPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256828.2	NM_006660	
C15orf59	388135	broad.mit.edu	37	15	74032367	74032367	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:74032367T>G	ENST00000569673.1	-	3	1977	c.773A>C	c.(772-774)cAg>cCg	p.Q258P	C15orf59_ENST00000379822.4_Missense_Mutation_p.Q258P|C15orf59_ENST00000558834.1_5'UTR			Q2T9L4	CO059_HUMAN	chromosome 15 open reading frame 59	258								p.Q258P(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CCTTCGAGTCTGTTCAGGGGC	0.632																																					p.Q258P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A773C	15						.						101.0	106.0	104.0					15																	74032367		2198	4297	6495	71819420	SO:0001583	missense	388135	exon2				CCDS32289.1	15q24.1	2012-09-27			ENSG00000205363	ENSG00000205363			33753	protein-coding gene	gene with protein product							Standard	XM_005254369		Approved	MGC131524, LOC388135	uc002avy.3	Q2T9L4	OTTHUMG00000172556	ENST00000569673.1:c.773A>C	15.37:g.74032367T>G	ENSP00000457205:p.Gln258Pro	Somatic		Capture	Illumina HiSeq	Phase_I	71819420	NM_001039614		Missense_Mutation	SNP	ENST00000569673.1	37	CCDS32289.1	.	.	.	.	.	.	.	.	.	.	T	7.782	0.709760	0.15239	.	.	ENSG00000205363	ENST00000379822	T	0.46063	0.88	5.1	3.94	0.45596	.	0.566316	0.16986	N	0.191492	T	0.20618	0.0496	N	0.20766	0.605	0.30605	N	0.760093	B	0.02656	0.0	B	0.06405	0.002	T	0.31668	-0.9935	10	0.02654	T	1	.	5.1221	0.14865	0.0:0.0937:0.1853:0.721	.	258	Q2T9L4	CO059_HUMAN	P	258	ENSP00000369150:Q258P	ENSP00000369150:Q258P	Q	-	2	0	C15orf59	71819420	1.000000	0.71417	0.981000	0.43875	0.214000	0.24535	2.302000	0.43637	0.739000	0.32628	0.459000	0.35465	CAG		0.632	C15orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419077.2	NM_001039614	
PML	5371	broad.mit.edu	37	15	74290480	74290480	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:74290480C>A	ENST00000268058.3	+	2	361	c.265C>A	c.(265-267)Ccc>Acc	p.P89T	PML_ENST00000395132.2_Missense_Mutation_p.P89T|PML_ENST00000395135.3_Missense_Mutation_p.P89T|PML_ENST00000563500.1_Missense_Mutation_p.P89T|PML_ENST00000359928.4_Missense_Mutation_p.P89T|PML_ENST00000564428.1_Missense_Mutation_p.P89T|PML_ENST00000569477.1_Missense_Mutation_p.P89T|PML_ENST00000435786.2_Missense_Mutation_p.P89T|PML_ENST00000436891.3_Missense_Mutation_p.P89T|PML_ENST00000567543.1_Missense_Mutation_p.P89T|PML_ENST00000354026.6_Missense_Mutation_p.P89T|PML_ENST00000569965.1_Missense_Mutation_p.P89T|PML_ENST00000565898.1_Missense_Mutation_p.P89T|PML_ENST00000268059.6_Missense_Mutation_p.P89T	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	89					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P89T(2)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						CATGCAGTGCCCCATCTGCCA	0.652			T	"""RARA, PAX5"""	"""APL, ALL"""																																p.P89T			Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C265A	15						.						43.0	40.0	41.0					15																	74290480		2198	4297	6495	72077533	SO:0001583	missense	5371	exon2			AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.265C>A	15.37:g.74290480C>A	ENSP00000268058:p.Pro89Thr	Somatic		Capture	Illumina HiSeq	Phase_I	72077533	NM_033238	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Missense_Mutation	SNP	ENST00000268058.3	37	CCDS10255.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.340051	0.60963	.	.	ENSG00000140464	ENST00000395135;ENST00000435786;ENST00000359928;ENST00000436891;ENST00000268058;ENST00000395132;ENST00000268059;ENST00000354026;ENST00000418568	T	0.65364	-0.15	4.78	3.86	0.44501	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.097389	0.45867	D	0.000328	T	0.81059	0.4744	M	0.91920	3.255	0.35847	D	0.826475	D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.987;0.998;0.999;0.998;0.998;0.995;1.0;0.998;0.999;0.995;1.0;0.993	D;D;D;D;D;P;D;D;D;D;D;D	0.76071	0.936;0.911;0.941;0.941;0.987;0.878;0.987;0.959;0.959;0.911;0.987;0.931	D	0.86656	0.1901	10	0.87932	D	0	-23.4939	10.1553	0.42818	0.0:0.9048:0.0:0.0952	.	39;89;89;89;89;89;89;89;89;89;89;92	Q59GQ8;P29590;P29590-11;P29590-12;P29590-5;E9PBR7;P29590-13;P29590-4;P29590-2;P29590-14;P29590-8;Q59H09	.;PML_HUMAN;.;.;.;.;.;.;.;.;.;.	T	89	ENSP00000268058:P89T	ENSP00000268058:P89T	P	+	1	0	PML	72077533	0.995000	0.38212	0.993000	0.49108	0.751000	0.42716	2.019000	0.41001	1.009000	0.39289	0.561000	0.74099	CCC		0.652	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675	
PEAK1	79834	broad.mit.edu	37	15	77472802	77472802	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:77472802G>A	ENST00000560626.2	-	4	1942	c.1467C>T	c.(1465-1467)ctC>ctT	p.L489L	PEAK1_ENST00000312493.4_Silent_p.L489L|PEAK1_ENST00000558305.1_Silent_p.L489L			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	489					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.L489L(2)									CAGGGCCCTCGAGGTGCTCAC	0.488																																					p.L489L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1467T	15						.						137.0	129.0	132.0					15																	77472802		2007	4171	6178	75259857	SO:0001819	synonymous_variant	79834	exon3				CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.1467C>T	15.37:g.77472802G>A		Somatic		Capture	Illumina HiSeq	Phase_I	75259857	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Silent	SNP	ENST00000560626.2	37	CCDS42062.1																																																																																				0.488	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
LINGO1	84894	broad.mit.edu	37	15	77907618	77907618	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:77907618G>T	ENST00000355300.6	-	2	805	c.631C>A	c.(631-633)Ctg>Atg	p.L211M	LINGO1_ENST00000561030.1_Missense_Mutation_p.L205M	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	211					central nervous system neuron development (GO:0021954)|negative regulation of axonogenesis (GO:0050771)|negative regulation of oligodendrocyte differentiation (GO:0048715)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein kinase B signaling (GO:0043491)|regulation of axonogenesis (GO:0050770)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L205M(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31						AGGTGGGACAGCGCCTCGGTG	0.602																																					p.L211M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C631A	15						.						107.0	117.0	113.0					15																	77907618		2180	4272	6452	75694673	SO:0001583	missense	84894	exon2			AK027500	CCDS45313.1, CCDS73766.1	15q24	2013-01-11	2007-02-01	2007-02-01		ENSG00000169783		"""Immunoglobulin superfamily / I-set domain containing"""	21205	protein-coding gene	gene with protein product		609791	"""leucine rich repeat neuronal 6A"""	LRRN6A		14686891	Standard	XM_006720723		Approved	FLJ14594, LERN1	uc002bct.1	Q96FE5		ENST00000355300.6:c.631C>A	15.37:g.77907618G>T	ENSP00000347451:p.Leu211Met	Somatic		Capture	Illumina HiSeq	Phase_I	75694673	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Missense_Mutation	SNP	ENST00000355300.6	37	CCDS45313.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.760193	0.49468	.	.	ENSG00000169783	ENST00000355300	D	0.83591	-1.74	5.47	3.58	0.41010	.	0.059850	0.64402	D	0.000002	D	0.90858	0.7128	M	0.86268	2.805	0.47094	D	0.999313	D	0.89917	1.0	D	0.83275	0.996	D	0.91789	0.5442	10	0.72032	D	0.01	.	12.2297	0.54480	0.1404:0.0:0.8596:0.0	.	211	Q96FE5	LIGO1_HUMAN	M	211	ENSP00000347451:L211M	ENSP00000347451:L211M	L	-	1	2	LINGO1	75694673	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.174000	0.65015	1.325000	0.45301	-0.258000	0.10820	CTG		0.602	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808	
CTSH	1512	broad.mit.edu	37	15	79223815	79223815	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:79223815A>G	ENST00000220166.5	-	7	635	c.526T>C	c.(526-528)Ttc>Ctc	p.F176L	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	176					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|bradykinin catabolic process (GO:0010815)|cellular response to thyroid hormone stimulus (GO:0097067)|dichotomous subdivision of terminal units involved in lung branching (GO:0060448)|ERK1 and ERK2 cascade (GO:0070371)|immune response-regulating signaling pathway (GO:0002764)|membrane protein proteolysis (GO:0033619)|metanephros development (GO:0001656)|negative regulation of apoptotic process (GO:0043066)|neuropeptide catabolic process (GO:0010813)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidase activity (GO:0010952)|protein destabilization (GO:0031648)|proteolysis (GO:0006508)|response to retinoic acid (GO:0032526)|spermatogenesis (GO:0007283)|surfactant homeostasis (GO:0043129)|T cell mediated cytotoxicity (GO:0001913)|zymogen activation (GO:0031638)	acrosomal vesicle (GO:0001669)|alveolar lamellar body (GO:0097208)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|outer dense fiber (GO:0001520)	aminopeptidase activity (GO:0004177)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)|HLA-A specific activating MHC class I receptor activity (GO:0030108)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|thyroid hormone binding (GO:0070324)	p.F176L(1)		central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)	10						TGATTATTGAAGTCCTGGGCG	0.587																																					p.F176L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T526C	15						.						130.0	105.0	114.0					15																	79223815		2196	4293	6489	77010870	SO:0001583	missense	1512	exon7			X07549	CCDS10308.1	15q25.1	2014-01-28			ENSG00000103811	ENSG00000103811	3.4.22.16	"""Cathepsins"""	2535	protein-coding gene	gene with protein product		116820		CPSB		2849458	Standard	NM_004390		Approved	ACC-4, ACC-5	uc021srk.1	P09668	OTTHUMG00000144171	ENST00000220166.5:c.526T>C	15.37:g.79223815A>G	ENSP00000220166:p.Phe176Leu	Somatic		Capture	Illumina HiSeq	Phase_I	77010870	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Missense_Mutation	SNP	ENST00000220166.5	37	CCDS10308.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.547737	0.65311	.	.	ENSG00000103811	ENST00000220166;ENST00000394758;ENST00000528741	T;T	0.20463	2.07;2.07	3.92	3.92	0.45320	Peptidase C1A, papain C-terminal (2);	0.057404	0.64402	D	0.000001	T	0.37785	0.1016	M	0.64567	1.98	0.52099	D	0.999943	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.08700	-1.0709	10	0.25106	T	0.35	.	9.3512	0.38140	1.0:0.0:0.0:0.0	.	176;164	P09668;E9PBP2	CATH_HUMAN;.	L	176;164;100	ENSP00000220166:F176L;ENSP00000435329:F100L	ENSP00000220166:F176L	F	-	1	0	CTSH	77010870	1.000000	0.71417	1.000000	0.80357	0.566000	0.35808	7.219000	0.78000	1.780000	0.52325	0.379000	0.24179	TTC		0.587	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390	
IL16	3603	broad.mit.edu	37	15	81558058	81558058	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:81558058G>A	ENST00000302987.4	+	3	480	c.480G>A	c.(478-480)gcG>gcA	p.A160A	IL16_ENST00000394660.2_Silent_p.A160A			Q14005	IL16_HUMAN	interleukin 16	160					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.A160A(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						AATCTGCAGCGCCCACGGACA	0.463											OREG0023362	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A160A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G480A	15						.						62.0	58.0	59.0					15																	81558058		1916	4130	6046	79345113	SO:0001819	synonymous_variant	3603	exon4			U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.480G>A	15.37:g.81558058G>A		Somatic	1207	Capture	Illumina HiSeq	Phase_I	79345113	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																				0.463	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
MEX3B	84206	broad.mit.edu	37	15	82336623	82336623	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:82336623C>T	ENST00000329713.4	-	2	1023	c.588G>A	c.(586-588)acG>acA	p.T196T	AC026956.1_ENST00000410589.1_RNA|MEX3B_ENST00000558133.1_3'UTR	NM_032246.4	NP_115622.2	Q6ZN04	MEX3B_HUMAN	mex-3 RNA binding family member B	196	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.T196T(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)	19						CCCGGCTGGGCGTCACGATGT	0.637																																					p.T196T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G588A	15						.						113.0	109.0	111.0					15																	82336623		2203	4300	6503	80123678	SO:0001819	synonymous_variant	84206	exon2			AK131424	CCDS10319.1	15q25.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000183496	ENSG00000183496		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	25297	protein-coding gene	gene with protein product		611008	"""ring finger and KH domain containing 3"", ""mex-3 homolog B (C. elegans)"""	RKHD3		11230166, 17267406	Standard	NM_032246		Approved	DKFZp434J0617, RNF195	uc002bgq.2	Q6ZN04	OTTHUMG00000147356	ENST00000329713.4:c.588G>A	15.37:g.82336623C>T		Somatic		Capture	Illumina HiSeq	Phase_I	80123678	NM_032246	Q4G0W1|Q8IVG2|Q9H0J0	Silent	SNP	ENST00000329713.4	37	CCDS10319.1																																																																																				0.637	MEX3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304000.1	XM_290645	
SH3GL3	6457	broad.mit.edu	37	15	84245389	84245389	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:84245389C>T	ENST00000427482.2	+	6	826	c.520C>T	c.(520-522)Cga>Tga	p.R174*	SH3GL3_ENST00000535412.1_Nonsense_Mutation_p.R174*|SH3GL3_ENST00000434347.1_Nonsense_Mutation_p.R182*|SH3GL3_ENST00000324537.5_Nonsense_Mutation_p.R182*	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	174	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)	p.R182*(1)		central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						TAAAAAGAAACGAGTAGGTAA	0.398																																					p.R174X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C520T	15						.						53.0	57.0	56.0					15																	84245389		2203	4300	6503	82036393	SO:0001587	stop_gained	6457	exon6			AF036271	CCDS10325.2, CCDS73772.1	15q24	2006-11-24			ENSG00000140600	ENSG00000140600			10832	protein-coding gene	gene with protein product		603362				9169142	Standard	NR_026799		Approved	SH3D2C, SH3P13, CNSA3, EEN-B2, HsT19371	uc002bjw.3	Q99963	OTTHUMG00000147361	ENST00000427482.2:c.520C>T	15.37:g.84245389C>T	ENSP00000391372:p.Arg174*	Somatic		Capture	Illumina HiSeq	Phase_I	82036393	NM_003027	O43553|O43554	Nonsense_Mutation	SNP	ENST00000427482.2	37	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	C	40	8.270094	0.98735	.	.	ENSG00000140600	ENST00000427482;ENST00000535412;ENST00000324537;ENST00000434347	.	.	.	5.05	1.87	0.25490	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-36.172	13.1358	0.59409	0.4152:0.5848:0.0:0.0	.	.	.	.	X	174;174;182;182	.	ENSP00000320092:R182X	R	+	1	2	SH3GL3	82036393	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	3.693000	0.54735	0.615000	0.30124	-1.312000	0.01307	CGA		0.398	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027	
ZNF592	9640	broad.mit.edu	37	15	85334047	85334047	+	Missense_Mutation	SNP	C	C	T	rs376104089		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:85334047C>T	ENST00000560079.2	+	5	2620	c.2332C>T	c.(2332-2334)Cgc>Tgc	p.R778C	ZNF592_ENST00000299927.3_Missense_Mutation_p.R778C	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	778					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R778C(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GGTCCTCTGCCGCTCTGCCTA	0.587																																					p.R778C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2332T	15						.	C	CYS/ARG	0,4406		0,0,2203	122.0	105.0	111.0		2332	5.6	1.0	15		111	1,8597	1.2+/-3.3	0,1,4298	no	missense	ZNF592	NM_014630.2	180	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	778/1268	85334047	1,13003	2203	4299	6502	83135051	SO:0001583	missense	9640	exon5			D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.2332C>T	15.37:g.85334047C>T	ENSP00000452877:p.Arg778Cys	Somatic		Capture	Illumina HiSeq	Phase_I	83135051	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.489176	0.84962	0.0	1.16E-4	ENSG00000166716	ENST00000299927	T	0.29655	1.56	5.61	5.61	0.85477	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.48642	0.1511	L	0.50993	1.605	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.45687	-0.9244	10	0.87932	D	0	-33.6825	12.1385	0.53984	0.1711:0.8289:0.0:0.0	.	778	Q92610	ZN592_HUMAN	C	778	ENSP00000299927:R778C	ENSP00000299927:R778C	R	+	1	0	ZNF592	83135051	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	3.772000	0.55325	2.646000	0.89796	0.563000	0.77884	CGC		0.587	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630	
ALPK3	57538	broad.mit.edu	37	15	85400117	85400117	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:85400117G>A	ENST00000258888.5	+	6	2921	c.2754G>A	c.(2752-2754)gcG>gcA	p.A918A		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	918					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A918A(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AGGGGAGCGCGCCCACAGCCA	0.617																																					p.A918A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2754A	15						.						105.0	111.0	109.0					15																	85400117		2203	4299	6502	83201121	SO:0001819	synonymous_variant	57538	exon6			AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.2754G>A	15.37:g.85400117G>A		Somatic		Capture	Illumina HiSeq	Phase_I	83201121	NM_020778	Q9P2L6	Silent	SNP	ENST00000258888.5	37	CCDS10333.1																																																																																				0.617	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
KLHL25	64410	broad.mit.edu	37	15	86312711	86312711	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:86312711C>T	ENST00000337975.5	-	2	605	c.331G>A	c.(331-333)Gcc>Acc	p.A111T	KLHL25_ENST00000536947.1_Missense_Mutation_p.A111T|KLHL25_ENST00000559131.1_Intron|MIR1276_ENST00000408707.1_RNA	NM_022480.3	NP_071925.2	Q9H0H3	KLH25_HUMAN	kelch-like family member 25	111	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of translational initiation (GO:0006446)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)		p.A111T(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	25						TCGTTGATGGCGATGCGTGAG	0.607																																					p.A111T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G331A	15						.						98.0	88.0	92.0					15																	86312711		2202	4299	6501	84113715	SO:0001583	missense	64410	exon2				CCDS10339.1	15q25.3	2013-02-22	2013-02-22		ENSG00000183655	ENSG00000183655		"""Kelch-like"", ""BTB/POZ domain containing"""	25732	protein-coding gene	gene with protein product	"""ectodermal-neural cortex 2"""		"""kelch-like 25 (Drosophila)"""				Standard	XM_006720635		Approved	FLJ12587, ENC2, ENC-2	uc002bly.3	Q9H0H3	OTTHUMG00000148672	ENST00000337975.5:c.331G>A	15.37:g.86312711C>T	ENSP00000336800:p.Ala111Thr	Somatic		Capture	Illumina HiSeq	Phase_I	84113715	NM_022480	B2RDH2|B3KRT7	Missense_Mutation	SNP	ENST00000337975.5	37	CCDS10339.1	.	.	.	.	.	.	.	.	.	.	C	13.32	2.200667	0.38905	.	.	ENSG00000183655	ENST00000337975;ENST00000538153;ENST00000536947	T;T	0.66280	-0.2;-0.2	4.79	3.75	0.43078	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.358989	0.27080	N	0.021024	T	0.23249	0.0562	N	0.01003	-1.06	0.24154	N	0.995688	B	0.02656	0.0	B	0.04013	0.001	T	0.24440	-1.0160	10	0.09843	T	0.71	.	3.4607	0.07532	0.0:0.6317:0.0:0.3683	.	111	Q9H0H3	ENC2_HUMAN	T	111;80;111	ENSP00000336800:A111T;ENSP00000444739:A111T	ENSP00000336800:A111T	A	-	1	0	KLHL25	84113715	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.444000	0.52914	2.234000	0.73211	0.442000	0.29010	GCC		0.607	KLHL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309023.1	NM_022480	
MRPL46	26589	broad.mit.edu	37	15	89002977	89002977	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:89002977G>T	ENST00000312475.4	-	4	748	c.707C>A	c.(706-708)gCa>gAa	p.A236E	MRPL46_ENST00000559538.1_5'UTR	NM_022163.3	NP_071446.2	Q9H2W6	RM46_HUMAN	mitochondrial ribosomal protein L46	236						mitochondrion (GO:0005739)|ribosome (GO:0005840)	hydrolase activity (GO:0016787)	p.A236E(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			TAATAGCAGTGCTTTGAAGAA	0.488																																					p.A236E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C707A	15						.						108.0	98.0	101.0					15																	89002977		2201	4299	6500	86803981	SO:0001583	missense	26589	exon4			AF210056	CCDS10341.1	15q25.3	2012-10-08	2001-12-10	2001-12-14	ENSG00000259494	ENSG00000259494		"""Mitochondrial ribosomal proteins / large subunits"""	1192	protein-coding gene	gene with protein product		611851	"""chromosome 15 open reading frame 4"""	C15orf4		11761714, 11551941	Standard	NM_022163		Approved	LIECG2, P2ECSL	uc002bmj.2	Q9H2W6	OTTHUMG00000148683	ENST00000312475.4:c.707C>A	15.37:g.89002977G>T	ENSP00000312311:p.Ala236Glu	Somatic		Capture	Illumina HiSeq	Phase_I	86803981	NM_022163	B2RD75|Q9HBU8	Missense_Mutation	SNP	ENST00000312475.4	37	CCDS10341.1	.	.	.	.	.	.	.	.	.	.	G	34	5.328032	0.95733	.	.	ENSG00000173867	ENST00000312475	T	0.56275	0.47	6.17	6.17	0.99709	NUDIX hydrolase domain (1);	0.000000	0.85682	D	0.000000	T	0.79598	0.4473	M	0.89968	3.075	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81810	-0.0762	10	0.72032	D	0.01	.	19.8676	0.96824	0.0:0.0:1.0:0.0	.	236	Q9H2W6	RM46_HUMAN	E	236	ENSP00000312311:A236E	ENSP00000312311:A236E	A	-	2	0	MRPL46	86803981	1.000000	0.71417	0.992000	0.48379	0.893000	0.52053	9.275000	0.95738	2.941000	0.99782	0.655000	0.94253	GCA		0.488	MRPL46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309073.1	NM_022163	
ACAN	176	broad.mit.edu	37	15	89401305	89401305	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:89401305C>A	ENST00000561243.1	+	11	5489	c.5489C>A	c.(5488-5490)aCa>aAa	p.T1830K	ACAN_ENST00000439576.2_Missense_Mutation_p.T1830K|ACAN_ENST00000352105.7_Missense_Mutation_p.T1830K|ACAN_ENST00000559004.1_Missense_Mutation_p.T1830K			P16112	PGCA_HUMAN	aggrecan	1865	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)	p.T1716K(1)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TCTGGGATTACATTTGTGGAC	0.537																																					p.T1830K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5489A	15						.						54.0	52.0	53.0					15																	89401305		1892	4102	5994	87202309	SO:0001583	missense	176	exon12			M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.5489C>A	15.37:g.89401305C>A	ENSP00000453342:p.Thr1830Lys	Somatic		Capture	Illumina HiSeq	Phase_I	87202309	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	C	11.02	1.514722	0.27123	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.03124	4.27;4.04	5.56	5.56	0.83823	.	0.255174	0.20740	N	0.086557	T	0.17109	0.0411	M	0.78916	2.43	0.09310	N	0.999997	D;D	0.76494	0.999;0.998	D;D	0.79784	0.993;0.954	T	0.03922	-1.0992	10	0.54805	T	0.06	-5.1755	11.9107	0.52737	0.0:0.9209:0.0:0.0791	.	1830;1830	E7ENV9;E7EX88	.;.	K	1830;1830;1716	ENSP00000387356:T1830K;ENSP00000341615:T1830K	ENSP00000268134:T1716K	T	+	2	0	ACAN	87202309	0.970000	0.33590	0.961000	0.40146	0.997000	0.91878	2.263000	0.43293	2.618000	0.88619	0.655000	0.94253	ACA		0.537	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
HAPLN3	145864	broad.mit.edu	37	15	89421427	89421427	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:89421427C>T	ENST00000359595.3	-	5	1071	c.857G>A	c.(856-858)tGc>tAc	p.C286Y	HAPLN3_ENST00000562889.1_Missense_Mutation_p.C348Y	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	286	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)	p.C286Y(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	ATCTTCCTGGCAGGCCTCCCT	0.652																																					p.C286Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G857A	15						.						148.0	136.0	140.0					15																	89421427		2200	4299	6499	87222431	SO:0001583	missense	145864	exon5			AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"""Immunoglobulin superfamily / V-set domain containing"""	21446	protein-coding gene	gene with protein product			"""extracellular link domain containing, 1"""	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.857G>A	15.37:g.89421427C>T	ENSP00000352606:p.Cys286Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	87222431	NM_178232	A8K7P0	Missense_Mutation	SNP	ENST00000359595.3	37	CCDS10346.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.414914	0.62511	.	.	ENSG00000140511	ENST00000359595	T	0.76839	-1.05	4.7	4.7	0.59300	C-type lectin fold (1);Link (4);C-type lectin-like (1);	0.000000	0.85682	D	0.000000	D	0.92328	0.7566	H	0.97732	4.065	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95110	0.8237	10	0.87932	D	0	-47.7485	16.5998	0.84810	0.0:1.0:0.0:0.0	.	286;286	A8K7T8;Q96S86	.;HPLN3_HUMAN	Y	286	ENSP00000352606:C286Y	ENSP00000352606:C286Y	C	-	2	0	HAPLN3	87222431	1.000000	0.71417	0.996000	0.52242	0.217000	0.24651	7.391000	0.79828	2.306000	0.77630	0.655000	0.94253	TGC		0.652	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232	
RLBP1	6017	broad.mit.edu	37	15	89760482	89760482	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:89760482G>A	ENST00000268125.5	-	5	654	c.215C>T	c.(214-216)gCg>gTg	p.A72V		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	72					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)	p.A72V(2)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	GGCCGCCTGCGCCTGCACCAT	0.652																																					p.A72V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C215T	15						.						66.0	66.0	66.0					15																	89760482		2200	4299	6499	87561486	SO:0001583	missense	6017	exon5			BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"""retinaldehyde-binding protein 1"""			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.215C>T	15.37:g.89760482G>A	ENSP00000268125:p.Ala72Val	Somatic		Capture	Illumina HiSeq	Phase_I	87561486	NM_000326	B2R667	Missense_Mutation	SNP	ENST00000268125.5	37	CCDS32324.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.424948	0.43020	.	.	ENSG00000140522	ENST00000268125	D	0.88818	-2.43	5.03	-3.3	0.05003	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.357463	0.32120	N	0.006555	T	0.79782	0.4505	L	0.31157	0.91	0.32085	N	0.592676	B	0.27166	0.17	B	0.20955	0.032	T	0.66476	-0.5914	10	0.52906	T	0.07	-12.9063	13.9826	0.64315	0.0:0.0762:0.1304:0.7935	.	72	P12271	RLBP1_HUMAN	V	72	ENSP00000268125:A72V	ENSP00000268125:A72V	A	-	2	0	RLBP1	87561486	1.000000	0.71417	0.177000	0.23020	0.793000	0.44817	1.783000	0.38664	-0.854000	0.04131	-1.431000	0.01090	GCG		0.652	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326	
ANPEP	290	broad.mit.edu	37	15	90349315	90349315	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:90349315T>C	ENST00000300060.6	-	2	813	c.500A>G	c.(499-501)aAg>aGg	p.K167R		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	167	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)	p.K167R(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	CAGGGAGCCCTTGAGGTGCAC	0.632																																					p.K167R	NSCLC(30;827 977 2459 19669 26125)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A500G	15						.						85.0	80.0	81.0					15																	90349315		2200	4299	6499	88150319	SO:0001583	missense	290	exon2			M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.500A>G	15.37:g.90349315T>C	ENSP00000300060:p.Lys167Arg	Somatic		Capture	Illumina HiSeq	Phase_I	88150319	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	37	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	T	0.479	-0.880803	0.02530	.	.	ENSG00000166825	ENST00000300060	T	0.04156	3.69	4.97	-0.266	0.12942	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	1.230610	0.05328	N	0.527747	T	0.03827	0.0108	L	0.33485	1.01	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.47182	-0.9137	10	0.17369	T	0.5	.	1.9353	0.03335	0.1182:0.1515:0.2427:0.4876	.	167	P15144	AMPN_HUMAN	R	167	ENSP00000300060:K167R	ENSP00000300060:K167R	K	-	2	0	ANPEP	88150319	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	-0.169000	0.09911	-0.664000	0.05324	-3.624000	0.00027	AAG		0.632	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
IDH2	3418	broad.mit.edu	37	15	90631935	90631935	+	Missense_Mutation	SNP	G	G	A	rs267606870		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:90631935G>A	ENST00000330062.3	-	4	531	c.418C>T	c.(418-420)Cgg>Tgg	p.R140W	IDH2_ENST00000559482.1_Intron|IDH2_ENST00000540499.2_Missense_Mutation_p.R88W|IDH2_ENST00000539790.1_Missense_Mutation_p.R10W	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	140	Substrate binding. {ECO:0000250}.		R -> G (in D2HGA2). {ECO:0000269|PubMed:20847235}.|R -> Q (in D2HGA2). {ECO:0000269|PubMed:20847235}.		2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R140W(10)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			AGGATGTTCCGGATAGTTCCA	0.532			M		GBM																																p.R140W			Dom	yes		15	15q26.1	3418	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """		M	.	.	10	Substitution - Missense(10)	haematopoietic_and_lymphoid_tissue(9)|large_intestine(1)	c.C418T	15						.						101.0	101.0	101.0					15																	90631935		2200	4298	6498	88432939	SO:0001583	missense	3418	exon4				CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.418C>T	15.37:g.90631935G>A	ENSP00000331897:p.Arg140Trp	Somatic		Capture	Illumina HiSeq	Phase_I	88432939	NM_002168	B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	ENST00000330062.3	37	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.512369	0.44660	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.87491	-2.26;-2.26;-2.26	5.67	3.65	0.41850	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.95130	0.8422	H	0.98446	4.235	0.48762	D	0.999708	D	0.89917	1.0	D	0.97110	1.0	D	0.93898	0.7186	10	0.87932	D	0	.	6.0524	0.19792	0.0955:0.0:0.6033:0.3012	.	140	P48735	IDHP_HUMAN	W	140;10;88	ENSP00000331897:R140W;ENSP00000438457:R10W;ENSP00000446147:R88W	ENSP00000331897:R140W	R	-	1	2	IDH2	88432939	1.000000	0.71417	1.000000	0.80357	0.067000	0.16453	1.013000	0.29937	1.393000	0.46605	0.561000	0.74099	CGG		0.532	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1		
MAN2A2	4122	broad.mit.edu	37	15	91453436	91453436	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:91453436G>A	ENST00000559717.1	+	10	1950	c.1491G>A	c.(1489-1491)gcG>gcA	p.A497A	MAN2A2_ENST00000360468.3_Silent_p.A497A|MAN2A2_ENST00000430376.2_5'Flank|MAN2A2_ENST00000431652.2_Intron			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	497					cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)	p.A497A(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			TCTCCTATGCGGACCGGGAGG	0.577																																					p.A497A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1491A	15						.						85.0	86.0	86.0					15																	91453436		2198	4298	6496	89254440	SO:0001819	synonymous_variant	4122	exon9			L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		ENST00000559717.1:c.1491G>A	15.37:g.91453436G>A		Somatic		Capture	Illumina HiSeq	Phase_I	89254440	NM_006122	A6NH12|A8K1E8|Q13754	Silent	SNP	ENST00000559717.1	37	CCDS32332.1																																																																																				0.577	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122	
LRRC28	123355	broad.mit.edu	37	15	99874262	99874262	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:99874262C>T	ENST00000301981.3	+	6	760	c.520C>T	c.(520-522)Cgc>Tgc	p.R174C	LRRC28_ENST00000559399.1_3'UTR|LRRC28_ENST00000422500.2_Intron|LRRC28_ENST00000558879.1_Intron|LRRC28_ENST00000442993.2_Missense_Mutation_p.A142V|LRRC28_ENST00000331450.5_Intron|LRRC28_ENST00000447360.2_Missense_Mutation_p.R174C	NM_144598.2	NP_653199.2	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28	174								p.R174C(1)		endometrium(2)|large_intestine(3)|lung(6)|prostate(1)	12	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			GTATGTGCCGCGCCATCTCTG	0.488																																					p.R174C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C520T	15						.						144.0	123.0	130.0					15																	99874262		2197	4297	6494	97691785	SO:0001583	missense	123355	exon6			AK091588	CCDS10380.1, CCDS66873.1	15q26.3	2004-06-29			ENSG00000168904	ENSG00000168904			28355	protein-coding gene	gene with protein product						12975309	Standard	XM_005254861		Approved	MGC24976, FLJ34269, FLJ45242	uc002bva.1	Q86X40	OTTHUMG00000149854	ENST00000301981.3:c.520C>T	15.37:g.99874262C>T	ENSP00000304923:p.Arg174Cys	Somatic		Capture	Illumina HiSeq	Phase_I	97691785	NM_144598	A8KA22|Q6UY49|Q6ZSS6	Missense_Mutation	SNP	ENST00000301981.3	37	CCDS10380.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.204994|5.204994	0.95033|0.95033	.|.	.|.	ENSG00000168904|ENSG00000168904	ENST00000442993|ENST00000301981;ENST00000447360	T|T;T	0.43688|0.30182	0.94|1.54;1.54	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.54447|0.54447	0.1859|0.1859	L|L	0.59436|0.59436	1.845|1.845	0.38960|0.38960	D|D	0.958534|0.958534	.|D;D	.|0.89917	.|1.0;0.999	.|D;P	.|0.81914	.|0.995;0.719	T|T	0.54029|0.54029	-0.8354|-0.8354	7|10	0.30078|0.59425	T|D	0.28|0.04	.|.	19.1152|19.1152	0.93336|0.93336	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|174;174	.|Q86X40-2;Q86X40	.|.;LRC28_HUMAN	V|C	142|174	ENSP00000404206:A142V|ENSP00000304923:R174C;ENSP00000404520:R174C	ENSP00000404206:A142V|ENSP00000304923:R174C	A|R	+|+	2|1	0|0	LRRC28|LRRC28	97691785|97691785	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.998000|0.998000	0.95712|0.95712	7.210000|7.210000	0.77924|0.77924	2.775000|2.775000	0.95449|0.95449	0.585000|0.585000	0.79938|0.79938	GCG|CGC		0.488	LRRC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313546.1	NM_144598	
CERS3	204219	broad.mit.edu	37	15	101024839	101024839	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:101024839A>G	ENST00000394113.1	-	7	1013	c.323T>C	c.(322-324)tTg>tCg	p.L108S	CERS3_ENST00000538112.2_Missense_Mutation_p.L108S|CERS3_ENST00000284382.4_Missense_Mutation_p.L108S|CERS3_ENST00000560944.1_Intron			Q8IU89	CERS3_HUMAN	ceramide synthase 3	108					ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)	p.L108S(1)									GCGCTCCGTCAAGTTACACTT	0.483																																					p.L108S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T323C	15						.						78.0	66.0	70.0					15																	101024839		2203	4300	6503	98842362	SO:0001583	missense	204219	exon6				CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"""Homeoboxes / CERS class"""	23752	protein-coding gene	gene with protein product		615276	"""LAG1 longevity assurance homolog 3 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 3"""	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.323T>C	15.37:g.101024839A>G	ENSP00000377672:p.Leu108Ser	Somatic		Capture	Illumina HiSeq	Phase_I	98842362	NM_178842	Q8NE64|Q8NEN6	Missense_Mutation	SNP	ENST00000394113.1	37	CCDS10384.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.791177	0.50102	.	.	ENSG00000154227	ENST00000284382;ENST00000394113;ENST00000538112	D;D	0.98493	-4.96;-4.96	5.26	2.84	0.33178	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.319150	0.35646	N	0.003074	D	0.96661	0.8910	M	0.83774	2.66	0.36195	D	0.850363	P	0.43231	0.801	B	0.38106	0.265	D	0.96965	0.9704	10	0.72032	D	0.01	-16.0798	6.4201	0.21738	0.6338:0.225:0.0:0.1412	.	108	Q8IU89	CERS3_HUMAN	S	108;119;108	ENSP00000284382:L108S;ENSP00000437640:L108S	ENSP00000284382:L108S	L	-	2	0	CERS3	98842362	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.339000	0.33885	1.982000	0.57802	0.533000	0.62120	TTG		0.483	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842	
ZNF280D	54816	broad.mit.edu	37	15	56935186	56935186	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:56935186delT	ENST00000267807.7	-	20	2439	c.2223delA	c.(2221-2223)aaafs	p.K741fs	ZNF280D_ENST00000559237.1_Frame_Shift_Del_p.K728fs	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	741					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E742fs*62(1)		endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		CGGGAGCTTCTTTTTTTAATC	0.274																																					p.K741fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2223delA	15						.						20.0	19.0	19.0					15																	56935186		2156	4172	6328	54722478	SO:0001589	frameshift_variant	54816	exon20			AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 4 (Drosophila)"""	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.2223delA	15.37:g.56935186delT	ENSP00000267807:p.Lys741fs	Somatic		Capture	Illumina HiSeq	Phase_I	54722478	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Frame_Shift_Del	DEL	ENST00000267807.7	37	CCDS32245.1																																																																																				0.274	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867	
DENND4A	10260	broad.mit.edu	37	15	65983285	65983286	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	AG	AG	AG	-	AG	AG	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:65983285_65983286delAG	ENST00000431932.2	-	22	3722_3723	c.3514_3515delCT	c.(3514-3516)cttfs	p.L1173fs	DENND4A_ENST00000443035.3_Frame_Shift_Del_p.L1216fs|DENND4A_ENST00000567323.1_5'Flank	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1173					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.L1174fs*4(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						AGCAACCAAAAGAGAGAGGGGA	0.416																																					p.1215_1215del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3643_3644del	15						.																																			63770340	SO:0001589	frameshift_variant	10260	exon23			AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"""DENN/MADD domain containing"""	24321	protein-coding gene	gene with protein product		600382	"""c-myc promoter binding protein"""	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.3514_3515delCT	15.37:g.65983291_65983292delAG	ENSP00000396830:p.Leu1173fs	Somatic		Capture	Illumina HiSeq	Phase_I	63770339	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Frame_Shift_Del	DEL	ENST00000431932.2	37	CCDS45285.1																																																																																				0.416	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	
SCAMP2	10066	broad.mit.edu	37	15	75140996	75140996	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:75140996delA	ENST00000268099.9	-	7	788	c.679delT	c.(679-681)tgtfs	p.C227fs		NM_005697.3	NP_005688.2	O15127	SCAM2_HUMAN	secretory carrier membrane protein 2	227					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)|trans-Golgi network membrane (GO:0032588)|transport vesicle (GO:0030133)		p.C227fs*3(1)		kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	9						CCTATTTGACAAAAAAATACA	0.488																																					p.C227fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.679delT	15						.						60.0	56.0	57.0					15																	75140996		2197	4295	6492	72928049	SO:0001589	frameshift_variant	10066	exon7			AF005038	CCDS10271.1	15q23-q25	2013-02-21			ENSG00000140497	ENSG00000140497		"""Secretory carrier membrane proteins"""	10564	protein-coding gene	gene with protein product		606912				9378760	Standard	NM_005697		Approved		uc002azb.1	O15127	OTTHUMG00000142817	ENST00000268099.9:c.679delT	15.37:g.75140996delA	ENSP00000268099:p.Cys227fs	Somatic		Capture	Illumina HiSeq	Phase_I	72928049	NM_005697	B2RDF0|Q9BQE8	Frame_Shift_Del	DEL	ENST00000268099.9	37	CCDS10271.1																																																																																				0.488	SCAMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286403.3	NM_005697	
C15orf39	56905	broad.mit.edu	37	15	75498964	75498964	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:75498964delG	ENST00000360639.2	+	2	895	c.575delG	c.(574-576)cggfs	p.R192fs	C15orf39_ENST00000394987.4_Frame_Shift_Del_p.R192fs|C15orf39_ENST00000567617.1_Frame_Shift_Del_p.R192fs			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	192						cytoplasm (GO:0005737)		p.V194fs*132(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						ACCTTCTTGCGGGGGGTGCCA	0.627																																					p.R192fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.575delG	15						.						37.0	41.0	40.0					15																	75498964		2197	4291	6488	73286017	SO:0001589	frameshift_variant	56905	exon2			AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 38~Name Same As HGNC:28782"""				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.575delG	15.37:g.75498964delG	ENSP00000353854:p.Arg192fs	Somatic		Capture	Illumina HiSeq	Phase_I	73286017	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Frame_Shift_Del	DEL	ENST00000360639.2	37	CCDS10276.1																																																																																				0.627	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492	
CHSY1	22856	broad.mit.edu	37	15	101718591	101718591	+	Missense_Mutation	SNP	C	C	T	rs373782542		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr15:101718591C>T	ENST00000254190.3	-	3	1886	c.1411G>A	c.(1411-1413)Gcg>Acg	p.A471T	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	471					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)	p.A471T(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGTAAATACGCGTGCCTCCTC	0.498													C|||	1	0.000199681	0.0	0.0	5008	,	,		20340	0.0		0.001	False		,,,				2504	0.0				p.A471T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1411A	15						.	C	THR/ALA	0,4406		0,0,2203	46.0	44.0	45.0		1411	5.8	0.3	15		45	1,8599	1.2+/-3.3	0,1,4299	no	missense	CHSY1	NM_014918.4	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	471/803	101718591	1,13005	2203	4300	6503	99536114	SO:0001583	missense	22856	exon3			AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	17198	protein-coding gene	gene with protein product		608183	"""carbohydrate (chondroitin) synthase 1"""			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.1411G>A	15.37:g.101718591C>T	ENSP00000254190:p.Ala471Thr	Somatic		Capture	Illumina HiSeq	Phase_I	99536114	NM_014918	Q6UX38|Q7LFU5|Q9Y2J5	Missense_Mutation	SNP	ENST00000254190.3	37	CCDS10390.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.416209	0.83449	0.0	1.16E-4	ENSG00000131873	ENST00000254190;ENST00000543813	T	0.16324	2.35	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.47746	0.1462	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.33420	-0.9869	10	0.35671	T	0.21	-42.432	20.063	0.97692	0.0:1.0:0.0:0.0	.	471	Q86X52	CHSS1_HUMAN	T	471;199	ENSP00000254190:A471T	ENSP00000254190:A471T	A	-	1	0	CHSY1	99536114	1.000000	0.71417	0.338000	0.25549	0.927000	0.56198	7.627000	0.83176	2.735000	0.93741	0.655000	0.94253	GCG		0.498	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918	
ATF7IP2	80063	broad.mit.edu	37	16	10565991	10565991	+	Silent	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:10565991T>A	ENST00000396560.2	+	8	1604	c.1377T>A	c.(1375-1377)atT>atA	p.I459I	ATF7IP2_ENST00000396559.1_Silent_p.I459I|ATF7IP2_ENST00000356427.2_Silent_p.I459I|ATF7IP2_ENST00000324570.5_Silent_p.I459I|ATF7IP2_ENST00000543967.1_Silent_p.I3I	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	459					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.I459I(1)		large_intestine(3)	3						TTATGTTGATTTCTGTGGAAA	0.294																																					p.I459I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1377A	16						.						77.0	73.0	74.0					16																	10565991		2195	4287	6482	10473492	SO:0001819	synonymous_variant	80063	exon7			AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.1377T>A	16.37:g.10565991T>A		Somatic		Capture	Illumina HiSeq	Phase_I	10473492	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Silent	SNP	ENST00000396560.2	37	CCDS10540.1																																																																																				0.294	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
UBE2I	7329	broad.mit.edu	37	16	1364044	1364044	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:1364044G>A	ENST00000355803.4	+	2	564	c.13G>A	c.(13-15)Gcc>Acc	p.A5T	UBE2I_ENST00000397514.3_Missense_Mutation_p.A5T|UBE2I_ENST00000403747.2_Missense_Mutation_p.A5T|UBE2I_ENST00000402301.1_Missense_Mutation_p.A5T|UBE2I_ENST00000325437.5_Missense_Mutation_p.A5T|UBE2I_ENST00000566587.1_Missense_Mutation_p.A5T|UBE2I_ENST00000397515.2_Missense_Mutation_p.A5T|UBE2I_ENST00000406620.1_Missense_Mutation_p.A5T	NM_194260.2	NP_919236.1	P63279	UBC9_HUMAN	ubiquitin-conjugating enzyme E2I	5					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intracellular steroid hormone receptor signaling pathway (GO:0033145)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein sumoylation (GO:0016925)|regulation of receptor activity (GO:0010469)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|fibrillar center (GO:0001650)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|synapse (GO:0045202)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RING-like zinc finger domain binding (GO:0071535)|SUMO ligase activity (GO:0019789)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)	p.A5T(1)		breast(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)	5		Hepatocellular(780;0.00369)				GTCGGGGATCGCCCTCAGCAG	0.632																																					p.A5T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G13A	16						.						109.0	113.0	111.0					16																	1364044		2198	4300	6498	1304045	SO:0001583	missense	7329	exon3			D45050	CCDS10433.1	16p13.3	2011-05-19	2011-05-19		ENSG00000103275	ENSG00000103275	6.3.2.19	"""Ubiquitin-conjugating enzymes E2"""	12485	protein-coding gene	gene with protein product		601661	"""ubiquitin-conjugating enzyme E2I (homologous to yeast UBC9)"", ""ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast)"""			8565643	Standard	NM_003345		Approved	UBC9	uc002cld.2	P63279	OTTHUMG00000047845	ENST00000355803.4:c.13G>A	16.37:g.1364044G>A	ENSP00000348056:p.Ala5Thr	Somatic		Capture	Illumina HiSeq	Phase_I	1304045	NM_194259	D3DU69|P50550|Q15698|Q59GX1|Q86VB3	Missense_Mutation	SNP	ENST00000355803.4	37	CCDS10433.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.852357	0.51270	.	.	ENSG00000103275	ENST00000325437;ENST00000355803;ENST00000397514;ENST00000397515;ENST00000406620;ENST00000403747;ENST00000402301	T;T;T;T;T;T;T	0.76316	-0.32;-0.32;-0.32;-0.32;-0.32;-0.32;-1.01	5.21	4.26	0.50523	Ubiquitin-conjugating enzyme/RWD-like (2);	0.056695	0.64402	D	0.000001	T	0.80138	0.4568	M	0.92691	3.335	0.80722	D	1	P;P	0.50528	0.936;0.838	B;B	0.37833	0.259;0.098	D	0.83766	0.0217	10	0.66056	D	0.02	.	11.4208	0.49980	0.0884:0.0:0.9116:0.0	.	5;5	B0QYN7;P63279	.;UBC9_HUMAN	T	5	ENSP00000324897:A5T;ENSP00000348056:A5T;ENSP00000380649:A5T;ENSP00000380650:A5T;ENSP00000384568:A5T;ENSP00000385009:A5T;ENSP00000384361:A5T	ENSP00000324897:A5T	A	+	1	0	UBE2I	1304045	1.000000	0.71417	0.998000	0.56505	0.312000	0.27988	9.622000	0.98378	1.211000	0.43351	0.655000	0.94253	GCC		0.632	UBE2I-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250317.2	NM_003345	
LITAF	9516	broad.mit.edu	37	16	11647526	11647526	+	Silent	SNP	G	G	A	rs149184234		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:11647526G>A	ENST00000571688.1	-	3	470	c.240C>T	c.(238-240)taC>taT	p.Y80Y	LITAF_ENST00000570904.1_Silent_p.Y80Y|LITAF_ENST00000381810.3_Silent_p.Y80Y|LITAF_ENST00000572255.1_De_novo_Start_OutOfFrame|LITAF_ENST00000576036.1_Silent_p.Y80Y|LITAF_ENST00000571459.1_Intron|LITAF_ENST00000571976.1_Silent_p.Y80Y|LITAF_ENST00000574763.1_Silent_p.Y80Y|LITAF_ENST00000413364.2_Silent_p.Y80Y|LITAF_ENST00000339430.5_Silent_p.Y80Y	NM_001136472.1	NP_001129944.1	Q99732	LITAF_HUMAN	lipopolysaccharide-induced TNF factor	80					aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of cytokine production (GO:0001817)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)	p.Y80Y(1)		endometrium(1)|large_intestine(1)|liver(1)|lung(3)|skin(1)	7						GGTGCTGCACGTAGACCGTCT	0.512																																					p.Y80Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C240T	16						.	G	,,	0,4394		0,0,2197	118.0	70.0	86.0		240,240,240	-2.2	0.5	16	dbSNP_134	86	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	LITAF	NM_001136472.1,NM_001136473.1,NM_004862.3	,,	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	,,	80/162,80/153,80/162	11647526	1,12993	2197	4300	6497	11555027	SO:0001819	synonymous_variant	9516	exon3			AB034747	CCDS32386.1, CCDS45411.1	16p13.3-p12	2014-09-17							16841	protein-coding gene	gene with protein product		603795				9305847, 10200294	Standard	NM_004862		Approved	PIG7, SIMPLE, FLJ38636, TP53I7	uc002dbb.3	Q99732		ENST00000571688.1:c.240C>T	16.37:g.11647526G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11555027	NM_001136473	D3DUG1|G5E9K0|Q05DW0|Q9C0L6	Silent	SNP	ENST00000571688.1	37	CCDS32386.1																																																																																				0.512	LITAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436794.2	NM_004862	
IFT140	9742	broad.mit.edu	37	16	1634251	1634251	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:1634251G>A	ENST00000426508.2	-	11	1689	c.1326C>T	c.(1324-1326)acC>acT	p.T442T	LA16c-395F10.2_ENST00000563162.1_RNA|IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	442					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)		p.T442T(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				TGTGCATGTCGGTGCGCAGGC	0.612																																					p.T442T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1326T	16						.						47.0	39.0	42.0					16																	1634251		2199	4300	6499	1574252	SO:0001819	synonymous_variant	9742	exon11			AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.1326C>T	16.37:g.1634251G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1574252	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																				0.612	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
BFAR	51283	broad.mit.edu	37	16	14758808	14758808	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:14758808T>A	ENST00000261658.2	+	7	1317	c.1040T>A	c.(1039-1041)tTt>tAt	p.F347Y	BFAR_ENST00000426842.2_Missense_Mutation_p.F219Y|BFAR_ENST00000563971.1_Missense_Mutation_p.F222Y	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	347					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)	p.F347Y(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	11						ATTGCTGAGTTTGCTTGGGAC	0.433																																					p.F347Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1040A	16						.						241.0	203.0	216.0					16																	14758808		2197	4300	6497	14666309	SO:0001583	missense	51283	exon7			AF173003	CCDS10554.1	16p13.2	2013-01-10			ENSG00000103429	ENSG00000103429		"""RING-type (C3HC4) zinc fingers"", ""Sterile alpha motif (SAM) domain containing"""	17613	protein-coding gene	gene with protein product						10716992	Standard	NM_016561		Approved	BAR, RNF47	uc002dco.3	Q9NZS9	OTTHUMG00000129848	ENST00000261658.2:c.1040T>A	16.37:g.14758808T>A	ENSP00000261658:p.Phe347Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	14666309	NM_016561	A8K4Z9|B4DUT0|D3DUG8	Missense_Mutation	SNP	ENST00000261658.2	37	CCDS10554.1	.	.	.	.	.	.	.	.	.	.	T	33	5.226507	0.95173	.	.	ENSG00000103429	ENST00000261658;ENST00000426842	T;T	0.60171	2.54;0.21	5.81	5.81	0.92471	.	0.053759	0.85682	D	0.000000	T	0.65523	0.2699	L	0.27053	0.805	0.80722	D	1	P;D;D	0.69078	0.935;0.997;0.997	P;D;D	0.77004	0.492;0.989;0.989	T	0.69694	-0.5076	10	0.87932	D	0	.	15.3502	0.74376	0.0:0.0:0.0:1.0	.	219;347;347	B4DUT0;B2R9R6;Q9NZS9	.;.;BFAR_HUMAN	Y	347;219	ENSP00000261658:F347Y;ENSP00000400634:F219Y	ENSP00000261658:F347Y	F	+	2	0	BFAR	14666309	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	7.769000	0.85360	2.213000	0.71641	0.533000	0.62120	TTT		0.433	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561	
ABCC1	4363	broad.mit.edu	37	16	16139754	16139754	+	Missense_Mutation	SNP	G	G	A	rs200520366		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:16139754G>A	ENST00000399410.3	+	9	1277	c.1102G>A	c.(1102-1104)Gtg>Atg	p.V368M	ABCC1_ENST00000399408.2_Missense_Mutation_p.V368M|ABCC1_ENST00000345148.5_Missense_Mutation_p.V368M|ABCC1_ENST00000346370.5_Missense_Mutation_p.V368M|ABCC1_ENST00000351154.5_Missense_Mutation_p.V368M|ABCC1_ENST00000349029.5_Missense_Mutation_p.V368M	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	368	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.V368M(1)		breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	CTTCTACACCGTGCTGCTGTT	0.547											OREG0023639	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V368M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1102A	16						.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	1,4203		0,1,2101	62.0	66.0	65.0		1102,1102,1102,1102,1102	5.1	0.3	16		65	2,8470		0,2,4234	yes	missense,missense,missense,missense,missense	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	21,21,21,21,21	0,3,6335	AA,AG,GG		0.0236,0.0238,0.0237	benign,benign,benign,benign,benign	368/1532,368/1473,368/1476,368/1417,368/1467	16139754	3,12673	2102	4236	6338	16047255	SO:0001583	missense	4363	exon9			L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.1102G>A	16.37:g.16139754G>A	ENSP00000382342:p.Val368Met	Somatic	708	Capture	Illumina HiSeq	Phase_I	16047255	NM_019862	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.622812	0.28889	2.38E-4	2.36E-4	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	D;D;D;D;D;D	0.90324	-2.65;-2.65;-2.65;-2.65;-2.65;-2.65	5.05	5.05	0.67936	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.486244	0.21807	N	0.068834	D	0.90310	0.6969	M	0.62016	1.91	0.09310	N	1	P;P;P;P;P;P;P	0.46512	0.799;0.799;0.864;0.853;0.799;0.879;0.853	B;B;P;P;B;P;P	0.46144	0.188;0.121;0.498;0.489;0.121;0.505;0.498	D	0.85445	0.1157	10	0.56958	D	0.05	-16.7341	12.4791	0.55831	0.0:0.0:0.8328:0.1672	.	368;368;368;368;368;368;368	P33527-6;P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;.;MRP1_HUMAN;.	M	368;368;368;368;368;368;42	ENSP00000382342:V368M;ENSP00000382340:V368M;ENSP00000263019:V368M;ENSP00000263017:V368M;ENSP00000263014:V368M;ENSP00000263016:V368M	ENSP00000263014:V368M	V	+	1	0	ABCC1	16047255	0.646000	0.27295	0.300000	0.25030	0.025000	0.11179	3.956000	0.56722	2.328000	0.79073	0.549000	0.68633	GTG		0.547	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
ABCC1	4363	broad.mit.edu	37	16	16225782	16225782	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:16225782G>T	ENST00000399410.3	+	27	4131	c.3956G>T	c.(3955-3957)gGg>gTg	p.G1319V	ABCC1_ENST00000399408.2_Missense_Mutation_p.G1329V|ABCC1_ENST00000345148.5_Missense_Mutation_p.G1319V|ABCC1_ENST00000346370.5_Missense_Mutation_p.G1263V|ABCC1_ENST00000351154.5_Missense_Mutation_p.G1260V|ABCC1_ENST00000349029.5_Missense_Mutation_p.G1204V	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1319	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.G1319V(1)		breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	ACGATCAATGGGGGAGAAAAG	0.607																																					p.G1260V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3779T	16						.						71.0	68.0	69.0					16																	16225782		2070	4221	6291	16133283	SO:0001583	missense	4363	exon26			L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.3956G>T	16.37:g.16225782G>T	ENSP00000382342:p.Gly1319Val	Somatic		Capture	Illumina HiSeq	Phase_I	16133283	NM_019862	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	G	13.91	2.379255	0.42207	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	D;D;D;D;D;D	0.93659	-3.26;-3.26;-3.26;-3.26;-3.26;-3.26	5.11	5.11	0.69529	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.112962	0.64402	D	0.000013	D	0.94291	0.8166	N	0.25426	0.745	0.80722	D	1	D;D;D;D;D;D	0.89917	0.963;0.998;0.999;1.0;0.998;0.999	P;D;D;D;D;D	0.97110	0.775;0.975;0.988;1.0;0.973;0.988	D	0.95327	0.8426	10	0.72032	D	0.01	-17.6911	17.5407	0.87846	0.0:0.0:1.0:0.0	.	1204;1319;1263;1260;1319;1329	P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;MRP1_HUMAN;.	V	1319;1329;1263;1260;1319;1204;1003	ENSP00000382342:G1319V;ENSP00000382340:G1329V;ENSP00000263019:G1263V;ENSP00000263017:G1260V;ENSP00000263014:G1319V;ENSP00000263016:G1204V	ENSP00000263014:G1319V	G	+	2	0	ABCC1	16133283	1.000000	0.71417	0.169000	0.22859	0.043000	0.13939	3.805000	0.55575	2.387000	0.81309	0.655000	0.94253	GGG		0.607	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
NOMO3	408050	broad.mit.edu	37	16	16350009	16350009	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:16350009C>T	ENST00000399336.4	+	11	1386	c.1214C>T	c.(1213-1215)gCa>gTa	p.A405V	NOMO3_ENST00000538468.1_Missense_Mutation_p.A238V|NOMO3_ENST00000263012.6_Missense_Mutation_p.A405V	NM_001004067.3	NP_001004067.1	P69849	NOMO3_HUMAN	NODAL modulator 3	405						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.A405V(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	8				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)		GACATTGTTGCAACAGGGTAA	0.473																																					p.A405V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1214T	16						.						120.0	142.0	135.0					16																	16350009		2044	4292	6336	16257510	SO:0001583	missense	408050	exon11			AK125530	CCDS42123.1	16p13	2004-11-24				ENSG00000103226			25242	protein-coding gene	gene with protein product		609159				15257293	Standard	NM_001004067		Approved		uc002deq.3	P69849	OTTHUMG00000170525	ENST00000399336.4:c.1214C>T	16.37:g.16350009C>T	ENSP00000382274:p.Ala405Val	Somatic		Capture	Illumina HiSeq	Phase_I	16257510	NM_001004067		Missense_Mutation	SNP	ENST00000399336.4	37	CCDS42123.1	.	.	.	.	.	.	.	.	.	.	.	17.89	3.500231	0.64298	.	.	ENSG00000103226	ENST00000263012;ENST00000399336;ENST00000538468	T;T;T	0.04502	3.61;3.63;3.64	3.28	3.28	0.37604	Carboxypeptidase-like, regulatory domain (1);	0.201019	0.42682	D	0.000664	T	0.05640	0.0148	L	0.38175	1.15	0.49299	D	0.999779	B;B;B	0.31548	0.328;0.057;0.167	B;B;B	0.34242	0.178;0.035;0.053	T	0.47497	-0.9113	10	0.31617	T	0.26	-7.1206	13.9407	0.64052	0.0:1.0:0.0:0.0	.	238;405;405	F5H826;P69849;Q5JPE7-2	.;NOMO3_HUMAN;.	V	405;405;238	ENSP00000263012:A405V;ENSP00000382274:A405V;ENSP00000443768:A238V	ENSP00000263012:A405V	A	+	2	0	NOMO3	16257510	1.000000	0.71417	0.985000	0.45067	0.938000	0.57974	7.478000	0.81082	1.576000	0.49790	0.425000	0.28330	GCA		0.473	NOMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409528.13	NM_001004067	
RAB26	25837	broad.mit.edu	37	16	2203403	2203403	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:2203403C>T	ENST00000210187.6	+	9	912	c.752C>T	c.(751-753)gCc>gTc	p.A251V	RP11-304L19.5_ENST00000563192.1_lincRNA|RAB26_ENST00000541451.1_Missense_Mutation_p.A185V|SNORD60_ENST00000383903.1_RNA|TRAF7_ENST00000326181.6_5'Flank	NM_014353.4	NP_055168.2	Q9ULW5	RAB26_HUMAN	RAB26, member RAS oncogene family	251					exocrine system development (GO:0035272)|Golgi to plasma membrane protein transport (GO:0043001)|regulated secretory pathway (GO:0045055)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	Golgi membrane (GO:0000139)|intrinsic component of plasma membrane (GO:0031226)|secretory granule membrane (GO:0030667)	GMP binding (GO:0019002)|GTP binding (GO:0005525)	p.A185V(1)		kidney(1)|large_intestine(1)|lung(3)	5						GGTCGAGGGGCCTCCTGCTGC	0.632																																					p.A251V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C752T	16						.						35.0	40.0	38.0					16																	2203403		2197	4299	6496	2143404	SO:0001583	missense	25837	exon9			AB027137	CCDS10460.1	16p13.3	2008-07-28			ENSG00000167964	ENSG00000167964		"""RAB, member RAS oncogene"""	14259	protein-coding gene	gene with protein product		605455				11043516	Standard	NM_014353		Approved		uc002cou.3	Q9ULW5	OTTHUMG00000128829	ENST00000210187.6:c.752C>T	16.37:g.2203403C>T	ENSP00000210187:p.Ala251Val	Somatic		Capture	Illumina HiSeq	Phase_I	2143404	NM_014353	B2RAA6|Q3L6K5|Q6NXS7	Missense_Mutation	SNP	ENST00000210187.6	37	CCDS10460.1	.	.	.	.	.	.	.	.	.	.	C	8.430	0.848492	0.17034	.	.	ENSG00000167964	ENST00000541451;ENST00000210187	T;T	0.63913	-0.07;0.1	4.42	1.2	0.21068	.	0.932844	0.08873	N	0.881235	T	0.46521	0.1397	N	0.20986	0.625	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37291	-0.9712	10	0.54805	T	0.06	.	7.8537	0.29470	0.0:0.5562:0.3483:0.0954	.	251	Q9ULW5	RAB26_HUMAN	V	185;251	ENSP00000441580:A185V;ENSP00000210187:A251V	ENSP00000210187:A251V	A	+	2	0	RAB26	2143404	0.000000	0.05858	0.040000	0.18447	0.023000	0.10783	0.159000	0.16442	0.101000	0.17610	0.313000	0.20887	GCC		0.632	RAB26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250767.2		
XYLT1	64131	broad.mit.edu	37	16	17235124	17235124	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:17235124G>A	ENST00000261381.6	-	7	1557	c.1473C>T	c.(1471-1473)ggC>ggT	p.G491G	CTD-2576D5.4_ENST00000567344.1_RNA	NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	491					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)	p.G491G(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						AGTCCGAACCGCCATCCACGG	0.572																																					p.G491G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1473T	16						.						110.0	112.0	112.0					16																	17235124		2197	4300	6497	17142625	SO:0001819	synonymous_variant	64131	exon7			AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	15516	protein-coding gene	gene with protein product	"""protein xylosyltransferase 1"""	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.1473C>T	16.37:g.17235124G>A		Somatic		Capture	Illumina HiSeq	Phase_I	17142625	NM_022166	Q9H1B6	Silent	SNP	ENST00000261381.6	37	CCDS10569.1																																																																																				0.572	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	
OTOA	146183	broad.mit.edu	37	16	21696626	21696626	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:21696626G>A	ENST00000286149.4	+	6	344	c.343G>A	c.(343-345)Gcc>Acc	p.A115T	OTOA_ENST00000388956.4_Missense_Mutation_p.A36T|OTOA_ENST00000388958.3_Missense_Mutation_p.A115T			Q7RTW8	OTOAN_HUMAN	otoancorin	115					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)		p.A115T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		GAAGACAGACGCCCAGCAGTT	0.592																																					p.A115T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G343A	16						.						66.0	60.0	62.0					16																	21696626		2199	4300	6499	21604127	SO:0001583	missense	146183	exon6			AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"""cancer/testis antigen 108"""	607038	"""deafness, autosomal recessive 22"""	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.343G>A	16.37:g.21696626G>A	ENSP00000286149:p.Ala115Thr	Somatic		Capture	Illumina HiSeq	Phase_I	21604127	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	37		.	.	.	.	.	.	.	.	.	.	G	6.024	0.372804	0.11409	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956	T;T;T	0.12774	2.65;2.65;2.65	5.84	1.25	0.21368	.	0.906562	0.09545	N	0.787717	T	0.07413	0.0187	L	0.40543	1.245	0.09310	N	1	P;P	0.42039	0.769;0.769	B;B	0.28305	0.088;0.062	T	0.29852	-0.9998	10	0.27785	T	0.31	-0.6907	3.2105	0.06681	0.156:0.1905:0.5314:0.1221	.	36;115	B3KWU3;E9PF51	.;.	T	115;115;36	ENSP00000373610:A115T;ENSP00000286149:A115T;ENSP00000373608:A36T	ENSP00000286149:A115T	A	+	1	0	OTOA	21604127	0.040000	0.19996	0.002000	0.10522	0.305000	0.27757	0.967000	0.29344	0.791000	0.33826	-0.150000	0.13652	GCC		0.592	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1		
PLK1	5347	broad.mit.edu	37	16	23701260	23701260	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:23701260G>A	ENST00000300093.4	+	10	1799	c.1688G>A	c.(1687-1689)cGc>cAc	p.R563H	CTD-2196E14.5_ENST00000566143.1_RNA	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	563	POLO box 2. {ECO:0000255|PROSITE- ProRule:PRU00154}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.R563H(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		CGCACATACCGCCTGAGTCTC	0.622																																					p.R563H	Colon(12;240 564 27038 33155)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1688A	16						.						99.0	84.0	89.0					16																	23701260		2197	4300	6497	23608761	SO:0001583	missense	5347	exon10				CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"""polo-like kinase (Drosophila)"""	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984	ENST00000300093.4:c.1688G>A	16.37:g.23701260G>A	ENSP00000300093:p.Arg563His	Somatic		Capture	Illumina HiSeq	Phase_I	23608761	NM_005030	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	37	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.034065	0.54896	.	.	ENSG00000166851	ENST00000300093;ENST00000425844	T	0.11277	2.79	5.13	2.93	0.34026	POLO box duplicated domain (2);	0.159369	0.53938	D	0.000051	T	0.12092	0.0294	M	0.74389	2.26	0.44477	D	0.997411	B	0.25743	0.133	B	0.22152	0.038	T	0.05954	-1.0854	10	0.49607	T	0.09	-25.1891	4.7849	0.13220	0.3854:0.0:0.6146:0.0	.	563	P53350	PLK1_HUMAN	H	563;466	ENSP00000300093:R563H	ENSP00000300093:R563H	R	+	2	0	PLK1	23608761	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	5.071000	0.64382	1.144000	0.42321	0.555000	0.69702	CGC		0.622	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030	
CACNG3	10368	broad.mit.edu	37	16	24366258	24366258	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:24366258G>A	ENST00000005284.3	+	3	1602	c.400G>A	c.(400-402)Gtc>Atc	p.V134I		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	134					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.V134I(2)		NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		CAGACACAACGTCATTCTCAG	0.582																																					p.V134I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G400A	16						.						63.0	55.0	58.0					16																	24366258		2197	4300	6497	24273759	SO:0001583	missense	10368	exon3			AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"""Calcium channel subunits"""	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.400G>A	16.37:g.24366258G>A	ENSP00000005284:p.Val134Ile	Somatic		Capture	Illumina HiSeq	Phase_I	24273759	NM_006539		Missense_Mutation	SNP	ENST00000005284.3	37	CCDS10620.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.381210	0.24944	.	.	ENSG00000006116	ENST00000005284	T	0.80653	-1.4	5.41	5.41	0.78517	.	0.064498	0.64402	D	0.000010	T	0.54351	0.1853	N	0.00926	-1.1	0.54753	D	0.99998	B	0.23806	0.091	B	0.23852	0.049	T	0.61282	-0.7094	10	0.02654	T	1	-25.1551	18.9864	0.92771	0.0:0.0:1.0:0.0	.	134	O60359	CCG3_HUMAN	I	134	ENSP00000005284:V134I	ENSP00000005284:V134I	V	+	1	0	CACNG3	24273759	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	3.533000	0.53561	2.815000	0.96918	0.561000	0.74099	GTC		0.582	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539	
SRRM2	23524	broad.mit.edu	37	16	2817202	2817202	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:2817202G>A	ENST00000301740.8	+	11	7222	c.6673G>A	c.(6673-6675)Gca>Aca	p.A2225T	AC092117.2_ENST00000581119.1_RNA	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2225	Ala-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)	p.A2225T(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						AACCGCACCAGCAGCCAACCT	0.622																																					p.A2225T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6673A	16						.						58.0	65.0	63.0					16																	2817202		2198	4300	6498	2757203	SO:0001583	missense	23524	exon11			AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.6673G>A	16.37:g.2817202G>A	ENSP00000301740:p.Ala2225Thr	Somatic		Capture	Illumina HiSeq	Phase_I	2757203	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	G	12.90	2.077365	0.36662	.	.	ENSG00000167978	ENST00000301740;ENST00000544933	T	0.78595	-1.19	5.82	5.82	0.92795	.	0.000000	0.64402	D	0.000005	T	0.81418	0.4818	L	0.27053	0.805	0.35909	D	0.830962	D	0.63880	0.993	D	0.74674	0.984	D	0.85488	0.1183	10	0.62326	D	0.03	-16.7209	15.5894	0.76512	0.0:0.0:1.0:0.0	.	2225	Q9UQ35	SRRM2_HUMAN	T	2225;1477	ENSP00000301740:A2225T	ENSP00000301740:A2225T	A	+	1	0	SRRM2	2757203	1.000000	0.71417	1.000000	0.80357	0.596000	0.36781	3.438000	0.52871	2.761000	0.94854	0.655000	0.94253	GCA		0.622	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
GTF3C1	2975	broad.mit.edu	37	16	27503681	27503681	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:27503681G>A	ENST00000356183.4	-	19	3144	c.3129C>T	c.(3127-3129)tgC>tgT	p.C1043C	GTF3C1_ENST00000561623.1_Silent_p.C1043C	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1043					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.C1043C(1)		breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						TGAGGCAGACGCACTGCAGGT	0.552																																					p.C1043C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3129T	16						.						67.0	68.0	68.0					16																	27503681		2197	4300	6497	27411182	SO:0001819	synonymous_variant	2975	exon19			U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.3129C>T	16.37:g.27503681G>A		Somatic		Capture	Illumina HiSeq	Phase_I	27411182	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Silent	SNP	ENST00000356183.4	37	CCDS32414.1																																																																																				0.552	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
SULT1A1	6817	broad.mit.edu	37	16	28619841	28619841	+	Missense_Mutation	SNP	G	G	A	rs201320226		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:28619841G>A	ENST00000395607.1	-	3	505	c.232C>T	c.(232-234)Cgg>Tgg	p.R78W	SULT1A1_ENST00000569554.1_Missense_Mutation_p.R78W|SULT1A1_ENST00000395609.1_Missense_Mutation_p.R78W|SULT1A1_ENST00000314752.7_Missense_Mutation_p.R78W|SULT1A1_ENST00000350842.4_Intron	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	78					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)	p.R78W(1)		endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	AAGGGCACCCGCATGAAGATG	0.587													.|||	1	0.000199681	0.0	0.0	5008	,	,		24966	0.001		0.0	False		,,,				2504	0.0				p.R78W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C232T	16						.						124.0	95.0	105.0					16																	28619841		2197	4300	6497	28527342	SO:0001583	missense	6817	exon3			U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.232C>T	16.37:g.28619841G>A	ENSP00000378971:p.Arg78Trp	Somatic		Capture	Illumina HiSeq	Phase_I	28527342	NM_177529	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Missense_Mutation	SNP	ENST00000395607.1	37	CCDS32420.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	.	17.50	3.406407	0.62399	.	.	ENSG00000196502	ENST00000314752;ENST00000395609;ENST00000395607	D;D;D	0.84070	-1.8;-1.8;-1.8	2.53	1.5	0.22942	Sulfotransferase domain (1);	0.000000	0.64402	D	0.000005	D	0.92564	0.7638	H	0.96805	3.885	0.27040	N	0.964039	D	0.89917	1.0	D	0.97110	1.0	D	0.84828	0.0800	10	0.87932	D	0	.	8.4211	0.32700	0.0:0.0:0.765:0.235	.	78	P50225	ST1A1_HUMAN	W	78	ENSP00000321988:R78W;ENSP00000378972:R78W;ENSP00000378971:R78W	ENSP00000321988:R78W	R	-	1	2	SULT1A1	28527342	0.246000	0.23909	0.348000	0.25681	0.747000	0.42532	1.054000	0.30455	0.592000	0.29728	0.306000	0.20318	CGG		0.587	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
ATP2A1	487	broad.mit.edu	37	16	28913516	28913516	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:28913516C>T	ENST00000357084.3	+	17	2600	c.2333C>T	c.(2332-2334)aCc>aTc	p.T778I	ATP2A1_ENST00000395503.4_Missense_Mutation_p.T778I|ATP2A1_ENST00000536376.1_Missense_Mutation_p.T653I	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	778					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)	p.T778I(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						ATCTTCCTGACCGCTGCCCTG	0.662																																					p.T778I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2333T	16						.						76.0	75.0	75.0					16																	28913516		2197	4300	6497	28821017	SO:0001583	missense	487	exon17				CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.2333C>T	16.37:g.28913516C>T	ENSP00000349595:p.Thr778Ile	Somatic		Capture	Illumina HiSeq	Phase_I	28821017	NM_004320	A8K5J9|B3KY17|O14984	Missense_Mutation	SNP	ENST00000357084.3	37	CCDS10643.1	.	.	.	.	.	.	.	.	.	.	C	18.23	3.578365	0.65878	.	.	ENSG00000196296	ENST00000357084;ENST00000395503;ENST00000395498;ENST00000536376	D;D;D	0.97186	-4.28;-4.28;-4.28	4.95	4.95	0.65309	ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.97791	0.9275	L	0.58669	1.825	0.80722	D	1	D;P;P	0.59767	0.986;0.879;0.926	D;D;D	0.66847	0.924;0.923;0.947	D	0.98616	1.0665	10	0.87932	D	0	.	17.0954	0.86633	0.0:1.0:0.0:0.0	.	653;778;778	B3KY17;O14983;O14983-2	.;AT2A1_HUMAN;.	I	778;778;815;653	ENSP00000349595:T778I;ENSP00000378879:T778I;ENSP00000443101:T653I	ENSP00000349595:T778I	T	+	2	0	ATP2A1	28821017	1.000000	0.71417	0.978000	0.43139	0.401000	0.30781	5.903000	0.69877	2.566000	0.86566	0.561000	0.74099	ACC		0.662	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
RABEP2	79874	broad.mit.edu	37	16	28922463	28922463	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:28922463C>T	ENST00000358201.4	-	6	1520	c.932G>A	c.(931-933)cGc>cAc	p.R311H	RABEP2_ENST00000544477.1_Missense_Mutation_p.R240H|RABEP2_ENST00000357573.6_Intron	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	311					endocytosis (GO:0006897)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.R311H(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	16						GTCCCGCTCGCGACTGACGCT	0.662																																					p.R311H	Pancreas(66;639 1284 10093 31061 49099)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G932A	16						.						47.0	57.0	54.0					16																	28922463		2144	4245	6389	28829964	SO:0001583	missense	79874	exon6			AK026935	CCDS42140.1	16p11.2	2014-09-11			ENSG00000177548	ENSG00000177548			24817	protein-coding gene	gene with protein product		611869				12477932	Standard	NM_024816		Approved	FRA, FLJ23282	uc002drq.3	Q9H5N1	OTTHUMG00000176593	ENST00000358201.4:c.932G>A	16.37:g.28922463C>T	ENSP00000350934:p.Arg311His	Somatic		Capture	Illumina HiSeq	Phase_I	28829964	NM_024816		Missense_Mutation	SNP	ENST00000358201.4	37	CCDS42140.1	.	.	.	.	.	.	.	.	.	.	C	19.19	3.780499	0.70222	.	.	ENSG00000177548	ENST00000358201;ENST00000544477	T;T	0.33865	1.39;1.39	5.03	3.05	0.35203	Rabaptin coiled-coil domain (1);	0.613150	0.16089	N	0.230155	T	0.33352	0.0860	N	0.22421	0.69	0.24734	N	0.993074	D;P;P	0.57899	0.981;0.887;0.901	P;P;P	0.52189	0.692;0.603;0.553	T	0.08889	-1.0700	10	0.72032	D	0.01	-10.7362	9.2432	0.37509	0.0:0.7594:0.0:0.2406	.	240;311;311	B4DHR0;Q49AT6;Q9H5N1	.;.;RABE2_HUMAN	H	311;240	ENSP00000350934:R311H;ENSP00000442798:R240H	ENSP00000350934:R311H	R	-	2	0	RABEP2	28829964	0.001000	0.12720	0.821000	0.32701	0.942000	0.58702	0.057000	0.14279	1.127000	0.42034	0.561000	0.74099	CGC		0.662	RABEP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432691.1	NM_024816	
KCTD13	253980	broad.mit.edu	37	16	29937181	29937181	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:29937181G>T	ENST00000568000.1	-	1	1175	c.174C>A	c.(172-174)acC>acA	p.T58T	CTD-2574D22.2_ENST00000450909.3_RNA|KCTD13_ENST00000561540.1_Silent_p.T58T|KCTD13_ENST00000568721.1_5'UTR	NM_178863.3	NP_849194.1	Q8WZ19	BACD1_HUMAN	potassium channel tetramerization domain containing 13	58	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell migration (GO:0016477)|DNA replication (GO:0006260)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of DNA replication (GO:0045740)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)	GTP-Rho binding (GO:0017049)	p.T58T(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	7						GTCCCGTGAGGGTGCGCAGCG	0.667																																					p.T58T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C174A	16						.						74.0	55.0	62.0					16																	29937181		2197	4300	6497	29844682	SO:0001819	synonymous_variant	253980	exon1			AF289573	CCDS10661.1	16p11.2	2013-06-20	2013-06-20		ENSG00000174943	ENSG00000174943			22234	protein-coding gene	gene with protein product	"""polymerase delta-interacting protein 1"", ""TNFAIP1-like"""	608947	"""potassium channel tetramerisation domain containing 13"""			11593007	Standard	NM_178863		Approved	PDIP1, FKSG86, POLDIP1	uc002duv.4	Q8WZ19	OTTHUMG00000132120	ENST00000568000.1:c.174C>A	16.37:g.29937181G>T		Somatic		Capture	Illumina HiSeq	Phase_I	29844682	NM_178863	A8K0R5|Q96P93|Q96SA1	Silent	SNP	ENST00000568000.1	37	CCDS10661.1																																																																																				0.667	KCTD13-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255162.2	NM_178863	
CLDN6	9074	broad.mit.edu	37	16	3065879	3065879	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:3065879C>A	ENST00000396925.1	-	3	572	c.144G>T	c.(142-144)gaG>gaT	p.E48D	CLDN6_ENST00000572154.1_Intron|CLDN6_ENST00000328796.4_Missense_Mutation_p.E48D|TNFRSF12A_ENST00000573001.1_5'Flank			P56747	CLD6_HUMAN	claudin 6	48					calcium-independent cell-cell adhesion (GO:0016338)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	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.E48D(1)		kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	10						TCCACAGGCCCTCCCACACCA	0.642																																					p.E48D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G144T	16						.						148.0	115.0	126.0					16																	3065879		2198	4300	6498	3005880	SO:0001583	missense	9074	exon2			AJ249735	CCDS10488.1	16p13.3	2008-08-01			ENSG00000184697	ENSG00000184697		"""Claudins"""	2048	protein-coding gene	gene with protein product		615798				9892664, 18234789	Standard	NM_021195		Approved		uc002csu.4	P56747	OTTHUMG00000128999	ENST00000396925.1:c.144G>T	16.37:g.3065879C>A	ENSP00000380131:p.Glu48Asp	Somatic		Capture	Illumina HiSeq	Phase_I	3005880	NM_021195	B3KQP9|D3DUA5	Missense_Mutation	SNP	ENST00000396925.1	37	CCDS10488.1	.	.	.	.	.	.	.	.	.	.	C	14.07	2.426469	0.43020	.	.	ENSG00000184697	ENST00000396925;ENST00000328796	D;D	0.89123	-2.47;-2.47	4.61	2.66	0.31614	.	0.000000	0.85682	D	0.000000	D	0.86777	0.6014	M	0.77820	2.39	0.37945	D	0.932461	B	0.31790	0.34	B	0.35114	0.196	D	0.84920	0.0853	10	0.44086	T	0.13	.	5.6295	0.17501	0.0:0.6952:0.0:0.3048	.	48	P56747	CLD6_HUMAN	D	48	ENSP00000380131:E48D;ENSP00000328674:E48D	ENSP00000328674:E48D	E	-	3	2	CLDN6	3005880	0.997000	0.39634	1.000000	0.80357	0.981000	0.71138	0.513000	0.22770	1.302000	0.44855	0.655000	0.94253	GAG		0.642	CLDN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250988.1	NM_021195	
ZNF205	7755	broad.mit.edu	37	16	3165534	3165534	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:3165534G>A	ENST00000382192.3	+	3	441	c.236G>A	c.(235-237)gGc>gAc	p.G79D	ZNF205_ENST00000219091.4_Missense_Mutation_p.G79D|ZNF205-AS1_ENST00000572691.1_RNA|RP11-473M20.14_ENST00000576490.1_RNA|RP11-473M20.14_ENST00000575139.1_RNA	NM_001278158.1|NM_003456.2	NP_001265087.1|NP_003447.2	O95201	ZN205_HUMAN	zinc finger protein 205	79					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hydrogen peroxide biosynthetic process (GO:0010729)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G79D(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20						CTAAGTCACGGCTCTAAGGAG	0.632																																					p.G79D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G236A	16						.						36.0	35.0	35.0					16																	3165534		2197	4300	6497	3105535	SO:0001583	missense	7755	exon3			AF060865	CCDS10494.2	16p13.3	2013-01-08			ENSG00000122386	ENSG00000122386		"""Zinc fingers, C2H2-type"", ""-"""	12996	protein-coding gene	gene with protein product		603436		ZNF210		9787081	Standard	NM_003456		Approved	Zfp13	uc002cub.3	O95201	OTTHUMG00000148676	ENST00000382192.3:c.236G>A	16.37:g.3165534G>A	ENSP00000371627:p.Gly79Asp	Somatic		Capture	Illumina HiSeq	Phase_I	3105535	NM_001042428	A8MZK0|D3DUB4|Q9BU95	Missense_Mutation	SNP	ENST00000382192.3	37	CCDS10494.2	.	.	.	.	.	.	.	.	.	.	G	17.35	3.368088	0.61513	.	.	ENSG00000122386	ENST00000382192;ENST00000219091;ENST00000444510;ENST00000414351	T;T;T;T	0.49139	3.14;3.14;0.79;3.08	4.74	3.54	0.40534	.	0.000000	0.41294	D	0.000901	T	0.36717	0.0977	L	0.46157	1.445	0.21256	N	0.999749	P	0.46987	0.888	B	0.41571	0.36	T	0.34204	-0.9838	10	0.48119	T	0.1	-29.5909	5.9434	0.19205	0.1734:0.0:0.8266:0.0	.	79	O95201	ZN205_HUMAN	D	79	ENSP00000371627:G79D;ENSP00000219091:G79D;ENSP00000394360:G79D;ENSP00000403306:G79D	ENSP00000219091:G79D	G	+	2	0	ZNF205	3105535	0.000000	0.05858	0.487000	0.27428	0.042000	0.13812	-0.050000	0.11904	2.371000	0.80710	0.591000	0.81541	GGC		0.632	ZNF205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309057.1	NM_003456	
ALDOA	226	broad.mit.edu	37	16	30078884	30078884	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:30078884G>T	ENST00000566897.1	+	6	1378	c.226G>T	c.(226-228)Ggt>Tgt	p.G76C	ALDOA_ENST00000395248.1_Missense_Mutation_p.G130C|ALDOA_ENST00000395240.3_Missense_Mutation_p.G76C|ALDOA_ENST00000563060.2_Missense_Mutation_p.G76C|ALDOA_ENST00000564595.2_Missense_Mutation_p.G130C|ALDOA_ENST00000564546.1_Missense_Mutation_p.G76C|ALDOA_ENST00000569798.1_Missense_Mutation_p.G76C|ALDOA_ENST00000569545.1_Missense_Mutation_p.G76C|ALDOA_ENST00000412304.2_Missense_Mutation_p.G76C|ALDOA_ENST00000338110.5_Missense_Mutation_p.G76C			P04075	ALDOA_HUMAN	aldolase A, fructose-bisphosphate	76					actin filament organization (GO:0007015)|ATP biosynthetic process (GO:0006754)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homotetramerization (GO:0051289)|regulation of cell shape (GO:0008360)|small molecule metabolic process (GO:0044281)|striated muscle contraction (GO:0006941)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|membrane (GO:0016020)|nucleus (GO:0005634)|platelet alpha granule lumen (GO:0031093)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|fructose binding (GO:0070061)|fructose-bisphosphate aldolase activity (GO:0004332)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|tubulin binding (GO:0015631)	p.G76C(1)		breast(2)|cervix(1)|endometrium(4)|large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	17						CTGCATTGGGGGTGTCATCCT	0.597																																					p.G76C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G226T	16						.						51.0	54.0	53.0					16																	30078884		2197	4300	6497	29986385	SO:0001583	missense	226	exon3			X05236	CCDS10668.1, CCDS58450.1	16p11.2	2008-03-06			ENSG00000149925	ENSG00000149925	4.1.2.13		414	protein-coding gene	gene with protein product		103850				3570299	Standard	NM_000034		Approved		uc010veg.2	P04075	OTTHUMG00000132107	ENST00000566897.1:c.226G>T	16.37:g.30078884G>T	ENSP00000455724:p.Gly76Cys	Somatic		Capture	Illumina HiSeq	Phase_I	29986385	NM_184041	B4DXI7|Q6FH76|Q6FI10|Q96B15|Q9BWD9|Q9UCN2	Missense_Mutation	SNP	ENST00000566897.1	37	CCDS10668.1	.	.	.	.	.	.	.	.	.	.	G	34	5.318402	0.95682	.	.	ENSG00000149925	ENST00000395248;ENST00000338110;ENST00000412304;ENST00000395240	D;D;D;D	0.96200	-3.94;-3.94;-3.94;-3.94	5.54	5.54	0.83059	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.98748	0.9579	H	0.97852	4.09	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99616	1.0982	10	0.87932	D	0	.	18.2468	0.89989	0.0:0.0:1.0:0.0	.	76	P04075	ALDOA_HUMAN	C	130;76;76;76	ENSP00000378669:G130C;ENSP00000336927:G76C;ENSP00000400452:G76C;ENSP00000378661:G76C	ENSP00000336927:G76C	G	+	1	0	ALDOA	29986385	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	9.807000	0.99171	2.607000	0.88179	0.561000	0.74099	GGT		0.597	ALDOA-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435360.1	NM_000034	
CREBBP	1387	broad.mit.edu	37	16	3778833	3778833	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:3778833C>T	ENST00000262367.5	-	31	7024	c.6215G>A	c.(6214-6216)cGg>cAg	p.R2072Q	CREBBP_ENST00000382070.3_Missense_Mutation_p.R2034Q	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2072					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R2072Q(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CTTCAGGGTCCGCAGCAGGTC	0.617			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.R2072Q			Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6215A	16						.						42.0	48.0	46.0					16																	3778833		2197	4299	6496	3718834	SO:0001583	missense	1387	exon31			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.6215G>A	16.37:g.3778833C>T	ENSP00000262367:p.Arg2072Gln	Somatic		Capture	Illumina HiSeq	Phase_I	3718834	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	c	13.17	2.156273	0.38021	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.83837	-1.77;-1.68	5.11	5.11	0.69529	Nuclear receptor coactivator, CREB-bp-like, interlocking (2);Nuclear receptor coactivator, interlocking (1);	0.085601	0.48767	D	0.000170	T	0.82093	0.4962	L	0.35542	1.07	0.80722	D	1	D;D	0.62365	0.991;0.991	P;P	0.53313	0.723;0.723	T	0.78443	-0.2202	10	0.16896	T	0.51	-21.2134	18.1476	0.89662	0.0:1.0:0.0:0.0	.	2102;2072	Q4LE28;Q92793	.;CBP_HUMAN	Q	2072;2102;2034;607	ENSP00000262367:R2072Q;ENSP00000371502:R2034Q	ENSP00000262367:R2072Q	R	-	2	0	CREBBP	3718834	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.728000	0.62000	2.387000	0.81309	0.655000	0.94253	CGG		0.617	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
ITGAD	3681	broad.mit.edu	37	16	31429471	31429471	+	Missense_Mutation	SNP	C	C	T	rs150295058	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:31429471C>T	ENST00000389202.2	+	21	2624	c.2575C>T	c.(2575-2577)Cgc>Tgc	p.R859C		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	859					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.R859C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						AAGAAGCAGCCGCTGCAGTGT	0.557													c|||	5	0.000998403	0.0038	0.0	5008	,	,		17576	0.0		0.0	False		,,,				2504	0.0				p.R859C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2575T	16						.	C	CYS/ARG	6,4388	11.4+/-27.6	0,6,2191	129.0	122.0	125.0		2575	-1.7	0.8	16	dbSNP_134	125	0,8600		0,0,4300	yes	missense	ITGAD	NM_005353.2	180	0,6,6491	TT,TC,CC		0.0,0.1365,0.0462	possibly-damaging	859/1162	31429471	6,12988	2197	4300	6497	31336972	SO:0001583	missense	3681	exon21			U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.2575C>T	16.37:g.31429471C>T	ENSP00000373854:p.Arg859Cys	Somatic		Capture	Illumina HiSeq	Phase_I	31336972	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	37	CCDS32438.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	13.11	2.138720	0.37728	0.001365	0.0	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.49432	0.78	5.06	-1.71	0.08133	Integrin alpha-2 (1);	.	.	.	.	T	0.46308	0.1386	L	0.38175	1.15	0.23449	N	0.997656	D;D	0.65815	0.995;0.991	P;P	0.56788	0.806;0.806	T	0.39961	-0.9588	9	0.72032	D	0.01	.	5.9642	0.19316	0.3778:0.4488:0.1733:0.0	.	875;859	Q59H14;Q13349	.;ITAD_HUMAN	C	875;859	ENSP00000373854:R859C	ENSP00000373854:R859C	R	+	1	0	ITGAD	31336972	0.003000	0.15002	0.763000	0.31416	0.030000	0.12068	-0.489000	0.06490	-0.310000	0.08766	-0.262000	0.10625	CGC		0.557	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
DNAJA2	10294	broad.mit.edu	37	16	46991040	46991040	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:46991040T>C	ENST00000317089.5	-	9	1355	c.1140A>G	c.(1138-1140)cgA>cgG	p.R380R		NM_005880.3	NP_005871.1	O60884	DNJA2_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 2	380					positive regulation of cell proliferation (GO:0008284)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)	p.R380R(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	14		all_cancers(37;0.00125)|all_lung(18;0.00338)|all_epithelial(9;0.00358)|Lung NSC(13;0.0309)|Breast(268;0.116)				CTCCTGAGCCTCGAGTGCTAT	0.463																																					p.R380R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1140G	16						.						269.0	263.0	265.0					16																	46991040		2203	4300	6503	45548541	SO:0001819	synonymous_variant	10294	exon9			AF116720	CCDS10726.1	16q12.1	2011-09-02			ENSG00000069345	ENSG00000069345		"""Heat shock proteins / DNAJ (HSP40)"""	14884	protein-coding gene	gene with protein product		611322				9710638, 11147971	Standard	NM_005880		Approved	HIRIP4, DNAJ, CPR3, DNJ3	uc002eeo.2	O60884	OTTHUMG00000133104	ENST00000317089.5:c.1140A>G	16.37:g.46991040T>C		Somatic		Capture	Illumina HiSeq	Phase_I	45548541	NM_005880	B2R7L7|O14711	Silent	SNP	ENST00000317089.5	37	CCDS10726.1																																																																																				0.463	DNAJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256769.2		
ABCC12	94160	broad.mit.edu	37	16	48149439	48149439	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:48149439G>T	ENST00000311303.3	-	13	2221	c.1876C>A	c.(1876-1878)Ctg>Atg	p.L626M	ABCC12_ENST00000416054.1_Nonsense_Mutation_p.C601*|ABCC12_ENST00000448542.1_Missense_Mutation_p.L626M	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	626	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.L626M(1)		NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				GGGTCGTCCAGCAGGTAGAGC	0.632																																					p.L626M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1876A	16						.						92.0	83.0	86.0					16																	48149439		2201	4300	6501	46706940	SO:0001583	missense	94160	exon13			AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.1876C>A	16.37:g.48149439G>T	ENSP00000311030:p.Leu626Met	Somatic		Capture	Illumina HiSeq	Phase_I	46706940	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.4|23.4	4.409653|4.409653	0.83340|0.83340	.|.	.|.	ENSG00000140798|ENSG00000140798	ENST00000416054|ENST00000311303;ENST00000448542;ENST00000449939	.|D;D	.|0.95205	.|-3.64;-3.64	5.09|5.09	2.03|2.03	0.26663|0.26663	.|ATPase, AAA+ type, core (1);ABC transporter-like (2);	.|0.000000	.|0.64402	.|D	.|0.000001	.|D	.|0.95166	.|0.8433	L|L	0.51914|0.51914	1.62|1.62	0.80722|0.80722	A|A	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	.|D	.|0.95475	.|0.8555	.|9	0.87932|0.87932	D|D	0|0	.|.	9.0515|9.0515	0.36378|0.36378	0.3183:0.0:0.6817:0.0|0.3183:0.0:0.6817:0.0	.|.	.|626	.|Q96J65	.|MRP9_HUMAN	X|M	601|626;626;568	.|ENSP00000311030:L626M;ENSP00000401855:L626M	ENSP00000413046:C601X|ENSP00000311030:L626M	C|L	-|-	3|1	2|2	ABCC12|ABCC12	46706940|46706940	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.028000|0.028000	0.11728|0.11728	2.557000|2.557000	0.45871|0.45871	0.656000|0.656000	0.30886|0.30886	-0.251000|-0.251000	0.11542|0.11542	TGC|CTG		0.632	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
ZNF423	23090	broad.mit.edu	37	16	49672560	49672560	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:49672560C>T	ENST00000561648.1	-	4	556	c.503G>A	c.(502-504)tGc>tAc	p.C168Y	ZNF423_ENST00000262383.2_Missense_Mutation_p.C168Y|ZNF423_ENST00000535559.1_Missense_Mutation_p.C51Y|ZNF423_ENST00000562520.1_Missense_Mutation_p.C108Y|ZNF423_ENST00000567169.1_Missense_Mutation_p.C51Y|ZNF423_ENST00000563137.2_Missense_Mutation_p.C108Y|ZNF423_ENST00000562871.1_Missense_Mutation_p.C108Y	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	168					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C168Y(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GCAGTAGGTGCACTTGAACGG	0.577																																					p.C168Y												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G503A	16						.						52.0	47.0	49.0					16																	49672560		2198	4300	6498	48230061	SO:0001583	missense	23090	exon5			AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.503G>A	16.37:g.49672560C>T	ENSP00000455426:p.Cys168Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	48230061	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.282426	0.59867	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.58358	0.34;0.34	4.7	4.7	0.59300	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.78904	0.4357	M	0.91920	3.255	0.58432	D	0.999995	D	0.89917	1.0	D	0.87578	0.998	D	0.84426	0.0574	9	.	.	.	.	18.0102	0.89221	0.0:1.0:0.0:0.0	.	168	Q2M1K9	ZN423_HUMAN	Y	168;51	ENSP00000262383:C168Y;ENSP00000442321:C51Y	.	C	-	2	0	ZNF423	48230061	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.776000	0.85560	2.331000	0.79229	0.561000	0.74099	TGC		0.577	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
NAGPA	51172	broad.mit.edu	37	16	5075659	5075659	+	Silent	SNP	C	C	T	rs185563042		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:5075659C>T	ENST00000312251.3	-	10	1387	c.1368G>A	c.(1366-1368)gcG>gcA	p.A456A	RP11-165E7.1_ENST00000588778.1_RNA|NAGPA_ENST00000381955.3_Silent_p.A422A	NM_016256.3	NP_057340.2	Q9UK23	NAGPA_HUMAN	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	456					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|lysosome organization (GO:0007040)|protein glycosylation (GO:0006486)|protein targeting to lysosome (GO:0006622)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity (GO:0003944)	p.A456A(2)		endometrium(4)|large_intestine(4)|lung(3)|urinary_tract(1)	12					N-Acetyl-D-glucosamine(DB00141)	GGAAGGCCAGCGCCAGGGTGA	0.642													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16819	0.0		0.0	False		,,,				2504	0.0				p.A456A												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.G1368A	16						.						25.0	27.0	26.0					16																	5075659		2196	4300	6496	5015660	SO:0001819	synonymous_variant	51172	exon10			AF187072	CCDS10527.1	16p13.3	2008-02-05			ENSG00000103174	ENSG00000103174	3.1.4.45		17378	protein-coding gene	gene with protein product		607985				10551838, 12058031	Standard	NM_016256		Approved	APAA, UCE	uc002cyg.3	Q9UK23	OTTHUMG00000090515	ENST00000312251.3:c.1368G>A	16.37:g.5075659C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5015660	NM_016256	B2RAS1|Q96EJ8	Silent	SNP	ENST00000312251.3	37	CCDS10527.1																																																																																				0.642	NAGPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207003.1	NM_016256	
SALL1	6299	broad.mit.edu	37	16	51172927	51172927	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:51172927G>T	ENST00000251020.4	-	2	3239	c.3206C>A	c.(3205-3207)cCc>cAc	p.P1069H	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.P972H	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1069					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P1069H(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GTTCTGATTGGGGCCAAGGTT	0.512																																					p.P1069H	GBM(103;1352 1446 1855 4775 8890)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3206A	16						.						85.0	81.0	82.0					16																	51172927		2198	4300	6498	49730428	SO:0001583	missense	6299	exon2			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3206C>A	16.37:g.51172927G>T	ENSP00000251020:p.Pro1069His	Somatic		Capture	Illumina HiSeq	Phase_I	49730428	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	19.81	3.896219	0.72639	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.08720	3.06;3.07	5.42	5.42	0.78866	.	0.048468	0.85682	D	0.000000	T	0.12135	0.0295	L	0.38175	1.15	0.80722	D	1	D	0.53151	0.958	P	0.46718	0.525	T	0.06862	-1.0803	10	0.30854	T	0.27	.	19.2277	0.93824	0.0:0.0:1.0:0.0	.	1069	Q9NSC2	SALL1_HUMAN	H	1069;972;1033	ENSP00000251020:P1069H;ENSP00000407914:P972H	ENSP00000251020:P1069H	P	-	2	0	SALL1	49730428	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.013000	0.88655	2.529000	0.85273	0.563000	0.77884	CCC		0.512	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
FTO	79068	broad.mit.edu	37	16	53913779	53913779	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:53913779T>C	ENST00000471389.1	+	6	1221	c.999T>C	c.(997-999)taT>taC	p.Y333Y	FTO_ENST00000394647.3_Silent_p.Y37Y	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	333					adipose tissue development (GO:0060612)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|oxidative demethylation (GO:0070989)|oxidative single-stranded DNA demethylation (GO:0035552)|oxidative single-stranded RNA demethylation (GO:0035553)|regulation of lipid storage (GO:0010883)|regulation of multicellular organism growth (GO:0040014)|regulation of respiratory system process (GO:0044065)|regulation of white fat cell proliferation (GO:0070350)|RNA repair (GO:0042245)|temperature homeostasis (GO:0001659)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|oxidative DNA demethylase activity (GO:0035516)|oxidative RNA demethylase activity (GO:0035515)	p.Y333Y(1)		endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						CCTTGGATTATATTTTACAAC	0.408																																					p.Y333Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T999C	16						.						178.0	166.0	170.0					16																	53913779		2198	4300	6498	52471280	SO:0001819	synonymous_variant	79068	exon6			BC003583	CCDS32448.1	16q12.2	2013-11-15			ENSG00000140718	ENSG00000140718		"""Alkylation repair homologs"""	24678	protein-coding gene	gene with protein product	"""AlkB homolog 9"", ""alpha-ketoglutarate-dependent dioxygenase"""	610966				17434869, 17991826, 22002720	Standard	NM_001080432		Approved	KIAA1752, MGC5149, ALKBH9	uc002ehr.3	Q9C0B1	OTTHUMG00000158780	ENST00000471389.1:c.999T>C	16.37:g.53913779T>C		Somatic		Capture	Illumina HiSeq	Phase_I	52471280	NM_001080432	A2RUH1|B2RNS0|Q0P676|Q7Z785	Silent	SNP	ENST00000471389.1	37	CCDS32448.1																																																																																				0.408	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432	
IRX5	10265	broad.mit.edu	37	16	54966485	54966485	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:54966485T>C	ENST00000394636.4	+	2	662	c.325T>C	c.(325-327)Tac>Cac	p.Y109H	IRX5_ENST00000320990.5_Missense_Mutation_p.Y109H|CTD-3032H12.2_ENST00000560487.1_lincRNA|IRX5_ENST00000560154.1_Intron|IRX5_ENST00000558597.1_Missense_Mutation_p.Y43H			P78411	IRX5_HUMAN	iroquois homeobox 5	109					embryonic cranial skeleton morphogenesis (GO:0048701)|gonad development (GO:0008406)|neuron maturation (GO:0042551)|regulation of heart rate (GO:0002027)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|vitamin D binding (GO:0005499)	p.Y109H(1)		kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						CCTGGGATCGTACCCTTACGG	0.662																																					p.Y109H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T325C	16						.						81.0	74.0	77.0					16																	54966485		2198	4300	6498	53523986	SO:0001583	missense	10265	exon2			U90309	CCDS10751.1, CCDS58462.1	16q12.2	2011-06-20	2007-07-13		ENSG00000176842	ENSG00000176842		"""Homeoboxes / TALE class"""	14361	protein-coding gene	gene with protein product		606195					Standard	NM_005853		Approved	IRX-2a	uc002ehv.3	P78411	OTTHUMG00000133201	ENST00000394636.4:c.325T>C	16.37:g.54966485T>C	ENSP00000378132:p.Tyr109His	Somatic		Capture	Illumina HiSeq	Phase_I	53523986	NM_005853	H0YMS7|P78416|Q7Z2E1	Missense_Mutation	SNP	ENST00000394636.4	37	CCDS10751.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.616045	0.46631	.	.	ENSG00000176842	ENST00000394636;ENST00000320990	T;T	0.64085	-0.08;-0.08	4.58	4.58	0.56647	Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.78904	0.4357	M	0.80183	2.485	0.58432	D	0.999999	D	0.89917	1.0	D	0.75484	0.986	T	0.81955	-0.0696	10	0.62326	D	0.03	-11.9254	13.7791	0.63073	0.0:0.0:0.0:1.0	.	109	P78411	IRX5_HUMAN	H	109	ENSP00000378132:Y109H;ENSP00000316250:Y109H	ENSP00000316250:Y109H	Y	+	1	0	IRX5	53523986	1.000000	0.71417	0.240000	0.24138	0.131000	0.20780	7.730000	0.84881	1.917000	0.55516	0.533000	0.62120	TAC		0.662	IRX5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256911.2		
CES1	1066	broad.mit.edu	37	16	55854296	55854296	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:55854296C>G	ENST00000361503.4	-	6	916	c.786G>C	c.(784-786)aaG>aaC	p.K262N	CES1_ENST00000360526.3_Missense_Mutation_p.K263N|CES1_ENST00000566555.1_5'Flank|CES1_ENST00000422046.2_Missense_Mutation_p.K262N			P23141	EST1_HUMAN	carboxylesterase 1	262					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)	p.K263N(1)							all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	CAGCCAAGGGCTTGACATCAC	0.567																																					p.K262N	NSCLC(162;1801 2756 42904 52896)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G786C	16						.						10.0	12.0	12.0					16																	55854296		2162	4250	6412	54411797	SO:0001583	missense	1066	exon6			BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.786G>C	16.37:g.55854296C>G	ENSP00000355193:p.Lys262Asn	Somatic		Capture	Illumina HiSeq	Phase_I	54411797	NM_001266	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	.	.	.	.	.	.	.	.	.	.	.	11.97	1.796740	0.31777	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046;ENST00000426667	T;T;T	0.67865	-0.29;-0.29;-0.29	3.6	-0.16	0.13375	Carboxylesterase, type B (1);	0.527468	0.17039	N	0.189409	T	0.51991	0.1707	N	0.20845	0.615	0.09310	N	1	D;D;D	0.55605	0.972;0.972;0.965	P;P;P	0.51415	0.669;0.669;0.539	T	0.44390	-0.9331	10	0.54805	T	0.06	.	2.7213	0.05201	0.2134:0.3416:0.0:0.445	.	262;262;263	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	N	263;262;262;127	ENSP00000353720:K263N;ENSP00000355193:K262N;ENSP00000390492:K262N	ENSP00000353720:K263N	K	-	3	2	CES1	54411797	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.453000	0.06778	0.182000	0.20032	0.456000	0.33151	AAG		0.567	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
GNAO1	2775	broad.mit.edu	37	16	56362650	56362650	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:56362650C>T	ENST00000262493.6	+	4	1257	c.411C>T	c.(409-411)atC>atT	p.I137I	GNAO1_ENST00000262494.7_Silent_p.I137I	NM_020988.2	NP_066268.1	P09471	GNAO_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O	137					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|dopamine receptor signaling pathway (GO:0007212)|forebrain development (GO:0030900)|locomotory behavior (GO:0007626)|muscle contraction (GO:0006936)|negative regulation of calcium ion transport (GO:0051926)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|regulation of heart contraction (GO:0008016)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to morphine (GO:0043278)	heterotrimeric G-protein complex (GO:0005834)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	corticotropin-releasing hormone receptor 1 binding (GO:0051430)|G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|mu-type opioid receptor binding (GO:0031852)|signal transducer activity (GO:0004871)	p.I137I(2)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)	17		all_neural(199;0.159)				ACTCAGGAATCCAAGAGTGCT	0.597																																					p.I137I												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C411T	16						.						85.0	80.0	82.0					16																	56362650		2198	4300	6498	54920151	SO:0001819	synonymous_variant	2775	exon4				CCDS10756.1, CCDS10757.1	16q13	2008-08-01			ENSG00000087258	ENSG00000087258			4389	protein-coding gene	gene with protein product		139311				1899283, 11395521	Standard	NM_020988		Approved	G-ALPHA-o	uc002eit.4	P09471	OTTHUMG00000133241	ENST00000262493.6:c.411C>T	16.37:g.56362650C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54920151	NM_138736	P29777|Q8TD72|Q9UMV4	Silent	SNP	ENST00000262493.6	37	CCDS10756.1																																																																																				0.597	GNAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256981.2	NM_020988	
CETP	1071	broad.mit.edu	37	16	57015082	57015082	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:57015082A>G	ENST00000566128.1	+	12	1231	c.964A>G	c.(964-966)Acc>Gcc	p.T322A	CETP_ENST00000379780.2_Missense_Mutation_p.T327A|CETP_ENST00000200676.3_Missense_Mutation_p.T387A					cholesteryl ester transfer protein, plasma									p.T387A(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						TATCGTGACTACCGTCCAGGC	0.527																																					p.T387A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1159G	16						.						86.0	91.0	90.0					16																	57015082		2198	4300	6498	55572583	SO:0001583	missense	1071	exon12			M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"""BPI fold containing"""	1869	protein-coding gene	gene with protein product	"""BPI fold containing family F"""	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000566128.1:c.964A>G	16.37:g.57015082A>G	ENSP00000456276:p.Thr322Ala	Somatic		Capture	Illumina HiSeq	Phase_I	55572583	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	37		.	.	.	.	.	.	.	.	.	.	A	5.290	0.238830	0.10023	.	.	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.07444	3.19;3.19	3.9	2.77	0.32553	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.491195	0.20604	U	0.089090	T	0.14485	0.0350	L	0.32530	0.975	0.09310	N	1	D;B	0.61697	0.99;0.271	D;B	0.73380	0.98;0.125	T	0.02588	-1.1137	10	0.56958	D	0.05	-3.4012	6.3435	0.21337	0.8745:0.0:0.1255:0.0	.	327;387	P11597-2;P11597	.;CETP_HUMAN	A	387;327	ENSP00000200676:T387A;ENSP00000369106:T327A	ENSP00000200676:T387A	T	+	1	0	CETP	55572583	0.000000	0.05858	0.002000	0.10522	0.156000	0.22039	0.665000	0.25083	1.559000	0.49555	0.260000	0.18958	ACC		0.527	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078	
NLRC5	84166	broad.mit.edu	37	16	57060670	57060670	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:57060670C>T	ENST00000262510.6	+	6	2040	c.1815C>T	c.(1813-1815)cgC>cgT	p.R605R	NLRC5_ENST00000436936.1_Silent_p.R605R|NLRC5_ENST00000539144.1_Silent_p.R605R|NLRC5_ENST00000308149.7_Silent_p.R605R	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	605					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)	p.R605R(1)		NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				TGGCCACCCGCAAGCTCACAG	0.597																																					p.R605R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1815T	16						.						82.0	63.0	70.0					16																	57060670		2198	4300	6498	55618171	SO:0001819	synonymous_variant	84166	exon6			AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.1815C>T	16.37:g.57060670C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55618171	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	37	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	C	3.254	-0.152718	0.06585	.	.	ENSG00000140853	ENST00000538805	.	.	.	5.27	-1.38	0.09027	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.0035	0.03472	0.2373:0.4246:0.1061:0.2319	.	.	.	.	X	358	.	.	Q	+	1	0	NLRC5	55618171	0.044000	0.20184	0.006000	0.13384	0.625000	0.37756	0.117000	0.15583	-0.045000	0.13468	-0.314000	0.08810	CAA		0.597	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
DRC7	84229	broad.mit.edu	37	16	57732056	57732056	+	Silent	SNP	G	G	A	rs377738081		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:57732056G>A	ENST00000360716.3	+	3	416	c.195G>A	c.(193-195)gcG>gcA	p.A65A	CCDC135_ENST00000336825.8_Silent_p.A65A|RP11-405F3.4_ENST00000563062.1_RNA|CCDC135_ENST00000394337.4_Silent_p.A65A			Q8IY82	CC135_HUMAN		65					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)		p.A65A(1)		breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						CTGTCTCAGCGGAGCTCCCGT	0.617																																					p.A65A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G195A	16						.	G		1,4395	2.1+/-5.4	0,1,2197	70.0	69.0	69.0		195	-2.6	0.0	16		69	0,8600		0,0,4300	no	coding-synonymous	CCDC135	NM_032269.5		0,1,6497	AA,AG,GG		0.0,0.0227,0.0077		65/875	57732056	1,12995	2198	4300	6498	56289557	SO:0001819	synonymous_variant	84229	exon2																														ENST00000360716.3:c.195G>A	16.37:g.57732056G>A		Somatic		Capture	Illumina HiSeq	Phase_I	56289557	NM_032269	A8K943|Q8NAA0|Q9H080	Silent	SNP	ENST00000360716.3	37	CCDS10787.1																																																																																				0.617	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
ZNF319	57567	broad.mit.edu	37	16	58031328	58031328	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:58031328G>A	ENST00000299237.2	-	2	1464	c.842C>T	c.(841-843)tCg>tTg	p.S281L	USB1_ENST00000561743.1_5'Flank	NM_020807.1	NP_065858.1	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	281					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S281L(1)		large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8						GTGCTCGCCCGAGTGCGCGTA	0.647																																					p.S281L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C842T	16						.						57.0	56.0	57.0					16																	58031328		2198	4300	6498	56588829	SO:0001583	missense	57567	exon2			AB037809	CCDS32462.1	16q21	2013-01-08				ENSG00000166188		"""Zinc fingers, C2H2-type"""	13644	protein-coding gene	gene with protein product						10718198, 11161788	Standard	XM_005256069		Approved	KIAA1388, Zfp319	uc002emx.1	Q9P2F9		ENST00000299237.2:c.842C>T	16.37:g.58031328G>A	ENSP00000299237:p.Ser281Leu	Somatic		Capture	Illumina HiSeq	Phase_I	56588829	NM_020807	Q52LH8	Missense_Mutation	SNP	ENST00000299237.2	37	CCDS32462.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.654242	0.67472	.	.	ENSG00000166188	ENST00000299237	T	0.07908	3.15	5.0	5.0	0.66597	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.076127	0.56097	U	0.000036	T	0.08670	0.0215	L	0.48986	1.54	0.58432	D	0.999997	P	0.50066	0.931	B	0.31390	0.129	T	0.12218	-1.0556	10	0.72032	D	0.01	-13.8633	17.2788	0.87122	0.0:0.0:1.0:0.0	.	281	Q9P2F9	ZN319_HUMAN	L	281	ENSP00000299237:S281L	ENSP00000299237:S281L	S	-	2	0	ZNF319	56588829	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	9.860000	0.99555	2.330000	0.79161	0.561000	0.74099	TCG		0.647	ZNF319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430317.1		
MMP15	4324	broad.mit.edu	37	16	58074002	58074002	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:58074002G>A	ENST00000219271.3	+	4	1449	c.664G>A	c.(664-666)Gcc>Acc	p.A222T		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	222					cellular protein modification process (GO:0006464)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)|response to estradiol (GO:0032355)	extracellular matrix (GO:0031012)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.A222T(1)		breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	18					Marimastat(DB00786)	TCTGGCCCACGCCTATTTCCC	0.632																																					p.A222T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G664A	16						.						54.0	51.0	52.0					16																	58074002		2198	4300	6498	56631503	SO:0001583	missense	4324	exon4			Z48482	CCDS10792.1	16q13	2008-05-14	2005-08-08		ENSG00000102996	ENSG00000102996			7161	protein-coding gene	gene with protein product		602261	"""matrix metalloproteinase 15 (membrane-inserted)"""			9070935, 9119382	Standard	NM_002428		Approved	MT2-MMP, MTMMP2, SMCP-2	uc002ena.3	P51511	OTTHUMG00000133466	ENST00000219271.3:c.664G>A	16.37:g.58074002G>A	ENSP00000219271:p.Ala222Thr	Somatic		Capture	Illumina HiSeq	Phase_I	56631503	NM_002428	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	.	.	.	.	.	.	.	.	.	.	G	36	5.667515	0.96745	.	.	ENSG00000102996	ENST00000219271	T	0.35789	1.29	4.89	4.89	0.63831	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.67011	0.2848	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75230	-0.3391	10	0.87932	D	0	.	17.0351	0.86473	0.0:0.0:1.0:0.0	.	222	P51511	MMP15_HUMAN	T	222	ENSP00000219271:A222T	ENSP00000219271:A222T	A	+	1	0	MMP15	56631503	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.869000	0.99810	2.270000	0.75569	0.462000	0.41574	GCC		0.632	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428	
CNOT1	23019	broad.mit.edu	37	16	58577422	58577422	+	Intron	SNP	G	G	A	rs372828610		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:58577422G>A	ENST00000317147.5	-	31	4767				CNOT1_ENST00000569240.1_Intron|CNOT1_ENST00000441024.2_Missense_Mutation_p.A1508V|CNOT1_ENST00000245138.4_Intron	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1						gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)	p.A1508V(1)		breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		aagtggtaacgcccagtgcca	0.343																																					p.A1508V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4523T	16						.	G	,VAL/ALA	0,2626		0,0,1313	49.0	55.0	53.0		,4523	-5.9	0.0	16		53	1,4617		0,1,2308	no	intron,missense	CNOT1	NM_016284.3,NM_206999.1	,64	0,1,3621	AA,AG,GG		0.0217,0.0,0.0138	,	,1508/1552	58577422	1,7243	1313	2309	3622	57134923	SO:0001627	intron_variant	23019	exon31			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.4434+88C>T	16.37:g.58577422G>A		Somatic		Capture	Illumina HiSeq	Phase_I	57134923	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	G	12.06	1.823563	0.32237	0.0	2.17E-4	ENSG00000125107	ENST00000441024	T	0.47177	0.85	3.52	-5.89	0.02282	.	.	.	.	.	T	0.30039	0.0752	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35574	-0.9783	8	0.87932	D	0	.	5.6745	0.17741	0.6643:0.0:0.186:0.1498	.	1508	A5YKK6-4	.	V	1508	ENSP00000413113:A1508V	ENSP00000413113:A1508V	A	-	2	0	CNOT1	57134923	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.098000	0.01347	-0.905000	0.03871	-0.384000	0.06662	GCG		0.343	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
CNOT1	23019	broad.mit.edu	37	16	58612736	58612736	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:58612736A>C	ENST00000317147.5	-	13	1783	c.1451T>G	c.(1450-1452)cTg>cGg	p.L484R	CNOT1_ENST00000569240.1_Missense_Mutation_p.L484R|CNOT1_ENST00000441024.2_Missense_Mutation_p.L484R	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	484					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)	p.L484R(2)		breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GGCCAATACCAGCATGTCTGG	0.448																																					p.L484R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1451G	16						.						219.0	205.0	210.0					16																	58612736		2198	4300	6498	57170237	SO:0001583	missense	23019	exon13			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.1451T>G	16.37:g.58612736A>C	ENSP00000320949:p.Leu484Arg	Somatic		Capture	Illumina HiSeq	Phase_I	57170237	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.798431	0.90538	.	.	ENSG00000125107	ENST00000317147;ENST00000394200;ENST00000441024	T;T	0.60920	0.27;0.15	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.80019	0.4547	M	0.89287	3.02	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.87578	0.994;0.998;0.995	D	0.83591	0.0123	9	.	.	.	-8.9623	15.8755	0.79159	1.0:0.0:0.0:0.0	.	484;484;484	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	R	484	ENSP00000320949:L484R;ENSP00000413113:L484R	.	L	-	2	0	CNOT1	57170237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.324000	0.96373	2.154000	0.67381	0.454000	0.30748	CTG		0.448	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
GOT2	2806	broad.mit.edu	37	16	58750701	58750701	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:58750701G>A	ENST00000245206.5	-	7	847	c.719C>T	c.(718-720)gCg>gTg	p.A240V	GOT2_ENST00000564400.1_Intron|GOT2_ENST00000434819.2_Missense_Mutation_p.A197V	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	240					2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)	p.A240V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	GTCAAAGAACGCAAAGAGATT	0.453																																					p.A240V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C719T	16						.						67.0	60.0	62.0					16																	58750701		2198	4300	6498	57308202	SO:0001583	missense	2806	exon7				CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"""kynurenine aminotransferase IV"", ""aspartate aminotransferase 2"", ""aspartate transaminase 2"""	138150	"""glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"""			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.719C>T	16.37:g.58750701G>A	ENSP00000245206:p.Ala240Val	Somatic		Capture	Illumina HiSeq	Phase_I	57308202	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Missense_Mutation	SNP	ENST00000245206.5	37	CCDS10801.1	.	.	.	.	.	.	.	.	.	.	G	14.46	2.542178	0.45280	.	.	ENSG00000125166	ENST00000245206;ENST00000434819	D;D	0.88896	-2.44;-2.44	5.54	5.54	0.83059	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.268081	0.42548	D	0.000681	T	0.78836	0.4346	N	0.15975	0.35	0.35404	D	0.791843	B;B	0.24186	0.025;0.099	B;B	0.15870	0.01;0.014	T	0.77440	-0.2587	9	.	.	.	-1.302	14.0955	0.65019	0.0744:0.0:0.9256:0.0	.	197;240	E7ERW2;P00505	.;AATM_HUMAN	V	240;197	ENSP00000245206:A240V;ENSP00000394100:A197V	.	A	-	2	0	GOT2	57308202	0.955000	0.32602	0.965000	0.40720	0.973000	0.67179	2.666000	0.46799	2.779000	0.95612	0.591000	0.81541	GCG		0.453	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
C16orf13	84326	broad.mit.edu	37	16	684632	684632	+	Missense_Mutation	SNP	C	C	T	rs142689363		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:684632C>T	ENST00000301686.8	-	6	591	c.580G>A	c.(580-582)Gcc>Acc	p.A194T	C16orf13_ENST00000397665.2_Missense_Mutation_p.S151N|C16orf13_ENST00000338401.4_Missense_Mutation_p.A97T|C16orf13_ENST00000397664.4_Missense_Mutation_p.A117T|C16orf13_ENST00000397666.2_Missense_Mutation_p.S171N	NM_032366.3	NP_115742.3	Q96S19	CP013_HUMAN	chromosome 16 open reading frame 13	194								p.A97T(1)		large_intestine(1)	1		Hepatocellular(780;0.00335)				TTGTTGTTGGCTGGCATGTCC	0.612																																					p.S171N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G512A	16						.	C	ASN/SER,THR/ALA,THR/ALA,ASN/SER,THR/ALA	1,4401	2.1+/-5.4	0,1,2200	178.0	200.0	192.0		512,289,349,452,580	4.3	1.0	16	dbSNP_134	192	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	C16orf13	NM_001040160.1,NM_001040161.1,NM_001040162.1,NM_001040165.1,NM_032366.3	46,58,58,46,58	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	171/206,97/108,117/128,151/186,194/205	684632	1,13001	2201	4300	6501	624633	SO:0001583	missense	84326	exon5				CCDS32352.1, CCDS42090.1, CCDS42091.1, CCDS45367.1, CCDS45368.1, CCDS73798.1	16p13.3	2012-10-09			ENSG00000130731	ENSG00000130731			14141	protein-coding gene	gene with protein product							Standard	NM_001040160		Approved	MGC13114	uc002chw.1	Q96S19	OTTHUMG00000047855	ENST00000301686.8:c.580G>A	16.37:g.684632C>T	ENSP00000445926:p.Ala194Thr	Somatic		Capture	Illumina HiSeq	Phase_I	624633	NM_001040160	A8MTR1|A8MWJ8|A8MZA1|B4DG95|B4DIJ3|D6REA6|F6TF62|F6VM53|Q96IW1|Q96MD6	Missense_Mutation	SNP	ENST00000301686.8	37	CCDS45368.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.4|21.4	4.148456|4.148456	0.78001|0.78001	2.27E-4|2.27E-4	0.0|0.0	ENSG00000130731|ENSG00000130731	ENST00000301686;ENST00000397664;ENST00000338401|ENST00000397666;ENST00000397665	T;T;T|T	0.52754|0.47528	0.65;0.65;0.65|0.84	4.31|4.31	4.31|4.31	0.51392|0.51392	.|.	0.254805|.	0.38058|.	N|.	0.001829|.	T|T	0.60011|0.60011	0.2236|0.2236	M|M	0.87097|0.87097	2.86|2.86	0.33754|0.33754	D|D	0.620958|0.620958	D;D;D|P;P	0.89917|0.48016	1.0;1.0;0.999|0.904;0.835	D;D;D|P;P	0.91635|0.45232	0.998;0.999;0.97|0.474;0.474	T|T	0.78391|0.78391	-0.2222|-0.2222	10|9	0.72032|0.62326	D|D	0.01|0.03	-38.653|-38.653	16.1364|16.1364	0.81491|0.81491	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	97;117;194|151;171	Q96S19-3;D6REA6;Q96S19|F6TF62;F6VM53	.;.;CP013_HUMAN|.;.	T|N	194;117;97|171;151	ENSP00000445926:A194T;ENSP00000440475:A117T;ENSP00000444140:A97T|ENSP00000440765:S171N	ENSP00000445926:A194T|ENSP00000444460:S151N	A|S	-|-	1|2	0|0	Z84479.1|Z84479.1	624633|624633	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.892000|0.892000	0.51952|0.51952	4.015000|4.015000	0.57152|0.57152	2.105000|2.105000	0.64084|0.64084	0.555000|0.555000	0.69702|0.69702	GCC|AGC		0.612	C16orf13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109081.2	NM_001040160	
CDH8	1006	broad.mit.edu	37	16	61935340	61935340	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:61935340T>G	ENST00000577390.1	-	3	1244	c.290A>C	c.(289-291)aAg>aCg	p.K97T	CDH8_ENST00000299345.6_Missense_Mutation_p.K97T|CDH8_ENST00000577730.1_Missense_Mutation_p.K97T|CDH8_ENST00000584337.1_Missense_Mutation_p.K97T	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	97	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)	p.K97T(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		TAGGATATACTTGATTTTTTT	0.378																																					p.K97T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A290C	16						.						82.0	78.0	80.0					16																	61935340		2203	4300	6503	60492841	SO:0001583	missense	1006	exon3			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"""Cadherins / Major cadherins"""	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.290A>C	16.37:g.61935340T>G	ENSP00000462701:p.Lys97Thr	Somatic		Capture	Illumina HiSeq	Phase_I	60492841	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.556137	0.86231	.	.	ENSG00000150394	ENST00000299345	T	0.51574	0.7	6.17	6.17	0.99709	Cadherin (4);Cadherin-like (1);	0.042248	0.85682	D	0.000000	T	0.55146	0.1902	L	0.28274	0.84	0.80722	D	1	P	0.48230	0.907	P	0.59357	0.856	T	0.57963	-0.7720	10	0.72032	D	0.01	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	97	P55286	CADH8_HUMAN	T	97	ENSP00000299345:K97T	ENSP00000299345:K97T	K	-	2	0	CDH8	60492841	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.869000	0.63028	2.371000	0.80710	0.533000	0.62120	AAG		0.378	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
DYNC1LI2	1783	broad.mit.edu	37	16	66770062	66770062	+	Silent	SNP	G	G	A	rs570710697		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:66770062G>A	ENST00000258198.2	-	5	821	c.615C>T	c.(613-615)tcC>tcT	p.S205S	DYNC1LI2_ENST00000440564.2_Silent_p.S166S|DYNC1LI2_ENST00000379482.2_Intron|DYNC1LI2_ENST00000443351.2_Silent_p.S128S|RP11-63M22.1_ENST00000565082.1_lincRNA	NM_006141.2	NP_006132.1	O43237	DC1L2_HUMAN	dynein, cytoplasmic 1, light intermediate chain 2	205					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|centrosome localization (GO:0051642)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based movement (GO:0007018)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.S205S(1)		central_nervous_system(3)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(4)|stomach(1)	15		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0907)|Epithelial(162;0.212)		TTTCTTCATCGGAGCCTGAGG	0.517													g|||	1	0.000199681	0.0008	0.0	5008	,	,		17448	0.0		0.0	False		,,,				2504	0.0				p.S205S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C615T	16						.						123.0	114.0	117.0					16																	66770062		2200	4300	6500	65327563	SO:0001819	synonymous_variant	1783	exon5			AF035812	CCDS10818.1, CCDS67049.1	16q22.1	2008-02-05	2005-11-25	2005-11-25	ENSG00000135720	ENSG00000135720		"""Cytoplasmic dyneins"""	2966	protein-coding gene	gene with protein product		611406	"""dynein, cytoplasmic, light intermediate polypeptide 2"""	DNCLI2		16260502	Standard	NM_006141		Approved		uc002eqb.1	O43237	OTTHUMG00000137523	ENST00000258198.2:c.615C>T	16.37:g.66770062G>A		Somatic		Capture	Illumina HiSeq	Phase_I	65327563	NM_006141	A8K6V1|B4DZP4|Q8TAT3	Silent	SNP	ENST00000258198.2	37	CCDS10818.1																																																																																				0.517	DYNC1LI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268846.1	NM_006141	
EXOC3L1	283849	broad.mit.edu	37	16	67221434	67221434	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:67221434C>T	ENST00000314586.6	-	5	974	c.734G>A	c.(733-735)cGt>cAt	p.R245H	EXOC3L1_ENST00000562887.1_Intron	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	245	Mediates interaction with EXOC2, EXOC4 and EXOC5. {ECO:0000250}.				exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)		p.R245H(2)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						ACAGCGCTGACGCCAGTCCCG	0.692																																					p.R245H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G734A	16						.						23.0	29.0	27.0					16																	67221434		2195	4284	6479	65778935	SO:0001583	missense	283849	exon5			AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"""exocyst complex component 3-like"""	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.734G>A	16.37:g.67221434C>T	ENSP00000325674:p.Arg245His	Somatic		Capture	Illumina HiSeq	Phase_I	65778935	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Missense_Mutation	SNP	ENST00000314586.6	37	CCDS10832.1	.	.	.	.	.	.	.	.	.	.	C	18.37	3.608163	0.66558	.	.	ENSG00000179044	ENST00000314586;ENST00000545725;ENST00000314553	T;T	0.29655	2.86;1.56	5.7	3.76	0.43208	.	0.099149	0.64402	D	0.000003	T	0.52256	0.1723	M	0.73598	2.24	0.50813	D	0.999899	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.70935	0.951;0.971;0.968	T	0.54241	-0.8323	10	0.72032	D	0.01	-24.5861	11.183	0.48640	0.0:0.8503:0.0:0.1497	.	184;184;245	F5H4W1;B7Z6U0;Q86VI1	.;.;EX3L1_HUMAN	H	245;184;189	ENSP00000325674:R245H;ENSP00000439910:R184H	ENSP00000325008:R189H	R	-	2	0	EXOC3L1	65778935	0.961000	0.32948	1.000000	0.80357	0.700000	0.40528	2.354000	0.44098	0.771000	0.33359	0.555000	0.69702	CGT		0.692	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516	
FHOD1	29109	broad.mit.edu	37	16	67271201	67271201	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:67271201G>A	ENST00000258201.4	-	9	1181	c.934C>T	c.(934-936)Cgc>Tgc	p.R312C		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	312	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)	p.R312C(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		CCCAGGTGGCGCTGGACCAGC	0.667																																					p.R312C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C934T	16						.						43.0	45.0	44.0					16																	67271201		2198	4300	6498	65828702	SO:0001583	missense	29109	exon9			AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.934C>T	16.37:g.67271201G>A	ENSP00000258201:p.Arg312Cys	Somatic		Capture	Illumina HiSeq	Phase_I	65828702	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Missense_Mutation	SNP	ENST00000258201.4	37	CCDS10834.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.216714	0.58452	.	.	ENSG00000135723	ENST00000258201	D	0.84873	-1.91	5.66	4.63	0.57726	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);	0.367165	0.27539	N	0.018904	T	0.80592	0.4652	L	0.38838	1.175	0.48975	D	0.999735	D	0.61697	0.99	B	0.43155	0.41	T	0.83009	-0.0173	10	0.52906	T	0.07	.	16.1475	0.81580	0.0:0.0:0.8577:0.1423	.	312	Q9Y613	FHOD1_HUMAN	C	312	ENSP00000258201:R312C	ENSP00000258201:R312C	R	-	1	0	FHOD1	65828702	1.000000	0.71417	0.957000	0.39632	0.993000	0.82548	4.190000	0.58365	2.666000	0.90696	0.655000	0.94253	CGC		0.667	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2		
EDC4	23644	broad.mit.edu	37	16	67913677	67913677	+	Splice_Site	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:67913677G>T	ENST00000358933.5	+	15	2060	c.1821G>T	c.(1819-1821)caG>caT	p.Q607H	EDC4_ENST00000574770.1_3'UTR|AC040162.1_ENST00000408599.1_RNA|CTC-479C5.10_ENST00000572067.1_lincRNA	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	607	Ser-rich.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)		p.Q607H(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		CCTTGCAGCAGGTACTCTCCC	0.592																																					p.Q607H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1821T	16						.						137.0	115.0	122.0					16																	67913677		2197	4291	6488	66471178	SO:0001630	splice_region_variant	23644	exon15			U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.1821+1G>T	16.37:g.67913677G>T		Somatic		Capture	Illumina HiSeq	Phase_I	66471178	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	37	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.462336	0.63513	.	.	ENSG00000038358	ENST00000358933;ENST00000536072	.	.	.	5.78	4.83	0.62350	.	0.270678	0.39475	N	0.001348	T	0.63129	0.2485	N	0.24115	0.695	0.48830	D	0.999714	D;D;D	0.64830	0.99;0.994;0.99	D;D;D	0.75484	0.969;0.986;0.979	T	0.65455	-0.6164	9	0.48119	T	0.1	-19.067	14.2364	0.65929	0.0717:0.0:0.9283:0.0	.	539;226;607	B7Z7V8;Q6P2E9-2;Q6P2E9	.;.;EDC4_HUMAN	H	607;539	.	ENSP00000351811:Q607H	Q	+	3	2	EDC4	66471178	1.000000	0.71417	1.000000	0.80357	0.706000	0.40770	7.165000	0.77544	1.450000	0.47717	0.655000	0.94253	CAG		0.592	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329	Missense_Mutation
NFATC3	4775	broad.mit.edu	37	16	68224771	68224771	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:68224771A>G	ENST00000346183.3	+	9	2223	c.2199A>G	c.(2197-2199)tcA>tcG	p.S733S	NFATC3_ENST00000575270.1_Silent_p.S733S|NFATC3_ENST00000329524.4_Silent_p.S733S|NFATC3_ENST00000535127.2_3'UTR|SNORA48_ENST00000391143.1_RNA|NFATC3_ENST00000349223.5_Silent_p.S733S	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	733					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.S733S(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		CCTCTGATTCAGGGTGTTCAC	0.468																																					p.S733S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A2199G	16						.						102.0	88.0	92.0					16																	68224771		2198	4300	6498	66782272	SO:0001819	synonymous_variant	4775	exon9			L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"""Nuclear factor of activated T-cells"""	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.2199A>G	16.37:g.68224771A>G		Somatic		Capture	Illumina HiSeq	Phase_I	66782272	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Silent	SNP	ENST00000346183.3	37	CCDS10860.1																																																																																				0.468	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555	
HAS3	3038	broad.mit.edu	37	16	69147349	69147349	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:69147349C>T	ENST00000306560.1	+	3	798	c.642C>T	c.(640-642)tgC>tgT	p.C214C	HAS3_ENST00000569188.1_Silent_p.C214C|HAS3_ENST00000219322.3_Silent_p.C214C	NM_005329.2	NP_005320.2	O00219	HYAS3_HUMAN	hyaluronan synthase 3	214					carbohydrate metabolic process (GO:0005975)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of transcription, DNA-templated (GO:0045893)|small molecule metabolic process (GO:0044281)	hyaluranon cable (GO:0036117)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)	p.C214C(2)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(2)	16		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)		TGCAGGTGTGCGACTCTGACA	0.612											OREG0023905	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C214C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C642T	16						.						107.0	95.0	99.0					16																	69147349		2198	4300	6498	67704850	SO:0001819	synonymous_variant	3038	exon3			BC021853	CCDS10870.1, CCDS10871.1	16q22.1	2013-02-22			ENSG00000103044	ENSG00000103044	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4820	protein-coding gene	gene with protein product		602428				9169154, 9083017	Standard	NM_005329		Approved		uc010cfh.3	O00219	OTTHUMG00000137562	ENST00000306560.1:c.642C>T	16.37:g.69147349C>T		Somatic	1112	Capture	Illumina HiSeq	Phase_I	67704850	NM_005329	A8K5T5|Q8WTZ0|Q9NYP0	Silent	SNP	ENST00000306560.1	37	CCDS10871.1																																																																																				0.612	HAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268898.2	NM_138612	
DDX19A	55308	broad.mit.edu	37	16	70395384	70395384	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:70395384G>T	ENST00000302243.7	+	5	520	c.357G>T	c.(355-357)gaG>gaT	p.E119D	RP11-529K1.3_ENST00000567706.1_Intron|DDX19A_ENST00000417604.2_Intron|DDX19A_ENST00000562509.1_3'UTR|DDX19A_ENST00000443119.2_Missense_Mutation_p.E29D	NM_018332.3	NP_060802.1	Q9NUU7	DD19A_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19A	119	N-terminal lobe. {ECO:0000250}.				mRNA transport (GO:0051028)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)	p.E119D(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(3)|urinary_tract(1)	11		Ovarian(137;0.221)				AGATACAAGAGAACGCATTAC	0.493																																					p.E119D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G357T	16						.						144.0	112.0	123.0					16																	70395384		2198	4300	6498	68952885	SO:0001583	missense	55308	exon5			AF183422	CCDS10889.1	16q22.1	2012-02-23	2012-02-23	2005-07-13	ENSG00000168872	ENSG00000168872		"""DEAD-boxes"""	25628	protein-coding gene	gene with protein product			"""DEAD (Asp-Glu-Ala-As) box polypeptide 19-like"""	DDX19L		12477932	Standard	NM_018332		Approved	FLJ11126		Q9NUU7	OTTHUMG00000137579	ENST00000302243.7:c.357G>T	16.37:g.70395384G>T	ENSP00000306117:p.Glu119Asp	Somatic		Capture	Illumina HiSeq	Phase_I	68952885	NM_018332	B2RPL0|B4DRZ7|Q53FM0	Missense_Mutation	SNP	ENST00000302243.7	37	CCDS10889.1	.	.	.	.	.	.	.	.	.	.	G	18.94	3.730211	0.69074	.	.	ENSG00000168872	ENST00000302243;ENST00000302227;ENST00000443119	T;T	0.15487	2.42;2.42	5.09	3.1	0.35709	RNA helicase, DEAD-box type, Q motif (1);DEAD-like helicase (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.36496	0.0969	M	0.77313	2.365	0.80722	D	1	P;B;D	0.58620	0.769;0.326;0.983	P;B;P	0.62014	0.714;0.271;0.897	T	0.19910	-1.0291	10	0.72032	D	0.01	.	9.919	0.41453	0.1738:0.0:0.8262:0.0	.	29;119;120	B4DRZ7;Q9NUU7;Q7Z4W5	.;DD19A_HUMAN;.	D	119;11;29	ENSP00000306117:E119D;ENSP00000399208:E29D	ENSP00000306209:E11D	E	+	3	2	DDX19A	68952885	1.000000	0.71417	0.993000	0.49108	0.445000	0.32107	2.609000	0.46317	1.141000	0.42275	0.491000	0.48974	GAG		0.493	DDX19A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268967.2	NM_018332	
ZFHX3	463	broad.mit.edu	37	16	72991976	72991976	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:72991976A>G	ENST00000268489.5	-	2	2741	c.2069T>C	c.(2068-2070)aTg>aCg	p.M690T	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	690					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.M690T(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CTTCTCCTTCATGTGTGCCTC	0.592																																					p.M690T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2069C	16						.						48.0	54.0	52.0					16																	72991976		2196	4300	6496	71549477	SO:0001583	missense	463	exon2			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.2069T>C	16.37:g.72991976A>G	ENSP00000268489:p.Met690Thr	Somatic		Capture	Illumina HiSeq	Phase_I	71549477	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	A	9.063	0.994973	0.19043	.	.	ENSG00000140836	ENST00000268489	T	0.79247	-1.25	5.29	5.29	0.74685	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.64402	D	0.000016	D	0.88100	0.6346	M	0.80422	2.495	0.80722	D	1	D	0.59357	0.985	D	0.71184	0.972	D	0.89826	0.3992	10	0.87932	D	0	.	15.5353	0.75998	1.0:0.0:0.0:0.0	.	690	Q15911	ZFHX3_HUMAN	T	690	ENSP00000268489:M690T	ENSP00000268489:M690T	M	-	2	0	ZFHX3	71549477	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.229000	0.95273	2.123000	0.65237	0.533000	0.62120	ATG		0.592	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
FA2H	79152	broad.mit.edu	37	16	74760155	74760155	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:74760155C>T	ENST00000219368.3	-	4	650	c.581G>A	c.(580-582)gGc>gAc	p.G194D	FA2H_ENST00000544337.1_Intron	NM_024306.4	NP_077282.3	Q7L5A8	FA2H_HUMAN	fatty acid 2-hydroxylase	194					cell death (GO:0008219)|central nervous system myelin maintenance (GO:0032286)|fatty acid biosynthetic process (GO:0006633)|lipid modification (GO:0030258)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of cell proliferation (GO:0042127)|regulation of hair cycle (GO:0042634)|sebaceous gland cell differentiation (GO:0001949)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	fatty acid alpha-hydroxylase activity (GO:0080132)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.G194D(1)		endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						TCGGACGTTGCCCTGGGCAAA	0.552																																					p.G194D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G581A	16						.						113.0	94.0	101.0					16																	74760155		2198	4300	6498	73317656	SO:0001583	missense	79152	exon4			BC002679	CCDS10911.1	16q23	2013-03-04	2003-10-29	2003-10-31	ENSG00000103089	ENSG00000103089		"""Fatty acid hydroxylase domain containing"""	21197	protein-coding gene	gene with protein product	"""fatty acid hydroxylase"""	611026	"""fatty acid hydroxylase domain containing 1"", ""spastic paraplegia 35 (autosomal recessive)"""	FAXDC1, SPG35		20104589	Standard	NM_024306		Approved	FAAH, FLJ25287	uc002fde.2	Q7L5A8	OTTHUMG00000137603	ENST00000219368.3:c.581G>A	16.37:g.74760155C>T	ENSP00000219368:p.Gly194Asp	Somatic		Capture	Illumina HiSeq	Phase_I	73317656	NM_024306	B7Z8T6|O75213|Q96DK1|Q9H1A5	Missense_Mutation	SNP	ENST00000219368.3	37	CCDS10911.1	.	.	.	.	.	.	.	.	.	.	C	9.280	1.047876	0.19827	.	.	ENSG00000103089	ENST00000219368	D	0.86497	-2.13	5.68	3.51	0.40186	.	0.193105	0.53938	N	0.000044	T	0.77184	0.4093	N	0.25647	0.755	0.80722	D	1	B	0.22683	0.073	B	0.20384	0.029	T	0.69899	-0.5020	10	0.20046	T	0.44	-13.7337	10.8871	0.46972	0.0:0.7942:0.0:0.2058	.	194	Q7L5A8	FA2H_HUMAN	D	194	ENSP00000219368:G194D	ENSP00000219368:G194D	G	-	2	0	FA2H	73317656	1.000000	0.71417	1.000000	0.80357	0.213000	0.24496	2.462000	0.45049	1.370000	0.46153	0.563000	0.77884	GGC		0.552	FA2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269015.2	NM_024306	
CNTNAP4	85445	broad.mit.edu	37	16	76513347	76513347	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:76513347G>A	ENST00000476707.1	+	11	1942	c.1803G>A	c.(1801-1803)aaG>aaA	p.K601K	CNTNAP4_ENST00000307431.8_Silent_p.K597K|CNTNAP4_ENST00000478060.1_Silent_p.K525K|CNTNAP4_ENST00000377504.4_Silent_p.K549K|CNTNAP4_ENST00000469589.1_3'UTR			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	598	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)		p.K573K(1)|p.K525K(1)|p.K597K(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						AAGCCTATAAGCACAGAGGAA	0.343																																					p.S598N												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.G1793A	16						.						117.0	125.0	123.0					16																	76513347		2198	4298	6496	75070848	SO:0001819	synonymous_variant	85445	exon12			AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.1803G>A	16.37:g.76513347G>A		Somatic		Capture	Illumina HiSeq	Phase_I	75070848	NM_033401	E9PFZ6|Q86YZ7	Silent	SNP	ENST00000476707.1	37																																																																																					0.343	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	
CDYL2	124359	broad.mit.edu	37	16	80646563	80646563	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:80646563C>G	ENST00000570137.2	-	5	1333	c.1178G>C	c.(1177-1179)tGc>tCc	p.C393S	CDYL2_ENST00000562812.1_Missense_Mutation_p.C394S|CDYL2_ENST00000566173.1_Missense_Mutation_p.C394S|CDYL2_ENST00000563890.1_Missense_Mutation_p.C394S	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	393						nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.C393S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						GTAGGAGGAGCAGCCAGCAGG	0.637																																					p.C393S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1178C	16						.						85.0	86.0	85.0					16																	80646563		2203	4300	6503	79204064	SO:0001583	missense	124359	exon5			AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"""chromodomain Y-like protein 2"""			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.1178G>C	16.37:g.80646563C>G	ENSP00000476295:p.Cys393Ser	Somatic		Capture	Illumina HiSeq	Phase_I	79204064	NM_152342	Q7Z5I8	Missense_Mutation	SNP	ENST00000570137.2	37	CCDS32493.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.939073	0.92526	.	.	ENSG00000166446	ENST00000299564	T	0.41400	1.0	4.95	4.95	0.65309	Crotonase, core (1);	0.107851	0.64402	D	0.000004	T	0.62258	0.2413	M	0.79011	2.435	0.80722	D	1	D	0.58268	0.982	P	0.58013	0.831	T	0.68014	-0.5521	10	0.87932	D	0	.	17.3496	0.87320	0.0:1.0:0.0:0.0	.	393	Q8N8U2	CDYL2_HUMAN	S	393	ENSP00000299564:C393S	ENSP00000299564:C393S	C	-	2	0	CDYL2	79204064	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.562000	0.86427	0.650000	0.86243	TGC		0.637	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342	
GAN	8139	broad.mit.edu	37	16	81391440	81391440	+	Nonsense_Mutation	SNP	C	C	T	rs370358470		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:81391440C>T	ENST00000568107.2	+	5	1039	c.877C>T	c.(877-879)Cga>Tga	p.R293*		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	293					cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R293*(2)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				AGCAGCGATGCGATGCATGTG	0.443																																					p.R293X	GBM(106;1239 1507 7582 9741 33976)											.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C877T	16	GRCh37	CM002982	GAN	M		.	C	stop/ARG	0,4404		0,0,2202	187.0	163.0	171.0		877	5.9	1.0	16		171	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	GAN	NM_022041.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		293/598	81391440	1,13003	2202	4300	6502	79948941	SO:0001587	stop_gained	8139	exon5			AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"""Kelch-like"", ""BTB/POZ domain containing"""	4137	protein-coding gene	gene with protein product	"""kelch-like family member 16"""	605379	"""giant axonal neuropathy (gigaxonin)"""			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.877C>T	16.37:g.81391440C>T	ENSP00000476795:p.Arg293*	Somatic		Capture	Illumina HiSeq	Phase_I	79948941	NM_022041		Nonsense_Mutation	SNP	ENST00000568107.2	37	CCDS10935.1	.	.	.	.	.	.	.	.	.	.	C	40	8.149539	0.98678	0.0	1.16E-4	ENSG00000127688	ENST00000248272	.	.	.	5.94	5.94	0.96194	.	0.105066	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	20.3552	0.98837	0.0:1.0:0.0:0.0	.	.	.	.	X	293	.	ENSP00000248272:R293X	R	+	1	2	GAN	79948941	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	5.861000	0.69553	2.812000	0.96745	0.557000	0.71058	CGA		0.443	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3		
HSDL1	83693	broad.mit.edu	37	16	84163352	84163352	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:84163352A>T	ENST00000219439.4	-	5	871	c.695T>A	c.(694-696)tTg>tAg	p.L232*	HSDL1_ENST00000434463.3_Nonsense_Mutation_p.L177*	NM_001146051.1|NM_031463.4	NP_001139523.1|NP_113651.4	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1	232						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)	p.L232*(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7						TTCATATTGCAAGGCTCTGCT	0.423																																					p.L232X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.T695A	16						.						69.0	69.0	69.0					16																	84163352		2200	4300	6500	82720853	SO:0001587	stop_gained	83693	exon5			AF237684	CCDS10942.1, CCDS54046.1	16q24	2011-09-20			ENSG00000103160	ENSG00000103160		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	16475	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 12C, member 3"""					12153137, 19027726	Standard	NM_031463		Approved	SDR12C3	uc002fhk.2	Q3SXM5	OTTHUMG00000137635	ENST00000219439.4:c.695T>A	16.37:g.84163352A>T	ENSP00000219439:p.Leu232*	Somatic		Capture	Illumina HiSeq	Phase_I	82720853	NM_031463	B4DSL2|D3DUL4|Q3SXM4|Q8NC98|Q9BY22	Nonsense_Mutation	SNP	ENST00000219439.4	37	CCDS10942.1	.	.	.	.	.	.	.	.	.	.	A	29.7	5.027049	0.93518	.	.	ENSG00000103160	ENST00000434463;ENST00000219439	.	.	.	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.6442	0.68748	1.0:0.0:0.0:0.0	.	.	.	.	X	177;232	.	ENSP00000219439:L232X	L	-	2	0	HSDL1	82720853	1.000000	0.71417	0.908000	0.35775	0.756000	0.42949	8.575000	0.90766	1.927000	0.55829	0.383000	0.25322	TTG		0.423	HSDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269076.3	NM_031463	
DNAAF1	123872	broad.mit.edu	37	16	84188196	84188196	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:84188196G>T	ENST00000378553.5	+	4	491	c.367G>T	c.(367-369)Gag>Tag	p.E123*	DNAAF1_ENST00000334315.5_Nonsense_Mutation_p.E123*	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	123					axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)	p.E123*(1)		NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						TGATCGCATTGAGAACCTGGA	0.502																																					p.E123X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G367T	16						.						93.0	89.0	90.0					16																	84188196		2200	4300	6500	82745697	SO:0001587	stop_gained	123872	exon4			BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"""outer row dynein assembly 7 homolog (Chlamydomonas)"""	613190	"""leucine rich repeat containing 50"""	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.367G>T	16.37:g.84188196G>T	ENSP00000367815:p.Glu123*	Somatic		Capture	Illumina HiSeq	Phase_I	82745697	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Nonsense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	.	.	.	.	.	.	.	.	.	.	G	36	5.662955	0.96745	.	.	ENSG00000154099	ENST00000334315;ENST00000378553	.	.	.	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-22.827	13.7829	0.63093	0.0:0.153:0.847:0.0	.	.	.	.	X	123	.	ENSP00000334593:E123X	E	+	1	0	DNAAF1	82745697	1.000000	0.71417	0.999000	0.59377	0.748000	0.42578	7.526000	0.81920	2.306000	0.77630	0.650000	0.86243	GAG		0.502	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
FAM92B	339145	broad.mit.edu	37	16	85143979	85143979	+	Silent	SNP	C	C	T	rs143497220		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:85143979C>T	ENST00000539556.1	-	2	263	c.108G>A	c.(106-108)acG>acA	p.T36T		NM_198491.1	NP_940893.1	Q6ZTR7	FA92B_HUMAN	family with sequence similarity 92, member B	36								p.T36T(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	16						CCGTCTTGCGCGTGTAGGCGG	0.647																																					p.T36T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G108A	16						.	C		1,4395	2.1+/-5.4	0,1,2197	50.0	52.0	52.0		108	0.0	1.0	16	dbSNP_134	52	0,8600		0,0,4300	no	coding-synonymous	FAM92B	NM_198491.1		0,1,6497	TT,TC,CC		0.0,0.0227,0.0077		36/305	85143979	1,12995	2198	4300	6498	83701480	SO:0001819	synonymous_variant	339145	exon2				CCDS32500.1	16q24.1	2005-09-22				ENSG00000153789			24781	protein-coding gene	gene with protein product						12477932	Standard	NM_198491		Approved	FLJ44299	uc021tlz.1	Q6ZTR7		ENST00000539556.1:c.108G>A	16.37:g.85143979C>T		Somatic		Capture	Illumina HiSeq	Phase_I	83701480	NM_198491		Silent	SNP	ENST00000539556.1	37	CCDS32500.1																																																																																				0.647	FAM92B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_198491	
FOXL1	2300	broad.mit.edu	37	16	86612596	86612596	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:86612596C>A	ENST00000320241.3	+	1	482	c.267C>A	c.(265-267)aaC>aaA	p.N89K		NM_005250.2	NP_005241.1	Q12952	FOXL1_HUMAN	forkhead box L1	89					heart development (GO:0007507)|multicellular organismal development (GO:0007275)|organ morphogenesis (GO:0009887)|Peyer's patch morphogenesis (GO:0061146)|proteoglycan biosynthetic process (GO:0030166)|regulation of Wnt signaling pathway (GO:0030111)|transcription, DNA-templated (GO:0006351)|visceral mesoderm-endoderm interaction involved in midgut development (GO:0007495)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N89K(5)		central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(2)|prostate(3)|skin(1)|urinary_tract(1)	15						ACCACGACAACCGGCAGGGCT	0.637																																					p.N89K	NSCLC(163;308 2020 10889 11476 18208)											.	.	5	Substitution - Missense(5)	endometrium(4)|large_intestine(1)	c.C267A	16						.						100.0	104.0	102.0					16																	86612596		2198	4300	6498	85170097	SO:0001583	missense	2300	exon1			AF315075	CCDS10959.1	16q24	2014-07-15			ENSG00000176678	ENSG00000176678		"""Forkhead boxes"""	3817	protein-coding gene	gene with protein product		603252		FKHL11		7957066	Standard	NM_005250		Approved	FREAC7, FKH6	uc002fjr.3	Q12952	OTTHUMG00000137653	ENST00000320241.3:c.267C>A	16.37:g.86612596C>A	ENSP00000326272:p.Asn89Lys	None		Capture	Illumina HiSeq	Phase_I	85170097	NM_005250	Q17RR1|Q9H242	Missense_Mutation	SNP	ENST00000320241.3	37	CCDS10959.1	.	.	.	.	.	.	.	.	.	.	C	18.99	3.738877	0.69304	.	.	ENSG00000176678	ENST00000320241	D	0.95412	-3.7	4.02	2.05	0.26809	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	D	0.96122	0.8736	M	0.64170	1.965	0.51012	D	0.999901	D	0.62365	0.991	D	0.67548	0.952	D	0.94458	0.7673	10	0.56958	D	0.05	.	9.0799	0.36545	0.0:0.8168:0.0:0.1832	.	89	Q12952	FOXL1_HUMAN	K	89	ENSP00000326272:N89K	ENSP00000326272:N89K	N	+	3	2	FOXL1	85170097	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.995000	0.49441	0.358000	0.24211	0.491000	0.48974	AAC		0.637	FOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269105.2	NM_005250	
METTL22	79091	broad.mit.edu	37	16	8729136	8729136	+	Missense_Mutation	SNP	G	G	A	rs201872412		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:8729136G>A	ENST00000381920.3	+	5	925	c.667G>A	c.(667-669)Gca>Aca	p.A223T	METTL22_ENST00000568967.1_3'UTR|METTL22_ENST00000561758.1_Missense_Mutation_p.A167T	NM_024109.2	NP_077014.2	Q9BUU2	MET22_HUMAN	methyltransferase like 22	223						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)	p.A223T(1)		large_intestine(5)|lung(4)	9						TAGCATCATCGCAGCCACCAT	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		20133	0.0		0.001	False		,,,				2504	0.0				p.A223T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G667A	16						.						48.0	53.0	51.0					16																	8729136		2052	4209	6261	8636637	SO:0001583	missense	79091	exon5			AK022495	CCDS10533.2	16p13.2	2014-07-15	2011-03-03	2011-03-03	ENSG00000067365	ENSG00000067365			28368	protein-coding gene	gene with protein product		615261	"""chromosome 16 open reading frame 68"""	C16orf68		24140279	Standard	XM_005255570		Approved	FLJ12433,MGC2654	uc002cyz.3	Q9BUU2	OTTHUMG00000129694	ENST00000381920.3:c.667G>A	16.37:g.8729136G>A	ENSP00000371345:p.Ala223Thr	Somatic		Capture	Illumina HiSeq	Phase_I	8636637	NM_024109	B2RD29|D3DUF2|Q6XYB4|Q9HA03	Missense_Mutation	SNP	ENST00000381920.3	37	CCDS10533.2	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	9.932	1.215019	0.22373	.	.	ENSG00000067365	ENST00000381920	T	0.54279	0.58	4.99	2.58	0.30949	.	0.169857	0.45361	D	0.000370	T	0.46014	0.1371	M	0.76002	2.32	0.33902	D	0.638578	B	0.26041	0.14	B	0.20384	0.029	T	0.51733	-0.8668	10	0.25106	T	0.35	-13.6938	7.0624	0.25133	0.339:0.0:0.661:0.0	.	223	Q9BUU2	MET22_HUMAN	T	223	ENSP00000371345:A223T	ENSP00000371345:A223T	A	+	1	0	METTL22	8636637	0.998000	0.40836	0.919000	0.36401	0.271000	0.26615	1.688000	0.37690	1.082000	0.41137	0.655000	0.94253	GCA		0.572	METTL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251901.1	NM_024109	
ZCCHC14	23174	broad.mit.edu	37	16	87446070	87446070	+	Missense_Mutation	SNP	C	C	T	rs138569077		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:87446070C>T	ENST00000268616.4	-	12	2063	c.1846G>A	c.(1846-1848)Gtg>Atg	p.V616M		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	616							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)	p.V616M(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		CTGGTCTCCACGACCAGGGCC	0.637																																					p.V616M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1846A	16						.	C	MET/VAL	1,4395	2.1+/-5.4	0,1,2197	46.0	55.0	52.0		1846	4.9	0.0	16	dbSNP_134	52	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZCCHC14	NM_015144.2	21	0,2,6496	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	616/950	87446070	2,12994	2198	4300	6498	86003571	SO:0001583	missense	23174	exon12			AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.1846G>A	16.37:g.87446070C>T	ENSP00000268616:p.Val616Met	Somatic		Capture	Illumina HiSeq	Phase_I	86003571	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Missense_Mutation	SNP	ENST00000268616.4	37	CCDS10961.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.493828	0.44352	2.27E-4	1.16E-4	ENSG00000140948	ENST00000268616	T	0.25912	1.77	5.83	4.88	0.63580	.	0.337642	0.30076	N	0.010480	T	0.37019	0.0988	L	0.29908	0.895	0.27101	N	0.962629	D;D	0.76494	0.999;0.986	D;P	0.63877	0.919;0.65	T	0.22452	-1.0216	10	0.72032	D	0.01	-1.4204	14.6699	0.68937	0.0:0.9304:0.0:0.0696	.	616;616	Q8WYQ9-2;Q8WYQ9	.;ZCH14_HUMAN	M	616	ENSP00000268616:V616M	ENSP00000268616:V616M	V	-	1	0	ZCCHC14	86003571	0.728000	0.28080	0.002000	0.10522	0.117000	0.20001	3.797000	0.55514	1.452000	0.47756	0.563000	0.77884	GTG		0.637	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
BANP	54971	broad.mit.edu	37	16	88052096	88052096	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:88052096G>A	ENST00000393207.1	+	7	915	c.694G>A	c.(694-696)Gcc>Acc	p.A232T	BANP_ENST00000286122.7_Missense_Mutation_p.A232T|BANP_ENST00000355022.4_Missense_Mutation_p.A201T|BANP_ENST00000538234.1_Missense_Mutation_p.A240T|BANP_ENST00000355163.5_Missense_Mutation_p.A207T|BANP_ENST00000393208.2_Missense_Mutation_p.A201T|BANP_ENST00000479780.2_Missense_Mutation_p.A201T	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	232	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.|Interaction with CUX1 and HDAC1. {ECO:0000250}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A201T(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		GGTACGCTGCGCCATCATCCC	0.612																																					p.A232T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G694A	16						.						79.0	68.0	72.0					16																	88052096		2198	4300	6498	86609597	SO:0001583	missense	54971	exon7			AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"""BEN domain containing"""	13450	protein-coding gene	gene with protein product	"""BEN domain containing 1"""	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.694G>A	16.37:g.88052096G>A	ENSP00000376902:p.Ala232Thr	Somatic		Capture	Illumina HiSeq	Phase_I	86609597	NM_001173543	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Missense_Mutation	SNP	ENST00000393207.1	37	CCDS54054.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.768720	0.90020	.	.	ENSG00000172530	ENST00000286122;ENST00000355163;ENST00000289484;ENST00000479780;ENST00000393208;ENST00000540932;ENST00000355022;ENST00000538234;ENST00000393207	T;T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92;1.92	5.11	5.11	0.69529	BEN domain (1);	0.052985	0.85682	D	0.000000	T	0.25232	0.0613	N	0.03608	-0.345	0.45515	D	0.998475	B;B;P;D;P;P	0.89917	0.11;0.158;0.897;1.0;0.938;0.948	B;B;B;D;B;P	0.78314	0.01;0.033;0.151;0.991;0.29;0.57	T	0.25984	-1.0116	9	.	.	.	.	12.7226	0.57149	0.0:0.2817:0.7183:0.0	.	240;207;201;232;201;201	B4DE54;B4DNJ9;B2RCF7;Q8N9N5;Q8N9N5-2;Q8N9N5-4	.;.;.;BANP_HUMAN;.;.	T	232;207;197;201;201;201;201;240;232	ENSP00000286122:A232T;ENSP00000347290:A207T;ENSP00000432508:A201T;ENSP00000376903:A201T;ENSP00000347125:A201T;ENSP00000444352:A240T;ENSP00000376902:A232T	.	A	+	1	0	BANP	86609597	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	6.319000	0.72871	2.357000	0.79964	0.491000	0.48974	GCC		0.612	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869	
ANKRD11	29123	broad.mit.edu	37	16	89345819	89345819	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:89345819G>A	ENST00000301030.4	-	9	7591	c.7131C>T	c.(7129-7131)gaC>gaT	p.D2377D	ANKRD11_ENST00000378330.2_Silent_p.D2377D	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2377					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.D2377D(1)		breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		CCTGGGCGTCGTCGTCCTCGG	0.716																																					p.D2377D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C7131T	16						.						2.0	2.0	2.0					16																	89345819		1332	2736	4068	87873320	SO:0001819	synonymous_variant	29123	exon9			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.7131C>T	16.37:g.89345819G>A		Somatic		Capture	Illumina HiSeq	Phase_I	87873320	NM_013275	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	37	CCDS32513.1																																																																																				0.716	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275	
GRIN2A	2903	broad.mit.edu	37	16	9857483	9857483	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:9857483C>T	ENST00000396573.2	-	14	4227	c.3918G>A	c.(3916-3918)agG>agA	p.R1306R	GRIN2A_ENST00000562109.1_Intron|GRIN2A_ENST00000404927.2_Intron|GRIN2A_ENST00000535259.1_Intron|GRIN2A_ENST00000396575.2_Silent_p.R1306R|GRIN2A_ENST00000330684.3_Silent_p.R1306R	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1306					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.R1306R(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)	TCCGGGAGGGCCTGCTAAGGT	0.488																																					p.R1306R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3918A	16						.						123.0	114.0	117.0					16																	9857483		2197	4300	6497	9764984	SO:0001819	synonymous_variant	2903	exon14				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.3918G>A	16.37:g.9857483C>T		Somatic		Capture	Illumina HiSeq	Phase_I	9764984	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																				0.488	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
GRIN2A	2903	broad.mit.edu	37	16	9892158	9892158	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:9892158C>T	ENST00000396573.2	-	12	2641	c.2332G>A	c.(2332-2334)Gcc>Acc	p.A778T	GRIN2A_ENST00000562109.1_Missense_Mutation_p.A778T|GRIN2A_ENST00000404927.2_Missense_Mutation_p.A778T|GRIN2A_ENST00000535259.1_Missense_Mutation_p.A621T|GRIN2A_ENST00000396575.2_Missense_Mutation_p.A778T|GRIN2A_ENST00000330684.3_Missense_Mutation_p.A778T	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	778					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.A778T(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)	TGAAGCAAGGCCAGGTCGATC	0.557																																					p.A778T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2332A	16						.						90.0	68.0	75.0					16																	9892158		2197	4300	6497	9799659	SO:0001583	missense	2903	exon11				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.2332G>A	16.37:g.9892158C>T	ENSP00000379818:p.Ala778Thr	Somatic		Capture	Illumina HiSeq	Phase_I	9799659	NM_001134408	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	32	5.192322	0.94960	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23	5.03	5.03	0.67393	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.161948	0.53938	D	0.000044	T	0.64305	0.2586	M	0.84219	2.685	0.80722	D	1	P;P;D	0.76494	0.626;0.676;0.999	B;B;D	0.85130	0.179;0.199;0.997	T	0.68655	-0.5351	9	.	.	.	.	17.3567	0.87338	0.0:1.0:0.0:0.0	.	621;778;778	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	T	778;778;621;778;778	ENSP00000379818:A778T;ENSP00000385872:A778T;ENSP00000441572:A621T;ENSP00000332549:A778T;ENSP00000379820:A778T	.	A	-	1	0	GRIN2A	9799659	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	7.681000	0.84073	2.337000	0.79520	0.557000	0.71058	GCC		0.557	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
GTF3C1	2975	broad.mit.edu	37	16	27517363	27517364	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	CT	CT	CT	-	CT	CT	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:27517363_27517364delCT	ENST00000356183.4	-	10	1641_1642	c.1626_1627delAG	c.(1624-1629)agagccfs	p.RA542fs	GTF3C1_ENST00000561623.1_Frame_Shift_Del_p.RA542fs	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	542					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.R542fs*35(1)		breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CTCTGGCAGGCTCTCTCTTCAG	0.554																																					p.542_543del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1626_1627del	16						.																																			27424865	SO:0001589	frameshift_variant	2975	exon10			U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.1626_1627delAG	16.37:g.27517369_27517370delCT	ENSP00000348510:p.Arg542fs	Somatic		Capture	Illumina HiSeq	Phase_I	27424864	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Frame_Shift_Del	DEL	ENST00000356183.4	37	CCDS32414.1																																																																																				0.554	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
IL27	246778	broad.mit.edu	37	16	28513344	28513344	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:28513344delC	ENST00000356897.1	-	4	437	c.415delG	c.(415-417)gccfs	p.A139fs		NM_145659.3	NP_663634.2	Q8TAD2	IL17D_HUMAN	interleukin 27	95					inflammatory response (GO:0006954)	extracellular space (GO:0005615)		p.A139fs*2(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	10						AGCCTCATGGCCCACAGCTGC	0.657																																					p.A139fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.415delG	16						.						83.0	85.0	84.0					16																	28513344		2197	4300	6497	28420845	SO:0001589	frameshift_variant	246778	exon4			AY099296	CCDS10633.1	16p11	2011-07-21	2003-12-17	2003-12-19	ENSG00000197272	ENSG00000197272		"""Interleukins and interleukin receptors"""	19157	protein-coding gene	gene with protein product		608273	"""interleukin 30"""	IL30		12121660	Standard	NM_145659		Approved	IL-27, p28, IL27p28, IL-27A, IL27A, MGC71873	uc002dqc.3	Q8NEV9	OTTHUMG00000097023	ENST00000356897.1:c.415delG	16.37:g.28513344delC	ENSP00000349365:p.Ala139fs	Somatic		Capture	Illumina HiSeq	Phase_I	28420845	NM_145659	B1AM69	Frame_Shift_Del	DEL	ENST00000356897.1	37	CCDS10633.1																																																																																				0.657	IL27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214114.1	NM_145659	
ANKRD11	29123	broad.mit.edu	37	16	89348651	89348651	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr16:89348651G>A	ENST00000301030.4	-	9	4759	c.4299C>T	c.(4297-4299)tcC>tcT	p.S1433S	ANKRD11_ENST00000378330.2_Silent_p.S1433S	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1433	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S1433S(1)		breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GTTCTCTCTCGGAATCATTTT	0.363																																					p.S1433S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4299T	16						.						100.0	98.0	99.0					16																	89348651		2198	4300	6498	87876152	SO:0001819	synonymous_variant	29123	exon9			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.4299C>T	16.37:g.89348651G>A		Somatic		Capture	Illumina HiSeq	Phase_I	87876152	NM_013275	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	37	CCDS32513.1																																																																																				0.363	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275	
MYH13	8735	broad.mit.edu	37	17	10212578	10212578	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:10212578G>A	ENST00000418404.3	-	34	5305	c.5142C>T	c.(5140-5142)agC>agT	p.S1714S	MYH13_ENST00000252172.4_Silent_p.S1714S|RP11-401O9.4_ENST00000609088.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1714					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.S1714S(2)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						GCACGCGGTCGCTGGCGTCCA	0.672																																					p.S1714S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C5142T	17						.						23.0	25.0	24.0					17																	10212578		2097	4214	6311	10153303	SO:0001819	synonymous_variant	8735	exon35			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.5142C>T	17.37:g.10212578G>A		Somatic		Capture	Illumina HiSeq	Phase_I	10153303	NM_003802	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	37	CCDS45613.1																																																																																				0.672	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	
MYH13	8735	broad.mit.edu	37	17	10213005	10213005	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:10213005G>T	ENST00000418404.3	-	33	4962	c.4799C>A	c.(4798-4800)gCc>gAc	p.A1600D	MYH13_ENST00000252172.4_Missense_Mutation_p.A1600D|RP11-401O9.4_ENST00000609088.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1600					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.A1600D(2)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						GCTCTGCAGGGCCTCTGCTGC	0.537																																					p.A1600D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C4799A	17						.						52.0	54.0	53.0					17																	10213005		2158	4275	6433	10153730	SO:0001583	missense	8735	exon34			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.4799C>A	17.37:g.10213005G>T	ENSP00000404570:p.Ala1600Asp	Somatic		Capture	Illumina HiSeq	Phase_I	10153730	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	G	14.44	2.535848	0.45176	.	.	ENSG00000006788	ENST00000252172	T	0.77098	-1.07	4.18	4.18	0.49190	Myosin tail (1);	.	.	.	.	T	0.60077	0.2241	N	0.02315	-0.6	0.47341	D	0.99939	B	0.23058	0.079	B	0.29440	0.102	T	0.63677	-0.6583	9	0.87932	D	0	.	17.0639	0.86554	0.0:0.0:1.0:0.0	.	1600	Q9UKX3	MYH13_HUMAN	D	1600	ENSP00000252172:A1600D	ENSP00000252172:A1600D	A	-	2	0	MYH13	10153730	1.000000	0.71417	1.000000	0.80357	0.288000	0.27193	9.544000	0.98092	2.326000	0.78906	0.462000	0.41574	GCC		0.537	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	
MYH13	8735	broad.mit.edu	37	17	10233837	10233837	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:10233837A>C	ENST00000418404.3	-	20	2465	c.2302T>G	c.(2302-2304)Ttt>Gtt	p.F768V	MYH13_ENST00000252172.4_Missense_Mutation_p.F768V|RP11-401O9.3_ENST00000577743.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	768	Actin-binding. {ECO:0000250}.|Myosin motor.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.F768V(2)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						GCTTTGAAAAACACCTGCATT	0.552																																					p.F768V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T2302G	17						.						46.0	47.0	47.0					17																	10233837		2059	4240	6299	10174562	SO:0001583	missense	8735	exon21			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.2302T>G	17.37:g.10233837A>C	ENSP00000404570:p.Phe768Val	Somatic		Capture	Illumina HiSeq	Phase_I	10174562	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.369781	0.82573	.	.	ENSG00000006788	ENST00000252172;ENST00000418404	D	0.94417	-3.42	3.94	3.94	0.45596	Myosin head, motor domain (2);	.	.	.	.	D	0.98811	0.9599	H	0.99764	4.76	0.48511	D	0.999667	B	0.25351	0.124	P	0.57283	0.817	D	0.98323	1.0529	9	0.87932	D	0	.	13.2824	0.60224	1.0:0.0:0.0:0.0	.	768	Q9UKX3	MYH13_HUMAN	V	768;443	ENSP00000252172:F768V	ENSP00000252172:F768V	F	-	1	0	MYH13	10174562	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	9.106000	0.94253	1.779000	0.52309	0.460000	0.39030	TTT		0.552	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	
MYH2	4620	broad.mit.edu	37	17	10442867	10442867	+	Missense_Mutation	SNP	G	G	A	rs527337606		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:10442867G>A	ENST00000245503.5	-	13	1544	c.1160C>T	c.(1159-1161)gCg>gTg	p.A387V	MYH2_ENST00000397183.2_Missense_Mutation_p.A387V|RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000532183.2_Missense_Mutation_p.A387V|CTC-297N7.11_ENST00000587182.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	387	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.A387V(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						GAGGTAGGCCGCCTTGTCAGC	0.428													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17231	0.0		0.0	False		,,,				2504	0.0				p.A387V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1160T	17						.						88.0	90.0	89.0					17																	10442867		2203	4300	6503	10383592	SO:0001583	missense	4620	exon13				CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.1160C>T	17.37:g.10442867G>A	ENSP00000245503:p.Ala387Val	Somatic		Capture	Illumina HiSeq	Phase_I	10383592	NM_001100112	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	37	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.459682	0.43736	.	.	ENSG00000125414	ENST00000532183;ENST00000245503;ENST00000397183	D;D;D	0.86366	-2.11;-2.11;-2.11	5.1	5.1	0.69264	Myosin head, motor domain (2);	0.000000	0.39020	U	0.001488	D	0.85128	0.5626	L	0.28054	0.825	0.48511	D	0.999666	B;P	0.51791	0.008;0.948	B;P	0.54431	0.003;0.752	T	0.80527	-0.1343	10	0.08381	T	0.77	.	17.6807	0.88242	0.0:0.0:1.0:0.0	.	387;387	Q567P6;Q9UKX2	.;MYH2_HUMAN	V	387	ENSP00000433944:A387V;ENSP00000245503:A387V;ENSP00000380367:A387V	ENSP00000245503:A387V	A	-	2	0	MYH2	10383592	0.962000	0.33011	0.986000	0.45419	0.883000	0.51084	3.669000	0.54561	2.653000	0.90120	0.585000	0.79938	GCG		0.428	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	
ZNF18	7566	broad.mit.edu	37	17	11881453	11881453	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:11881453G>T	ENST00000322748.3	-	9	2075	c.1471C>A	c.(1471-1473)Ccc>Acc	p.P491T	ZNF18_ENST00000580306.2_Missense_Mutation_p.P491T|ZNF18_ENST00000454073.3_Missense_Mutation_p.P490T|RP11-1096G20.5_ENST00000580270.1_RNA	NM_144680.2	NP_653281.2	P17022	ZNF18_HUMAN	zinc finger protein 18	491					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.P491T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	14				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)		CATTTATAGGGTTTCTCTCCT	0.423																																					p.P491T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1471A	17						.						109.0	112.0	111.0					17																	11881453		2203	4300	6503	11822178	SO:0001583	missense	7566	exon9			X52342	CCDS32568.1	17p12	2013-01-09	2006-05-10		ENSG00000154957	ENSG00000154957		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12969	protein-coding gene	gene with protein product		194524	"""zinc finger protein 18 (KOX 11)"""			15702252	Standard	XM_005256786		Approved	ZKSCAN6, KOX11, HDSG1, Zfp535, ZNF535, ZSCAN38	uc002gng.1	P17022	OTTHUMG00000178307	ENST00000322748.3:c.1471C>A	17.37:g.11881453G>T	ENSP00000315664:p.Pro491Thr	Somatic		Capture	Illumina HiSeq	Phase_I	11822178	NM_144680	Q5QHQ3|Q8IYC4|Q8NAH6	Missense_Mutation	SNP	ENST00000322748.3	37	CCDS32568.1	.	.	.	.	.	.	.	.	.	.	G	14.32	2.500767	0.44455	.	.	ENSG00000154957	ENST00000454073;ENST00000322748	T	0.16897	2.31	5.51	5.51	0.81932	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.52532	D	0.000061	T	0.44582	0.1300	M	0.77103	2.36	0.45995	D	0.998805	D;D	0.89917	1.0;1.0	D;D	0.81914	0.991;0.995	T	0.34329	-0.9833	10	0.54805	T	0.06	-16.1584	16.9299	0.86188	0.0:0.0:1.0:0.0	.	490;491	P17022-2;P17022	.;ZNF18_HUMAN	T	491	ENSP00000315664:P491T	ENSP00000315664:P491T	P	-	1	0	ZNF18	11822178	1.000000	0.71417	0.998000	0.56505	0.903000	0.53119	7.872000	0.87187	2.596000	0.87737	0.557000	0.71058	CCC		0.423	ZNF18-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441450.2	XM_085596	
MAP2K4	6416	broad.mit.edu	37	17	11984741	11984741	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:11984741A>T	ENST00000353533.5	+	3	350	c.287A>T	c.(286-288)gAt>gTt	p.D96V	MIR744_ENST00000578242.1_RNA|MAP2K4_ENST00000581941.1_3'UTR|MAP2K4_ENST00000415385.3_Missense_Mutation_p.D107V	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	96					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(1)|p.D96V(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		CAACACTGGGATTTCACTGCA	0.428			"""D, Mis, N"""		"""pancreatic, breast, colorectal"""																																p.D96V			Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	.	.	12	Whole gene deletion(10)|Substitution - Missense(1)|Unknown(1)	ovary(4)|breast(4)|large_intestine(2)|biliary_tract(1)|pancreas(1)	c.A287T	17						.						87.0	82.0	83.0					17																	11984741		2203	4300	6503	11925466	SO:0001583	missense	6416	exon3			L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.287A>T	17.37:g.11984741A>T	ENSP00000262445:p.Asp96Val	Somatic		Capture	Illumina HiSeq	Phase_I	11925466	NM_003010	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Missense_Mutation	SNP	ENST00000353533.5	37	CCDS11162.1	.	.	.	.	.	.	.	.	.	.	A	16.82	3.227922	0.58777	.	.	ENSG00000065559	ENST00000353533;ENST00000415385;ENST00000538465	T;T	0.19532	2.14;2.14	5.27	5.27	0.74061	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.24470	0.0593	M	0.64997	1.995	0.80722	D	1	B;B	0.23249	0.082;0.049	B;B	0.20767	0.031;0.014	T	0.02505	-1.1149	10	0.35671	T	0.21	.	14.456	0.67416	1.0:0.0:0.0:0.0	.	107;96	P45985-2;P45985	.;MP2K4_HUMAN	V	96;107;73	ENSP00000262445:D96V;ENSP00000410402:D107V	ENSP00000262445:D96V	D	+	2	0	MAP2K4	11925466	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.123000	0.65237	0.459000	0.35465	GAT		0.428	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1		
INPP5K	51763	broad.mit.edu	37	17	1399385	1399385	+	Missense_Mutation	SNP	C	C	T	rs138972043		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:1399385C>T	ENST00000421807.2	-	11	1647	c.1259G>A	c.(1258-1260)cGt>cAt	p.R420H	INPP5K_ENST00000542125.1_Missense_Mutation_p.R324H|INPP5K_ENST00000320345.6_Missense_Mutation_p.R344H|INPP5K_ENST00000397335.3_Missense_Mutation_p.R328H|INPP5K_ENST00000406424.4_Missense_Mutation_p.R344H	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	420	Required for ruffle localization.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)	p.R420H(1)|p.R344H(1)		endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						CACCACAGAACGCAGACTGTT	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		23371	0.001		0.0	False		,,,				2504	0.0				p.R420H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1259A	17						.						104.0	90.0	95.0					17																	1399385		2203	4300	6503	1346135	SO:0001583	missense	51763	exon11				CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"""skeletal muscle and kidney enriched inositol phosphatase"""	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.1259G>A	17.37:g.1399385C>T	ENSP00000413937:p.Arg420His	Somatic		Capture	Illumina HiSeq	Phase_I	1346135	NM_016532	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Missense_Mutation	SNP	ENST00000421807.2	37	CCDS11004.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	0.292	-0.979706	0.02197	.	.	ENSG00000132376	ENST00000421807;ENST00000406424;ENST00000350761;ENST00000320345;ENST00000397335;ENST00000542125	D;D;D;D	0.97959	-4.63;-4.63;-4.57;-4.51	5.66	3.24	0.37175	.	0.585611	0.20140	N	0.098396	D	0.88952	0.6577	N	0.01152	-0.98	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.001;0.002	T	0.81745	-0.0792	10	0.33940	T	0.23	-0.7907	6.6726	0.23076	0.0:0.2335:0.0:0.7665	.	324;420	F5GXZ0;Q9BT40	.;INP5K_HUMAN	H	344;344;420;344;328;324	ENSP00000385177:R344H;ENSP00000318476:R344H;ENSP00000380496:R328H;ENSP00000440147:R324H	ENSP00000318476:R344H	R	-	2	0	INPP5K	1346135	0.000000	0.05858	0.019000	0.16419	0.253000	0.25986	-0.067000	0.11579	0.349000	0.23975	-0.378000	0.06908	CGT		0.552	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4		
ELAC2	60528	broad.mit.edu	37	17	12899972	12899972	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:12899972A>G	ENST00000338034.4	-	17	1790	c.1551T>C	c.(1549-1551)ggT>ggC	p.G517G	ELAC2_ENST00000395962.2_Silent_p.G498G|ELAC2_ENST00000426905.3_Silent_p.G477G	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	517					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.G517G(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						ATGTGCCCTCACCACAGTCCA	0.582																																					p.G477G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1431C	17						.						65.0	52.0	57.0					17																	12899972		2203	4300	6503	12840697	SO:0001819	synonymous_variant	60528	exon16			AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"""tRNase Z (long form)"""	605367	"""elaC (E. coli) homolog 2"", ""elaC homolog 2 (E. coli)"""			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.1551T>C	17.37:g.12899972A>G		Somatic		Capture	Illumina HiSeq	Phase_I	12840697	NM_001165962	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Silent	SNP	ENST00000338034.4	37	CCDS11164.1																																																																																				0.582	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5		
COX10	1352	broad.mit.edu	37	17	14095434	14095434	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:14095434C>T	ENST00000261643.3	+	6	901	c.824C>T	c.(823-825)aCa>aTa	p.T275I	COX10_ENST00000536205.1_Missense_Mutation_p.T83I|COX10_ENST00000537334.1_Missense_Mutation_p.T58I	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	275					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)	p.T275I(1)		cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		TGCTGCTACACACCACTGAAA	0.577																																					p.T275I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C824T	17						.						57.0	55.0	56.0					17																	14095434		2202	4278	6480	14036159	SO:0001583	missense	1352	exon6			U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"""Mitochondrial respiratory chain complex assembly factors"""	2260	protein-coding gene	gene with protein product	"""heme A: farnesyltransferase"", ""protoheme IX farnesyltransferase, mitochondrial"", ""heme O synthase"""	602125	"""COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)"", ""COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"""			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.824C>T	17.37:g.14095434C>T	ENSP00000261643:p.Thr275Ile	Somatic		Capture	Illumina HiSeq	Phase_I	14036159	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Missense_Mutation	SNP	ENST00000261643.3	37	CCDS11166.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.565115	0.86439	.	.	ENSG00000006695	ENST00000261643;ENST00000536205;ENST00000537334	D;D;D	0.94184	-3.37;-3.37;-3.37	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	D	0.97692	0.9243	H	0.95539	3.685	0.80722	D	1	D;D	0.89917	0.994;1.0	P;D	0.83275	0.896;0.996	D	0.98988	1.0807	10	0.87932	D	0	-32.2213	16.1943	0.82015	0.0:1.0:0.0:0.0	.	83;275	B4DJ50;Q12887	.;COX10_HUMAN	I	275;83;58	ENSP00000261643:T275I;ENSP00000439494:T83I;ENSP00000443354:T58I	ENSP00000261643:T275I	T	+	2	0	COX10	14036159	1.000000	0.71417	0.950000	0.38849	0.993000	0.82548	7.109000	0.77062	2.334000	0.79466	0.655000	0.94253	ACA		0.577	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303	
CDRT1	374286	broad.mit.edu	37	17	15496685	15496685	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:15496685C>T	ENST00000395906.3	-	11	1971	c.1972G>A	c.(1972-1974)Gat>Aat	p.D658N	RP11-385D13.1_ENST00000455584.2_Intron|CDRT1_ENST00000354433.3_Missense_Mutation_p.D158N|CDRT1_ENST00000583965.1_Intron	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	658								p.D658N(2)|p.D158N(2)		endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		AGCACAGGATCGCCTCTGCCA	0.468																																					p.D658N												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G1972A	17						.						275.0	279.0	278.0					17																	15496685		2203	4300	6503	15437410	SO:0001583	missense	374286	exon11			U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	14379	protein-coding gene	gene with protein product		604596	"""F-box and WD repeat domain containing 10 pseudogene 1"", ""F-box and WD-40 domain protein 10 pseudogene 1"""	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.1972G>A	17.37:g.15496685C>T	ENSP00000379242:p.Asp658Asn	Somatic		Capture	Illumina HiSeq	Phase_I	15437410	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	.	.	.	.	.	.	.	.	.	.	c	16.69	3.192445	0.58017	.	.	ENSG00000241322;ENSG00000251537;ENSG00000251537	ENST00000354433;ENST00000261644;ENST00000395906	T;T	0.72282	-0.64;0.23	4.44	3.46	0.39613	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.64746	0.2626	M	0.71036	2.16	0.80722	D	1	P	0.37141	0.584	B	0.28849	0.095	T	0.63821	-0.6550	9	0.31617	T	0.26	.	13.0173	0.58764	0.1627:0.8373:0.0:0.0	.	658	O95170	CDRT1_HUMAN	N	158;688;658	ENSP00000346416:D158N;ENSP00000379242:D658N	ENSP00000346416:D158N	D	-	1	0	CDRT1;RP11-385D13.1	15437410	0.902000	0.30710	0.997000	0.53966	0.795000	0.44927	1.655000	0.37345	0.994000	0.38892	0.650000	0.86243	GAT		0.468	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
MYO15A	51168	broad.mit.edu	37	17	18054162	18054162	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:18054162A>G	ENST00000205890.5	+	38	7746	c.7408A>G	c.(7408-7410)Acc>Gcc	p.T2470A	MYO15A_ENST00000418233.3_5'Flank	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2470	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.T2470A(1)		breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CCGGGAGATGACCCTGCAGGC	0.672																																					p.T2470A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A7408G	17						.						23.0	30.0	27.0					17																	18054162		2034	4168	6202	17994887	SO:0001583	missense	51168	exon37			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.7408A>G	17.37:g.18054162A>G	ENSP00000205890:p.Thr2470Ala	Somatic		Capture	Illumina HiSeq	Phase_I	17994887	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.064420	0.55432	.	.	ENSG00000091536	ENST00000205890	D	0.88896	-2.44	4.01	4.01	0.46588	.	.	.	.	.	D	0.88164	0.6363	L	0.54323	1.7	0.80722	D	1	D	0.52996	0.957	P	0.50352	0.638	D	0.87681	0.2547	9	0.56958	D	0.05	.	8.4336	0.32773	0.8251:0.0:0.0:0.1749	.	2470	Q9UKN7	MYO15_HUMAN	A	2470	ENSP00000205890:T2470A	ENSP00000205890:T2470A	T	+	1	0	MYO15A	17994887	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.935000	0.70145	1.824000	0.53156	0.529000	0.55759	ACC		0.672	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
MYO15A	51168	broad.mit.edu	37	17	18075481	18075481	+	Silent	SNP	C	C	T	rs199520412		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:18075481C>T	ENST00000205890.5	+	64	10565	c.10227C>T	c.(10225-10227)agC>agT	p.S3409S	MYO15A_ENST00000451725.2_Missense_Mutation_p.A203V|MYO15A_ENST00000418233.3_Silent_p.S673S|RP11-258F1.1_ENST00000577847.1_RNA	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3409	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.S3409S(1)		breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					GCCTCCTCAGCGCCTTACCTA	0.587													C|||	1	0.000199681	0.0	0.0014	5008	,	,		21058	0.0		0.0	False		,,,				2504	0.0				p.S3409S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C10227T	17						.						92.0	101.0	98.0					17																	18075481		2121	4226	6347	18016206	SO:0001819	synonymous_variant	51168	exon63			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.10227C>T	17.37:g.18075481C>T		Somatic		Capture	Illumina HiSeq	Phase_I	18016206	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	13.64	2.297114	0.40694	.	.	ENSG00000091536	ENST00000451725	D	0.98105	-4.72	5.81	-4.33	0.03677	.	.	.	.	.	D	0.92691	0.7677	.	.	.	0.26034	N	0.981706	B	0.16166	0.016	B	0.06405	0.002	D	0.85218	0.1025	8	0.87932	D	0	.	12.7307	0.57197	0.0:0.3447:0.0:0.6553	.	203	B4DQJ3	.	V	203	ENSP00000409098:A203V	ENSP00000409098:A203V	A	+	2	0	MYO15A	18016206	0.001000	0.12720	0.950000	0.38849	0.208000	0.24298	-1.381000	0.02549	-0.485000	0.06754	-1.105000	0.02106	GCG		0.587	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
LGALS9	3965	broad.mit.edu	37	17	25974349	25974349	+	Missense_Mutation	SNP	G	G	A	rs147965169		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:25974349G>A	ENST00000395473.2	+	10	2280	c.812G>A	c.(811-813)cGt>cAt	p.R271H	LGALS9_ENST00000313648.6_Intron|LGALS9_ENST00000413914.2_Intron|LGALS9_ENST00000310394.5_Missense_Mutation_p.R227H|LGALS9_ENST00000302228.5_Missense_Mutation_p.R239H	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	271	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|galactose binding (GO:0005534)|signal transducer activity (GO:0004871)	p.R271H(1)		endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		CTGAACCCCCGTTTTGATGAG	0.577																																					p.R271H	Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G812A	17						.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	94.0	88.0	90.0		716,812	2.3	0.5	17	dbSNP_134	90	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	LGALS9	NM_002308.3,NM_009587.2	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	239/324,271/356	25974349	1,13005	2203	4300	6503	22998476	SO:0001583	missense	3965	exon10			AB006782	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961		"""Lectins, galactoside-binding"""	6570	protein-coding gene	gene with protein product	"""galectin 9"""	601879				9045665	Standard	NM_009587		Approved	LGALS9A	uc002gzp.3	O00182	OTTHUMG00000179831	ENST00000395473.2:c.812G>A	17.37:g.25974349G>A	ENSP00000378856:p.Arg271His	Somatic		Capture	Illumina HiSeq	Phase_I	22998476	NM_009587	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Missense_Mutation	SNP	ENST00000395473.2	37	CCDS11222.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.138544	0.77775	0.0	1.16E-4	ENSG00000168961	ENST00000395473;ENST00000302228;ENST00000310394	T;T;T	0.22134	1.97;1.97;1.97	4.36	2.34	0.29019	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.056820	0.64402	D	0.000001	T	0.41442	0.1159	M	0.86864	2.845	0.80722	D	1	D;D;D	0.67145	0.992;0.989;0.996	P;P;P	0.59889	0.865;0.782;0.821	T	0.30909	-0.9962	10	0.87932	D	0	.	6.6923	0.23179	0.0965:0.0:0.726:0.1774	.	182;239;271	B4DJD7;Q3B8N1;O00182	.;.;LEG9_HUMAN	H	271;239;227	ENSP00000378856:R271H;ENSP00000306228:R239H;ENSP00000312259:R227H	ENSP00000306228:R239H	R	+	2	0	LGALS9	22998476	0.997000	0.39634	0.547000	0.28179	0.968000	0.65278	4.284000	0.58983	0.467000	0.27218	0.467000	0.42956	CGT		0.577	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1	NM_009587	
LYRM9	201229	broad.mit.edu	37	17	26207353	26207353	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:26207353T>A	ENST00000379103.3	-	4	454	c.166A>T	c.(166-168)Atc>Ttc	p.I56F	RP11-138P22.1_ENST00000581901.1_RNA|LYRM9_ENST00000508862.1_Missense_Mutation_p.I56F|LYRM9_ENST00000503642.1_Missense_Mutation_p.I56F|LYRM9_ENST00000460380.2_Missense_Mutation_p.I56F|RP1-66C13.4_ENST00000582441.1_Missense_Mutation_p.I56F|LYRM9_ENST00000379102.3_Missense_Mutation_p.I56F	NM_001076680.1	NP_001070148.1	A8MSI8	LYRM9_HUMAN	LYR motif containing 9	56								p.I56F(1)									ATCTGCTGGATTCTCTCAGGG	0.468											OREG0024270	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I56F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A166T	17						.						79.0	83.0	82.0					17																	26207353		1918	4135	6053	23231480	SO:0001583	missense	201229	exon3			BC018092	CCDS45631.1	17q11.2	2014-06-05	2012-10-23	2012-10-23	ENSG00000232859	ENSG00000232859		"""LYR motif containing"""	27314	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 108"""	C17orf108		12477932	Standard	NM_001076680		Approved	HSD24	uc002gzx.3	A8MSI8	OTTHUMG00000132829	ENST00000379103.3:c.166A>T	17.37:g.26207353T>A	ENSP00000368397:p.Ile56Phe	Somatic	784	Capture	Illumina HiSeq	Phase_I	23231480	NM_001076680	A6NJT7|Q6X7B8	Missense_Mutation	SNP	ENST00000379103.3	37	CCDS45631.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.94|15.94	2.980935|2.980935	0.53827|0.53827	.|.	.|.	ENSG00000232859|ENSG00000232859	ENST00000379103|ENST00000379102;ENST00000503642	.|T	.|0.78003	.|-1.14	5.29|5.29	4.18|4.18	0.49190|0.49190	.|.	.|.	.|.	.|.	.|.	D|D	0.82825|0.82825	0.5121|0.5121	.|.	.|.	.|.	0.51233|0.51233	D|D	0.999915|0.999915	B|D;P	0.28350|0.56521	0.208|0.976;0.94	B|P;P	0.26094|0.54706	0.066|0.759;0.583	D|D	0.83379|0.83379	0.0011|0.0011	7|8	0.87932|0.87932	D|D	0|0	.|.	10.3623|10.3623	0.44001|0.44001	0.0:0.0:0.1651:0.8349|0.0:0.0:0.1651:0.8349	.|.	108|65;56	F2Z3P6|D6RAR2;A8MSI8	.|.;CQ108_HUMAN	D|F	108|56;65	.|ENSP00000368396:I56F	ENSP00000368397:E108D|ENSP00000368396:I56F	E|I	-|-	3|1	2|0	C17orf108|C17orf108	23231480|23231480	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	5.361000|5.361000	0.66092|0.66092	0.804000|0.804000	0.34136|0.34136	0.533000|0.533000	0.62120|0.62120	GAA|ATC		0.468	LYRM9-001	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256294.3	NM_001076680	
TMEM199	147007	broad.mit.edu	37	17	26687807	26687807	+	Silent	SNP	G	G	A	rs371468040		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:26687807G>A	ENST00000292114.3	+	5	558	c.468G>A	c.(466-468)acG>acA	p.T156T	CTB-96E2.7_ENST00000577850.1_RNA|TMEM199_ENST00000395404.3_De_novo_Start_InFrame|CTB-96E2.3_ENST00000591482.1_RNA|MIR4723_ENST00000585070.1_RNA|TMEM199_ENST00000509083.1_Silent_p.T156T	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199	156						integral component of membrane (GO:0016021)		p.T156T(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		TCATTGTCACGGTGGTTGCTG	0.522																																					p.T156T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G468A	17						.	G		1,4405	2.1+/-5.4	0,1,2202	101.0	98.0	99.0		468	-2.8	1.0	17		99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TMEM199	NM_152464.1		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		156/209	26687807	2,13004	2203	4300	6503	23711934	SO:0001819	synonymous_variant	147007	exon5			AY074907	CCDS11228.1	17q11.2	2007-12-17	2007-12-17	2007-12-17	ENSG00000244045	ENSG00000244045			18085	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 32"""	C17orf32			Standard	NM_152464		Approved	MGC45714	uc002hba.3	Q8N511	OTTHUMG00000132498	ENST00000292114.3:c.468G>A	17.37:g.26687807G>A		Somatic		Capture	Illumina HiSeq	Phase_I	23711934	NM_152464		Silent	SNP	ENST00000292114.3	37	CCDS11228.1																																																																																				0.522	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2	NM_152464	
FOXN1	8456	broad.mit.edu	37	17	26851603	26851603	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:26851603G>A	ENST00000226247.2	+	2	235	c.206G>A	c.(205-207)cGc>cAc	p.R69H	FOXN1_ENST00000579795.1_Missense_Mutation_p.R69H	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	69			R -> C (in dbSNP:rs2071587).		defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R69H(2)		endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					CACAGCCCCCGCATTGCGTCA	0.647																																					p.R69H												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.G206A	17						.						44.0	48.0	47.0					17																	26851603		2203	4300	6503	23875730	SO:0001583	missense	8456	exon2			Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"""Forkhead boxes"""	12765	protein-coding gene	gene with protein product		600838	"""winged-helix nude"", ""Rowett nude"""	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.206G>A	17.37:g.26851603G>A	ENSP00000226247:p.Arg69His	Somatic		Capture	Illumina HiSeq	Phase_I	23875730	NM_003593	B2R9Q7|O15352	Missense_Mutation	SNP	ENST00000226247.2	37	CCDS11232.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.866705	0.51588	.	.	ENSG00000109101	ENST00000226247	D	0.92397	-3.03	5.54	5.54	0.83059	.	0.063200	0.64402	D	0.000002	D	0.84401	0.5464	N	0.08118	0	0.27921	N	0.93824	B	0.17268	0.021	B	0.04013	0.001	T	0.77400	-0.2602	10	0.72032	D	0.01	.	16.5484	0.84457	0.0:0.0:1.0:0.0	.	69	O15353	FOXN1_HUMAN	H	69	ENSP00000226247:R69H	ENSP00000226247:R69H	R	+	2	0	FOXN1	23875730	0.965000	0.33210	0.972000	0.41901	0.368000	0.29767	1.535000	0.36061	2.768000	0.95171	0.561000	0.74099	CGC		0.647	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1		
KIAA0100	9703	broad.mit.edu	37	17	26942116	26942116	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:26942116G>C	ENST00000528896.2	-	39	6748	c.6674C>G	c.(6673-6675)cCt>cGt	p.P2225R	KIAA0100_ENST00000579924.2_5'Flank|SGK494_ENST00000469832.3_5'Flank|KIAA0100_ENST00000544884.1_Missense_Mutation_p.P2082R|KIAA0100_ENST00000389003.3_Missense_Mutation_p.P2082R|SGK494_ENST00000301037.5_5'Flank|SPAG5-AS1_ENST00000554154.1_RNA|RP11-192H23.4_ENST00000577790.1_5'Flank|RP11-192H23.4_ENST00000534850.1_5'Flank|SPAG5-AS1_ENST00000424210.1_RNA|SPAG5-AS1_ENST00000414744.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	2225						extracellular region (GO:0005576)		p.P2225R(1)|p.P2225H(1)		breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					CTTCTTGCCAGGGTTCTTGTC	0.537																																					p.P2225R												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C6674G	17						.						235.0	226.0	229.0					17																	26942116		2203	4300	6503	23966243	SO:0001583	missense	9703	exon39			D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"""cancer/testis antigen 101"", ""breast cancer overexpressed gene 1"""	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.6674C>G	17.37:g.26942116G>C	ENSP00000436773:p.Pro2225Arg	Somatic		Capture	Illumina HiSeq	Phase_I	23966243	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	G	10.04	1.241909	0.22796	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.24350	1.86;1.86	5.94	3.73	0.42828	.	0.145727	0.64402	D	0.000004	T	0.14830	0.0358	N	0.19112	0.55	0.36421	D	0.864305	B	0.31125	0.309	B	0.22386	0.039	T	0.13522	-1.0506	10	0.44086	T	0.13	.	10.4636	0.44594	0.0742:0.0:0.7953:0.1304	.	2225	Q14667	K0100_HUMAN	R	2225;2195;2225;2082	ENSP00000436773:P2225R;ENSP00000446443:P2082R	ENSP00000005905:P2225R	P	-	2	0	KIAA0100	23966243	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.265000	0.72534	0.696000	0.31696	0.561000	0.74099	CCT		0.537	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680	
PAFAH1B1	5048	broad.mit.edu	37	17	2570332	2570332	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:2570332C>T	ENST00000397195.5	+	5	690	c.239C>T	c.(238-240)aCg>aTg	p.T80M	PAFAH1B1_ENST00000572915.2_3'UTR	NM_000430.3	NP_000421.1			platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa)									p.T80M(1)		endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(1)|skin(1)	11						GAAGAATTTACGTCAGGTGGA	0.393																																					p.T80M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C239T	17						.						67.0	64.0	65.0					17																	2570332		2203	4300	6503	2517082	SO:0001583	missense	5048	exon5			L25107	CCDS32528.1	17p13.3	2014-04-04	2010-02-10		ENSG00000007168	ENSG00000007168		"""WD repeat domain containing"""	8574	protein-coding gene	gene with protein product	"""lissencephaly-1"""	601545	"""platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit (45kD)"", ""Miller-Dieker syndrome chromosome region"", ""platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa"", ""platelet-activating factor acetylhydrolase, isoform Ib, subunit 1 (45kDa)"""	MDCR, MDS		8355785, 9063735	Standard	NM_000430		Approved	LIS1, PAFAH	uc002fuw.4	P43034	OTTHUMG00000177574	ENST00000397195.5:c.239C>T	17.37:g.2570332C>T	ENSP00000380378:p.Thr80Met	Somatic		Capture	Illumina HiSeq	Phase_I	2517082	NM_000430		Missense_Mutation	SNP	ENST00000397195.5	37	CCDS32528.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.837580	0.50951	.	.	ENSG00000007168	ENST00000397195	T	0.55760	0.5	4.87	4.87	0.63330	.	0.048725	0.85682	D	0.000000	T	0.39064	0.1064	N	0.24115	0.695	0.80722	D	1	P	0.42908	0.793	B	0.35607	0.206	T	0.42085	-0.9472	10	0.48119	T	0.1	.	17.3274	0.87252	0.0:1.0:0.0:0.0	.	80	P43034	LIS1_HUMAN	M	80	ENSP00000380378:T80M	ENSP00000380378:T80M	T	+	2	0	PAFAH1B1	2517082	1.000000	0.71417	0.997000	0.53966	0.970000	0.65996	4.785000	0.62418	2.399000	0.81585	0.585000	0.79938	ACG		0.393	PAFAH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437797.2	NM_000430	
RAP1GAP2	23108	broad.mit.edu	37	17	2898742	2898742	+	Silent	SNP	C	C	A	rs530398634		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:2898742C>A	ENST00000254695.8	+	13	1116	c.1026C>A	c.(1024-1026)acC>acA	p.T342T	RAP1GAP2_ENST00000540393.2_Silent_p.T323T|RAP1GAP2_ENST00000366401.4_Silent_p.T327T|RAP1GAP2_ENST00000542807.1_Silent_p.T342T	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	342	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)	p.T342T(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						TGCCATTTACCGACGGAGACG	0.597																																					p.T342T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1026A	17						.						77.0	80.0	79.0					17																	2898742		2179	4297	6476	2845492	SO:0001819	synonymous_variant	23108	exon13			AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1026C>A	17.37:g.2898742C>A		Somatic		Capture	Illumina HiSeq	Phase_I	2845492	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																				0.597	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
SUPT6H	6830	broad.mit.edu	37	17	27031809	27031809	+	IGR	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:27031809C>T	ENST00000314616.6	+	0	6518				PROCA1_ENST00000579650.1_5'UTR|PROCA1_ENST00000581289.1_Intron|PROCA1_ENST00000439862.3_Silent_p.G50G|PROCA1_ENST00000301039.2_Silent_p.G48G	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)						chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G48G(1)		NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					AGATGATGTGCCCAGTGCACT	0.592																																					p.G48G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G144A	17						.						133.0	106.0	115.0					17																	27031809		2203	4300	6503	24055936	SO:0001628	intergenic_variant	147011	exon2			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85			17.37:g.27031809C>T		Somatic		Capture	Illumina HiSeq	Phase_I	24055936	NM_152465	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	37	CCDS32596.1																																																																																				0.592	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
NLE1	54475	broad.mit.edu	37	17	33463440	33463440	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:33463440C>T	ENST00000442241.4	-	8	944	c.905G>A	c.(904-906)cGc>cAc	p.R302H	NLE1_ENST00000593176.1_5'Flank|NLE1_ENST00000360831.5_Missense_Mutation_p.R260H|NLE1_ENST00000586869.1_Missense_Mutation_p.R10H	NM_001014445.1|NM_018096.3	NP_001014445.1|NP_060566.2	Q9NVX2	NLE1_HUMAN	notchless homolog 1 (Drosophila)	302					hematopoietic stem cell homeostasis (GO:0061484)|inner cell mass cell differentiation (GO:0001826)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of mitotic cell cycle (GO:0045930)|Notch signaling pathway (GO:0007219)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|ribosomal large subunit biogenesis (GO:0042273)	nucleolus (GO:0005730)|nucleus (GO:0005634)		p.R302H(1)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	22		Ovarian(249;0.17)				GGCCCCAGTGCGCAGGGCATA	0.602																																					p.R10H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G29A	17						.						117.0	125.0	122.0					17																	33463440		2203	4300	6503	30487553	SO:0001583	missense	54475	exon7				CCDS11291.1, CCDS45647.1	17q12	2013-01-10		2005-08-09	ENSG00000073536	ENSG00000073536		"""WD repeat domain containing"""	19889	protein-coding gene	gene with protein product	"""Notchless gene homolog, (Drosophila)"""						Standard	XM_005257989		Approved	FLJ10458	uc002hiy.1	Q9NVX2	OTTHUMG00000132928	ENST00000442241.4:c.905G>A	17.37:g.33463440C>T	ENSP00000413572:p.Arg302His	Somatic		Capture	Illumina HiSeq	Phase_I	30487553	NM_001014445	O60868|Q59GJ8|Q9BU54	Missense_Mutation	SNP	ENST00000442241.4	37	CCDS11291.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.306394|5.306394	0.95629|0.95629	.|.	.|.	ENSG00000073536|ENSG00000073536	ENST00000436188|ENST00000442241;ENST00000360831;ENST00000537697	.|T	.|0.28255	.|1.62	5.44|5.44	5.44|5.44	0.79542|0.79542	.|WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.60222|0.60222	0.2252|0.2252	M|M	0.84326|0.84326	2.69|2.69	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.994;0.999	T|T	0.63857|0.63857	-0.6542|-0.6542	5|10	.|0.72032	.|D	.|0.01	-25.7974|-25.7974	16.8112|16.8112	0.85720|0.85720	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|278;302	.|B4E074;Q9NVX2	.|.;NLE1_HUMAN	T|H	82|302;10;278	.|ENSP00000413572:R302H	.|ENSP00000354075:R10H	A|R	-|-	1|2	0|0	NLE1|NLE1	30487553|30487553	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.947000|0.947000	0.59692|0.59692	7.033000|7.033000	0.76504|0.76504	2.837000|2.837000	0.97791|0.97791	0.655000|0.655000	0.94253|0.94253	GCA|CGC		0.602	NLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256441.2	NM_018096	
RDM1	201299	broad.mit.edu	37	17	34247203	34247203	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:34247203G>A	ENST00000293273.6	-	6	786	c.741C>T	c.(739-741)caC>caT	p.H247H	RDM1_ENST00000425909.3_Intron|RDM1_ENST00000394529.3_Silent_p.H224H|RDM1_ENST00000431884.2_Silent_p.H214H|RDM1_ENST00000591402.1_Intron|RDM1_ENST00000419453.2_Silent_p.H191H	NM_145654.3	NP_663629.1	Q8NG50	RDM1_HUMAN	RAD52 motif containing 1	247					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.H247H(1)		breast(1)|kidney(3)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)	9		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GAATTAAACCGTGTAGTTCTT	0.368								Other identified genes with known or suspected DNA repair function																													p.H191H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C573T	17						.						146.0	138.0	141.0					17																	34247203		2203	4300	6503	31271316	SO:0001819	synonymous_variant	201299	exon4			AB080728	CCDS11301.1, CCDS42299.1, CCDS54111.1, CCDS54108.1, CCDS54109.1, CCDS54110.1, CCDS59280.1, CCDS59281.1	17q11.2	2014-04-10	2014-04-10	2005-10-20	ENSG00000187456	ENSG00000278023		"""RNA binding motif (RRM) containing"""	19950	protein-coding gene	gene with protein product		612896	"""RAD52 homolog B (S. cerevisiae)"", ""RAD52 motif 1"""	RAD52B		15611051	Standard	NM_001163120		Approved	MGC33977	uc002hkh.3	Q8NG50	OTTHUMG00000188399	ENST00000293273.6:c.741C>T	17.37:g.34247203G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31271316	NM_001163122	A0JP55|A8MV46|A8MY68|A8MZ92|A8RCS5|A8RCT0|A8RCT5|A8RCT8|A8RCU3|A8RCU8|A8RCW0|A8RCW5	Silent	SNP	ENST00000293273.6	37	CCDS11301.1																																																																																				0.368	RDM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256588.2	NM_145654	
CCL23	6368	broad.mit.edu	37	17	34340844	34340844	+	Missense_Mutation	SNP	G	G	A	rs142522197		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:34340844G>A	ENST00000591423.1	-	3	255	c.191C>T	c.(190-192)cCg>cTg	p.P64L	CCL23_ENST00000293280.2_Missense_Mutation_p.P81L|RP11-104J23.1_ENST00000588294.1_RNA|RP11-104J23.2_ENST00000590149.1_lincRNA	NM_145898.1	NP_665905.1	P55773	CCL23_HUMAN	chemokine (C-C motif) ligand 23	64					cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|monocyte chemotaxis (GO:0002548)|negative regulation of C-C chemokine binding (GO:2001264)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)	p.P81L(1)		large_intestine(2)|liver(1)|lung(2)|prostate(1)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GAGTGAACACGGGATGCTTCG	0.522																																					p.P64L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C191T	17						.	G	LEU/PRO,LEU/PRO	7,4399	14.3+/-33.2	0,7,2196	133.0	108.0	116.0		242,191	-7.4	0.2	17	dbSNP_134	116	0,8600		0,0,4300	no	missense,missense	CCL23	NM_005064.3,NM_145898.1	98,98	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	probably-damaging,probably-damaging	81/138,64/121	34340844	7,12999	2203	4300	6503	31364957	SO:0001583	missense	6368	exon3			U58913	CCDS11305.1, CCDS59282.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000167236	ENSG00000274736		"""Chemokine ligands"", ""Endogenous ligands"""	10622	protein-coding gene	gene with protein product		602494	"""small inducible cytokine subfamily A (Cys-Cys), member 23"""	SCYA23		9104803, 10409433	Standard	XR_429910		Approved	Ckb-8, MPIF-1, MIP-3, CKb8	uc002hks.1	P55773	OTTHUMG00000188409	ENST00000591423.1:c.191C>T	17.37:g.34340844G>A	ENSP00000465954:p.Pro64Leu	Somatic		Capture	Illumina HiSeq	Phase_I	31364957	NM_145898	B7ZKQ3|O00174|O75950|Q52LD4	Missense_Mutation	SNP	ENST00000591423.1	37	CCDS59282.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.155200	0.38021	0.001589	0.0	ENSG00000167236	ENST00000293280	T	0.07908	3.15	3.7	-7.4	0.01397	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.609303	0.13779	N	0.363351	T	0.18635	0.0447	M	0.90759	3.145	0.30996	N	0.720826	D;D	0.67145	0.992;0.996	P;P	0.54372	0.617;0.75	T	0.00630	-1.1636	10	0.52906	T	0.07	.	7.6013	0.28077	0.0:0.1775:0.4775:0.345	.	64;81	P55773;P55773-2	CCL23_HUMAN;.	L	81	ENSP00000293280:P81L	ENSP00000293280:P81L	P	-	2	0	CCL23	31364957	0.000000	0.05858	0.203000	0.23512	0.054000	0.15201	-2.440000	0.01016	-1.708000	0.01401	-0.416000	0.06073	CCG		0.522	CCL23-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450228.1	NM_005064, NM_145898	
AATF	26574	broad.mit.edu	37	17	35307578	35307578	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:35307578A>G	ENST00000225402.5	+	2	407	c.156A>G	c.(154-156)gtA>gtG	p.V52V		NM_012138.3	NP_036270.1	Q9NY61	AATF_HUMAN	apoptosis antagonizing transcription factor	52					apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|embryonic cleavage (GO:0040016)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of apoptotic process (GO:0043066)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of superoxide anion generation (GO:0032929)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mitotic cell cycle (GO:0007346)|ribosome biogenesis (GO:0042254)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	leucine zipper domain binding (GO:0043522)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V52V(1)		cervix(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)	18		Breast(25;0.00607)				ATTTCCTAGTAGTGGGTAGCA	0.488																																					p.V52V	NSCLC(49;901 1159 19183 41572 46244)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A156G	17						.						145.0	141.0	142.0					17																	35307578		2203	4300	6503	32381691	SO:0001819	synonymous_variant	26574	exon2			AF083208	CCDS32632.1	17q12	2014-05-06			ENSG00000108270	ENSG00000275700			19235	protein-coding gene	gene with protein product		608463				11027528, 10783144	Standard	NM_012138		Approved	DED, CHE-1, CHE1, BFR2	uc002hni.3	Q9NY61	OTTHUMG00000188458	ENST00000225402.5:c.156A>G	17.37:g.35307578A>G		Somatic		Capture	Illumina HiSeq	Phase_I	32381691	NM_012138	A6NCJ6|B3KQ26|Q9P0A4|Q9UNX5	Silent	SNP	ENST00000225402.5	37	CCDS32632.1																																																																																				0.488	AATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451543.1	NM_012138	
OR3A3	8392	broad.mit.edu	37	17	3324554	3324554	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:3324554A>G	ENST00000291231.1	+	1	693	c.693A>G	c.(691-693)gtA>gtG	p.V231V		NM_012373.2	NP_036505.2	P47888	OR3A3_HUMAN	olfactory receptor, family 3, subfamily A, member 3	231					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V231V(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(1)	9						CCCATGTGGTAGCTGCTGTGC	0.562																																					p.V231V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A693G	17						.						106.0	96.0	99.0					17																	3324554		2203	4300	6503	3271304	SO:0001819	synonymous_variant	8392	exon1			U04688	CCDS11025.1	17p13.3	2012-08-09			ENSG00000159961	ENSG00000159961		"""GPCR / Class A : Olfactory receptors"""	8284	protein-coding gene	gene with protein product				OR3A6, OR3A7, OR3A8P		8004088, 9500546	Standard	NM_012373		Approved	OR17-201, OR17-137, OR17-16	uc010vrd.2	P47888	OTTHUMG00000090649	ENST00000291231.1:c.693A>G	17.37:g.3324554A>G		Somatic		Capture	Illumina HiSeq	Phase_I	3271304	NM_012373	Q2VPE4|Q6IFM6|Q9P1Q4|Q9UBE7	Silent	SNP	ENST00000291231.1	37	CCDS11025.1																																																																																				0.562	OR3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207309.1		
ACACA	31	broad.mit.edu	37	17	35597475	35597475	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:35597475C>T	ENST00000394406.2	-	24	3117	c.2927G>A	c.(2926-2928)cGa>cAa	p.R976Q	ACACA_ENST00000360679.3_Missense_Mutation_p.R918Q|ACACA_ENST00000335166.5_Missense_Mutation_p.R898Q|ACACA_ENST00000353139.5_Missense_Mutation_p.R1013Q	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	976					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.R1013Q(1)|p.R918Q(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	GATGCCACTTCGGTACCTAGG	0.478																																					p.R1013Q	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3038A	17						.						69.0	59.0	63.0					17																	35597475		2203	4300	6503	32671588	SO:0001583	missense	31	exon24			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.2927G>A	17.37:g.35597475C>T	ENSP00000377928:p.Arg976Gln	Somatic		Capture	Illumina HiSeq	Phase_I	32671588	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.166212	0.78339	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.37	5.37	0.77165	Acetyl-CoA carboxylase, central domain (1);	0.000000	0.85682	D	0.000000	T	0.62307	0.2417	M	0.62723	1.935	0.80722	D	1	D;P;P	0.89917	1.0;0.892;0.625	D;B;B	0.91635	0.999;0.283;0.119	T	0.55270	-0.8167	10	0.30078	T	0.28	-7.2335	18.2839	0.90107	0.0:1.0:0.0:0.0	.	1013;976;918	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	Q	1013;918;976;1000;898	ENSP00000344789:R1013Q;ENSP00000353898:R918Q;ENSP00000377928:R976Q;ENSP00000335323:R898Q	ENSP00000335323:R898Q	R	-	2	0	ACACA	32671588	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.793000	0.96121	0.563000	0.77884	CGA		0.478	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
DDX52	11056	broad.mit.edu	37	17	35978412	35978412	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:35978412A>G	ENST00000349699.2	-	14	1710	c.1667T>C	c.(1666-1668)aTg>aCg	p.M556T	DDX52_ENST00000394367.3_Missense_Mutation_p.M448T	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	556	Lys-rich.					membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)	p.M556T(1)		biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				TTTCTTAATCATCTTTTTCTT	0.299																																					p.M556T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1667C	17						.						140.0	127.0	132.0					17																	35978412		2203	4299	6502	33052525	SO:0001583	missense	11056	exon14			AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"""DEAD-boxes"""	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.1667T>C	17.37:g.35978412A>G	ENSP00000268854:p.Met556Thr	Somatic		Capture	Illumina HiSeq	Phase_I	33052525	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Missense_Mutation	SNP	ENST00000349699.2	37	CCDS11323.1	.	.	.	.	.	.	.	.	.	.	A	12.01	1.808525	0.31961	.	.	ENSG00000141141	ENST00000349699;ENST00000394367	T;T	0.13420	2.59;2.62	5.37	5.37	0.77165	.	0.358288	0.30392	N	0.009727	T	0.14743	0.0356	L	0.51422	1.61	0.41332	D	0.987246	B	0.16166	0.016	B	0.14023	0.01	T	0.05131	-1.0904	10	0.23302	T	0.38	.	14.5893	0.68351	1.0:0.0:0.0:0.0	.	556	Q9Y2R4	DDX52_HUMAN	T	556;448	ENSP00000268854:M556T;ENSP00000377893:M448T	ENSP00000268854:M556T	M	-	2	0	DDX52	33052525	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	6.982000	0.76173	2.032000	0.59987	0.528000	0.53228	ATG		0.299	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300	
MLLT6	4302	broad.mit.edu	37	17	36872991	36872991	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:36872991G>A	ENST00000325718.7	+	10	1499	c.1408G>A	c.(1408-1410)Gcc>Acc	p.A470T	MIR4726_ENST00000577947.1_RNA|CTB-58E17.9_ENST00000579499.1_RNA	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	470					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.A470T(1)		breast(3)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(7;4.43e-21)					GAAGCACAAAGCCAGCAAGAG	0.667			T	MLL	AL																																p.A470T			Dom	yes		17	17q21	4302	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1408A	17						.						23.0	29.0	27.0					17																	36872991		2197	4295	6492	34126517	SO:0001583	missense	4302	exon10				CCDS11327.1	17q21	2014-04-10	2001-11-28		ENSG00000108292	ENSG00000275023		"""Zinc fingers, PHD-type"""	7138	protein-coding gene	gene with protein product	"""Myeloid/lymphoid or mixed-lineage leukemia, translocated to, 6"", ""trithorax homolog"""	600328	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 6"""			8058765	Standard	NM_005937		Approved	AF17, FLJ23480	uc002hqi.4	P55198	OTTHUMG00000188498	ENST00000325718.7:c.1408G>A	17.37:g.36872991G>A	ENSP00000316426:p.Ala470Thr	Somatic		Capture	Illumina HiSeq	Phase_I	34126517	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Missense_Mutation	SNP	ENST00000325718.7	37	CCDS11327.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.952173	0.92660	.	.	ENSG00000108292	ENST00000325718	T	0.15256	2.44	5.17	5.17	0.71159	.	0.217177	0.40728	N	0.001030	T	0.15046	0.0363	L	0.36672	1.1	0.44142	D	0.996932	P	0.38395	0.629	B	0.32465	0.146	T	0.02491	-1.1151	10	0.66056	D	0.02	.	16.2014	0.82084	0.0:0.0:1.0:0.0	.	470	P55198	AF17_HUMAN	T	470	ENSP00000316426:A470T	ENSP00000316426:A470T	A	+	1	0	MLLT6	34126517	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.879000	0.75572	2.700000	0.92200	0.561000	0.74099	GCC		0.667	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937	
TOP2A	7153	broad.mit.edu	37	17	38552631	38552631	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:38552631A>G	ENST00000423485.1	-	28	3782	c.3624T>C	c.(3622-3624)gcT>gcC	p.A1208A		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1208					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)	p.A1208A(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	GCAAAACTTCAGCCATTTGTG	0.418																																					p.A1208A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3624C	17						.						104.0	96.0	99.0					17																	38552631		1849	4087	5936	35806157	SO:0001819	synonymous_variant	7153	exon28				CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.3624T>C	17.37:g.38552631A>G		Somatic		Capture	Illumina HiSeq	Phase_I	35806157	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	37	CCDS45672.1																																																																																				0.418	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
TOP2A	7153	broad.mit.edu	37	17	38556144	38556144	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:38556144A>G	ENST00000423485.1	-	24	3334	c.3176T>C	c.(3175-3177)aTa>aCa	p.I1059T		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1059					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)	p.I1059T(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	TTTGCCATCTATTTTCTCTAA	0.328																																					p.I1059T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3176C	17						.						60.0	56.0	57.0					17																	38556144		1832	4076	5908	35809670	SO:0001583	missense	7153	exon24				CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.3176T>C	17.37:g.38556144A>G	ENSP00000411532:p.Ile1059Thr	Somatic		Capture	Illumina HiSeq	Phase_I	35809670	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Missense_Mutation	SNP	ENST00000423485.1	37	CCDS45672.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.937481	0.73557	.	.	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	T	0.27890	1.64	5.41	5.41	0.78517	DNA topoisomerase, type IIA, subunit A/C-terminal (2);DNA topoisomerase, type IIA, subunit A, alpha-helical (1);DNA topoisomerase, type IIA, central (1);	0.000000	0.85682	D	0.000000	T	0.60025	0.2237	M	0.87900	2.915	0.80722	D	1	D	0.58970	0.984	D	0.66497	0.944	T	0.66905	-0.5805	10	0.59425	D	0.04	.	15.738	0.77863	1.0:0.0:0.0:0.0	.	1059	P11388	TOP2A_HUMAN	T	1059;1139;1082;1095	ENSP00000411532:I1059T	ENSP00000269577:I1139T	I	-	2	0	TOP2A	35809670	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.212000	0.95126	2.178000	0.69098	0.533000	0.62120	ATA		0.328	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
KRT34	3885	broad.mit.edu	37	17	39534378	39534378	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:39534378G>A	ENST00000394001.1	-	7	1274	c.1244C>T	c.(1243-1245)gCc>gTc	p.A415V		NM_021013.3	NP_066293.2	O76011	KRT34_HUMAN	keratin 34	415	Tail.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.A415V(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Breast(137;0.000496)				ATTGGTGGTGGCGCATGGGTT	0.478																																					p.A415V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1244T	17						.						107.0	102.0	104.0					17																	39534378		2203	4300	6503	36787904	SO:0001583	missense	3885	exon7			Y16790	CCDS11390.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131737	ENSG00000131737		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6452	protein-coding gene	gene with protein product	"""hard keratin type I 4"""	602763	"""keratin, hair, acidic, 4"""	KRTHA4		2431943, 9756910, 16831889	Standard	NM_021013		Approved	Ha-4	uc002hwm.3	O76011	OTTHUMG00000133436	ENST00000394001.1:c.1244C>T	17.37:g.39534378G>A	ENSP00000377570:p.Ala415Val	Somatic		Capture	Illumina HiSeq	Phase_I	36787904	NM_021013	Q8IUT8|Q8N4W2	Missense_Mutation	SNP	ENST00000394001.1	37	CCDS11390.1	.	.	.	.	.	.	.	.	.	.	-	15.91	2.971047	0.53614	.	.	ENSG00000131737	ENST00000394001;ENST00000251648	.	.	.	5.54	4.58	0.56647	.	0.216591	0.32459	N	0.006063	T	0.47469	0.1447	M	0.72118	2.19	0.25260	N	0.989607	B	0.15473	0.013	B	0.20767	0.031	T	0.48603	-0.9021	9	0.59425	D	0.04	.	10.6243	0.45497	0.0887:0.0:0.9113:0.0	.	415	O76011	KRT34_HUMAN	V	373;415	.	ENSP00000251648:A415V	A	-	2	0	KRT34	36787904	1.000000	0.71417	0.986000	0.45419	0.906000	0.53458	2.951000	0.49089	1.380000	0.46344	-0.161000	0.13427	GCC		0.478	KRT34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257304.3	NM_021013	
ACLY	47	broad.mit.edu	37	17	40030091	40030091	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:40030091A>G	ENST00000352035.2	-	23	2745	c.2615T>C	c.(2614-2616)gTc>gCc	p.V872A	ACLY_ENST00000590151.1_Missense_Mutation_p.V872A|ACLY_ENST00000393896.2_Missense_Mutation_p.V862A|ACLY_ENST00000537919.1_Missense_Mutation_p.V601A|ACLY_ENST00000353196.1_Missense_Mutation_p.V862A	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	872				V -> A (in Ref. 1; CAA45614). {ECO:0000305}.	ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)	p.V872A(1)	NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				GAGGCCGAGGACCCCGCCAAT	0.562																																					p.V862A	Colon(64;807 1396 15971 30971)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2585C	17						.						68.0	71.0	70.0					17																	40030091		2203	4300	6503	37283617	SO:0001583	missense	47	exon22			X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"""ATP citrate synthase"""	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.2615T>C	17.37:g.40030091A>G	ENSP00000253792:p.Val872Ala	Somatic		Capture	Illumina HiSeq	Phase_I	37283617	NM_198830	B4DIM0|B4E3P0|Q13037|Q9BRL0	Missense_Mutation	SNP	ENST00000352035.2	37	CCDS11412.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.223357	0.79464	.	.	ENSG00000131473	ENST00000352035;ENST00000401700;ENST00000353196;ENST00000537919;ENST00000393896	T;T;T;T	0.26660	1.72;1.72;1.72;1.72	5.93	5.93	0.95920	Citrate synthase-like, core (1);	0.248378	0.40818	N	0.001004	T	0.55577	0.1929	M	0.93150	3.385	0.58432	D	0.999997	P;B;P;P;B	0.43662	0.595;0.361;0.549;0.814;0.307	B;B;P;P;B	0.51833	0.138;0.183;0.469;0.681;0.089	T	0.66666	-0.5866	10	0.72032	D	0.01	.	16.3797	0.83452	1.0:0.0:0.0:0.0	.	601;916;926;862;872	B4E3P0;B4DIM0;E7ENH9;G3XAI4;P53396	.;.;.;.;ACLY_HUMAN	A	872;926;862;601;862	ENSP00000253792:V872A;ENSP00000345398:V862A;ENSP00000445349:V601A;ENSP00000377474:V862A	ENSP00000253792:V872A	V	-	2	0	ACLY	37283617	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	5.038000	0.64177	2.271000	0.75665	0.533000	0.62120	GTC		0.562	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096	
CNP	1267	broad.mit.edu	37	17	40117186	40117186	+	5'Flank	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:40117186T>C	ENST00000393892.3	+	0	0				CNP_ENST00000591072.1_5'Flank|CNP_ENST00000393888.1_5'Flank|CNP_ENST00000472031.1_5'Flank|TTC25_ENST00000591658.1_RNA	NM_033133.4	NP_149124.3	P09543	CN37_HUMAN	2',3'-cyclic nucleotide 3' phosphodiesterase						adult locomotory behavior (GO:0008344)|aging (GO:0007568)|axonogenesis (GO:0007409)|cyclic nucleotide catabolic process (GO:0009214)|microtubule cytoskeleton organization (GO:0000226)|oligodendrocyte differentiation (GO:0048709)|regulation of mitochondrial membrane permeability (GO:0046902)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule (GO:0005874)|microvillus (GO:0005902)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|myelin sheath abaxonal region (GO:0035748)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity (GO:0004113)|cyclic nucleotide binding (GO:0030551)|RNA binding (GO:0003723)	p.S568S(1)		breast(1)|kidney(2)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	9		all_cancers(22;2.38e-06)|all_epithelial(22;6.79e-05)|Breast(137;0.000143)		UCEC - Uterine corpus endometrioid carcinoma (308;0.171)		GAAAGCAGAGTGTGGAAGCAG	0.527																																					p.S504S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1512C	17						.						36.0	39.0	38.0					17																	40117186		1961	4150	6111	37370712	SO:0001631	upstream_gene_variant	83538	exon11				CCDS11414.2	17q21	2008-02-05			ENSG00000173786	ENSG00000173786	3.1.4.37		2158	protein-coding gene	gene with protein product		123830				1322358	Standard	XM_006721701		Approved		uc002hyl.1	P09543	OTTHUMG00000133502		17.37:g.40117186T>C	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	37370712	NM_031421		Silent	SNP	ENST00000393892.3	37	CCDS11414.2																																																																																				0.527	CNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257443.2		
STAT5A	6776	broad.mit.edu	37	17	40458436	40458436	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:40458436C>T	ENST00000345506.4	+	14	2293	c.1651C>T	c.(1651-1653)Ctg>Ttg	p.L551L	STAT5A_ENST00000590949.1_Silent_p.L551L|STAT5A_ENST00000587646.1_Silent_p.L39L|STAT5A_ENST00000452307.2_Silent_p.L551L|STAT5A_ENST00000588868.1_Silent_p.L520L|STAT5A_ENST00000546010.2_Silent_p.L521L	NM_003152.3	NP_003143.2	P42229	STA5A_HUMAN	signal transducer and activator of transcription 5A	551					2-oxoglutarate metabolic process (GO:0006103)|allantoin metabolic process (GO:0000255)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|luteinization (GO:0001553)|mammary gland epithelium development (GO:0061180)|natural killer cell differentiation (GO:0001779)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of mast cell apoptotic process (GO:0033026)|oxaloacetate metabolic process (GO:0006107)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mast cell differentiation (GO:0060376)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin signaling pathway (GO:0038161)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription, DNA-templated (GO:0006351)|valine metabolic process (GO:0006573)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	calcium ion binding (GO:0005509)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.L551L(1)		central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		CTACAGTGGCCTGTCCGTGTC	0.637																																					p.L551L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1651T	17						.						64.0	50.0	55.0					17																	40458436		2203	4300	6503	37711962	SO:0001819	synonymous_variant	6776	exon14			U43185	CCDS11424.1, CCDS74066.1, CCDS74067.1	17q11.2	2013-02-14			ENSG00000126561	ENSG00000126561		"""SH2 domain containing"""	11366	protein-coding gene	gene with protein product		601511		STAT5		7719937, 8631883	Standard	NM_003152		Approved	MGF	uc002hzj.2	P42229	OTTHUMG00000150725	ENST00000345506.4:c.1651C>T	17.37:g.40458436C>T		Somatic		Capture	Illumina HiSeq	Phase_I	37711962	NM_003152	Q1KLZ6	Silent	SNP	ENST00000345506.4	37	CCDS11424.1																																																																																				0.637	STAT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319804.1	NM_003152	
CNTNAP1	8506	broad.mit.edu	37	17	40839013	40839013	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:40839013C>T	ENST00000264638.4	+	7	1210	c.993C>T	c.(991-993)cgC>cgT	p.R331R	CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	331	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon cargo transport (GO:0008088)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|neuron projection morphogenesis (GO:0048812)|neuronal action potential propagation (GO:0019227)|paranodal junction assembly (GO:0030913)|positive regulation of signal transduction (GO:0009967)|protein localization to paranode region of axon (GO:0002175)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|paranode region of axon (GO:0033270)|voltage-gated potassium channel complex (GO:0008076)	receptor activity (GO:0004872)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)	p.R331R(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|lung(15)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		TCTTCAACCGCGTCAACATCG	0.612																																					p.R331R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C993T	17						.						54.0	49.0	51.0					17																	40839013		2203	4300	6503	38092539	SO:0001819	synonymous_variant	8506	exon7			U87223	CCDS11436.1	17q21	2008-07-18				ENSG00000108797			8011	protein-coding gene	gene with protein product	"""neurexin 4"""	602346		NRXN4		9118959	Standard	NM_003632		Approved	p190, Caspr, CNTNAP	uc002iay.3	P78357		ENST00000264638.4:c.993C>T	17.37:g.40839013C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38092539	NM_003632		Silent	SNP	ENST00000264638.4	37	CCDS11436.1																																																																																				0.612	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632	
AOC2	314	broad.mit.edu	37	17	41001199	41001199	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:41001199G>A	ENST00000253799.3	+	2	1712	c.1685G>A	c.(1684-1686)cGg>cAg	p.R562Q	AOC3_ENST00000308423.2_5'Flank|AOC2_ENST00000452774.2_Missense_Mutation_p.R562Q	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)	562					amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)	p.R562Q(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(14)|ovary(4)|skin(2)	30		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		CAGCTGACTCGGCAGGTCCTG	0.597																																					p.R562Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1685A	17						.						40.0	41.0	41.0					17																	41001199		2203	4300	6503	38254725	SO:0001583	missense	314	exon2			AF081363	CCDS11443.1, CCDS45690.1	17q21	2012-07-13				ENSG00000131480	1.4.3.21		549	protein-coding gene	gene with protein product		602268				9119395, 9722954	Standard	NM_001158		Approved	RAO, DAO2	uc002ibu.3	O75106		ENST00000253799.3:c.1685G>A	17.37:g.41001199G>A	ENSP00000253799:p.Arg562Gln	Somatic		Capture	Illumina HiSeq	Phase_I	38254725	NM_001158	A5PKW2|O00120|O75105|Q4TTW5|Q9UNY0	Missense_Mutation	SNP	ENST00000253799.3	37	CCDS11443.1	.	.	.	.	.	.	.	.	.	.	G	8.329	0.826087	0.16749	.	.	ENSG00000131480	ENST00000253799;ENST00000452774	T;T	0.03920	3.76;3.76	5.26	4.3	0.51218	Copper amine oxidase, C-terminal (3);	0.336335	0.30565	N	0.009350	T	0.04227	0.0117	L	0.39397	1.21	0.34808	D	0.737383	B;B	0.32031	0.352;0.28	B;B	0.31390	0.129;0.031	T	0.39231	-0.9624	10	0.25106	T	0.35	-34.1673	5.8598	0.18740	0.3111:0.0:0.6889:0.0	.	562;562	O75106;O75106-2	AOC2_HUMAN;.	Q	562	ENSP00000253799:R562Q;ENSP00000406134:R562Q	ENSP00000253799:R562Q	R	+	2	0	AOC2	38254725	0.036000	0.19791	0.973000	0.42090	0.561000	0.35649	2.522000	0.45572	1.458000	0.47871	-0.136000	0.14681	CGG		0.597	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1	NM_009590, NM_001158	
ZZEF1	23140	broad.mit.edu	37	17	3937343	3937343	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:3937343G>A	ENST00000381638.2	-	40	6674	c.6550C>T	c.(6550-6552)Ctg>Ttg	p.L2184L		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2184							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.L2184L(1)		central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						CTAAAGAGCAGGTGGGTGGTT	0.532																																					p.L2184L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C6550T	17						.						119.0	116.0	117.0					17																	3937343		2203	4300	6503	3884092	SO:0001819	synonymous_variant	23140	exon40			BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.6550C>T	17.37:g.3937343G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3884092	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	37	CCDS11043.1																																																																																				0.532	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
G6PC	2538	broad.mit.edu	37	17	41063361	41063361	+	Missense_Mutation	SNP	C	C	T	rs149486847	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:41063361C>T	ENST00000253801.2	+	5	1071	c.992C>T	c.(991-993)gCg>gTg	p.A331V	G6PC_ENST00000585489.1_3'UTR	NM_000151.3	NP_000142.2	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit	331					carbohydrate metabolic process (GO:0005975)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|hexose transport (GO:0008645)|multicellular organism growth (GO:0035264)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)|urate metabolic process (GO:0046415)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)|phosphate ion binding (GO:0042301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)	p.A331V(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		TGCAAGAGTGCGGTAGTGCCC	0.572													C|||	6	0.00119808	0.0	0.0	5008	,	,		20686	0.0		0.0	False		,,,				2504	0.0061				p.A331V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C992T	17						.	C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	131.0	128.0	129.0		992	4.9	0.9	17	dbSNP_134	129	2,8598	2.2+/-6.3	0,2,4298	yes	missense	G6PC	NM_000151.2	64	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign	331/358	41063361	3,13003	2203	4300	6503	38316887	SO:0001583	missense	2538	exon5			U01120	CCDS11446.1, CCDS59291.1	17q21	2014-09-17	2006-06-28			ENSG00000131482	3.1.3.9		4056	protein-coding gene	gene with protein product	"""glycogen storage disease type I, von Gierke disease"""	613742	"""glucose-6-phosphatase, catalytic (glycogen storage disease type I, von Gierke disease)"""	G6PT		7774924	Standard	NM_000151		Approved	GSD1a	uc002icb.2	P35575		ENST00000253801.2:c.992C>T	17.37:g.41063361C>T	ENSP00000253801:p.Ala331Val	Somatic		Capture	Illumina HiSeq	Phase_I	38316887	NM_000151	A1L4C0|B4E1C3|K7EL82	Missense_Mutation	SNP	ENST00000253801.2	37	CCDS11446.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658290	0.47467	2.27E-4	2.33E-4	ENSG00000131482	ENST00000253801	T	0.75821	-0.97	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.59390	0.2190	L	0.39397	1.21	0.80722	D	1	P	0.48230	0.907	B	0.33295	0.161	T	0.62863	-0.6764	10	0.36615	T	0.2	.	11.735	0.51759	0.0:0.9197:0.0:0.0803	.	331	P35575	G6PC_HUMAN	V	331	ENSP00000253801:A331V	ENSP00000253801:A331V	A	+	2	0	G6PC	38316887	0.999000	0.42202	0.930000	0.37139	0.781000	0.44180	3.926000	0.56491	2.552000	0.86080	0.637000	0.83480	GCG		0.572	G6PC-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452451.1	NM_000151	
ETV4	2118	broad.mit.edu	37	17	41611302	41611302	+	Missense_Mutation	SNP	C	C	T	rs368196782		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:41611302C>T	ENST00000319349.5	-	6	606	c.308G>A	c.(307-309)cGc>cAc	p.R103H	ETV4_ENST00000393664.2_Missense_Mutation_p.R103H|ETV4_ENST00000538265.1_Missense_Mutation_p.R64H|ETV4_ENST00000545954.1_Missense_Mutation_p.R64H|ETV4_ENST00000545089.1_Missense_Mutation_p.R103H|ETV4_ENST00000591713.1_Missense_Mutation_p.R103H	NM_001079675.2	NP_001073143.1	P43268	ETV4_HUMAN	ets variant 4	103					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|motor neuron axon guidance (GO:0008045)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)	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 RNA polymerase II transcription factor activity (GO:0000981)	p.R103H(1)	EWSR1/ETV4(6)|CANT1/ETV4(3)|TMPRSS2/ETV4(13)|DDX5_ENST00000540698/ETV4(2)|KLK2/ETV4(2)	ovary(2)|upper_aerodigestive_tract(1)	3		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)		CGGGTCTGTGCGGGGACTCTG	0.642			T	"""EWSR1, TMPRSS2, DDX5, KLK2, CANT1"""	"""Ewing sarcoma, Prostate carcinoma"""																																p.R103H	Esophageal Squamous(116;1540 1611 12927 31103 34118)		Dom	yes		17	17q21	2118	"""ets variant gene 4 (E1A enhancer binding protein, E1AF)"""		"""M, E"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G308A	17						.	C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	40.0	46.0	44.0		308,308	4.7	1.0	17		44	0,8600		0,0,4300	no	missense,missense	ETV4	NM_001079675.1,NM_001986.2	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	103/485,103/485	41611302	1,13005	2203	4300	6503	38966828	SO:0001583	missense	2118	exon6			U18018	CCDS11465.1, CCDS58553.1, CCDS59292.1	17q21	2014-04-30	2008-09-12			ENSG00000175832			3493	protein-coding gene	gene with protein product	"""E1A enhancer binding protein"""	600711	"""ets variant gene 4 (E1A enhancer-binding protein, E1AF)"""			8530053, 1547944	Standard	NM_001986		Approved	E1A-F, E1AF, PEA3	uc002idw.3	P43268		ENST00000319349.5:c.308G>A	17.37:g.41611302C>T	ENSP00000321835:p.Arg103His	Somatic		Capture	Illumina HiSeq	Phase_I	38966828	NM_001986	A8K314|B7Z5J3|B7Z9J6|Q96AW9	Missense_Mutation	SNP	ENST00000319349.5	37	CCDS11465.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.859275	0.71834	2.27E-4	0.0	ENSG00000175832	ENST00000319349;ENST00000393664;ENST00000538265;ENST00000545954;ENST00000545089	T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92	5.66	4.69	0.59074	PEA3-type ETS-domain transcription factor, N-terminal (1);	0.643065	0.16981	N	0.191701	T	0.34366	0.0895	L	0.54323	1.7	0.22858	N	0.998649	P;B;B	0.52316	0.952;0.016;0.068	P;B;B	0.51833	0.681;0.002;0.015	T	0.13629	-1.0502	10	0.52906	T	0.07	.	9.7089	0.40233	0.0:0.7718:0.1509:0.0773	.	103;64;103	B7Z5F4;B7Z5J3;P43268	.;.;ETV4_HUMAN	H	103;103;64;64;103	ENSP00000321835:R103H;ENSP00000377273:R103H;ENSP00000443846:R64H;ENSP00000440023:R64H;ENSP00000441749:R103H	ENSP00000321835:R103H	R	-	2	0	ETV4	38966828	1.000000	0.71417	0.954000	0.39281	0.905000	0.53344	2.343000	0.44001	1.380000	0.46344	-0.142000	0.14014	CGC		0.642	ETV4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453489.1	NM_001986	
MPP2	4355	broad.mit.edu	37	17	41959856	41959856	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:41959856G>A	ENST00000461854.1	-	7	634	c.549C>T	c.(547-549)ggC>ggT	p.G183G	MPP2_ENST00000536246.1_Silent_p.G148G|MPP2_ENST00000377184.3_Silent_p.G176G|MPP2_ENST00000520305.1_Silent_p.G20G|MPP2_ENST00000523501.1_Silent_p.G148G|MPP2_ENST00000473246.1_5'UTR|MPP2_ENST00000269095.4_Silent_p.G159G|MPP2_ENST00000518766.1_Silent_p.G204G			Q14168	MPP2_HUMAN	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	183					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)	p.G159G(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(4)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)		CCAGCTCGCCGCCCTCCACGC	0.572																																					p.G159G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C477T	17						.						49.0	49.0	49.0					17																	41959856		2203	4300	6503	39315382	SO:0001819	synonymous_variant	4355	exon6				CCDS11471.1, CCDS62206.1, CCDS62207.1, CCDS62208.1, CCDS62209.1, CCDS62210.1	17q12-q21	2008-07-18			ENSG00000108852	ENSG00000108852			7220	protein-coding gene	gene with protein product	"""MAGUK p55 subfamily member 2"", ""discs large, homolog 2"""	600723		DLG2		7590743	Standard	NM_001278370		Approved	DKFZp761D0712	uc002ieo.1	Q14168	OTTHUMG00000133840	ENST00000461854.1:c.549C>T	17.37:g.41959856G>A		Somatic		Capture	Illumina HiSeq	Phase_I	39315382	NM_005374	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Silent	SNP	ENST00000461854.1	37																																																																																					0.572	MPP2-003	KNOWN	non_canonical_polymorphism|basic	protein_coding	protein_coding	OTTHUMT00000258388.2	NM_005374	
UBTF	7343	broad.mit.edu	37	17	42287765	42287765	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:42287765C>T	ENST00000302904.4	-	14	1928	c.1436G>A	c.(1435-1437)gGc>gAc	p.G479D	UBTF_ENST00000533177.1_Missense_Mutation_p.G442D|UBTF_ENST00000393606.3_Missense_Mutation_p.G442D|UBTF_ENST00000343638.5_Missense_Mutation_p.G442D|UBTF_ENST00000436088.1_Missense_Mutation_p.G479D|UBTF_ENST00000527034.1_Missense_Mutation_p.G442D|UBTF_ENST00000526094.1_Missense_Mutation_p.G442D|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000529383.1_Missense_Mutation_p.G479D			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	479					chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.G479D(1)		breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		GGGCAGCTTGCCCCGTTCCTC	0.667											OREG0024456	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G442D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1325A	17						.						45.0	42.0	43.0					17																	42287765		2203	4300	6503	39643291	SO:0001583	missense	7343	exon13			BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.1436G>A	17.37:g.42287765C>T	ENSP00000302640:p.Gly479Asp	Somatic	907	Capture	Illumina HiSeq	Phase_I	39643291	NM_001076683	A8K6R8	Missense_Mutation	SNP	ENST00000302904.4	37	CCDS11480.1	.	.	.	.	.	.	.	.	.	.	c	22.5	4.295389	0.81025	.	.	ENSG00000108312	ENST00000343638;ENST00000302904;ENST00000527034;ENST00000533177;ENST00000436088;ENST00000393606;ENST00000526094;ENST00000529383;ENST00000529373	D;D;D;D;D;D;D;D;T	0.98280	-4.8;-4.08;-4.84;-4.8;-4.08;-4.8;-4.8;-4.08;1.95	4.61	4.61	0.57282	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (1);	0.173971	0.49916	D	0.000127	D	0.96062	0.8717	N	0.14661	0.345	0.43890	D	0.996515	D;P;D	0.56521	0.976;0.902;0.967	P;P;P	0.54924	0.654;0.498;0.764	D	0.94299	0.7535	10	0.20519	T	0.43	-16.0175	13.0528	0.58964	0.0:0.8382:0.1618:0.0	.	442;442;479	E9PKP7;P17480-2;P17480	.;.;UBF1_HUMAN	D	442;479;442;442;479;442;442;479;66	ENSP00000345297:G442D;ENSP00000302640:G479D;ENSP00000431539:G442D;ENSP00000437180:G442D;ENSP00000390669:G479D;ENSP00000377231:G442D;ENSP00000432925:G442D;ENSP00000435708:G479D;ENSP00000431295:G66D	ENSP00000302640:G479D	G	-	2	0	UBTF	39643291	1.000000	0.71417	0.994000	0.49952	0.757000	0.42996	2.272000	0.43373	2.392000	0.81423	0.467000	0.42956	GGC		0.667	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233	
ANKFY1	51479	broad.mit.edu	37	17	4088319	4088319	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:4088319G>A	ENST00000341657.4	-	12	1528	c.1493C>T	c.(1492-1494)gCg>gTg	p.A498V	CYB5D2_ENST00000573984.1_Intron|Y_RNA_ENST00000516003.1_RNA|ANKFY1_ENST00000573722.1_5'UTR|ANKFY1_ENST00000570535.1_Missense_Mutation_p.A540V|ANKFY1_ENST00000574367.1_Missense_Mutation_p.A498V	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	498					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)	p.A498V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						ATGCCGACACGCTGTGTGCAA	0.577																																					p.A498V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1493T	17						.						37.0	42.0	40.0					17																	4088319		2120	4247	6367	4035068	SO:0001583	missense	51479	exon12			AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"""Zinc fingers, FYVE domain containing"", ""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.1493C>T	17.37:g.4088319G>A	ENSP00000343362:p.Ala498Val	Somatic		Capture	Illumina HiSeq	Phase_I	4035068	NM_016376	A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	37		.	.	.	.	.	.	.	.	.	.	G	36	5.859707	0.97036	.	.	ENSG00000185722	ENST00000341657;ENST00000535427	T	0.80824	-1.42	5.86	5.86	0.93980	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.91680	0.7370	M	0.88979	2.995	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.994;0.999;0.999;0.999	D	0.92057	0.5653	10	0.59425	D	0.04	-17.3148	19.1747	0.93599	0.0:0.0:1.0:0.0	.	439;498;498;540	F5H754;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;ANFY1_HUMAN;.;.	V	498;439	ENSP00000343362:A498V	ENSP00000343362:A498V	A	-	2	0	ANKFY1	4035068	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	9.835000	0.99442	2.775000	0.95449	0.655000	0.94253	GCG		0.577	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376	
ANKFY1	51479	broad.mit.edu	37	17	4100823	4100823	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:4100823G>A	ENST00000341657.4	-	8	983	c.948C>T	c.(946-948)aaC>aaT	p.N316N	ANKFY1_ENST00000433651.1_Silent_p.N316N|ANKFY1_ENST00000570535.1_Silent_p.N358N|ANKFY1_ENST00000574367.1_Silent_p.N316N	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	316					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)	p.N316N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						GTGTAGCAGCGTTGACAAAGG	0.473																																					p.N316N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C948T	17						.						66.0	64.0	64.0					17																	4100823		1997	4177	6174	4047572	SO:0001819	synonymous_variant	51479	exon8			AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"""Zinc fingers, FYVE domain containing"", ""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.948C>T	17.37:g.4100823G>A		Somatic		Capture	Illumina HiSeq	Phase_I	4047572	NM_020740	A8KA65|Q5RKV4|Q9ULG5	Silent	SNP	ENST00000341657.4	37																																																																																					0.473	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376	
GRN	2896	broad.mit.edu	37	17	42428520	42428520	+	Missense_Mutation	SNP	C	C	A	rs529849967		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:42428520C>A	ENST00000053867.3	+	8	886	c.824C>A	c.(823-825)cCt>cAt	p.P275H	GRN_ENST00000589265.1_Intron|GRN_ENST00000589923.1_Intron	NM_002087.2	NP_002078.1	P28799	GRN_HUMAN	granulin	275			P -> L. {ECO:0000269|PubMed:20020531}.		blastocyst hatching (GO:0001835)|cell death (GO:0008219)|embryo implantation (GO:0007566)|positive regulation of epithelial cell proliferation (GO:0050679)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	growth factor activity (GO:0008083)|poly(A) RNA binding (GO:0044822)	p.P275H(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		ACTAAGCTGCCTGCGCACACA	0.587											OREG0024459	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P275H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C824A	17						.						95.0	92.0	93.0					17																	42428520		2203	4300	6503	39784046	SO:0001583	missense	2896	exon8			M75161	CCDS11483.1	17q21.32	2014-09-17				ENSG00000030582			4601	protein-coding gene	gene with protein product	"""progranulin"""	138945				1417868, 9826678	Standard	XM_005257253		Approved	PCDGF, PGRN, CLN11	uc002igp.1	P28799		ENST00000053867.3:c.824C>A	17.37:g.42428520C>A	ENSP00000053867:p.Pro275His	Somatic	908	Capture	Illumina HiSeq	Phase_I	39784046	NM_002087	D3DX55|P23781|P23782|P23783|P23784|Q53HQ8|Q53Y88|Q540U8|Q9BWE7|Q9H8S1|Q9UCH0	Missense_Mutation	SNP	ENST00000053867.3	37	CCDS11483.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.517694	0.44763	.	.	ENSG00000030582	ENST00000053867;ENST00000357351;ENST00000393566	T	0.71698	-0.59	4.66	3.68	0.42216	.	0.086772	0.48767	D	0.000169	T	0.71592	0.3358	L	0.34521	1.04	0.80722	D	1	D;D	0.71674	0.996;0.998	P;P	0.60012	0.754;0.867	T	0.72896	-0.4153	10	0.59425	D	0.04	-3.8852	10.78	0.46371	0.0:0.9059:0.0:0.0941	.	212;275	B4DJI2;P28799	.;GRN_HUMAN	H	275;275;95	ENSP00000053867:P275H	ENSP00000053867:P275H	P	+	2	0	GRN	39784046	0.011000	0.17503	0.803000	0.32268	0.249000	0.25844	1.223000	0.32527	1.164000	0.42652	0.491000	0.48974	CCT		0.587	GRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457766.1	NM_002087	
PLCD3	113026	broad.mit.edu	37	17	43190878	43190878	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:43190878A>G	ENST00000322765.5	-	13	2034	c.1921T>C	c.(1921-1923)Tgc>Cgc	p.C641R	PLCD3_ENST00000540511.1_5'UTR	NM_133373.3	NP_588614.1	Q8N3E9	PLCD3_HUMAN	phospholipase C, delta 3	642	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.C642R(1)|p.C641R(1)		breast(2)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	17						TGCCGCAGGCAGGCAGGTTTT	0.607																																					p.P641P												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1923C	17						.						54.0	59.0	58.0					17																	43190878		2060	4185	6245	40546404	SO:0001583	missense	113026	exon12			AC002117	CCDS74077.1	17q21	2012-04-20			ENSG00000161714	ENSG00000161714	3.1.4.11		9061	protein-coding gene	gene with protein product		608795				10702670, 9056492	Standard	NM_133373		Approved		uc002iib.3	Q8N3E9	OTTHUMG00000168029	ENST00000322765.5:c.1921T>C	17.37:g.43190878A>G	ENSP00000313731:p.Cys641Arg	Somatic		Capture	Illumina HiSeq	Phase_I	40546404	NM_133373	Q8TEC1|Q8TF37|Q96FL6	Missense_Mutation	SNP	ENST00000322765.5	37		.	.	.	.	.	.	.	.	.	.	A	13.58	2.279255	0.40294	.	.	ENSG00000161714	ENST00000322765	T	0.62639	0.01	4.84	3.76	0.43208	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.155988	0.56097	N	0.000023	T	0.52240	0.1722	.	.	.	0.52099	D	0.999947	B	0.09022	0.002	B	0.08055	0.003	T	0.51841	-0.8654	9	0.72032	D	0.01	.	9.8261	0.40912	0.9172:0.0:0.0828:0.0	.	642	Q8N3E9	PLCD3_HUMAN	R	641	ENSP00000313731:C641R	ENSP00000313731:C641R	C	-	1	0	PLCD3	40546404	0.995000	0.38212	0.977000	0.42913	0.535000	0.34838	3.651000	0.54431	0.984000	0.38629	0.454000	0.30748	TGC		0.607	PLCD3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_133373	
PLEKHM1	9842	broad.mit.edu	37	17	43555287	43555287	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:43555287A>G	ENST00000430334.3	-	3	408	c.275T>C	c.(274-276)cTc>cCc	p.L92P	PLEKHM1_ENST00000421073.2_Intron	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	92	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)	p.L92P(1)		breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					AGCTTTCAGGAGGGGCCAGAA	0.562																																					p.L92P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T275C	17						.						25.0	19.0	21.0					17																	43555287		2200	4279	6479	40911070	SO:0001583	missense	9842	exon3			X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.275T>C	17.37:g.43555287A>G	ENSP00000389913:p.Leu92Pro	Somatic		Capture	Illumina HiSeq	Phase_I	40911070	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Missense_Mutation	SNP	ENST00000430334.3	37	CCDS32671.1	.	.	.	.	.	.	.	.	.	.	A	14.09	2.430263	0.43122	.	.	ENSG00000225190	ENST00000430334	T	0.36520	1.25	5.03	5.03	0.67393	RUN (2);	0.000000	0.64402	D	0.000001	T	0.49270	0.1547	L	0.38531	1.155	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.47156	-0.9139	10	0.49607	T	0.09	.	13.7321	0.62794	1.0:0.0:0.0:0.0	.	92	Q9Y4G2	PKHM1_HUMAN	P	92	ENSP00000389913:L92P	ENSP00000389913:L92P	L	-	2	0	PLEKHM1	40911070	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.851000	0.92205	2.108000	0.64289	0.533000	0.62120	CTC		0.562	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
ITGB3	3690	broad.mit.edu	37	17	45364530	45364530	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:45364530T>C	ENST00000559488.1	+	6	888	c.872T>C	c.(871-873)aTt>aCt	p.I291T	ITGB3_ENST00000571680.1_Missense_Mutation_p.I291T|ITGB3_ENST00000560629.1_Silent_p.H279H|ITGB3_ENST00000435993.2_Missense_Mutation_p.I244T	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	291	VWFA.				activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.I291T(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	CTGGCAGGCATTGTCCAGCCT	0.483																																					p.I291T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T872C	17						.						173.0	119.0	137.0					17																	45364530		2203	4300	6503	42719529	SO:0001583	missense	3690	exon6				CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"""CD molecules"", ""Integrins"""	6156	protein-coding gene	gene with protein product	"""platelet glycoprotein IIIa"""	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.872T>C	17.37:g.45364530T>C	ENSP00000452786:p.Ile291Thr	Somatic		Capture	Illumina HiSeq	Phase_I	42719529	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	37	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.519039	0.85495	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.94723	-3.5	5.16	5.16	0.70880	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	D	0.98012	0.9345	H	0.95365	3.66	0.80722	D	1	D;D	0.76494	0.994;0.999	D;D	0.91635	0.978;0.999	D	0.99215	1.0877	10	0.87932	D	0	.	14.2503	0.66016	0.0:0.0:0.0:1.0	.	291;291	P05106;Q2YFE1	ITB3_HUMAN;.	T	291;244	ENSP00000407801:I244T	ENSP00000262017:I291T	I	+	2	0	C17orf57	42719529	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.071000	0.62044	0.459000	0.35465	ATT		0.483	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
NPEPPS	9520	broad.mit.edu	37	17	45656851	45656851	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:45656851C>T	ENST00000322157.4	+	4	751	c.514C>T	c.(514-516)Cgc>Tgc	p.R172C	NPEPPS_ENST00000525037.1_3'UTR|NPEPPS_ENST00000530173.1_Missense_Mutation_p.R168C|NPEPPS_ENST00000544660.1_Missense_Mutation_p.R128C	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	172					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R172C(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						TGGAGAGGTGCGCTATGCTGC	0.358																																					p.R172C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C514T	17						.						32.0	31.0	31.0					17																	45656851		1809	4069	5878	43011850	SO:0001583	missense	9520	exon4			Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"""puromycin-sensitive aminopeptidase"", ""metalloproteinase MP100"""	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.514C>T	17.37:g.45656851C>T	ENSP00000320324:p.Arg172Cys	Somatic		Capture	Illumina HiSeq	Phase_I	43011850	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Missense_Mutation	SNP	ENST00000322157.4	37	CCDS45721.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789374	0.90367	.	.	ENSG00000141279	ENST00000525007;ENST00000530173;ENST00000322157;ENST00000539572;ENST00000544660	T;T;T;T	0.04809	4.11;4.11;4.11;3.55	5.29	5.29	0.74685	Peptidase M1, membrane alanine aminopeptidase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.28167	0.0695	M	0.89658	3.05	0.80722	D	1	D;B;P	0.76494	0.999;0.426;0.947	D;B;B	0.65987	0.94;0.116;0.381	T	0.14755	-1.0461	10	0.66056	D	0.02	.	18.9359	0.92584	0.0:1.0:0.0:0.0	.	172;168;172	A6NEC2;E9PLK3;P55786	PSAL_HUMAN;.;PSA_HUMAN	C	159;168;172;159;128	ENSP00000437019:R159C;ENSP00000433287:R168C;ENSP00000320324:R172C;ENSP00000442461:R128C	ENSP00000320324:R172C	R	+	1	0	NPEPPS	43011850	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.809000	0.86057	2.487000	0.83934	0.585000	0.79938	CGC		0.358	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310	
ABI3	51225	broad.mit.edu	37	17	47293944	47293944	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:47293944G>A	ENST00000225941.1	+	2	667	c.169G>A	c.(169-171)Gca>Aca	p.A57T	ABI3_ENST00000419580.2_Missense_Mutation_p.A57T	NM_001135186.1|NM_016428.2	NP_001128658.1|NP_057512	Q9P2A4	ABI3_HUMAN	ABI family, member 3	57					cellular component movement (GO:0006928)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|membrane (GO:0016020)		p.A57T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	12			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)			CACTACCCAGGCACTGGCCAG	0.657										HNSCC(55;0.14)																											p.A57T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G169A	17						.						32.0	29.0	30.0					17																	47293944		2203	4300	6503	44648943	SO:0001583	missense	51225	exon2			AB037886	CCDS11546.1, CCDS45725.1	17q21.3	2011-03-04	2008-09-12		ENSG00000108798	ENSG00000108798			29859	protein-coding gene	gene with protein product		606363				10978530, 11956071	Standard	NM_001135186		Approved	NESH, SSH3BP3	uc002iop.1	Q9P2A4	OTTHUMG00000161306	ENST00000225941.1:c.169G>A	17.37:g.47293944G>A	ENSP00000225941:p.Ala57Thr	Somatic		Capture	Illumina HiSeq	Phase_I	44648943	NM_001135186	C9IZN8|Q9H0P6	Missense_Mutation	SNP	ENST00000225941.1	37	CCDS11546.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769692	0.90020	.	.	ENSG00000108798	ENST00000225941;ENST00000419580	D;D	0.92048	-2.96;-2.96	5.35	3.21	0.36854	.	0.080528	0.48767	D	0.000164	D	0.90321	0.6972	L	0.27053	0.805	0.45515	D	0.998476	D;D	0.59767	0.986;0.976	P;P	0.56163	0.793;0.626	D	0.90587	0.4534	10	0.87932	D	0	-23.7593	11.1713	0.48573	0.0:0.0:0.523:0.477	.	57;57	Q9P2A4-2;Q9P2A4	.;ABI3_HUMAN	T	57	ENSP00000225941:A57T;ENSP00000406651:A57T	ENSP00000225941:A57T	A	+	1	0	ABI3	44648943	1.000000	0.71417	0.994000	0.49952	0.933000	0.57130	5.046000	0.64226	1.220000	0.43490	0.563000	0.77884	GCA		0.657	ABI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364475.1	NM_016428	
COL1A1	1277	broad.mit.edu	37	17	48268238	48268238	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:48268238G>A	ENST00000225964.5	-	33	2401	c.2283C>T	c.(2281-2283)ggC>ggT	p.G761G		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	761	Triple-helical region.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)	p.G761G(3)	COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	GACCACGGACGCCATCTTTGC	0.587			T	"""PDGFB, USP6"""	"""dermatofibrosarcoma protuberans, aneurysmal bone cyst """		Osteogenesis imperfecta																														p.G761G			Dom	yes		17	17q21.31-q22	1277	"""collagen, type I, alpha 1"""	yes	M	.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C2283T	17						.						119.0	93.0	102.0					17																	48268238		2203	4300	6503	45623237	SO:0001819	synonymous_variant	1277	exon33			Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"""Collagens"""	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.2283C>T	17.37:g.48268238G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45623237	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Silent	SNP	ENST00000225964.5	37	CCDS11561.1																																																																																				0.587	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2		
XYLT2	64132	broad.mit.edu	37	17	48435581	48435581	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:48435581G>T	ENST00000017003.2	+	10	2004	c.1955G>T	c.(1954-1956)tGg>tTg	p.W652L	XYLT2_ENST00000507602.1_Intron	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	652					chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)	p.W652L(1)		endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					GGCACTGATTGGGACCCCAAA	0.622																																					p.W652L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1955T	17						.						18.0	18.0	18.0					17																	48435581		2198	4288	6486	45790580	SO:0001583	missense	64132	exon10			AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"""protein xylosyltransferase 2"""	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.1955G>T	17.37:g.48435581G>T	ENSP00000017003:p.Trp652Leu	Somatic		Capture	Illumina HiSeq	Phase_I	45790580	NM_022167	Q6UY41|Q86V00	Missense_Mutation	SNP	ENST00000017003.2	37	CCDS11563.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.365810	0.82463	.	.	ENSG00000015532	ENST00000017003	T	0.50277	0.75	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.69584	0.3127	M	0.77313	2.365	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.73575	-0.3939	10	0.56958	D	0.05	-17.8235	17.6889	0.88263	0.0:0.0:1.0:0.0	.	652	Q9H1B5	XYLT2_HUMAN	L	652	ENSP00000017003:W652L	ENSP00000017003:W652L	W	+	2	0	XYLT2	45790580	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	9.544000	0.98092	2.420000	0.82092	0.561000	0.74099	TGG		0.622	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167	
CACNA1G	8913	broad.mit.edu	37	17	48650181	48650181	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:48650181A>G	ENST00000359106.5	+	6	1013	c.1013A>G	c.(1012-1014)gAc>gGc	p.D338G	CACNA1G_ENST00000429973.2_Missense_Mutation_p.D338G|CACNA1G_ENST00000514717.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000358244.5_Missense_Mutation_p.D338G|CACNA1G_ENST00000502264.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000512389.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000352832.5_Missense_Mutation_p.D338G|CACNA1G_ENST00000503485.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000354983.4_Missense_Mutation_p.D338G|CACNA1G_ENST00000515765.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000507510.2_Missense_Mutation_p.D338G|CACNA1G_ENST00000360761.4_Missense_Mutation_p.D338G|CACNA1G_ENST00000416767.4_Missense_Mutation_p.D338G|CACNA1G_ENST00000514079.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000507609.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000510115.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000442258.2_Missense_Mutation_p.D338G|CACNA1G_ENST00000505165.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000515165.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000507336.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000513689.2_Missense_Mutation_p.D338G|CACNA1G_ENST00000515411.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000507896.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000514181.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000510366.1_Missense_Mutation_p.D338G|CACNA1G_ENST00000513964.1_Missense_Mutation_p.D338G	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	338					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)	p.D338G(3)		breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	ATCAACTTTGACAACATTGGC	0.597																																					p.D338G												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.A1013G	17						.						74.0	80.0	78.0					17																	48650181		2057	4181	6238	46005180	SO:0001583	missense	8913	exon6			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.1013A>G	17.37:g.48650181A>G	ENSP00000352011:p.Asp338Gly	Somatic		Capture	Illumina HiSeq	Phase_I	46005180	NM_198382	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	a	25.2	4.608852	0.87258	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97480	-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4;-4.4	5.55	5.55	0.83447	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98213	0.9409	M	0.74881	2.28	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;1.0;0.999;0.999;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.998;1.0;1.0;1.0;0.999;1.0;0.999;1.0;1.0;0.997	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.996;1.0;1.0;0.998;1.0;0.999;0.998;1.0;0.998;1.0;1.0;1.0;1.0;1.0;0.998;0.999;0.955;0.999;1.0;1.0;0.995;1.0;0.998;0.997;0.999;0.925	D	0.99410	1.0930	10	0.87932	D	0	.	15.6856	0.77409	1.0:0.0:0.0:0.0	.	338;338;338;338;338;338;338;338;338;338;338;338;338;338;338;338;338;338;338;338;338;338;338;338;338;338	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	G	338	ENSP00000353990:D338G;ENSP00000339302:D338G;ENSP00000392390:D338G;ENSP00000347078:D338G;ENSP00000409759:D338G;ENSP00000425522:D338G;ENSP00000426261:D338G;ENSP00000425451:D338G;ENSP00000422407:D338G;ENSP00000426814:D338G;ENSP00000427238:D338G;ENSP00000423112:D338G;ENSP00000420918:D338G;ENSP00000426172:D338G;ENSP00000423045:D338G;ENSP00000427173:D338G;ENSP00000426098:D338G;ENSP00000425698:D338G;ENSP00000426232:D338G;ENSP00000423317:D338G;ENSP00000350979:D338G;ENSP00000352011:D338G;ENSP00000414388:D338G;ENSP00000423155:D338G;ENSP00000422268:D338G;ENSP00000421518:D338G	ENSP00000339302:D338G	D	+	2	0	CACNA1G	46005180	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.882000	0.92420	2.113000	0.64589	0.418000	0.28097	GAC		0.597	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
RNF167	26001	broad.mit.edu	37	17	4848060	4848060	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:4848060T>C	ENST00000262482.6	+	10	1458	c.802T>C	c.(802-804)Tgc>Cgc	p.C268R	RNF167_ENST00000571816.1_Missense_Mutation_p.C268R|RNF167_ENST00000572430.1_Missense_Mutation_p.C268R|RNF167_ENST00000575111.1_Missense_Mutation_p.C268R|RNF167_ENST00000576229.1_Missense_Mutation_p.C233R	NM_015528.1	NP_056343.1	Q9H6Y7	RN167_HUMAN	ring finger protein 167	268					negative regulation of cell cycle (GO:0045786)|protein polyubiquitination (GO:0000209)	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.C268R(1)		endometrium(1)|large_intestine(2)|lung(1)	4						CCGGAAGACCTGCCCCATTTG	0.612																																					p.C268R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T802C	17						.						107.0	107.0	107.0					17																	4848060		2203	4300	6503	4788805	SO:0001583	missense	26001	exon10			AL050060	CCDS11060.1	17p13.3	2013-02-21			ENSG00000108523	ENSG00000108523		"""RING-type (C3HC4) zinc fingers"""	24544	protein-coding gene	gene with protein product		610431				23129617, 23353890	Standard	NM_015528		Approved	DKFZP566H073	uc002fzs.3	Q9H6Y7	OTTHUMG00000099397	ENST00000262482.6:c.802T>C	17.37:g.4848060T>C	ENSP00000262482:p.Cys268Arg	Somatic		Capture	Illumina HiSeq	Phase_I	4788805	NM_015528	D3DTK8|Q6XYE0|Q8NDC1|Q9Y3V1	Missense_Mutation	SNP	ENST00000262482.6	37	CCDS11060.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.413744	0.83449	.	.	ENSG00000108523	ENST00000262482	D	0.99809	-6.86	5.17	5.17	0.71159	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.050514	0.85682	D	0.000000	D	0.99898	0.9951	H	0.99794	4.785	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.998;1.0	D	0.96201	0.9145	10	0.87932	D	0	-0.2297	13.0078	0.58715	0.0:0.0:0.0:1.0	.	76;268	Q9Y4L6;Q9H6Y7	.;RN167_HUMAN	R	268	ENSP00000262482:C268R	ENSP00000262482:C268R	C	+	1	0	RNF167	4788805	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.130000	0.77235	2.176000	0.68965	0.455000	0.32223	TGC		0.612	RNF167-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216854.3	NM_015528	
CAMTA2	23125	broad.mit.edu	37	17	4876132	4876132	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:4876132A>G	ENST00000348066.3	-	15	2558	c.2435T>C	c.(2434-2436)cTa>cCa	p.L812P	RP5-1050D4.2_ENST00000430920.1_RNA|CAMTA2_ENST00000572543.1_Missense_Mutation_p.L817P|CAMTA2_ENST00000361571.5_Missense_Mutation_p.L811P|CAMTA2_ENST00000358183.4_Missense_Mutation_p.L812P|CAMTA2_ENST00000381311.5_Missense_Mutation_p.L814P|CAMTA2_ENST00000414043.3_Missense_Mutation_p.L835P	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	812					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)	p.L812P(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						CTGTCTCTGTAGTTCCTCAAG	0.612																																					p.L812P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2435C	17						.						102.0	109.0	107.0					17																	4876132		2203	4300	6503	4816856	SO:0001583	missense	23125	exon15			AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.2435T>C	17.37:g.4876132A>G	ENSP00000321813:p.Leu812Pro	Somatic		Capture	Illumina HiSeq	Phase_I	4816856	NM_015099	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	37	CCDS11063.1	.	.	.	.	.	.	.	.	.	.	A	19.16	3.773754	0.69992	.	.	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.39056	2.31;1.34;1.1;1.34;1.12	4.79	4.79	0.61399	.	0.000000	0.56097	D	0.000023	T	0.58119	0.2100	L	0.57536	1.79	0.80722	D	1	D;D;D;D;D	0.76494	0.997;0.999;0.999;0.998;0.997	D;D;D;D;D	0.85130	0.987;0.997;0.996;0.991;0.994	T	0.60637	-0.7224	10	0.66056	D	0.02	-9.8935	10.6951	0.45894	1.0:0.0:0.0:0.0	.	788;835;814;812;811	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	P	835;814;811;812;812	ENSP00000412886:L835P;ENSP00000370712:L814P;ENSP00000354828:L811P;ENSP00000350910:L812P;ENSP00000321813:L812P	ENSP00000321813:L812P	L	-	2	0	CAMTA2	4816856	1.000000	0.71417	0.995000	0.50966	0.685000	0.39939	8.928000	0.92853	2.034000	0.60081	0.519000	0.50382	CTA		0.612	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099	
ZFP3	124961	broad.mit.edu	37	17	4995093	4995093	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:4995093C>T	ENST00000318833.3	+	2	630	c.294C>T	c.(292-294)agC>agT	p.S98S		NM_153018.2	NP_694563.1	Q96NJ6	ZFP3_HUMAN	ZFP3 zinc finger protein	98					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S98S(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(3)|prostate(1)	20						GCAGTCCCAGCCCAAATCTGG	0.443																																					p.S98S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C294T	17						.						50.0	51.0	51.0					17																	4995093		2203	4300	6503	4935817	SO:0001819	synonymous_variant	124961	exon2			BX647638	CCDS11067.1	17p13.2	2013-01-08	2012-11-27		ENSG00000180787	ENSG00000180787		"""Zinc fingers, C2H2-type"""	12861	protein-coding gene	gene with protein product		194480	"""zinc finger protein homologous to Zfp-3 in mouse"", ""zinc finger protein 3 homolog (mouse)"""				Standard	NM_153018		Approved	FLJ30726, ZNF752	uc002gaq.3	Q96NJ6		ENST00000318833.3:c.294C>T	17.37:g.4995093C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4935817	NM_153018	A5PLL4	Silent	SNP	ENST00000318833.3	37	CCDS11067.1																																																																																				0.443	ZFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438979.1	NM_153018	
CACNA1G	8913	broad.mit.edu	37	17	48695268	48695268	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:48695268C>T	ENST00000359106.5	+	30	5204	c.5204C>T	c.(5203-5205)aCg>aTg	p.T1735M	CACNA1G_ENST00000429973.2_Missense_Mutation_p.T1717M|CACNA1G_ENST00000514717.1_Missense_Mutation_p.T1678M|CACNA1G_ENST00000358244.5_Missense_Mutation_p.T1701M|CACNA1G_ENST00000502264.1_Missense_Mutation_p.T1712M|CACNA1G_ENST00000512389.1_Missense_Mutation_p.T1724M|CACNA1G_ENST00000352832.5_Missense_Mutation_p.T1701M|CACNA1G_ENST00000503485.1_Missense_Mutation_p.T1701M|CACNA1G_ENST00000354983.4_Missense_Mutation_p.T1701M|CACNA1G_ENST00000515765.1_Missense_Mutation_p.T1724M|CACNA1G_ENST00000507510.2_Missense_Mutation_p.T1735M|CACNA1G_ENST00000360761.4_Missense_Mutation_p.T1712M|CACNA1G_ENST00000514079.1_Missense_Mutation_p.T1742M|CACNA1G_ENST00000507609.1_Splice_Site_p.T1735M|CACNA1G_ENST00000510115.1_Missense_Mutation_p.T1701M|CACNA1G_ENST00000442258.2_Missense_Mutation_p.T1694M|CACNA1G_ENST00000505165.1_Missense_Mutation_p.T1735M|CACNA1G_ENST00000515165.1_Missense_Mutation_p.T1735M|CACNA1G_ENST00000507336.1_Missense_Mutation_p.T1724M|CACNA1G_ENST00000513689.2_Missense_Mutation_p.T1690M|CACNA1G_ENST00000515411.1_Missense_Mutation_p.T1717M|CACNA1G_ENST00000507896.1_Missense_Mutation_p.T1724M|CACNA1G_ENST00000514181.1_Splice_Site_p.T1717M|CACNA1G_ENST00000510366.1_Missense_Mutation_p.T1683M|CACNA1G_ENST00000513964.1_Missense_Mutation_p.T1690M	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1735					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)	p.T1701M(1)|p.T1735M(1)		breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CTGCTGGACACGGTGATGCAG	0.657																																					p.T1712M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C5135T	17						.						47.0	51.0	49.0					17																	48695268		2001	4173	6174	46050267	SO:0001583	missense	8913	exon29			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.5204C>T	17.37:g.48695268C>T	ENSP00000352011:p.Thr1735Met	Somatic		Capture	Illumina HiSeq	Phase_I	46050267	NM_198382	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	c	20.3	3.965610	0.74131	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98602	-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-4.91;-5.02;-5.02;-4.91;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02	5.08	5.08	0.68730	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99184	0.9717	M	0.91140	3.18	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.997;1.0;1.0;0.999;1.0;1.0;0.999;1.0;0.999;1.0;1.0;0.999;1.0;1.0;0.998;0.999;0.999;0.998;1.0;0.999;0.998;0.999;1.0;0.998;0.993	D	0.99360	1.0917	10	0.87932	D	0	.	18.4894	0.90842	0.0:1.0:0.0:0.0	.	1678;1690;1683;1717;1690;1717;1742;1701;1735;1724;1735;1712;1724;1724;1717;1724;1735;1712;1735;1701;1694;1701;1712;1735;1701	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.	M	1712;1701;1701;1694;1712;1724;1690;1678;1683;1701;1735;1724;1690;1735;1701;1735;1717;1724;1742;1701;1735;1717;1717;1735;1724	ENSP00000353990:T1712M;ENSP00000339302:T1701M;ENSP00000347078:T1701M;ENSP00000409759:T1694M;ENSP00000425522:T1712M;ENSP00000426261:T1724M;ENSP00000425451:T1690M;ENSP00000422407:T1678M;ENSP00000426814:T1683M;ENSP00000427238:T1701M;ENSP00000423112:T1735M;ENSP00000420918:T1724M;ENSP00000426172:T1690M;ENSP00000423045:T1735M;ENSP00000427173:T1701M;ENSP00000426098:T1735M;ENSP00000425698:T1717M;ENSP00000426232:T1724M;ENSP00000423317:T1742M;ENSP00000350979:T1701M;ENSP00000352011:T1735M;ENSP00000414388:T1717M;ENSP00000423155:T1717M;ENSP00000422268:T1735M;ENSP00000421518:T1724M	ENSP00000339302:T1701M	T	+	2	0	CACNA1G	46050267	1.000000	0.71417	0.993000	0.49108	0.999000	0.98932	6.089000	0.71384	2.362000	0.80069	0.655000	0.94253	ACG		0.657	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
EPX	8288	broad.mit.edu	37	17	56274588	56274588	+	Missense_Mutation	SNP	C	C	T	rs573827983	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:56274588C>T	ENST00000225371.5	+	7	1200	c.1090C>T	c.(1090-1092)Cgc>Tgc	p.R364C		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	364			R -> H (in dbSNP:rs35232062). {ECO:0000269|Ref.2}.		defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.R364C(1)		breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	CCTCACCAACCGCTCGGCGCG	0.632																																					p.R364C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1090T	17						.						64.0	65.0	65.0					17																	56274588		2203	4300	6503	53629587	SO:0001583	missense	8288	exon7			M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.1090C>T	17.37:g.56274588C>T	ENSP00000225371:p.Arg364Cys	Somatic		Capture	Illumina HiSeq	Phase_I	53629587	NM_000502	Q4TVP3	Missense_Mutation	SNP	ENST00000225371.5	37	CCDS11602.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.547976	0.65311	.	.	ENSG00000121053	ENST00000225371	T	0.73469	-0.75	4.86	4.86	0.63082	.	0.210370	0.41823	D	0.000814	D	0.83599	0.5289	M	0.78456	2.415	0.45995	D	0.9988	D	0.89917	1.0	D	0.64776	0.929	D	0.85005	0.0902	10	0.62326	D	0.03	-10.3123	11.0265	0.47748	0.186:0.814:0.0:0.0	.	364	P11678	PERE_HUMAN	C	364	ENSP00000225371:R364C	ENSP00000225371:R364C	R	+	1	0	EPX	53629587	0.001000	0.12720	0.980000	0.43619	0.944000	0.59088	0.470000	0.22084	2.408000	0.81797	0.462000	0.41574	CGC		0.632	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502	
RNF43	54894	broad.mit.edu	37	17	56492691	56492691	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:56492691A>G	ENST00000584437.1	-	1	2203	c.248T>C	c.(247-249)aTg>aCg	p.M83T	RNF43_ENST00000407977.2_Missense_Mutation_p.M83T|RNF43_ENST00000577716.1_Missense_Mutation_p.M83T|RNF43_ENST00000583753.1_Missense_Mutation_p.M83T|RNF43_ENST00000500597.2_Missense_Mutation_p.M83T|RNF43_ENST00000581868.1_Intron|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000580014.1_5'Flank			Q68DV7	RNF43_HUMAN	ring finger protein 43	83					negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.M83T(1)		NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ACTTGCCTGCATTAATTTTCC	0.383																																					p.M83T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T248C	17						.						58.0	58.0	58.0					17																	56492691		2203	4300	6503	53847690	SO:0001583	missense	54894	exon2				CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.248T>C	17.37:g.56492691A>G	ENSP00000463069:p.Met83Thr	Somatic		Capture	Illumina HiSeq	Phase_I	53847690	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	A	17.39	3.377956	0.61735	.	.	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.08458	3.26;3.09	5.27	5.27	0.74061	.	0.265792	0.33732	N	0.004602	T	0.11537	0.0281	N	0.08118	0	0.42137	D	0.991493	D;D	0.67145	0.996;0.993	P;P	0.61477	0.889;0.777	T	0.36212	-0.9757	10	0.51188	T	0.08	-13.8568	14.669	0.68929	1.0:0.0:0.0:0.0	.	83;83	Q68DV7-2;Q68DV7	.;RNF43_HUMAN	T	83	ENSP00000385328:M83T;ENSP00000441969:M83T	ENSP00000385328:M83T	M	-	2	0	RNF43	53847690	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.449000	0.73473	2.115000	0.64714	0.533000	0.62120	ATG		0.383	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
TRIM37	4591	broad.mit.edu	37	17	57058099	57058099	+	IGR	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:57058099T>A	ENST00000393066.3	-	0	3622				PPM1E_ENST00000308249.2_Missense_Mutation_p.S659T	NM_001005207.2	NP_001005207.1	O94972	TRI37_HUMAN	tripartite motif containing 37						aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S659T(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					ACAGTTCAAATCCCCGGGAAA	0.423									Mulibrey Nanism																												p.S659T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1975A	17						.						149.0	159.0	155.0					17																	57058099		2203	4300	6503	54412881	SO:0001628	intergenic_variant	22843	exon7	Familial Cancer Database	Perheentupa syndrome	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	7523	protein-coding gene	gene with protein product	"""RING-B-box-coiled-coil protein"""	605073	"""tripartite motif-containing 37"""	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972			17.37:g.57058099T>A		Somatic		Capture	Illumina HiSeq	Phase_I	54412881	NM_014906	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000393066.3	37	CCDS45746.1	.	.	.	.	.	.	.	.	.	.	T	8.620	0.891176	0.17613	.	.	ENSG00000175175	ENST00000308249;ENST00000443121	T	0.19394	2.15	5.67	4.56	0.56223	.	1.935240	0.02312	N	0.072228	T	0.17066	0.0410	N	0.19112	0.55	0.19575	N	0.999962	B;B	0.22211	0.007;0.066	B;B	0.25506	0.042;0.061	T	0.12993	-1.0526	10	0.36615	T	0.2	-0.6384	6.3045	0.21131	0.0:0.1047:0.1599:0.7354	.	668;659	Q8WY54-3;Q8WY54-2	.;.	T	659;510	ENSP00000312411:S659T	ENSP00000312411:S659T	S	+	1	0	PPM1E	54412881	0.961000	0.32948	0.979000	0.43373	0.747000	0.42532	1.131000	0.31406	2.169000	0.68431	0.459000	0.35465	TCC		0.423	TRIM37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445928.1	NM_015294	
EFCAB3	146779	broad.mit.edu	37	17	60460394	60460394	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:60460394A>G	ENST00000305286.3	+	2	132	c.54A>G	c.(52-54)gtA>gtG	p.V18V	RNU7-52P_ENST00000516172.1_RNA|EFCAB3_ENST00000450662.2_Silent_p.V70V	NM_173503.3	NP_775774.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	18							calcium ion binding (GO:0005509)	p.V18V(1)		cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)	17			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			TAACAAAAGTACCCATCTCCC	0.323																																					p.V18V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A54G	17						.						73.0	66.0	68.0					17																	60460394		2203	4300	6503	57814126	SO:0001819	synonymous_variant	146779	exon2			AK098684	CCDS11632.1, CCDS45751.1	17q23.3	2013-01-10			ENSG00000172421	ENSG00000172421		"""EF-hand domain containing"""	26379	protein-coding gene	gene with protein product						12477932	Standard	NM_173503		Approved	FLJ25818	uc010wpc.2	Q8N7B9	OTTHUMG00000179175	ENST00000305286.3:c.54A>G	17.37:g.60460394A>G		Somatic		Capture	Illumina HiSeq	Phase_I	57814126	NM_173503	J3KQM8	Silent	SNP	ENST00000305286.3	37	CCDS11632.1																																																																																				0.323	EFCAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379114.1	NM_173503	
KCNH6	81033	broad.mit.edu	37	17	61611628	61611628	+	Missense_Mutation	SNP	G	G	A	rs560196120		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:61611628G>A	ENST00000583023.1	+	5	1068	c.1057G>A	c.(1057-1059)Gcc>Acc	p.A353T	KCNH6_ENST00000314672.5_Missense_Mutation_p.A353T|KCNH6_ENST00000580652.1_Missense_Mutation_p.A353T|KCNH6_ENST00000581784.1_Missense_Mutation_p.A353T|KCNH6_ENST00000456941.2_Missense_Mutation_p.A353T	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	353					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.A353T(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	CATGGTGGCCGCCATCCCTTT	0.622																																					p.A353T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1057A	17						.						139.0	105.0	117.0					17																	61611628		2203	4300	6503	58965360	SO:0001583	missense	81033	exon5			AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.1057G>A	17.37:g.61611628G>A	ENSP00000463533:p.Ala353Thr	Somatic		Capture	Illumina HiSeq	Phase_I	58965360	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	37	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.703581	0.48412	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	D;D	0.99818	-6.92;-6.92	4.14	4.14	0.48551	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99594	0.9853	L	0.39085	1.19	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;0.998;1.0	D;D;D;D;D	0.97110	1.0;0.983;1.0;0.992;0.996	D	0.97321	0.9944	10	0.87932	D	0	.	16.6049	0.84826	0.0:0.0:1.0:0.0	.	230;353;353;353;353	B4DPJ3;B4DKC0;Q9H252-2;Q9H252;Q9H252-3	.;.;.;KCNH6_HUMAN;.	T	353	ENSP00000318212:A353T;ENSP00000396900:A353T	ENSP00000318212:A353T	A	+	1	0	KCNH6	58965360	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	9.657000	0.98554	2.121000	0.65114	0.305000	0.20034	GCC		0.622	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779	
DCAF7	10238	broad.mit.edu	37	17	61666493	61666493	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:61666493G>A	ENST00000310827.4	+	8	1205	c.988G>A	c.(988-990)Gcc>Acc	p.A330T	DCAF7_ENST00000415273.2_Missense_Mutation_p.A130T|DCAF7_ENST00000577702.1_3'UTR|DCAF7_ENST00000431926.1_Intron	NM_005828.3	NP_005819.3	P61962	DCAF7_HUMAN	DDB1 and CUL4 associated factor 7	330					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)		p.A329T(2)		endometrium(6)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	18						CGACTGGATCGCCATCTGCTA	0.567																																					p.R330H												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G989A	17						.						104.0	102.0	103.0					17																	61666493		2053	4194	6247	59020225	SO:0001583	missense	10238	exon7			U94747	CCDS74127.1	17q23.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000136485		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30915	protein-coding gene	gene with protein product	"""seven-WD-repeat protein of the AN11 family-1"", ""human anthocyanin"""	605973	"""WD repeat domain 68"""	WDR68		9192870, 20940704	Standard	NM_005828		Approved	HAN11, SWAN-1	uc002jbc.4	P61962		ENST00000310827.4:c.988G>A	17.37:g.61666493G>A	ENSP00000308344:p.Ala330Thr	Somatic		Capture	Illumina HiSeq	Phase_I	59020225	NM_005828	B4E039|D3DU14|O15491|Q9DAE4	Missense_Mutation	SNP	ENST00000310827.4	37		.	.	.	.	.	.	.	.	.	.	G	32	5.189176	0.94923	.	.	ENSG00000136485	ENST00000310827;ENST00000415273	T;T	0.67171	-0.25;1.18	5.31	5.31	0.75309	WD40/YVTN repeat-like-containing domain (1);	0.105483	0.64402	D	0.000004	T	0.74253	0.3692	.	.	.	0.80722	D	1	D;D	0.61080	0.989;0.978	B;P	0.49922	0.436;0.626	T	0.78043	-0.2358	9	0.87932	D	0	-26.4677	19.1619	0.93537	0.0:0.0:1.0:0.0	.	130;330	B4E039;P61962	.;DCAF7_HUMAN	T	330;130	ENSP00000308344:A330T;ENSP00000403920:A130T	ENSP00000308344:A330T	A	+	1	0	DCAF7	59020225	1.000000	0.71417	0.982000	0.44146	0.992000	0.81027	9.657000	0.98554	2.758000	0.94735	0.563000	0.77884	GCC		0.567	DCAF7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005828	
MAP3K3	4215	broad.mit.edu	37	17	61769665	61769665	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:61769665G>A	ENST00000361733.3	+	15	1858	c.1538G>A	c.(1537-1539)cGc>cAc	p.R513H	MAP3K3_ENST00000577395.1_Missense_Mutation_p.R509H|MAP3K3_ENST00000579585.1_Missense_Mutation_p.R544H|MAP3K3_ENST00000361357.3_Missense_Mutation_p.R544H|MAP3K3_ENST00000584573.1_Missense_Mutation_p.R540H	NM_002401.3	NP_002392.2	Q99759	M3K3_HUMAN	mitogen-activated protein kinase kinase kinase 3	513	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)	p.R513H(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	28						GCCAGCAAACGCCTGCAGACG	0.612																																					p.R513H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1538A	17						.						68.0	66.0	67.0					17																	61769665		2203	4300	6503	59123397	SO:0001583	missense	4215	exon15			U78876	CCDS32701.1, CCDS32702.1	17q	2011-06-09				ENSG00000198909		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6855	protein-coding gene	gene with protein product	"""MAP/ERK kinase kinase 3"", ""MAPK/ERK kinase kinase 3"""	602539		MEKK3		9006902	Standard	NM_002401		Approved	MAPKKK3	uc002jbf.3	Q99759		ENST00000361733.3:c.1538G>A	17.37:g.61769665G>A	ENSP00000354485:p.Arg513His	Somatic		Capture	Illumina HiSeq	Phase_I	59123397	NM_002401	B2RCW2|D3DU15|Q5BKZ6|Q8N3I9	Missense_Mutation	SNP	ENST00000361733.3	37	CCDS32702.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.416175	0.83449	.	.	ENSG00000198909	ENST00000361357;ENST00000361733	T;T	0.65549	-0.16;-0.16	4.99	2.9	0.33743	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.107942	0.64402	D	0.000007	T	0.67795	0.2931	L	0.37800	1.135	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;0.989;0.988	D;D;P;P	0.87578	0.998;0.998;0.861;0.846	T	0.61187	-0.7113	10	0.14656	T	0.56	.	15.254	0.73571	0.0:0.2662:0.7338:0.0	.	509;481;513;544	Q1PBM3;Q96HN9;Q99759;Q99759-2	.;.;M3K3_HUMAN;.	H	544;513	ENSP00000354927:R544H;ENSP00000354485:R513H	ENSP00000354927:R544H	R	+	2	0	MAP3K3	59123397	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.813000	0.99286	0.569000	0.29329	0.556000	0.70494	CGC		0.612	MAP3K3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443867.1	NM_002401	
DDX42	11325	broad.mit.edu	37	17	61892935	61892935	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:61892935C>T	ENST00000578681.1	+	17	2516	c.1915C>T	c.(1915-1917)Cgg>Tgg	p.R639W	DDX42_ENST00000359353.5_Missense_Mutation_p.R520W|DDX42_ENST00000457800.2_Missense_Mutation_p.R639W|DDX42_ENST00000583590.1_Missense_Mutation_p.R639W|DDX42_ENST00000389924.2_Missense_Mutation_p.R639W	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	639					protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.R639W(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						TGCCTGGTTTCGGAAATCTCG	0.473																																					p.R639W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1915T	17						.						98.0	95.0	96.0					17																	61892935		2203	4300	6503	59246667	SO:0001583	missense	11325	exon16			BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"""DEAD-boxes"""	18676	protein-coding gene	gene with protein product	"""splicing factor 3b, subunit 8"""	613369	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"""			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.1915C>T	17.37:g.61892935C>T	ENSP00000464050:p.Arg639Trp	Somatic		Capture	Illumina HiSeq	Phase_I	59246667	NM_203499	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	37	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.295161	0.81025	.	.	ENSG00000198231	ENST00000389924;ENST00000457800;ENST00000359353	T;T	0.24151	1.87;1.87	5.26	4.29	0.51040	.	0.000000	0.85682	D	0.000000	T	0.50343	0.1610	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.55692	-0.8101	10	0.87932	D	0	-11.7417	13.3868	0.60801	0.0:0.9238:0.0:0.0762	.	185;639	B3KV84;Q86XP3	.;DDX42_HUMAN	W	639;639;356	ENSP00000374574:R639W;ENSP00000390121:R639W	ENSP00000352308:R356W	R	+	1	2	DDX42	59246667	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.228000	0.58619	1.362000	0.46000	0.467000	0.42956	CGG		0.473	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372	
HELZ	9931	broad.mit.edu	37	17	65162674	65162674	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:65162674A>G	ENST00000358691.5	-	15	1981	c.1815T>C	c.(1813-1815)taT>taC	p.Y605Y	HELZ_ENST00000580168.1_Silent_p.Y605Y	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	605						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.Y605Y(1)		NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TGTCTAGTGCATAGTGCATTT	0.383																																					p.Y605Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1815C	17						.						133.0	124.0	127.0					17																	65162674		1880	4122	6002	62593136	SO:0001819	synonymous_variant	9931	exon15			D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"""Zinc fingers, CCCH-type domain containing"""	16878	protein-coding gene	gene with protein product	"""down-regulated in human cancers"""	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.1815T>C	17.37:g.65162674A>G		Somatic		Capture	Illumina HiSeq	Phase_I	62593136	NM_014877	I6L9H4	Silent	SNP	ENST00000358691.5	37	CCDS42374.1																																																																																				0.383	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877	
PRKAR1A	5573	broad.mit.edu	37	17	66524030	66524030	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:66524030T>C	ENST00000589228.1	+	8	886	c.758T>C	c.(757-759)gTc>gCc	p.V253A	PRKAR1A_ENST00000586397.1_Missense_Mutation_p.V253A|PRKAR1A_ENST00000392711.1_Missense_Mutation_p.V253A|PRKAR1A_ENST00000536854.2_Missense_Mutation_p.V253A|PRKAR1A_ENST00000588188.2_Missense_Mutation_p.V253A|PRKAR1A_ENST00000358598.2_Missense_Mutation_p.V253A	NM_001276289.1|NM_001278433.1	NP_001263218.1|NP_001265362.1	P10644	KAP0_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, alpha	253					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cardiac muscle cell proliferation (GO:0060038)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|female meiotic division (GO:0007143)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sarcomere organization (GO:0045214)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)	p.V253A(1)		adrenal_gland(4)|breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|soft_tissue(2)|stomach(2)|testis(1)|thyroid(2)|upper_aerodigestive_tract(1)	31	Breast(10;1.64e-13)					CTTAGTAAAGTCTCTATTTTA	0.363			"""T, Mis, N, F, S"""	RET	papillary thyroid	"""myxoma, endocrine, papillary thyroid"""			Primary Pigmented Nodular Adrenocortical Disease, Familial;Carney Complex;Cardiac Myxomas, Familial Clustering of																												p.V253A	Ovarian(167;637 1670 33025 39608 46699 51856)	yes	"""Dom, Rec"""	yes	Carney complex	17	17q23-q24	5573	"""protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1)"""		"""E, M"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T758C	17						.						174.0	177.0	176.0					17																	66524030		2203	4300	6503	64035625	SO:0001583	missense	5573	exon8	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2;Carney syndrome, NAME syndrome, LAMB syndrome, Familial Myxoma syndrome;		CCDS11678.1, CCDS62307.1	17q24.2	2014-09-17	2012-07-31		ENSG00000108946	ENSG00000108946	2.7.11.1		9388	protein-coding gene	gene with protein product	"""Carney complex type 1"""	188830	"""tissue specific extinguisher 1"""	PRKAR1, TSE1		3479018, 10973256	Standard	NM_212471		Approved	CNC1	uc002jhg.4	P10644	OTTHUMG00000180128	ENST00000589228.1:c.758T>C	17.37:g.66524030T>C	ENSP00000464977:p.Val253Ala	Somatic		Capture	Illumina HiSeq	Phase_I	64035625	NM_212472	K7ER48|Q567S7	Missense_Mutation	SNP	ENST00000589228.1	37	CCDS11678.1	.	.	.	.	.	.	.	.	.	.	T	31	5.104096	0.94245	.	.	ENSG00000108946	ENST00000358598;ENST00000392711;ENST00000392710;ENST00000536854	T;T;T	0.72282	-0.64;-0.64;-0.64	5.74	5.74	0.90152	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.90133	0.6917	H	0.97918	4.105	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.77557	0.99;0.99	D	0.93734	0.7044	10	0.87932	D	0	-28.8816	16.0347	0.80617	0.0:0.0:0.0:1.0	.	253;253	B2R5T5;P10644	.;KAP0_HUMAN	A	253	ENSP00000351410:V253A;ENSP00000376475:V253A;ENSP00000445625:V253A	ENSP00000351410:V253A	V	+	2	0	PRKAR1A	64035625	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	8.040000	0.89188	2.183000	0.69458	0.528000	0.53228	GTC		0.363	PRKAR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449884.1		
ABCA6	23460	broad.mit.edu	37	17	67124900	67124900	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:67124900G>T	ENST00000284425.2	-	8	1153	c.979C>A	c.(979-981)Ctc>Atc	p.L327I		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	327					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.L327I(1)		breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					AAATTGGTGAGGACAGCTTTC	0.398																																					p.L327I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C979A	17						.						116.0	112.0	114.0					17																	67124900		2203	4300	6503	64636495	SO:0001583	missense	23460	exon8			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"""ATP binding cassette transporters / subfamily A"""	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.979C>A	17.37:g.67124900G>T	ENSP00000284425:p.Leu327Ile	Somatic		Capture	Illumina HiSeq	Phase_I	64636495	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	37	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	G	17.16	3.319927	0.60634	.	.	ENSG00000154262	ENST00000284425	D	0.82984	-1.67	5.61	3.6	0.41247	.	0.176734	0.26844	N	0.022220	D	0.83538	0.5276	M	0.76727	2.345	0.80722	D	1	B	0.31318	0.319	B	0.41691	0.364	T	0.79482	-0.1785	10	0.40728	T	0.16	.	7.8104	0.29228	0.0832:0.0:0.7577:0.1591	.	327	Q8N139	ABCA6_HUMAN	I	327	ENSP00000284425:L327I	ENSP00000284425:L327I	L	-	1	0	ABCA6	64636495	0.976000	0.34144	0.986000	0.45419	0.990000	0.78478	1.605000	0.36815	0.820000	0.34516	0.655000	0.94253	CTC		0.398	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284	
BCL6B	255877	broad.mit.edu	37	17	6928447	6928447	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:6928447A>G	ENST00000293805.5	+	5	909	c.817A>G	c.(817-819)Acc>Gcc	p.T273A		NM_181844.3	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B	273					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T273A(1)		skin(1)	1						TCCAGCCAGTACCCCCTACCT	0.552																																					p.T273A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A817G	17						.						95.0	104.0	102.0					17																	6928447		1946	4151	6097	6869171	SO:0001583	missense	255877	exon5			AI672318	CCDS42248.1	17p13.1	2014-06-10	2010-04-14		ENSG00000161940	ENSG00000161940		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	1002	protein-coding gene	gene with protein product		608992	"""zinc finger protein 62"", ""B-cell CLL/lymphoma 6, member B (zinc finger protein)"""	ZNF62		9632807	Standard	NM_181844		Approved	ZBTB28, BAZF	uc010clt.1	Q8N143	OTTHUMG00000177882	ENST00000293805.5:c.817A>G	17.37:g.6928447A>G	ENSP00000293805:p.Thr273Ala	Somatic		Capture	Illumina HiSeq	Phase_I	6869171	NM_181844	Q6PCB4	Missense_Mutation	SNP	ENST00000293805.5	37	CCDS42248.1	.	.	.	.	.	.	.	.	.	.	A	3.608	-0.080155	0.07141	.	.	ENSG00000161940	ENST00000293805	T	0.07444	3.19	4.79	3.72	0.42706	.	1.338990	0.04219	N	0.333217	T	0.06554	0.0168	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31194	-0.9952	10	0.33141	T	0.24	.	7.2578	0.26187	0.9034:0.0:0.0966:0.0	.	273	Q8N143	BCL6B_HUMAN	A	273	ENSP00000293805:T273A	ENSP00000293805:T273A	T	+	1	0	BCL6B	6869171	0.003000	0.15002	0.007000	0.13788	0.708000	0.40852	0.890000	0.28295	1.163000	0.42636	0.533000	0.62120	ACC		0.552	BCL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439455.2	NM_181844	
SSTR2	6752	broad.mit.edu	37	17	71166287	71166287	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:71166287G>A	ENST00000357585.2	+	2	1198	c.829G>A	c.(829-831)Gtt>Att	p.V277I	RP11-143K11.5_ENST00000580671.1_RNA|SSTR2_ENST00000315332.2_Missense_Mutation_p.V277I	NM_001050.2	NP_001041.1	P30874	SSR2_HUMAN	somatostatin receptor 2	277					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|peristalsis (GO:0030432)|regulation of muscle contraction (GO:0006937)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|somatostatin receptor activity (GO:0004994)	p.V277I(1)		endometrium(2)|large_intestine(5)|lung(2)|prostate(2)	11			LUSC - Lung squamous cell carcinoma(166;0.197)		Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	CATATTCAACGTTTCTTCCGT	0.512																																					p.V277I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G829A	17						.						224.0	184.0	198.0					17																	71166287		2203	4300	6503	68677882	SO:0001583	missense	6752	exon2				CCDS11691.1	17q24	2012-08-08				ENSG00000180616		"""GPCR / Class A : Somatostatin receptors"""	11331	protein-coding gene	gene with protein product		182452				8449518	Standard	NM_001050		Approved		uc002jje.3	P30874		ENST00000357585.2:c.829G>A	17.37:g.71166287G>A	ENSP00000350198:p.Val277Ile	Somatic		Capture	Illumina HiSeq	Phase_I	68677882	NM_001050	A8K3Y0|B2R9P7|Q4VBP0|Q96GE0|Q96TF2|Q9BWH1	Missense_Mutation	SNP	ENST00000357585.2	37	CCDS11691.1	.	.	.	.	.	.	.	.	.	.	G	1.159	-0.644430	0.03531	.	.	ENSG00000180616	ENST00000357585;ENST00000315332	T;T	0.34667	1.35;1.35	5.49	5.49	0.81192	GPCR, rhodopsin-like superfamily (1);	0.061338	0.64402	D	0.000004	T	0.16428	0.0395	N	0.02247	-0.625	0.58432	D	0.999993	B	0.19935	0.04	B	0.20184	0.028	T	0.17410	-1.0370	10	0.02654	T	1	.	18.9738	0.92725	0.0:0.0:1.0:0.0	.	277	P30874	SSR2_HUMAN	I	277	ENSP00000350198:V277I;ENSP00000326616:V277I	ENSP00000326616:V277I	V	+	1	0	SSTR2	68677882	1.000000	0.71417	0.928000	0.36995	0.640000	0.38277	5.802000	0.69122	2.577000	0.86979	0.655000	0.94253	GTT		0.512	SSTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441633.1		
SDK2	54549	broad.mit.edu	37	17	71364616	71364616	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:71364616G>A	ENST00000392650.3	-	37	5097	c.5097C>T	c.(5095-5097)agC>agT	p.S1699S	SDK2_ENST00000388726.3_Silent_p.S1680S|SDK2_ENST00000410094.1_5'UTR	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1699	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.S1699S(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						AGGCGGCCACGCTGACCATGT	0.652																																					p.S1699S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5097T	17						.						56.0	42.0	47.0					17																	71364616		2203	4300	6503	68876211	SO:0001819	synonymous_variant	54549	exon37			AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.5097C>T	17.37:g.71364616G>A		Somatic		Capture	Illumina HiSeq	Phase_I	68876211	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	37	CCDS45769.1																																																																																				0.652	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
PHF23	79142	broad.mit.edu	37	17	7139478	7139478	+	Silent	SNP	C	C	T	rs569508322	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:7139478C>T	ENST00000320316.3	-	4	994	c.768G>A	c.(766-768)gaG>gaA	p.E256E	PHF23_ENST00000570753.1_5'Flank|DVL2_ENST00000575458.1_5'Flank|PHF23_ENST00000454255.2_Silent_p.E252E|PHF23_ENST00000576955.1_Silent_p.E126E|PHF23_ENST00000571362.1_Silent_p.E189E|DVL2_ENST00000005340.5_5'Flank	NM_001284518.1|NM_024297.2	NP_001271447.1|NP_077273.2	Q9BUL5	PHF23_HUMAN	PHD finger protein 23	256	Poly-Glu.						zinc ion binding (GO:0008270)	p.E256E(1)		breast(4)|kidney(2)|large_intestine(6)|lung(3)	15						cttcttcttcctcttcctcct	0.602																																					p.E256E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G768A	17						.						67.0	77.0	74.0					17																	7139478		2014	4193	6207	7080202	SO:0001819	synonymous_variant	79142	exon4			AK122791	CCDS42250.1, CCDS67143.1, CCDS67144.1	17p13.1	2014-08-13			ENSG00000040633	ENSG00000040633		"""Zinc fingers, PHD-type"""	28428	protein-coding gene	gene with protein product		612910					Standard	NM_024297		Approved	MGC2941, FLJ16355	uc002gfa.3	Q9BUL5	OTTHUMG00000177972	ENST00000320316.3:c.768G>A	17.37:g.7139478C>T		Somatic		Capture	Illumina HiSeq	Phase_I	7080202	NM_024297	A1DZ74|B3KVH8|B4DLK6|D3DTN4|Q8IZK0|Q96HG7|Q9H5X0	Silent	SNP	ENST00000320316.3	37	CCDS42250.1																																																																																				0.602	PHF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440047.1	NM_024297	
GRIN2C	2905	broad.mit.edu	37	17	72846459	72846459	+	Silent	SNP	G	G	A	rs138691824	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:72846459G>A	ENST00000293190.5	-	6	1523	c.1377C>T	c.(1375-1377)atC>atT	p.I459I	GRIN2C_ENST00000347612.4_Silent_p.I459I|GRIN2C_ENST00000578159.1_5'Flank	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	459					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)	p.I459I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGAGGATGTCGATGCAGAATC	0.602													G|||	11	0.00219649	0.0061	0.0043	5008	,	,		19831	0.0		0.0	False		,,,				2504	0.0				p.I459I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1377T	17						.	G		27,4379	32.6+/-62.9	0,27,2176	142.0	130.0	134.0		1377	0.1	1.0	17	dbSNP_134	134	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GRIN2C	NM_000835.3		0,28,6475	AA,AG,GG		0.0116,0.6128,0.2153		459/1234	72846459	28,12978	2203	4300	6503	70358054	SO:0001819	synonymous_variant	2905	exon6				CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.1377C>T	17.37:g.72846459G>A		Somatic		Capture	Illumina HiSeq	Phase_I	70358054	NM_000835	B2RTT1	Silent	SNP	ENST00000293190.5	37	CCDS32724.1																																																																																				0.602	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1		
KIAA0195	9772	broad.mit.edu	37	17	73489025	73489025	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:73489025C>T	ENST00000314256.7	+	16	2322	c.1928C>T	c.(1927-1929)gCc>gTc	p.A643V	KIAA0195_ENST00000579208.1_Missense_Mutation_p.A294V|KIAA0195_ENST00000375248.5_Missense_Mutation_p.A653V	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	643						integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.A643V(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			ACTCCTGGGGCCAAGGAGCTT	0.607																																					p.A643V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1928T	17						.						75.0	81.0	79.0					17																	73489025		2203	4300	6503	71000620	SO:0001583	missense	9772	exon16				CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.1928C>T	17.37:g.73489025C>T	ENSP00000313885:p.Ala643Val	Somatic		Capture	Illumina HiSeq	Phase_I	71000620	NM_014738	O75536|Q86XF1	Missense_Mutation	SNP	ENST00000314256.7	37	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.895312	0.52121	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	D;D	0.89746	-2.56;-2.56	5.73	4.76	0.60689	.	0.000000	0.85682	D	0.000000	D	0.91422	0.7293	L	0.45422	1.42	0.80722	D	1	D;D;D	0.76494	0.996;0.999;0.999	D;D;D	0.71414	0.914;0.973;0.94	D	0.89736	0.3930	10	0.27082	T	0.32	-33.516	16.1586	0.81681	0.1346:0.8654:0.0:0.0	.	653;653;643	B4DGC6;C9JL75;Q12767	.;.;K0195_HUMAN	V	643;653	ENSP00000313885:A643V;ENSP00000364397:A653V	ENSP00000313885:A643V	A	+	2	0	KIAA0195	71000620	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.710000	0.84655	1.420000	0.47138	0.561000	0.74099	GCC		0.607	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738	
ITGB4	3691	broad.mit.edu	37	17	73723793	73723793	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:73723793G>A	ENST00000200181.3	+	5	513	c.326G>A	c.(325-327)cGt>cAt	p.R109H	ITGB4_ENST00000450894.3_Missense_Mutation_p.R109H|ITGB4_ENST00000449880.2_Missense_Mutation_p.R109H|ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000339591.3_Missense_Mutation_p.R109H|ITGB4_ENST00000579662.1_Missense_Mutation_p.R109H	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	109					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)	p.R109H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTGCGGGTCCGTCTGCGGCCC	0.632																																					p.R109H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G326A	17						.						37.0	34.0	35.0					17																	73723793		2203	4300	6503	71235388	SO:0001583	missense	3691	exon5				CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.326G>A	17.37:g.73723793G>A	ENSP00000200181:p.Arg109His	Somatic		Capture	Illumina HiSeq	Phase_I	71235388	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	12.10	1.837827	0.32513	.	.	ENSG00000132470	ENST00000450894;ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.92647	-3.08;-3.08;-3.08	4.92	2.75	0.32379	Integrin beta subunit, N-terminal (2);	0.603956	0.15782	N	0.244880	D	0.93442	0.7908	L	0.53729	1.69	0.35732	D	0.81803	P;D;D;D	0.62365	0.727;0.989;0.984;0.991	B;P;P;P	0.58454	0.145;0.666;0.839;0.839	D	0.94968	0.8114	10	0.62326	D	0.03	.	14.1365	0.65291	0.0:0.0:0.7297:0.2703	.	109;109;109;109	P16144-5;P16144-3;A0AVL6;P16144	.;.;.;ITB4_HUMAN	H	25;109;109;109	ENSP00000200181:R109H;ENSP00000344079:R109H;ENSP00000400217:R109H	ENSP00000200181:R109H	R	+	2	0	ITGB4	71235388	0.935000	0.31712	0.738000	0.30950	0.738000	0.42128	2.190000	0.42630	1.175000	0.42826	0.655000	0.94253	CGT		0.632	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
CDK3	1018	broad.mit.edu	37	17	73997958	73997958	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:73997958G>T	ENST00000425876.2	+	2	208	c.120G>T	c.(118-120)gaG>gaT	p.E40D	TEN1-CDK3_ENST00000567351.1_RNA|CDK3_ENST00000448471.1_Missense_Mutation_p.E40D			Q00526	CDK3_HUMAN	cyclin-dependent kinase 3	40	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|G0 to G1 transition (GO:0045023)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.E40D(1)		central_nervous_system(1)	1						CTTGCAGGGAGATGGAGGGGG	0.592																																					p.E40D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G120T	17						.						54.0	46.0	49.0					17																	73997958		2203	4300	6503	71509553	SO:0001583	missense	1018	exon3			X66357	CCDS11736.1	17q25.1	2012-09-20			ENSG00000250506	ENSG00000250506		"""Cyclin-dependent kinases"""	1772	protein-coding gene	gene with protein product		123828				1639063	Standard	NM_001258		Approved		uc010dgt.3	Q00526	OTTHUMG00000154861	ENST00000425876.2:c.120G>T	17.37:g.73997958G>T	ENSP00000410561:p.Glu40Asp	Somatic		Capture	Illumina HiSeq	Phase_I	71509553	NM_001258		Missense_Mutation	SNP	ENST00000425876.2	37	CCDS11736.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.121879	0.37436	.	.	ENSG00000250506	ENST00000448471;ENST00000425876	T;T	0.67523	-0.27;-0.27	4.68	1.47	0.22746	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	D	0.000080	T	0.48995	0.1531	N	0.21545	0.675	0.40950	D	0.984533	B	0.23854	0.092	B	0.25987	0.065	T	0.42682	-0.9437	10	0.51188	T	0.08	-9.8139	8.4277	0.32739	0.2699:0.0:0.7301:0.0	.	40	Q00526	CDK3_HUMAN	D	40	ENSP00000400088:E40D;ENSP00000410561:E40D	ENSP00000410561:E40D	E	+	3	2	CDK3	71509553	0.987000	0.35691	0.867000	0.34043	0.682000	0.39822	0.507000	0.22675	0.475000	0.27415	0.561000	0.74099	GAG		0.592	CDK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337389.2	NM_001258	
EVPL	2125	broad.mit.edu	37	17	74011613	74011613	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:74011613C>T	ENST00000301607.3	-	15	2060	c.1807G>A	c.(1807-1809)Gcc>Acc	p.A603T	EVPL_ENST00000586740.1_Missense_Mutation_p.A625T	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	603	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.A603T(1)		breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						AGCTGCAGGGCAGCGGGGCCC	0.637																																					p.A603T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1807A	17						.						63.0	57.0	59.0					17																	74011613		2203	4300	6503	71523208	SO:0001583	missense	2125	exon15			U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.1807G>A	17.37:g.74011613C>T	ENSP00000301607:p.Ala603Thr	Somatic		Capture	Illumina HiSeq	Phase_I	71523208	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.482166	0.44147	.	.	ENSG00000167880	ENST00000301607	T	0.38077	1.16	5.15	3.17	0.36434	.	0.148104	0.47093	N	0.000259	T	0.25606	0.0623	N	0.25380	0.74	0.38981	D	0.958952	B;B	0.15930	0.008;0.015	B;B	0.17433	0.006;0.018	T	0.06110	-1.0845	10	0.37606	T	0.19	-14.525	11.6669	0.51379	0.0:0.8557:0.0:0.1443	.	625;603	B7ZLH8;Q92817	.;EVPL_HUMAN	T	603	ENSP00000301607:A603T	ENSP00000301607:A603T	A	-	1	0	EVPL	71523208	0.090000	0.21635	0.566000	0.28421	0.673000	0.39480	0.493000	0.22451	0.586000	0.29626	0.455000	0.32223	GCC		0.637	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
POLR2A	5430	broad.mit.edu	37	17	7416220	7416220	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:7416220A>G	ENST00000322644.6	+	28	5133	c.4734A>G	c.(4732-4734)tcA>tcG	p.S1578S		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1578					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)	p.S1578S(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				CAGGTCCCTCAAGCCCCTACA	0.607																																					p.S1578S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A4734G	17						.						79.0	90.0	86.0					17																	7416220		2203	4300	6503	7356944	SO:0001819	synonymous_variant	5430	exon28					17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.4734A>G	17.37:g.7416220A>G		Somatic		Capture	Illumina HiSeq	Phase_I	7356944	NM_000937	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																				0.607	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
PRPSAP1	5635	broad.mit.edu	37	17	74326632	74326632	+	Splice_Site	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:74326632T>C	ENST00000446526.3	-	5	1024	c.579A>G	c.(577-579)gaA>gaG	p.E193E	PRPSAP1_ENST00000324684.4_Splice_Site_p.E90E	NM_002766.2	NP_002757.2	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 1	164					negative regulation of kinase activity (GO:0033673)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)	p.E164E(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17						GGTTCCTCACTTCTTCCTGGA	0.418																																					p.E193E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A579G	17						.						81.0	78.0	79.0					17																	74326632		2203	4300	6503	71838227	SO:0001630	splice_region_variant	5635	exon5			D61391	CCDS11743.2	17q24-q25	2008-07-18			ENSG00000161542	ENSG00000161542			9466	protein-coding gene	gene with protein product		601249				8660991	Standard	NM_002766		Approved	PAP39	uc010wta.1	Q14558	OTTHUMG00000155969	ENST00000446526.3:c.579+1A>G	17.37:g.74326632T>C		Somatic		Capture	Illumina HiSeq	Phase_I	71838227	NM_002766	B2R6M4|Q96H06	Silent	SNP	ENST00000446526.3	37	CCDS11743.2																																																																																				0.418	PRPSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342480.2	NM_002766	Silent
C1QTNF1	114897	broad.mit.edu	37	17	77043952	77043952	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:77043952C>T	ENST00000339142.2	+	5	1183	c.628C>T	c.(628-630)Cac>Tac	p.H210Y	C1QTNF1_ENST00000583904.1_Missense_Mutation_p.H210Y|C1QTNF1_ENST00000354124.3_Missense_Mutation_p.H220Y|C1QTNF1_ENST00000580454.1_Missense_Mutation_p.H210Y|C1QTNF1_ENST00000581774.1_Missense_Mutation_p.H210Y|C1QTNF1_ENST00000579760.1_Missense_Mutation_p.H210Y|C1QTNF1_ENST00000578229.1_Missense_Mutation_p.H128Y|C1QTNF1_ENST00000392445.2_Missense_Mutation_p.H210Y|C1QTNF1_ENST00000582625.1_3'UTR|C1QTNF1_ENST00000311661.4_Missense_Mutation_p.H128Y|C1QTNF1_ENST00000580474.1_Missense_Mutation_p.H210Y	NM_198593.3	NP_940995.1	Q9BXJ1	C1QT1_HUMAN	C1q and tumor necrosis factor related protein 1	210	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase B signaling (GO:0051897)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|regulation of glucose metabolic process (GO:0010906)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)	p.H128Y(1)|p.H210Y(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(2)	14			BRCA - Breast invasive adenocarcinoma(99;0.0294)|OV - Ovarian serous cystadenocarcinoma(97;0.201)			GACCTACCTGCACATCATGAA	0.567																																					p.H210Y												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C628T	17						.						165.0	139.0	148.0					17																	77043952		2203	4300	6503	74555547	SO:0001583	missense	114897	exon4			AF329840	CCDS11761.1, CCDS11762.1	17q25	2012-07-02			ENSG00000173918	ENSG00000173918			14324	protein-coding gene	gene with protein product	"""G protein coupled receptor interacting protein"""	610365				12409230	Standard	NM_198593		Approved	CTRP1, ZSIG37, GIP, FLJ90694	uc002jwp.4	Q9BXJ1	OTTHUMG00000177533	ENST00000339142.2:c.628C>T	17.37:g.77043952C>T	ENSP00000340864:p.His210Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	74555547	NM_198593	Q6ZMH6|Q96NF2|Q9GZR4	Missense_Mutation	SNP	ENST00000339142.2	37	CCDS11761.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.133782	0.77662	.	.	ENSG00000173918	ENST00000339142;ENST00000311661;ENST00000354124;ENST00000392444;ENST00000392445	T;T;T	0.75050	-0.9;-0.9;-0.9	4.71	4.71	0.59529	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.069211	0.56097	N	0.000029	D	0.87200	0.6118	M	0.83603	2.65	0.80722	D	1	P;D;D	0.89917	0.885;0.997;1.0	P;D;D	0.83275	0.833;0.968;0.996	D	0.89321	0.3640	10	0.66056	D	0.02	.	17.2569	0.87060	0.0:1.0:0.0:0.0	.	220;220;210	A8K7L9;Q6ZMH6;Q9BXJ1	.;.;C1QT1_HUMAN	Y	210;128;220;210;220	ENSP00000340864:H210Y;ENSP00000311265:H128Y;ENSP00000343230:H220Y	ENSP00000311265:H128Y	H	+	1	0	C1QTNF1	74555547	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.725000	0.84808	2.159000	0.67721	0.561000	0.74099	CAC		0.567	C1QTNF1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437388.2	NM_030968	
DNAH2	146754	broad.mit.edu	37	17	7669764	7669764	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:7669764C>T	ENST00000572933.1	+	22	5100	c.3640C>T	c.(3640-3642)Cag>Tag	p.Q1214*	DNAH2_ENST00000389173.2_Nonsense_Mutation_p.Q1214*			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1214	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.Q1214*(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CAAGATCGAGCAGCCACCCTC	0.567																																					p.Q1214X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C3640T	17						.						69.0	63.0	65.0					17																	7669764		2203	4300	6503	7610489	SO:0001587	stop_gained	146754	exon21			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.3640C>T	17.37:g.7669764C>T	ENSP00000458355:p.Gln1214*	Somatic		Capture	Illumina HiSeq	Phase_I	7610489	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Nonsense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	C	44	10.752175	0.99461	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	.	.	.	5.93	5.93	0.95920	.	0.131468	0.52532	D	0.000072	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	17.2605	0.87068	0.0:1.0:0.0:0.0	.	.	.	.	X	1214	.	ENSP00000353818:Q1214X	Q	+	1	0	DNAH2	7610489	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.769000	0.68865	2.815000	0.96918	0.561000	0.74099	CAG		0.567	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
RNF213	57674	broad.mit.edu	37	17	78341906	78341906	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:78341906C>T	ENST00000582970.1	+	44	12261	c.12118C>T	c.(12118-12120)Cca>Tca	p.P4040S	RNF213_ENST00000508628.2_Missense_Mutation_p.P4089S|CTD-2047H16.4_ENST00000572151.1_RNA|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.P2113S	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4040					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P2113S(1)|p.P4089S(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AACTGCCTTGCCAGACGAATT	0.517																																					p.P4089S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C12265T	17						.						156.0	149.0	151.0					17																	78341906		2203	4300	6503	75956501	SO:0001583	missense	57674	exon45			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.12118C>T	17.37:g.78341906C>T	ENSP00000464087:p.Pro4040Ser	Somatic		Capture	Illumina HiSeq	Phase_I	75956501	NM_020914	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.237360	0.58886	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.15834	2.39	4.67	4.67	0.58626	Zinc finger, RING/FYVE/PHD-type (1);	0.470395	0.22908	N	0.054170	T	0.23133	0.0559	L	0.37507	1.11	0.09310	N	0.999997	D;D	0.56521	0.976;0.963	P;P	0.56398	0.797;0.551	T	0.08432	-1.0722	10	0.18710	T	0.47	.	12.8981	0.58111	0.0:0.823:0.177:0.0	.	4089;2113	C9JCP4;Q63HN8	.;RN213_HUMAN	S	4040;4089;2113	ENSP00000338218:P2113S	ENSP00000338218:P2113S	P	+	1	0	RNF213	75956501	0.281000	0.24258	0.770000	0.31555	0.175000	0.22909	1.689000	0.37700	2.419000	0.82065	0.655000	0.94253	CCA		0.517	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
SGSM2	9905	broad.mit.edu	37	17	2282478	2282480	+	In_Frame_Del	DEL	CAT	CAT	-	rs143690160		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	CAT	CAT	CAT	-	CAT	CAT	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:2282478_2282480delCAT	ENST00000426855.2	+	22	3088_3090	c.2913_2915delCAT	c.(2911-2916)gacatc>gac	p.I973del	RP1-59D14.5_ENST00000574290.1_RNA|SGSM2_ENST00000268989.3_In_Frame_Del_p.I1018del|SGSM2_ENST00000574563.1_In_Frame_Del_p.I973del|RP1-59D14.5_ENST00000573007.1_RNA	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	973					late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)	p.I1018delI(1)		biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		ACTTCACTGACATCATCAAGTTT	0.581																																					p.971_972del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.2913_2915del	17						.																																			2229230	SO:0001651	inframe_deletion	9905	exon22			BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"""Small G protein signaling modulators"""	29026	protein-coding gene	gene with protein product		611418	"""RUN and TBC1 domain containing 1"""	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.2913_2915delCAT	17.37:g.2282481_2282483delCAT	ENSP00000415107:p.Ile973del	Somatic		Capture	Illumina HiSeq	Phase_I	2229228	NM_001098509	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	In_Frame_Del	DEL	ENST00000426855.2	37	CCDS45570.1																																																																																				0.581	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853	
CNTROB	116840	broad.mit.edu	37	17	7851028	7851028	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:7851028delT	ENST00000563694.1	+	14	3058	c.2133delT	c.(2131-2133)aatfs	p.N711fs	CNTROB_ENST00000565740.1_Frame_Shift_Del_p.N711fs|CNTROB_ENST00000380255.3_3'UTR|CNTROB_ENST00000380262.3_Frame_Shift_Del_p.N711fs	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	711	Pro-rich.|Required for centrosome localization.				centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)	p.L713fs*27(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				GCCTCAAGAATTTTTTGCACC	0.547																																					p.N711fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2133delT	17						.						79.0	86.0	84.0					17																	7851028		2203	4300	6503	7791753	SO:0001589	frameshift_variant	116840	exon14			AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"""centrobin"""	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.2133delT	17.37:g.7851028delT	ENSP00000456335:p.Asn711fs	Somatic		Capture	Illumina HiSeq	Phase_I	7791753	NM_053051	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Frame_Shift_Del	DEL	ENST00000563694.1	37	CCDS11126.1																																																																																				0.547	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051	
ALOXE3	59344	broad.mit.edu	37	17	8007505	8007505	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:8007505T>C	ENST00000448843.2	-	14	2053	c.1713A>G	c.(1711-1713)ggA>ggG	p.G571G	ALOXE3_ENST00000380149.1_Silent_p.G727G|ALOXE3_ENST00000318227.3_Silent_p.G703G	NM_021628.2	NP_067641.2	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3	571	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|fat cell differentiation (GO:0045444)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|sensory perception of pain (GO:0019233)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)	hepoxilin A3 synthase activity (GO:0051120)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)	p.G571G(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	31						TCACCATCTCTCCTGGGGTGC	0.592																																					p.G703G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2109G	17						.						100.0	83.0	89.0					17																	8007505		2203	4300	6503	7948230	SO:0001819	synonymous_variant	59344	exon14			AJ269499	CCDS11130.1, CCDS54084.1	17p13.1	2009-07-10			ENSG00000179148	ENSG00000179148	1.13.11.-	"""Arachidonate lipoxygenases"""	13743	protein-coding gene	gene with protein product		607206					Standard	NM_021628		Approved	eLOX3, E-LOX	uc010vuo.2	Q9BYJ1	OTTHUMG00000108179	ENST00000448843.2:c.1713A>G	17.37:g.8007505T>C		Somatic		Capture	Illumina HiSeq	Phase_I	7948230	NM_001165960	B2R981|B7Z3W0|Q3ZB74|Q9H4F2|Q9HC22	Silent	SNP	ENST00000448843.2	37	CCDS11130.1																																																																																				0.592	ALOXE3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441475.1		
ARHGEF15	22899	broad.mit.edu	37	17	8218491	8218491	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:8218491C>A	ENST00000361926.3	+	6	1266	c.1156C>A	c.(1156-1158)Cca>Aca	p.P386T	ARHGEF15_ENST00000421050.1_Missense_Mutation_p.P386T|AC135178.7_ENST00000458568.1_RNA	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	386					negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.P386T(1)		breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						ACCCACCTTCCCACGACCCCC	0.637																																					p.P386T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1156A	17						.						34.0	34.0	34.0					17																	8218491		2203	4300	6503	8159216	SO:0001583	missense	22899	exon6			AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"""Rho guanine nucleotide exchange factors"""	15590	protein-coding gene	gene with protein product	"""Rho guanine exchange factor (GEF) 15"""	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.1156C>A	17.37:g.8218491C>A	ENSP00000355026:p.Pro386Thr	Somatic		Capture	Illumina HiSeq	Phase_I	8159216	NM_173728	A8K6G1|Q8N449|Q9H8B4	Missense_Mutation	SNP	ENST00000361926.3	37	CCDS11139.1	.	.	.	.	.	.	.	.	.	.	c	1.124	-0.654542	0.03480	.	.	ENSG00000198844	ENST00000361926;ENST00000455564;ENST00000421050	T;T	0.69561	-0.41;-0.41	4.88	-9.76	0.00503	.	1.188700	0.05815	N	0.614760	T	0.34542	0.0901	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.16070	-1.0415	10	0.14252	T	0.57	-0.0112	1.0494	0.01576	0.224:0.1943:0.1383:0.4434	.	386;386	D3DTR7;O94989	.;ARHGF_HUMAN	T	386;176;386	ENSP00000355026:P386T;ENSP00000412505:P386T	ENSP00000355026:P386T	P	+	1	0	ARHGEF15	8159216	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-1.078000	0.03413	-1.573000	0.01659	-0.311000	0.09066	CCA		0.637	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728	
USP43	124739	broad.mit.edu	37	17	9613302	9613302	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:9613302T>C	ENST00000285199.7	+	13	2137	c.2041T>C	c.(2041-2043)Tgg>Cgg	p.W681R	USP43_ENST00000570475.1_Missense_Mutation_p.W676R|USP43_ENST00000570827.2_3'UTR	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	681	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.W682R(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						GGATGGCCAGTGGTACAGTTA	0.522																																					p.W681R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2041C	17						.						82.0	81.0	81.0					17																	9613302		1975	4166	6141	9554027	SO:0001583	missense	124739	exon13			AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"""Ubiquitin-specific peptidases"""	20072	protein-coding gene	gene with protein product			"""ubiquitin specific protease 43"""			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.2041T>C	17.37:g.9613302T>C	ENSP00000285199:p.Trp681Arg	Somatic		Capture	Illumina HiSeq	Phase_I	9554027	NM_153210	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	ENST00000285199.7	37	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.230712	0.79688	.	.	ENSG00000154914	ENST00000285199	T	0.21031	2.03	5.51	5.51	0.81932	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.61751	0.2372	H	0.97291	3.975	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	T	0.75938	-0.3141	10	0.87932	D	0	-17.1063	13.8717	0.63624	0.0:0.0:0.0:1.0	.	676;370;681;193	B7ZVX5;Q70EL4-3;Q70EL4;Q70EL4-2	.;.;UBP43_HUMAN;.	R	681	ENSP00000285199:W681R	ENSP00000285199:W681R	W	+	1	0	USP43	9554027	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	7.491000	0.81471	2.221000	0.72209	0.528000	0.53228	TGG		0.522	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210	
TRPV2	51393	broad.mit.edu	37	17	16330835	16330835	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:16330835delG	ENST00000338560.7	+	8	1723	c.1324delG	c.(1324-1326)gggfs	p.G443fs	AC093484.4_ENST00000441875.1_RNA|TRPV2_ENST00000577397.1_Frame_Shift_Del_p.G13fs	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	443					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)	p.I444fs*23(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TATCCTGCTAGGGGGGATCTA	0.567																																					p.G442fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1324delG	17						.						81.0	66.0	71.0					17																	16330835		2203	4300	6503	16271560	SO:0001589	frameshift_variant	51393	exon8			AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.1324delG	17.37:g.16330835delG	ENSP00000342222:p.Gly443fs	Somatic		Capture	Illumina HiSeq	Phase_I	16271560	NM_016113	A6NML2|A8K0Z0|Q9Y670	Frame_Shift_Del	DEL	ENST00000338560.7	37	CCDS32576.1																																																																																				0.567	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113	
KRT18P55	284085	broad.mit.edu	37	17	26604400	26604400	+	RNA	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:26604400T>G	ENST00000577198.1	-	0	561				AC061975.8_ENST00000385109.1_RNA	NR_028334.1				keratin 18 pseudogene 55																		AGGACTCAGGTTTTGACGGCC	0.443																																					.												.	.	0			.	17						.						54.0	54.0	54.0					17																	26604400		1942	4149	6091	23628527			284085	.					17q11.2	2013-06-25			ENSG00000265480	ENSG00000265480			26874	pseudogene	pseudogene							Standard	NR_028334		Approved		uc002has.3		OTTHUMG00000179422		17.37:g.26604400T>G		Somatic		Capture	Illumina HiSeq	Phase_I	23628527	.		Missense_Mutation	SNP	ENST00000577198.1	37																																																																																					0.443	KRT18P55-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000446194.1	NR_028334	
CORO6	84940	broad.mit.edu	37	17	27948270	27948270	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:27948270delC	ENST00000445145.2	-	1	171	c.170delG	c.(169-171)ggtfs	p.G57fs	CORO6_ENST00000580212.1_Frame_Shift_Del_p.G57fs|CORO6_ENST00000345068.5_Frame_Shift_Del_p.G57fs|CORO6_ENST00000577909.1_Intron|RP11-68I3.2_ENST00000581474.1_RNA|CORO6_ENST00000584969.1_Frame_Shift_Del_p.G57fs|CORO6_ENST00000388767.3_Frame_Shift_Del_p.G57fs|RP11-68I3.10_ENST00000582367.1_RNA			Q6QEF8	CORO6_HUMAN	coronin 6	57	Poly-Gly.				actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)	actin filament binding (GO:0051015)	p.G57fs*99(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(2)	14						GATGAAGGCACCCCCGCCTCC	0.592																																					p.G57fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.170delG	17						.						54.0	60.0	58.0					17																	27948270		2172	4287	6459	24972396	SO:0001589	frameshift_variant	84940	exon1			AF193039	CCDS11252.2	17q11.2	2013-01-10			ENSG00000167549	ENSG00000167549		"""Coronins"", ""WD repeat domain containing"""	21356	protein-coding gene	gene with protein product							Standard	NM_032854		Approved	FLJ14871	uc002hel.2	Q6QEF8	OTTHUMG00000132732	ENST00000445145.2:c.170delG	17.37:g.27948270delC	ENSP00000393624:p.Gly57fs	Somatic		Capture	Illumina HiSeq	Phase_I	24972396	NM_032854	B3KU26|Q71MF3|Q8WYH7|Q96K02	Frame_Shift_Del	DEL	ENST00000445145.2	37																																																																																					0.592	CORO6-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000447831.1	NM_032854	
ASIC2	40	broad.mit.edu	37	17	31351017	31351017	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:31351017delT	ENST00000359872.6	-	6	1819	c.1058delA	c.(1057-1059)aagfs	p.K353fs	ASIC2_ENST00000225823.2_Frame_Shift_Del_p.K404fs|ASIC2_ENST00000448983.1_5'UTR	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2	353					central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)	p.K404fs*14(1)|p.K353fs*14(1)								Amiloride(DB00594)	ATTGCTGTCCTTTTCCGCCAA	0.537																																					p.K404fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1211delA	17						.						132.0	117.0	122.0					17																	31351017		2203	4300	6503	28375130	SO:0001589	frameshift_variant	40	exon6			AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	99	protein-coding gene	gene with protein product	"""degenerin"""	601784	"""amiloride-sensitive cation channel 1, neuronal"""	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.1058delA	17.37:g.31351017delT	ENSP00000352934:p.Lys353fs	Somatic		Capture	Illumina HiSeq	Phase_I	28375130	NM_183377	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Frame_Shift_Del	DEL	ENST00000359872.6	37	CCDS42296.1																																																																																				0.537	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094	
KRT19	3880	broad.mit.edu	37	17	39684320	39684320	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:39684320delG	ENST00000361566.3	-	1	240	c.180delC	c.(178-180)gccfs	p.A60fs		NM_002276.4	NP_002267.2	P08727	K1C19_HUMAN	keratin 19	60	Head.		A -> G (in dbSNP:rs4602). {ECO:0000269|PubMed:10623642, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21269460, ECO:0000269|PubMed:2447559, ECO:0000269|PubMed:2448790, ECO:0000269|PubMed:2469734}.		cell differentiation involved in embryonic placenta development (GO:0060706)|response to estrogen (GO:0043627)|sarcomere organization (GO:0045214)|viral process (GO:0016032)	cell periphery (GO:0071944)|costamere (GO:0043034)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)	p.Y61fs*9(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12		Breast(137;0.00038)				CGCCGCCGTAGGCCCCCGAGG	0.721																																					p.A60fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.180delC	17						.						17.0	23.0	21.0					17																	39684320		2146	4209	6355	36937846	SO:0001589	frameshift_variant	3880	exon1				CCDS11399.1	17q21.2	2013-06-20			ENSG00000171345	ENSG00000171345		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6436	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 19"", ""keratin, type I, 40-kd"", ""cytokeratin 19"", ""40-kDa keratin intermediate filament"""	148020				16831889	Standard	NM_002276		Approved	K19, CK19, K1CS, MGC15366		P08727	OTTHUMG00000133422	ENST00000361566.3:c.180delC	17.37:g.39684320delG	ENSP00000355124:p.Ala60fs	Somatic		Capture	Illumina HiSeq	Phase_I	36937846	NM_002276	B2R874|Q5XG83|Q6NW33|Q7L5M9|Q96A53|Q96FV1|Q9BYF9|Q9P1Y4	Frame_Shift_Del	DEL	ENST00000361566.3	37	CCDS11399.1																																																																																				0.721	KRT19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257285.1	NM_002276	
PPM1D	8493	broad.mit.edu	37	17	58740624	58740624	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:58740624delA	ENST00000305921.3	+	6	1761	c.1529delA	c.(1528-1530)caafs	p.Q510fs	RNU6-623P_ENST00000363143.1_RNA	NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1D	510					G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of cell proliferation (GO:0008285)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.N512fs*2(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	15	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)			GTCATGGACCAAAAAAATTTG	0.378											OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.Q510fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1529delA	17						.						71.0	73.0	72.0					17																	58740624		2203	4300	6503	56095406	SO:0001589	frameshift_variant	8493	exon6			U78305	CCDS11625.1	17q23.3	2014-09-17	2010-03-05		ENSG00000170836	ENSG00000170836		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9277	protein-coding gene	gene with protein product	"""wild-type p53-induced phosphatase 1"", ""protein phosphatase 2C, delta isoform"""	605100	"""protein phosphatase 1D magnesium-dependent, delta isoform"""			9177166	Standard	NM_003620		Approved	Wip1, PP2C-DELTA	uc002iyt.2	O15297		ENST00000305921.3:c.1529delA	17.37:g.58740624delA	ENSP00000306682:p.Gln510fs	Somatic	1033	Capture	Illumina HiSeq	Phase_I	56095406	NM_003620	Q53XP4|Q6P991|Q8IVR6	Frame_Shift_Del	DEL	ENST00000305921.3	37	CCDS11625.1																																																																																				0.378	PPM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449474.1	NM_003620	
AXIN2	8313	broad.mit.edu	37	17	63533939	63533940	+	Frame_Shift_Del	DEL	CT	CT	-	rs376701878		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	CT	CT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:63533939_63533940delCT	ENST00000375702.5	-	5	1322_1323	c.1214_1215delAG	c.(1213-1215)gagfs	p.E405fs	AXIN2_ENST00000307078.5_Frame_Shift_Del_p.E405fs			Q9Y2T1	AXIN2_HUMAN	axin 2	405	Interaction with GSK3B. {ECO:0000250}.				bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)	p.E405fs*56(1)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						GCTCGGAGCCCTCTCTCTCTTC	0.624									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																												p.405_405del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1214_1215del	17						.																																			60964402	SO:0001589	frameshift_variant	8313	exon6	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"""conductin"", ""axil"""	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.1214_1215delAG	17.37:g.63533947_63533948delCT	ENSP00000364854:p.Glu405fs	Somatic		Capture	Illumina HiSeq	Phase_I	60964401	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Frame_Shift_Del	DEL	ENST00000375702.5	37																																																																																					0.624	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655	
SOX9	6662	broad.mit.edu	37	17	70120094	70120094	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:70120094delC	ENST00000245479.2	+	3	1468	c.1096delC	c.(1096-1098)cccfs	p.P367fs		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	367	Gln/Pro-rich.				astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P367fs*16(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			gcaggcggcgcccccacagca	0.771																																					p.P366fs	Pancreas(42;83 1041 2320 35205 39456)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1096delC	17						.																																			67631689	SO:0001589	frameshift_variant	6662	exon3			S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"""SRY (sex determining region Y)-boxes"""	11204	protein-coding gene	gene with protein product		608160	"""campomelic dysplasia, autosomal sex-reversal"""	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.1096delC	17.37:g.70120094delC	ENSP00000245479:p.Pro367fs	Somatic		Capture	Illumina HiSeq	Phase_I	67631689	NM_000346	Q53Y80	Frame_Shift_Del	DEL	ENST00000245479.2	37	CCDS11689.1																																																																																				0.771	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346	
SLC16A5	9121	broad.mit.edu	37	17	73096368	73096368	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:73096368delC	ENST00000450736.2	+	4	1025	c.610delC	c.(610-612)cccfs	p.P208fs	SLC16A5_ENST00000580123.1_Frame_Shift_Del_p.P208fs|SLC16A5_ENST00000538213.2_Frame_Shift_Del_p.P248fs|SLC16A5_ENST00000329783.4_Frame_Shift_Del_p.P208fs			O15375	MOT6_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 5	208					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)	p.P205fs*41(1)		central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)	CAAAGAATGTCCCCCGCCACC	0.632																																					p.P204fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.610delC	17						.						52.0	50.0	50.0					17																	73096368		2203	4300	6503	70607963	SO:0001589	frameshift_variant	9121	exon5			U59299	CCDS11713.1	17q25.1	2013-07-18	2013-07-18		ENSG00000170190	ENSG00000170190		"""Solute carriers"""	10926	protein-coding gene	gene with protein product		603879	"""solute carrier family 16 (monocarboxylic acid transporters), member 5"", ""solute carrier family 16, member 5 (monocarboxylic acid transporter 6)"""			9425115	Standard	NM_004695		Approved	MCT5, MCT6	uc002jmr.4	O15375	OTTHUMG00000179277	ENST00000450736.2:c.610delC	17.37:g.73096368delC	ENSP00000390564:p.Pro208fs	Somatic		Capture	Illumina HiSeq	Phase_I	70607963	NM_004695	B4E288	Frame_Shift_Del	DEL	ENST00000450736.2	37	CCDS11713.1																																																																																				0.632	SLC16A5-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445547.1	NM_004695	
C17orf62	79415	broad.mit.edu	37	17	80402447	80402447	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr17:80402447C>T	ENST00000437807.2	-	7	636	c.319G>A	c.(319-321)Gtc>Atc	p.V107I	C17orf62_ENST00000578913.1_Missense_Mutation_p.V107I|C17orf62_ENST00000434650.2_Missense_Mutation_p.V93I|C17orf62_ENST00000585064.1_Missense_Mutation_p.V107I|C17orf62_ENST00000585080.1_Missense_Mutation_p.V107I|C17orf62_ENST00000577732.1_Missense_Mutation_p.V107I|C17orf62_ENST00000583359.1_5'Flank|C17orf62_ENST00000336995.7_5'UTR|C17orf62_ENST00000578919.1_Missense_Mutation_p.V107I|C17orf62_ENST00000577436.1_Missense_Mutation_p.V93I|C17orf62_ENST00000342572.8_5'UTR|C17orf62_ENST00000583617.1_Missense_Mutation_p.V107I|C17orf62_ENST00000306645.5_Missense_Mutation_p.V107I	NM_001193653.1|NM_001193657.1	NP_001180582.1|NP_001180586.1	Q9BQA9	CQ062_HUMAN	chromosome 17 open reading frame 62	107						integral component of membrane (GO:0016021)		p.V107I(1)		breast(2)|large_intestine(2)|skin(2)|urinary_tract(2)	8	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			ACATCACGGACATCATGGAGC	0.652																																					p.V107I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G319A	17						.						170.0	123.0	139.0					17																	80402447		2203	4300	6503	77995736	SO:0001583	missense	79415	exon7			AK074950	CCDS32776.1, CCDS45817.1	17q25.3	2014-06-09			ENSG00000178927	ENSG00000178927			28672	protein-coding gene	gene with protein product							Standard	NM_001100407		Approved	MGC4368, FLJ90469	uc021ufr.1	Q9BQA9		ENST00000437807.2:c.319G>A	17.37:g.80402447C>T	ENSP00000388909:p.Val107Ile	Somatic		Capture	Illumina HiSeq	Phase_I	77995736	NM_001100407	E1B6X3|Q96NR1	Missense_Mutation	SNP	ENST00000437807.2	37	CCDS32776.1	.	.	.	.	.	.	.	.	.	.	C	0.013	-1.641201	0.00799	.	.	ENSG00000178927	ENST00000437807;ENST00000306645;ENST00000434650	.	.	.	4.84	1.34	0.21922	.	.	.	.	.	T	0.12902	0.0313	N	0.01048	-1.04	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.31475	-0.9942	8	0.02654	T	1	.	4.8896	0.13721	0.0:0.1754:0.1588:0.6658	.	93;107	E1B6X3;Q9BQA9	.;CQ062_HUMAN	I	107;107;93	.	ENSP00000307765:V107I	V	-	1	0	C17orf62	77995736	1.000000	0.71417	0.546000	0.28166	0.002000	0.02628	3.476000	0.53143	0.203000	0.20529	-0.367000	0.07326	GTC		0.652	C17orf62-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443260.1	NM_001033046	
IMPA2	3613	broad.mit.edu	37	18	11999060	11999061	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:11999060_11999061insA	ENST00000269159.3	+	2	346_347	c.104_105insA	c.(103-108)agaaaafs	p.RK35fs	IMPA2_ENST00000588927.1_Splice_Site|IMPA2_ENST00000589238.1_5'UTR|IMPA2_ENST00000588752.1_3'UTR	NM_014214.2	NP_055029.1	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2	35					inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)	p.A37fs*4(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|skin(2)|stomach(2)|urinary_tract(1)	12					Lithium(DB01356)	CAGATCATCAGAAAAGCCCTTA	0.406																																					p.R35fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.104_105insA	18						.																																			11989061	SO:0001589	frameshift_variant	3613	exon2			AF014398	CCDS11855.1	18p11.2	2008-03-18			ENSG00000141401	ENSG00000141401	3.1.3.25		6051	protein-coding gene	gene with protein product		605922				9322233	Standard	NM_014214		Approved		uc002kqp.2	O14732	OTTHUMG00000131693	ENST00000269159.3:c.108dupA	18.37:g.11999064_11999064dupA	ENSP00000269159:p.Arg35fs	Somatic		Capture	Illumina HiSeq	Phase_I	11989060	NM_014214	B0YJ29|Q9UJT3	Frame_Shift_Ins	INS	ENST00000269159.3	37	CCDS11855.1																																																																																				0.406	IMPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254601.1		
LAMA3	3909	broad.mit.edu	37	18	21422469	21422469	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:21422469C>T	ENST00000313654.9	+	28	3688	c.3447C>T	c.(3445-3447)ggC>ggT	p.G1149G	LAMA3_ENST00000399516.3_Silent_p.G1149G	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1149	Domain IV 1 (domain IV B).				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.G1149G(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					CGGTGGATGGCGGGTGGCCAC	0.602																																					p.G1149G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3447T	18						.						59.0	64.0	63.0					18																	21422469		2093	4205	6298	19676467	SO:0001819	synonymous_variant	3909	exon28			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.3447C>T	18.37:g.21422469C>T		Somatic		Capture	Illumina HiSeq	Phase_I	19676467	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																				0.602	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
LAMA3	3909	broad.mit.edu	37	18	21501017	21501017	+	Splice_Site	SNP	C	C	T	rs371915321		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:21501017C>T	ENST00000313654.9	+	61	8283	c.8042C>T	c.(8041-8043)tCg>tTg	p.S2681L	LAMA3_ENST00000269217.6_Splice_Site_p.S1072L|LAMA3_ENST00000399516.3_Splice_Site_p.S2625L|LAMA3_ENST00000587184.1_Splice_Site_p.S1016L|LAMA3_ENST00000588770.1_3'UTR	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2681	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.S2681L(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					AGAGACCATTCGGTACACCTT	0.383																																					p.S1016L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3047T	18						.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER	0,4406		0,0,2203	112.0	100.0	104.0		3215,7874,3047,8042	-4.6	0.0	18		104	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	145,145,145,145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign	1072/1725,2625/3278,1016/1669,2681/3334	21501017	1,13005	2203	4300	6503	19755015	SO:0001630	splice_region_variant	3909	exon23			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.8043+1C>T	18.37:g.21501017C>T		Somatic		Capture	Illumina HiSeq	Phase_I	19755015	NM_001127718	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	2.099	-0.406644	0.04832	0.0	1.16E-4	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.79033	-1.23;-1.23;-1.23	4.8	-4.58	0.03410	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.59211	0.2177	L	0.29908	0.895	0.09310	N	0.999999	B;B;B;B	0.14012	0.003;0.009;0.002;0.004	B;B;B;B	0.08055	0.002;0.003;0.003;0.003	T	0.40289	-0.9571	9	0.37606	T	0.19	.	4.8227	0.13400	0.11:0.2166:0.099:0.5744	.	1016;1072;2625;2681	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	L	2681;2625;1072	ENSP00000324532:S2681L;ENSP00000382432:S2625L;ENSP00000269217:S1072L	ENSP00000269217:S1072L	S	+	2	0	LAMA3	19755015	0.000000	0.05858	0.003000	0.11579	0.024000	0.10985	-1.194000	0.03046	-0.959000	0.03618	-0.781000	0.03364	TCG		0.383	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	Missense_Mutation
CABYR	26256	broad.mit.edu	37	18	21735975	21735975	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:21735975T>C	ENST00000399496.3	+	4	675	c.510T>C	c.(508-510)gcT>gcC	p.A170A	CABYR_ENST00000581397.1_Silent_p.A170A|CABYR_ENST00000399499.1_Silent_p.A170A|CABYR_ENST00000399481.2_Silent_p.A72A|CABYR_ENST00000415309.2_Silent_p.A170A|CABYR_ENST00000327201.6_Silent_p.A72A	NM_012189.2|NM_153769.1	NP_036321.2|NP_722453.1	O75952	CABYR_HUMAN	calcium binding tyrosine-(Y)-phosphorylation regulated	170					epithelial cilium movement (GO:0003351)|sperm capacitation (GO:0048240)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)	p.A170A(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(4)	11	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)					ACGTCCCAGCTGACCCAGCTC	0.493																																					p.A170A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T510C	18						.						129.0	97.0	108.0					18																	21735975		2203	4300	6503	19989973	SO:0001819	synonymous_variant	26256	exon4			AF088868	CCDS11881.1, CCDS11882.1, CCDS11883.1, CCDS42420.1, CCDS45840.1	18q11.2	2009-08-06	2007-11-22		ENSG00000154040	ENSG00000154040			15569	protein-coding gene	gene with protein product	"""fibrousheathin 2"", ""cancer/testis antigen 88"""	612135				11820818, 17317841, 16139264	Standard	NM_012189		Approved	FSP-2, CBP86, CT88	uc002kux.3	O75952	OTTHUMG00000037365	ENST00000399496.3:c.510T>C	18.37:g.21735975T>C		Somatic		Capture	Illumina HiSeq	Phase_I	19989973	NM_138644	B2R857|Q8WXW5|Q9HAY3|Q9HAY4|Q9HAY5|Q9HCY9	Silent	SNP	ENST00000399496.3	37	CCDS42420.1																																																																																				0.493	CABYR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090926.2	NM_153770	
DSC3	1825	broad.mit.edu	37	18	28605749	28605749	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:28605749G>A	ENST00000360428.4	-	5	687	c.607C>T	c.(607-609)Cgt>Tgt	p.R203C	DSC3_ENST00000434452.1_Missense_Mutation_p.R203C	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	203	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.R203C(2)		endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			TATTCTTCACGATCCACAGGC	0.338																																					p.R203C												.	.	2	Substitution - Missense(2)	large_intestine(1)|skin(1)	c.C607T	18						.						74.0	75.0	74.0					18																	28605749		2203	4299	6502	26859747	SO:0001583	missense	1825	exon5			X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.607C>T	18.37:g.28605749G>A	ENSP00000353608:p.Arg203Cys	Somatic		Capture	Illumina HiSeq	Phase_I	26859747	NM_001941	A6NN35|Q14200|Q9HAZ9	Missense_Mutation	SNP	ENST00000360428.4	37	CCDS32810.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.674758	0.88445	.	.	ENSG00000134762	ENST00000360428;ENST00000434452	T;T	0.59772	0.24;0.24	5.2	5.2	0.72013	Cadherin (5);Cadherin-like (1);	0.000000	0.33712	N	0.004626	D	0.84982	0.5593	H	0.97365	3.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89852	0.4010	10	0.87932	D	0	.	18.0367	0.89305	0.0:0.0:1.0:0.0	.	203;203	Q14574;Q14574-2	DSC3_HUMAN;.	C	203	ENSP00000353608:R203C;ENSP00000392068:R203C	ENSP00000353608:R203C	R	-	1	0	DSC3	26859747	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.479000	0.66813	2.854000	0.98071	0.655000	0.94253	CGT		0.338	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
DSG4	147409	broad.mit.edu	37	18	28956898	28956898	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:28956898C>T	ENST00000308128.4	+	1	159	c.24C>T	c.(22-24)aaC>aaT	p.N8N	RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA|DSG4_ENST00000359747.4_Silent_p.N8N	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	8					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N8N(1)		NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			TCTTCAGAAACATTTGCCTTT	0.433																																					p.N8N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C24T	18						.						114.0	97.0	103.0					18																	28956898		2203	4300	6503	27210896	SO:0001819	synonymous_variant	147409	exon1			AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.24C>T	18.37:g.28956898C>T		Somatic		Capture	Illumina HiSeq	Phase_I	27210896	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Silent	SNP	ENST00000308128.4	37	CCDS11897.1																																																																																				0.433	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	
TRAPPC8	22878	broad.mit.edu	37	18	29480952	29480952	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:29480952C>T	ENST00000283351.4	-	10	1761	c.1426G>A	c.(1426-1428)Gca>Aca	p.A476T	TRAPPC8_ENST00000582539.1_Missense_Mutation_p.A422T|TRAPPC8_ENST00000582513.1_Missense_Mutation_p.A476T	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	476					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)		p.A476T(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						GGCCTAGGTGCTCCTGGTTGA	0.358																																					p.A476T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1426A	18						.						88.0	86.0	86.0					18																	29480952		2203	4300	6503	27734950	SO:0001583	missense	22878	exon10			AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"""Trafficking protein particle complex"""	29169	protein-coding gene	gene with protein product	"""general sporulation gene 1 homolog (S. cerevisiae)"""	614136	"""KIAA1012"""	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.1426G>A	18.37:g.29480952C>T	ENSP00000283351:p.Ala476Thr	Somatic		Capture	Illumina HiSeq	Phase_I	27734950	NM_014939	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	37	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	C	17.77	3.470669	0.63625	.	.	ENSG00000153339	ENST00000283351	T	0.17528	2.27	5.5	5.5	0.81552	.	0.164235	0.53938	D	0.000058	T	0.19927	0.0479	L	0.34521	1.04	0.80722	D	1	B;P	0.41978	0.1;0.767	B;P	0.46144	0.098;0.505	T	0.01839	-1.1263	10	0.10902	T	0.67	.	19.8192	0.96586	0.0:1.0:0.0:0.0	.	476;476	Q6PCC9;Q9Y2L5	.;TPPC8_HUMAN	T	476	ENSP00000283351:A476T	ENSP00000283351:A476T	A	-	1	0	TRAPPC8	27734950	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.554000	0.67294	2.751000	0.94390	0.644000	0.83932	GCA		0.358	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939	
KLHL14	57565	broad.mit.edu	37	18	30260447	30260447	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:30260447G>A	ENST00000359358.4	-	6	1792	c.1354C>T	c.(1354-1356)Cgc>Tgc	p.R452C		NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	452						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)		p.R452C(2)		breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						GACACATAGCGCCATTCATTC	0.468																																					p.R452C												.	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.C1354T	18						.						131.0	126.0	128.0					18																	30260447		2203	4300	6503	28514445	SO:0001583	missense	57565	exon6			AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705		"""Kelch-like"", ""BTB/POZ domain containing"""	29266	protein-coding gene	gene with protein product	"""printor"""	613772	"""kelch-like 14 (Drosophila)"""			10718198, 19535332	Standard	NM_020805		Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.1354C>T	18.37:g.30260447G>A	ENSP00000352314:p.Arg452Cys	Somatic		Capture	Illumina HiSeq	Phase_I	28514445	NM_020805	A6NNW1|B4DHA0|Q8WU41	Missense_Mutation	SNP	ENST00000359358.4	37	CCDS32813.1	.	.	.	.	.	.	.	.	.	.	G	18.69	3.678853	0.68042	.	.	ENSG00000197705	ENST00000359358	T	0.79454	-1.27	5.58	5.58	0.84498	Galactose oxidase, beta-propeller (1);	0.143817	0.64402	D	0.000005	T	0.80675	0.4668	L	0.47190	1.495	0.80722	D	1	D	0.60575	0.988	P	0.51266	0.664	T	0.80982	-0.1139	10	0.52906	T	0.07	.	19.922	0.97089	0.0:0.0:1.0:0.0	.	452	Q9P2G3	KLH14_HUMAN	C	452	ENSP00000352314:R452C	ENSP00000352314:R452C	R	-	1	0	KLHL14	28514445	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.793000	0.69060	2.780000	0.95670	0.655000	0.94253	CGC		0.468	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1		
MYOM1	8736	broad.mit.edu	37	18	3067413	3067413	+	Silent	SNP	G	G	A	rs1042723		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:3067413G>A	ENST00000356443.4	-	38	5238	c.4905C>T	c.(4903-4905)ggC>ggT	p.G1635G	MYOM1_ENST00000261606.7_Silent_p.G1539G|MYOM1_ENST00000400569.3_Silent_p.G1635G	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1635	Ig-like C2-type 5.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.G1635G(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGGTGCTCACGCCGTTGATGG	0.592																																					p.G1539G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4617T	18						.	G	,	0,4406		0,0,2203	75.0	79.0	78.0		4905,4617	-5.4	0.0	18	dbSNP_86	78	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	1635/1686,1539/1590	3067413	1,13005	2203	4300	6503	3057413	SO:0001819	synonymous_variant	8736	exon37			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4905C>T	18.37:g.3067413G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3057413	NM_019856	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																				0.592	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
ASXL3	80816	broad.mit.edu	37	18	31323220	31323220	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:31323220G>T	ENST00000269197.5	+	12	3408	c.3408G>T	c.(3406-3408)aaG>aaT	p.K1136N		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1136					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K1136N(1)|p.K843N(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						TCAGCTCAAAGGAAGGGCCTC	0.478																																					p.K1136N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3408T	18						.						37.0	37.0	37.0					18																	31323220		1890	4105	5995	29577218	SO:0001583	missense	80816	exon12			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.3408G>T	18.37:g.31323220G>T	ENSP00000269197:p.Lys1136Asn	Somatic		Capture	Illumina HiSeq	Phase_I	29577218	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.149939	0.57151	.	.	ENSG00000141431	ENST00000269197	T	0.53857	0.6	5.8	3.99	0.46301	.	0.188231	0.38058	N	0.001833	T	0.61464	0.2349	L	0.44542	1.39	0.39629	D	0.970149	D	0.76494	0.999	D	0.80764	0.994	T	0.63198	-0.6691	10	0.49607	T	0.09	.	10.0829	0.42401	0.2079:0.0:0.7921:0.0	.	1136	Q9C0F0	ASXL3_HUMAN	N	1136	ENSP00000269197:K1136N	ENSP00000269197:K1136N	K	+	3	2	ASXL3	29577218	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.991000	0.40727	1.441000	0.47550	0.655000	0.94253	AAG		0.478	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
TPGS2	25941	broad.mit.edu	37	18	34376938	34376938	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:34376938T>C	ENST00000334295.4	-	7	1160	c.733A>G	c.(733-735)Aag>Gag	p.K245E	TPGS2_ENST00000590842.1_Intron|TPGS2_ENST00000593035.1_Missense_Mutation_p.K210E|TPGS2_ENST00000590652.1_Intron|TPGS2_ENST00000587129.1_Intron|TPGS2_ENST00000383056.3_Missense_Mutation_p.K202E	NM_015476.2	NP_056291.2	Q68CL5	TPGS2_HUMAN	tubulin polyglutamylase complex subunit 2	245						cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.K245E(1)									GGATCTAGCTTATTCACAAAG	0.468																																					p.K245E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A733G	18						.						191.0	189.0	190.0					18																	34376938		2203	4300	6503	32630936	SO:0001583	missense	25941	exon7			BC015178	CCDS32817.1, CCDS62421.1, CCDS62422.1, CCDS62423.1, CCDS62424.1, CCDS74214.1, CCDS74215.1	18q12.2	2011-11-25	2011-11-25	2011-11-25	ENSG00000134779	ENSG00000134779			24561	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 10"""	C18orf10		12477932	Standard	NM_015476		Approved	DKFZP586M1523, HsT3006	uc031rhw.1	Q68CL5		ENST00000334295.4:c.733A>G	18.37:g.34376938T>C	ENSP00000335144:p.Lys245Glu	Somatic		Capture	Illumina HiSeq	Phase_I	32630936	NM_015476	B4DIX2|K7EIJ9|Q4KN59|Q8WTU3|Q96BT9|Q9Y435	Missense_Mutation	SNP	ENST00000334295.4	37	CCDS32817.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.878409	0.91740	.	.	ENSG00000134779	ENST00000334295;ENST00000383056	T;T	0.53640	0.64;0.61	5.91	5.91	0.95273	.	0.230245	0.48767	D	0.000166	T	0.68412	0.2998	M	0.75264	2.295	0.80722	D	1	D;D;D	0.67145	0.996;0.992;0.992	D;D;P	0.66847	0.947;0.927;0.799	T	0.72020	-0.4416	10	0.72032	D	0.01	-3.9058	16.3483	0.83171	0.0:0.0:0.0:1.0	.	210;202;245	B4DIX2;Q68CL5-1;Q68CL5	.;.;TPGS2_HUMAN	E	245;202	ENSP00000335144:K245E;ENSP00000372530:K202E	ENSP00000335144:K245E	K	-	1	0	C18orf10	32630936	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	6.576000	0.74023	2.254000	0.74563	0.533000	0.62120	AAG		0.468	TPGS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440410.2	NM_015476	
TPGS2	25941	broad.mit.edu	37	18	34378466	34378466	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:34378466G>A	ENST00000334295.4	-	6	1030	c.603C>T	c.(601-603)ggC>ggT	p.G201G	TPGS2_ENST00000589049.1_Silent_p.G201G|TPGS2_ENST00000590842.1_Silent_p.G201G|TPGS2_ENST00000593035.1_Silent_p.G166G|TPGS2_ENST00000590652.1_5'UTR|TPGS2_ENST00000587129.1_Silent_p.G201G|TPGS2_ENST00000383056.3_Silent_p.G158G	NM_015476.2	NP_056291.2	Q68CL5	TPGS2_HUMAN	tubulin polyglutamylase complex subunit 2	201						cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.G201G(1)									ACTGGGGCAGGCCCAGGTGGG	0.502																																					p.G201G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C603T	18						.						130.0	128.0	129.0					18																	34378466		2203	4300	6503	32632464	SO:0001819	synonymous_variant	25941	exon6			BC015178	CCDS32817.1, CCDS62421.1, CCDS62422.1, CCDS62423.1, CCDS62424.1, CCDS74214.1, CCDS74215.1	18q12.2	2011-11-25	2011-11-25	2011-11-25	ENSG00000134779	ENSG00000134779			24561	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 10"""	C18orf10		12477932	Standard	NM_015476		Approved	DKFZP586M1523, HsT3006	uc031rhw.1	Q68CL5		ENST00000334295.4:c.603C>T	18.37:g.34378466G>A		Somatic		Capture	Illumina HiSeq	Phase_I	32632464	NM_015476	B4DIX2|K7EIJ9|Q4KN59|Q8WTU3|Q96BT9|Q9Y435	Silent	SNP	ENST00000334295.4	37	CCDS32817.1																																																																																				0.502	TPGS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440410.2	NM_015476	
SIGLEC15	284266	broad.mit.edu	37	18	43405733	43405733	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:43405733G>A	ENST00000389474.3	+	1	257	c.40G>A	c.(40-42)Gtt>Att	p.V14I		NM_213602.2	NP_998767.1	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15	14					cellular response to lipoprotein particle stimulus (GO:0071402)|innate immune response (GO:0045087)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of bone resorption (GO:0045124)|regulation of osteoclast development (GO:2001204)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)		p.V14I(1)		endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						CTTGGCGTGGGTTCTCCCGAC	0.597																																					p.V14I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G40A	18						.						129.0	95.0	107.0					18																	43405733		2203	4300	6503	41659731	SO:0001583	missense	284266	exon1			AK095432	CCDS32819.1	18q21.1	2014-01-28	2007-05-31	2007-05-31	ENSG00000197046	ENSG00000197046		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27596	protein-coding gene	gene with protein product			"""CD33 antigen-like 3"", ""CD33 molecule-like 3"""	CD33L3		17483134	Standard	NM_213602		Approved	HsT1361	uc002lbl.1	Q6ZMC9		ENST00000389474.3:c.40G>A	18.37:g.43405733G>A	ENSP00000374125:p.Val14Ile	Somatic		Capture	Illumina HiSeq	Phase_I	41659731	NM_213602	A8K2Y5|B4DVQ9	Missense_Mutation	SNP	ENST00000389474.3	37	CCDS32819.1	.	.	.	.	.	.	.	.	.	.	G	9.208	1.030226	0.19512	.	.	ENSG00000197046	ENST00000389474	T	0.32515	1.45	3.76	-2.9	0.05648	.	0.774566	0.10219	N	0.701187	T	0.11750	0.0286	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34527	-0.9825	10	0.05721	T	0.95	-10.1417	1.9709	0.03406	0.1846:0.1664:0.482:0.167	.	14	Q6ZMC9	SIG15_HUMAN	I	14	ENSP00000374125:V14I	ENSP00000374125:V14I	V	+	1	0	SIGLEC15	41659731	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.641000	0.05434	-0.308000	0.08792	0.456000	0.33151	GTT		0.597	SIGLEC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410768.2	NM_213602	
SMAD7	4092	broad.mit.edu	37	18	46448237	46448237	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:46448237G>A	ENST00000262158.2	-	4	1072	c.786C>T	c.(784-786)tgC>tgT	p.C262C	SMAD7_ENST00000591805.1_Silent_p.C47C|SMAD7_ENST00000589634.1_Silent_p.C261C|SMAD7_ENST00000585986.1_5'UTR	NM_001190821.1|NM_005904.3	NP_001177750.1|NP_005895.1	O15105	SMAD7_HUMAN	SMAD family member 7	262	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				adherens junction assembly (GO:0034333)|artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|cellular protein complex localization (GO:0034629)|cellular response to transforming growth factor beta stimulus (GO:0071560)|gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein stabilization (GO:0050821)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of cardiac muscle contraction (GO:0055117)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|response to laminar fluid shear stress (GO:0034616)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activin binding (GO:0048185)|beta-catenin binding (GO:0008013)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity (GO:0030617)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)	p.C262C(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	10	Colorectal(1;0.0518)					ATGCCACCACGCACCAGTGTG	0.537																																					p.C262C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C786T	18						.						50.0	55.0	54.0					18																	46448237		2199	4298	6497	44702235	SO:0001819	synonymous_variant	4092	exon4			AF010193	CCDS11936.1, CCDS54186.1, CCDS59317.1	18q21.1	2006-11-06	2006-11-06	2004-05-26	ENSG00000101665	ENSG00000101665		"""SMADs"""	6773	protein-coding gene	gene with protein product		602932	"""MAD, mothers against decapentaplegic homolog 7 (Drosophila)"", ""SMAD, mothers against DPP homolog 7 (Drosophila)"""	MADH8, MADH7		9256479, 9730599	Standard	NM_005904		Approved		uc002ldg.3	O15105	OTTHUMG00000132655	ENST00000262158.2:c.786C>T	18.37:g.46448237G>A		Somatic		Capture	Illumina HiSeq	Phase_I	44702235	NM_005904	B7Z773|K7EQ10|O14740|Q6DK23	Silent	SNP	ENST00000262158.2	37	CCDS11936.1																																																																																				0.537	SMAD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255906.1	NM_005904	
MBD1	4152	broad.mit.edu	37	18	47802020	47802020	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:47802020G>A	ENST00000591416.1	-	8	1173	c.742C>T	c.(742-744)Cgc>Tgc	p.R248C	MBD1_ENST00000398488.1_Missense_Mutation_p.R248C|MBD1_ENST00000347968.3_Missense_Mutation_p.R248C|MBD1_ENST00000457839.2_Missense_Mutation_p.R248C|MBD1_ENST00000590208.1_Missense_Mutation_p.R248C|MBD1_ENST00000269471.5_Missense_Mutation_p.R248C|MBD1_ENST00000349085.2_Missense_Mutation_p.R248C|MBD1_ENST00000585672.1_Missense_Mutation_p.R199C|MBD1_ENST00000436910.1_Missense_Mutation_p.R248C|MBD1_ENST00000424334.2_Missense_Mutation_p.R274C|MBD1_ENST00000398495.2_Missense_Mutation_p.R248C|MBD1_ENST00000585595.1_Missense_Mutation_p.R248C|MBD1_ENST00000339998.6_Missense_Mutation_p.R248C|MBD1_ENST00000353909.3_Missense_Mutation_p.R199C|MBD1_ENST00000269468.5_Missense_Mutation_p.R248C|MBD1_ENST00000587605.1_Missense_Mutation_p.R248C|MBD1_ENST00000382948.5_Missense_Mutation_p.R248C|MBD1_ENST00000398493.1_Missense_Mutation_p.R248C|MBD1_ENST00000591535.1_Missense_Mutation_p.R248C|MBD1_ENST00000588937.1_Missense_Mutation_p.R248C			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	248					negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R248C(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						AGACCAGGGCGGGGAGGGCGA	0.632																																					p.R199C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C595T	18						.						53.0	50.0	51.0					18																	47802020		2203	4300	6503	46056018	SO:0001583	missense	4152	exon7			Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.742C>T	18.37:g.47802020G>A	ENSP00000467017:p.Arg248Cys	Somatic		Capture	Illumina HiSeq	Phase_I	46056018	NM_015847	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Missense_Mutation	SNP	ENST00000591416.1	37	CCDS11943.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.016415	0.75161	.	.	ENSG00000141644	ENST00000382948;ENST00000353909;ENST00000349085;ENST00000269468;ENST00000347968;ENST00000436910;ENST00000269471;ENST00000424334;ENST00000339998;ENST00000398495;ENST00000457839;ENST00000398493;ENST00000398488	D;D;D;D;D;D;D;D;D;D;D;D;D	0.96300	-3.97;-3.83;-3.88;-3.97;-3.88;-3.89;-3.89;-3.84;-3.96;-3.87;-3.83;-3.88;-3.88	5.46	4.48	0.54585	Zinc finger, CXXC-type (2);	0.098131	0.41823	D	0.000806	D	0.96540	0.8871	L	0.44542	1.39	0.44402	D	0.997312	D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.997;0.999;0.993;0.997;0.993;0.998;0.994;0.985;0.997;0.995;0.997;0.999	D	0.95809	0.8840	10	0.87932	D	0	-15.9063	10.5472	0.45066	0.0:0.0:0.6916:0.3084	.	248;274;248;248;248;248;199;248;248;248;248;248	B4DUR3;B4DI41;Q9UIS9-8;A8K654;Q9UIS9-6;Q9UIS9-2;Q9UIS9-5;Q9UIS9-4;Q9UIS9;Q9UIS9-7;B4DXJ5;Q9UIS9-3	.;.;.;.;.;.;.;.;MBD1_HUMAN;.;.;.	C	248;199;248;248;248;248;248;274;248;248;248;248;248	ENSP00000372407:R248C;ENSP00000269469:R199C;ENSP00000342531:R248C;ENSP00000269468:R248C;ENSP00000285102:R248C;ENSP00000409561:R248C;ENSP00000269471:R248C;ENSP00000408846:R274C;ENSP00000339546:R248C;ENSP00000381508:R248C;ENSP00000405268:R248C;ENSP00000381506:R248C;ENSP00000381502:R248C	ENSP00000269468:R248C	R	-	1	0	MBD1	46056018	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.440000	0.44855	2.735000	0.93741	0.655000	0.94253	CGC		0.632	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846	
MEX3C	51320	broad.mit.edu	37	18	48702956	48702956	+	5'Flank	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:48702956T>C	ENST00000591040.1	-	0	799							Q5U5Q3	MEX3C_HUMAN	mex-3 RNA binding family member C						chondrocyte hypertrophy (GO:0003415)|energy homeostasis (GO:0097009)|regulation of fat cell differentiation (GO:0045598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.N387S(1)		endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|skin(1)	17		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		ATTGGTACCATTAGAAAAAGC	0.473																																					p.N582S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1745G	18						.						121.0	115.0	117.0					18																	48702956		2203	4300	6503	46956954	SO:0001631	upstream_gene_variant	51320	exon2			BC041122	CCDS11951.2	18q21.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000176624	ENSG00000176624		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	28040	protein-coding gene	gene with protein product		611005	"""ring finger and KH domain containing 2"", ""mex-3 homolog C (C. elegans)"""	RKHD2		17267406	Standard	NM_016626		Approved	FLJ38871, RNF194	uc002lfc.4	Q5U5Q3	OTTHUMG00000132693		18.37:g.48702956T>C	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	46956954	NM_016626	A1L022|Q9NZE3	Missense_Mutation	SNP	ENST00000591040.1	37		.	.	.	.	.	.	.	.	.	.	T	8.036	0.762908	0.15914	.	.	ENSG00000176624	ENST00000406189	T	0.27890	1.64	6.17	6.17	0.99709	.	0.146684	0.64402	D	0.000012	T	0.33352	0.0860	N	0.14661	0.345	0.39304	D	0.964964	D	0.58268	0.982	D	0.67548	0.952	T	0.09271	-1.0682	10	0.05833	T	0.94	-11.251	15.8048	0.78491	0.0:0.0:0.0:1.0	.	582	Q5U5Q3	MEX3C_HUMAN	S	582	ENSP00000385610:N582S	ENSP00000385610:N582S	N	-	2	0	MEX3C	46956954	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.837000	0.55820	2.371000	0.80710	0.533000	0.62120	AAT		0.473	MEX3C-003	KNOWN	mRNA_end_NF|basic	processed_transcript	protein_coding	OTTHUMT00000449559.1	NM_016626	
DCC	1630	broad.mit.edu	37	18	49867232	49867232	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:49867232G>A	ENST00000442544.2	+	1	691	c.75G>A	c.(73-75)gcG>gcA	p.A25A	RP11-25O3.1_ENST00000582700.1_lincRNA	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	25					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)	p.A25A(1)		NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		TGTTCAGCGCGCATCTTCAAG	0.493																																					p.A25A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G75A	18						.						193.0	171.0	178.0					18																	49867232		2203	4300	6503	48121230	SO:0001819	synonymous_variant	1630	exon1			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.75G>A	18.37:g.49867232G>A		Somatic		Capture	Illumina HiSeq	Phase_I	48121230	NM_005215		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																				0.493	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
DCC	1630	broad.mit.edu	37	18	51025696	51025696	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:51025696A>G	ENST00000442544.2	+	27	4543	c.3927A>G	c.(3925-3927)caA>caG	p.Q1309Q	DCC_ENST00000581580.1_Silent_p.Q942Q|RP11-671P2.1_ENST00000582064.1_RNA	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1309					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)	p.Q1309Q(1)		NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CTACCCAACAACCACCTATGC	0.507																																					p.Q1309Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A3927G	18						.						169.0	141.0	151.0					18																	51025696		2203	4300	6503	49279694	SO:0001819	synonymous_variant	1630	exon27			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.3927A>G	18.37:g.51025696A>G		Somatic		Capture	Illumina HiSeq	Phase_I	49279694	NM_005215		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																				0.507	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
DYNAP	284254	broad.mit.edu	37	18	52265293	52265293	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:52265293G>T	ENST00000321600.1	+	3	596	c.550G>T	c.(550-552)Gcc>Tcc	p.A184S	DYNAP_ENST00000585973.1_Missense_Mutation_p.A132S	NM_173629.1	NP_775900.1	Q8N1N2	DYNAP_HUMAN	dynactin associated protein	184	Thr-rich.				activation of protein kinase B activity (GO:0032148)|cellular response to ergosterol (GO:1901625)|positive regulation of cell proliferation (GO:0008284)|regulation of apoptotic process (GO:0042981)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A184S(1)									TGCAAGTACAGCCACTGAATC	0.463																																					p.A184S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G550T	18						.						122.0	105.0	111.0					18																	52265293		2203	4300	6503	50416291	SO:0001583	missense	284254	exon3			AK096425	CCDS11957.1	18q21.2	2012-10-24	2012-10-24	2012-10-24	ENSG00000178690	ENSG00000178690			26808	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 26"""	C18orf26		20978158	Standard	NM_173629		Approved	FLJ39106	uc002lfq.1	Q8N1N2	OTTHUMG00000132709	ENST00000321600.1:c.550G>T	18.37:g.52265293G>T	ENSP00000315265:p.Ala184Ser	Somatic		Capture	Illumina HiSeq	Phase_I	50416291	NM_173629		Missense_Mutation	SNP	ENST00000321600.1	37	CCDS11957.1	.	.	.	.	.	.	.	.	.	.	G	12.05	1.822469	0.32237	.	.	ENSG00000178690	ENST00000321600	T	0.38240	1.15	4.29	-8.58	0.00897	.	0.781535	0.11152	N	0.593998	T	0.11707	0.0285	N	0.08118	0	0.09310	N	1	B	0.18013	0.025	B	0.18871	0.023	T	0.14924	-1.0455	10	0.26408	T	0.33	-0.3734	3.3151	0.07030	0.1795:0.1887:0.4661:0.1658	.	184	Q8N1N2	CR026_HUMAN	S	184	ENSP00000315265:A184S	ENSP00000315265:A184S	A	+	1	0	C18orf26	50416291	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.657000	0.05335	-1.393000	0.02079	-0.320000	0.08662	GCC		0.463	DYNAP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256007.1	NM_173629	
EPB41L3	23136	broad.mit.edu	37	18	5395619	5395619	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:5395619G>A	ENST00000341928.2	-	20	3401	c.3061C>T	c.(3061-3063)Cac>Tac	p.H1021Y	EPB41L3_ENST00000427684.2_Missense_Mutation_p.H318Y|EPB41L3_ENST00000400111.3_Missense_Mutation_p.H799Y|EPB41L3_ENST00000544123.1_Missense_Mutation_p.H852Y|EPB41L3_ENST00000342933.3_Missense_Mutation_p.H1021Y|EPB41L3_ENST00000542146.1_Missense_Mutation_p.H326Y|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000540638.2_Missense_Mutation_p.H799Y	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	1021	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.H1021Y(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						TTGGTGATGTGCGTAGTGGTG	0.537																																					p.H1021Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3061T	18						.						347.0	267.0	294.0					18																	5395619		2203	4300	6503	5385619	SO:0001583	missense	23136	exon20			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.3061C>T	18.37:g.5395619G>A	ENSP00000343158:p.His1021Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	5385619	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	32	5.121984	0.94429	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	T;T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3;-1.3	5.71	5.71	0.89125	Band 4.1, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.90383	0.6990	M	0.83603	2.65	0.80722	D	1	D;D;D;D;D;P;D;D	0.89917	0.97;0.995;0.997;0.999;0.999;0.66;1.0;0.999	D;D;D;D;D;P;D;D	0.91635	0.961;0.985;0.971;0.99;0.996;0.454;0.999;0.988	D	0.87654	0.2530	10	0.25751	T	0.34	.	19.8677	0.96824	0.0:0.0:1.0:0.0	.	852;318;326;413;690;799;1021;256	F5GX05;E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;.;E41L3_HUMAN;.	Y	1021;690;852;690;318;326;1021;799	ENSP00000343158:H1021Y;ENSP00000441174:H852Y;ENSP00000392195:H318Y;ENSP00000442233:H326Y;ENSP00000341138:H1021Y;ENSP00000382981:H799Y	ENSP00000343158:H1021Y	H	-	1	0	EPB41L3	5385619	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.769000	0.98969	2.709000	0.92574	0.655000	0.94253	CAC		0.537	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
EPB41L3	23136	broad.mit.edu	37	18	5398137	5398137	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:5398137C>T	ENST00000341928.2	-	17	2695	c.2355G>A	c.(2353-2355)aaG>aaA	p.K785K	EPB41L3_ENST00000427684.2_Silent_p.K82K|EPB41L3_ENST00000400111.3_Intron|EPB41L3_ENST00000544123.1_Silent_p.K616K|EPB41L3_ENST00000342933.3_Silent_p.K785K|EPB41L3_ENST00000542146.1_Silent_p.K90K|EPB41L3_ENST00000542652.2_Intron|EPB41L3_ENST00000540638.2_Intron	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	785	Spectrin--actin-binding. {ECO:0000255}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.K785K(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						CAGAAGACTGCTTAGTCTGAG	0.428																																					p.K785K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2355A	18						.						183.0	198.0	193.0					18																	5398137		2203	4300	6503	5388137	SO:0001819	synonymous_variant	23136	exon17			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.2355G>A	18.37:g.5398137C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5388137	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Silent	SNP	ENST00000341928.2	37	CCDS11838.1																																																																																				0.428	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
EPB41L3	23136	broad.mit.edu	37	18	5433547	5433547	+	Missense_Mutation	SNP	G	G	A	rs376210046		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:5433547G>A	ENST00000341928.2	-	8	1173	c.833C>T	c.(832-834)aCg>aTg	p.T278M	EPB41L3_ENST00000400111.3_Missense_Mutation_p.T278M|EPB41L3_ENST00000544123.1_Missense_Mutation_p.T278M|EPB41L3_ENST00000342933.3_Missense_Mutation_p.T278M|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000540638.2_Missense_Mutation_p.T278M	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	278	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.T278M(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						TTCTGCTGGCGTCATTCCTCT	0.378																																					p.T278M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C833T	18						.						142.0	132.0	135.0					18																	5433547		2203	4300	6503	5423547	SO:0001583	missense	23136	exon8			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.833C>T	18.37:g.5433547G>A	ENSP00000343158:p.Thr278Met	Somatic		Capture	Illumina HiSeq	Phase_I	5423547	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.400318	0.83120	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111	T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27	5.96	5.96	0.96718	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);FERM conserved site (1);	0.092643	0.85682	D	0.000000	D	0.90981	0.7164	M	0.89601	3.045	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.995;0.985;0.986;0.995	D	0.91602	0.5296	10	0.72032	D	0.01	.	20.4008	0.98991	0.0:0.0:1.0:0.0	.	278;278;169;278;278	F5GX05;Q9Y2J2-3;A8K968;Q9Y2J2-2;Q9Y2J2	.;.;.;.;E41L3_HUMAN	M	278;169;278;169;278;278	ENSP00000343158:T278M;ENSP00000441174:T278M;ENSP00000341138:T278M;ENSP00000382981:T278M	ENSP00000343158:T278M	T	-	2	0	EPB41L3	5423547	1.000000	0.71417	0.986000	0.45419	0.985000	0.73830	7.903000	0.87398	2.826000	0.97356	0.655000	0.94253	ACG		0.378	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
ATP8B1	5205	broad.mit.edu	37	18	55328506	55328506	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:55328506G>A	ENST00000283684.4	-	21	2606	c.2607C>T	c.(2605-2607)acC>acT	p.T869T	RP11-35G9.3_ENST00000599199.1_RNA|RP11-35G9.3_ENST00000591854.1_RNA|RP11-35G9.3_ENST00000592201.1_RNA|RP11-35G9.5_ENST00000588925.1_RNA|ATP8B1_ENST00000536015.1_Silent_p.T869T			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	869					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.T869T(1)		breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				TCTGCTTGGGGGTGACGCGGC	0.547																																					p.T869T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2607T	18						.						95.0	84.0	88.0					18																	55328506		2203	4300	6503	53479504	SO:0001819	synonymous_variant	5205	exon22			AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"""ATPases / P-type"""	3706	protein-coding gene	gene with protein product		602397	"""ATPase, Class I, type 8B, member 1"", ""ATPase, class I, type 8B, member 1"""	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.2607C>T	18.37:g.55328506G>A		Somatic		Capture	Illumina HiSeq	Phase_I	53479504	NM_005603	Q9BTP8	Silent	SNP	ENST00000283684.4	37	CCDS11965.1																																																																																				0.547	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603	
LAMA1	284217	broad.mit.edu	37	18	7014009	7014009	+	Silent	SNP	G	G	A	rs147111783		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:7014009G>A	ENST00000389658.3	-	23	3261	c.3168C>T	c.(3166-3168)tgC>tgT	p.C1056C		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1056	Laminin EGF-like 12. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.C1056C(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TGACCACATCGCACCGATGAT	0.512													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19474	0.0		0.0	False		,,,				2504	0.0				p.C1056C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3168T	18						.	G		6,4400	11.4+/-27.6	0,6,2197	41.0	34.0	36.0		3168	-10.2	0.0	18	dbSNP_134	36	0,8600		0,0,4300	no	coding-synonymous	LAMA1	NM_005559.3		0,6,6497	AA,AG,GG		0.0,0.1362,0.0461		1056/3076	7014009	6,13000	2203	4300	6503	7004009	SO:0001819	synonymous_variant	284217	exon23			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.3168C>T	18.37:g.7014009G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7004009	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																				0.512	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
DSEL	92126	broad.mit.edu	37	18	65179474	65179474	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:65179474C>T	ENST00000310045.7	-	2	3875	c.2402G>A	c.(2401-2403)tGg>tAg	p.W801*	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	791					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)	p.W801*(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				GTAAAAACGCCATTGGAAAGT	0.328																																					p.W801X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G2402A	18						.						45.0	47.0	47.0					18																	65179474		2203	4300	6503	63330454	SO:0001587	stop_gained	92126	exon2			AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.2402G>A	18.37:g.65179474C>T	ENSP00000310565:p.Trp801*	Somatic		Capture	Illumina HiSeq	Phase_I	63330454	NM_032160	Q17RH1|Q6P5Z3	Nonsense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	C	50	17.171320	0.99880	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	.	.	.	4.98	4.98	0.66077	.	0.073778	0.56097	U	0.000032	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	17.8508	0.88747	0.0:1.0:0.0:0.0	.	.	.	.	X	801;791	.	ENSP00000310565:W801X	W	-	2	0	DSEL	63330454	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.951000	0.70273	2.309000	0.77851	0.455000	0.32223	TGG		0.328	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
ZADH2	284273	broad.mit.edu	37	18	72913712	72913712	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:72913712G>A	ENST00000322342.3	-	2	1082	c.793C>T	c.(793-795)Cgc>Tgc	p.R265C	ZADH2_ENST00000537114.2_Missense_Mutation_p.R142C	NM_175907.4	NP_787103.1	Q8N4Q0	ZADH2_HUMAN	zinc binding alcohol dehydrogenase domain containing 2	265						mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)	p.R265C(2)		endometrium(3)|large_intestine(3)|lung(8)|skin(1)	15		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)		ACTATCAAGCGCCCTTTCGTA	0.507																																					p.R265C												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C793T	18						.						98.0	85.0	89.0					18																	72913712		2203	4300	6503	71042700	SO:0001583	missense	284273	exon2			BC033780	CCDS12008.1	18q22.3	2008-05-29	2008-05-29		ENSG00000180011	ENSG00000180011			28697	protein-coding gene	gene with protein product						12477932	Standard	NM_175907		Approved	MGC45594	uc002llx.3	Q8N4Q0	OTTHUMG00000132858	ENST00000322342.3:c.793C>T	18.37:g.72913712G>A	ENSP00000323678:p.Arg265Cys	Somatic		Capture	Illumina HiSeq	Phase_I	71042700	NM_175907	A8KA15|B4DZ91	Missense_Mutation	SNP	ENST00000322342.3	37	CCDS12008.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.800760	0.70567	.	.	ENSG00000180011	ENST00000322342;ENST00000537114	T;T	0.05513	3.43;3.43	5.92	4.13	0.48395	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.24774	0.0601	M	0.93328	3.405	0.54753	D	0.999981	D	0.63880	0.993	P	0.55508	0.777	T	0.02037	-1.1225	10	0.56958	D	0.05	-2.6275	9.037	0.36293	0.2179:0.0:0.7821:0.0	.	265	Q8N4Q0	ZADH2_HUMAN	C	265;142	ENSP00000323678:R265C;ENSP00000440111:R142C	ENSP00000323678:R265C	R	-	1	0	ZADH2	71042700	1.000000	0.71417	0.999000	0.59377	0.800000	0.45204	2.663000	0.46774	0.327000	0.23409	0.650000	0.86243	CGC		0.507	ZADH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256332.1	NM_175907	
PTPRM	5797	broad.mit.edu	37	18	8253226	8253226	+	Splice_Site	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:8253226T>C	ENST00000332175.8	+	17	3566	c.2529T>C	c.(2527-2529)gaT>gaC	p.D843D	PTPRM_ENST00000444013.1_Splice_Site_p.D630D|PTPRM_ENST00000400053.4_Splice_Site_p.D781D|PTPRM_ENST00000580170.1_Splice_Site_p.D856D|PTPRM_ENST00000400060.4_Splice_Site_p.N857N	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	843					homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.D843D(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				TTTTCCTAGATGAAACCCACA	0.572																																					p.D843D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2529C	18						.						24.0	22.0	23.0					18																	8253226		2203	4300	6503	8243226	SO:0001630	splice_region_variant	5797	exon17			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.2528-1T>C	18.37:g.8253226T>C		Somatic		Capture	Illumina HiSeq	Phase_I	8243226	NM_002845	A7MBN1|D3DUH8|J3QL11	Silent	SNP	ENST00000332175.8	37	CCDS11840.1																																																																																				0.572	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		Silent
PTPRM	5797	broad.mit.edu	37	18	8384591	8384591	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:8384591A>G	ENST00000332175.8	+	28	4949	c.3912A>G	c.(3910-3912)gtA>gtG	p.V1304V	PTPRM_ENST00000444013.1_Silent_p.V1091V|PTPRM_ENST00000400053.4_Silent_p.V1242V|PTPRM_ENST00000580170.1_Silent_p.V1317V|PTPRM_ENST00000400060.4_Silent_p.V1318V	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1304	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.V1304V(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				AAAACGGAGTACACAGACACG	0.438																																					p.V1304V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A3912G	18						.						133.0	115.0	121.0					18																	8384591		2203	4300	6503	8374591	SO:0001819	synonymous_variant	5797	exon28			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.3912A>G	18.37:g.8384591A>G		Somatic		Capture	Illumina HiSeq	Phase_I	8374591	NM_002845	A7MBN1|D3DUH8|J3QL11	Silent	SNP	ENST00000332175.8	37	CCDS11840.1																																																																																				0.438	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		
RALBP1	10928	broad.mit.edu	37	18	9513198	9513198	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:9513198A>G	ENST00000019317.4	+	2	378	c.155A>G	c.(154-156)gAc>gGc	p.D52G	RALBP1_ENST00000383432.3_Missense_Mutation_p.D52G			Q15311	RBP1_HUMAN	ralA binding protein 1	52					ATP catabolic process (GO:0006200)|chemotaxis (GO:0006935)|positive regulation of Cdc42 GTPase activity (GO:0043089)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|transport (GO:0006810)	cytosol (GO:0005829)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ATPase activity, coupled to movement of substances (GO:0043492)|GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)	p.D52G(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	14					Carbamazepine(DB00564)|Doxorubicin(DB00997)|Sorafenib(DB00398)|Vincristine(DB00541)	CCTCCCCATGACATCCTCCAT	0.502																																					p.D52G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A155G	18						.						60.0	58.0	59.0					18																	9513198		2203	4300	6503	9503198	SO:0001583	missense	10928	exon2			L42542	CCDS11845.1	18p11.22	2006-04-22			ENSG00000017797	ENSG00000017797			9841	protein-coding gene	gene with protein product		605801				7673236	Standard	NM_006788		Approved	RLIP76, RIP1, RIP	uc002koc.3	Q15311	OTTHUMG00000131596	ENST00000019317.4:c.155A>G	18.37:g.9513198A>G	ENSP00000019317:p.Asp52Gly	Somatic		Capture	Illumina HiSeq	Phase_I	9503198	NM_006788	D3DUI0	Missense_Mutation	SNP	ENST00000019317.4	37	CCDS11845.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.518208	0.64634	.	.	ENSG00000017797	ENST00000019317;ENST00000383432;ENST00000458039	T;T	0.14766	2.48;2.48	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.18882	0.0453	L	0.36672	1.1	0.58432	D	0.999998	P	0.35612	0.512	B	0.44278	0.445	T	0.02512	-1.1148	10	0.62326	D	0.03	-26.4815	15.1696	0.72862	1.0:0.0:0.0:0.0	.	52	Q15311	RBP1_HUMAN	G	52	ENSP00000019317:D52G;ENSP00000372924:D52G	ENSP00000019317:D52G	D	+	2	0	RALBP1	9503198	1.000000	0.71417	1.000000	0.80357	0.355000	0.29361	8.998000	0.93550	2.038000	0.60285	0.379000	0.24179	GAC		0.502	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788	
PPP4R1	9989	broad.mit.edu	37	18	9547907	9547907	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:9547907C>T	ENST00000400556.3	-	20	2806	c.2733G>A	c.(2731-2733)gaG>gaA	p.E911E	PPP4R1_ENST00000400555.3_Silent_p.E894E	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	911					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)	p.E911E(1)		large_intestine(1)|skin(2)	3						TGATGGTCTGCTCCACAGCCT	0.507																																					p.E911E	Melanoma(188;1232 2082 5061 11948 35994)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2733A	18						.						78.0	80.0	79.0					18																	9547907		2052	4194	6246	9537907	SO:0001819	synonymous_variant	9989	exon20			AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.2733G>A	18.37:g.9547907C>T		Somatic		Capture	Illumina HiSeq	Phase_I	9537907	NM_001042388	Q99774|Q9UNQ7	Silent	SNP	ENST00000400556.3	37	CCDS42412.1																																																																																				0.507	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134	
TXNDC2	84203	broad.mit.edu	37	18	9888061	9888061	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:9888061delA	ENST00000306084.6	+	2	1784	c.1585delA	c.(1585-1587)aaafs	p.K530fs	TXNDC2_ENST00000536353.2_3'UTR|TXNDC2_ENST00000357775.5_Frame_Shift_Del_p.K463fs	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	530	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)	p.E464fs*22(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						TCAGTTTTATAAAAAAGAAGA	0.438																																					p.K529fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1585delA	18						.						45.0	46.0	45.0					18																	9888061		2203	4300	6503	9878061	SO:0001589	frameshift_variant	84203	exon2			AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 1"""					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.1585delA	18.37:g.9888061delA	ENSP00000304908:p.Lys530fs	Somatic		Capture	Illumina HiSeq	Phase_I	9878061	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Frame_Shift_Del	DEL	ENST00000306084.6	37	CCDS42414.1																																																																																				0.438	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
TTC39C	125488	broad.mit.edu	37	18	21662977	21662977	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:21662977delA	ENST00000317571.3	+	6	1152	c.916delA	c.(916-918)aaafs	p.K307fs	TTC39C_ENST00000304621.6_Frame_Shift_Del_p.K246fs|RP11-403A21.3_ENST00000578443.1_RNA	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	307								p.E247fs*20(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						AATTCTCCTTAAAAAAGAAGC	0.408																																					p.K306fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.916delA	18						.						126.0	130.0	128.0					18																	21662977		2203	4300	6503	19916975	SO:0001589	frameshift_variant	125488	exon6			AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"""Tetratricopeptide (TTC) repeat domain containing"""	26595	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 17"""	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.916delA	18.37:g.21662977delA	ENSP00000323645:p.Lys307fs	Somatic		Capture	Illumina HiSeq	Phase_I	19916975	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Frame_Shift_Del	DEL	ENST00000317571.3	37	CCDS45839.1																																																																																				0.408	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211	
DSG4	147409	broad.mit.edu	37	18	28991270	28991270	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:28991270delG	ENST00000308128.4	+	15	2349	c.2214delG	c.(2212-2214)atgfs	p.M738fs	RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA|DSG4_ENST00000359747.4_Frame_Shift_Del_p.M757fs	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	738					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T740fs*76(1)		NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ACACAGGTATGGGGACAGCCG	0.607																																					p.M757fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2271delG	18						.						75.0	70.0	71.0					18																	28991270		2203	4300	6503	27245268	SO:0001589	frameshift_variant	147409	exon14			AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.2214delG	18.37:g.28991270delG	ENSP00000311859:p.Met738fs	Somatic		Capture	Illumina HiSeq	Phase_I	27245268	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Frame_Shift_Del	DEL	ENST00000308128.4	37	CCDS11897.1																																																																																				0.607	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	
ATP8B1	5205	broad.mit.edu	37	18	55329760	55329760	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:55329760delA	ENST00000283684.4	-	20	2372	c.2373delT	c.(2371-2373)tttfs	p.F791fs	RP11-35G9.3_ENST00000599199.1_RNA|RP11-35G9.3_ENST00000591854.1_RNA|RP11-35G9.3_ENST00000592201.1_RNA|RP11-35G9.5_ENST00000588925.1_RNA|ATP8B1_ENST00000536015.1_Frame_Shift_Del_p.F791fs			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	791					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.P792fs*8(1)		breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				CACCGGGTGGAAAAAAAGATT	0.443																																					p.F791fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2373delT	18						.						94.0	88.0	90.0					18																	55329760		2203	4300	6503	53480758	SO:0001589	frameshift_variant	5205	exon21			AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"""ATPases / P-type"""	3706	protein-coding gene	gene with protein product		602397	"""ATPase, Class I, type 8B, member 1"", ""ATPase, class I, type 8B, member 1"""	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.2373delT	18.37:g.55329760delA	ENSP00000283684:p.Phe791fs	Somatic		Capture	Illumina HiSeq	Phase_I	53480758	NM_005603	Q9BTP8	Frame_Shift_Del	DEL	ENST00000283684.4	37	CCDS11965.1																																																																																				0.443	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603	
RTTN	25914	broad.mit.edu	37	18	67871492	67871492	+	Frame_Shift_Del	DEL	G	G	-	rs114765225	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:67871492delG	ENST00000255674.6	-	3	513	c.227delC	c.(226-228)ccafs	p.P76fs	RTTN_ENST00000454359.1_Frame_Shift_Del_p.P76fs|RTTN_ENST00000437017.1_Frame_Shift_Del_p.P76fs	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	76					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)		p.P76fs*12(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				TTGGACTGCTGGGGGATACTA	0.368																																					p.P76fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.227delC	18						.						92.0	92.0	92.0					18																	67871492		1854	4098	5952	66022472	SO:0001589	frameshift_variant	25914	exon3			AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.227delC	18.37:g.67871492delG	ENSP00000255674:p.Pro76fs	Somatic		Capture	Illumina HiSeq	Phase_I	66022472	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Frame_Shift_Del	DEL	ENST00000255674.6	37	CCDS42443.1																																																																																				0.368	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630	
CTDP1	9150	broad.mit.edu	37	18	77488928	77488928	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr18:77488928G>A	ENST00000299543.7	+	11	2586	c.2439G>A	c.(2437-2439)ccG>ccA	p.P813P	CTDP1_ENST00000075430.7_Intron	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	813					exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)	p.P813P(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		CACCCCAGCCGCAGATGTTTG	0.557																																					p.P813P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2439A	18						.						176.0	195.0	188.0					18																	77488928		2203	4300	6503	75589916	SO:0001819	synonymous_variant	9150	exon11			AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.2439G>A	18.37:g.77488928G>A		Somatic		Capture	Illumina HiSeq	Phase_I	75589916	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Silent	SNP	ENST00000299543.7	37	CCDS12017.1																																																																																				0.557	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
DCAF15	90379	broad.mit.edu	37	19	14069917	14069918	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:14069917_14069918insC	ENST00000254337.6	+	7	866_867	c.845_846insC	c.(844-849)agccccfs	p.SP282fs		NM_138353.2	NP_612362.2	Q66K64	DCA15_HUMAN	DDB1 and CUL4 associated factor 15	282					protein ubiquitination (GO:0016567)			p.E285fs*1(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)	11						GCGCCTGCCAGCCCCCCTGAGC	0.663																																					p.S282fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.845_846insC	19						.																																			13930918	SO:0001589	frameshift_variant	90379	exon7			BC002926	CCDS32926.1	19p13.12	2009-07-17	2009-07-17	2009-07-17	ENSG00000132017	ENSG00000132017		"""DDB1 and CUL4 associated factors"""	25095	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 72"""	C19orf72			Standard	NM_138353		Approved	MGC99481	uc002mxt.3	Q66K64		ENST00000254337.6:c.851dupC	19.37:g.14069923_14069923dupC	ENSP00000254337:p.Ser282fs	Somatic		Capture	Illumina HiSeq	Phase_I	13930917	NM_138353	B3KS86|Q96DW0|Q9BU31	Frame_Shift_Ins	INS	ENST00000254337.6	37	CCDS32926.1																																																																																				0.663	DCAF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458099.1	NM_138353	
ZNF790	388536	broad.mit.edu	37	19	37309501	37309502	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:37309501_37309502insT	ENST00000356725.4	-	5	1864_1865	c.1744_1745insA	c.(1744-1746)attfs	p.I582fs	CTD-2162K18.5_ENST00000587278.1_RNA|CTD-2162K18.5_ENST00000588906.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	582					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I582fs*3(1)		biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ACTATTATGAATTTTTTGTTCA	0.347																																					p.I582fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1745_1746insA	19						.																																			42001342	SO:0001589	frameshift_variant	388536	exon5			BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"""Zinc fingers, C2H2-type"", ""-"""	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.1745dupA	19.37:g.37309507_37309507dupT	ENSP00000349161:p.Ile582fs	Somatic		Capture	Illumina HiSeq	Phase_I	42001341	NM_206894		Frame_Shift_Ins	INS	ENST00000356725.4	37	CCDS12496.1																																																																																				0.347	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894	
FCGBP	8857	broad.mit.edu	37	19	40411852	40411853	+	Frame_Shift_Ins	INS	-	-	G	rs376544998		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-	-	G	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:40411852_40411853insG	ENST00000221347.6	-	7	3782_3783	c.3775_3776insC	c.(3775-3777)cacfs	p.H1259fs		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1259	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.H1259fs*44(1)|p.H1259N(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGTGGTGTAGTGGGGGTCTCCT	0.678																																					p.H1259fs												.	.	2	Substitution - Missense(1)|Insertion - Frameshift(1)	large_intestine(1)|endometrium(1)	c.3776_3777insC	19						.																																			45103693	SO:0001589	frameshift_variant	8857	exon7			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.3776dupC	19.37:g.40411857_40411857dupG	ENSP00000221347:p.His1259fs	Somatic		Capture	Illumina HiSeq	Phase_I	45103692	NM_003890	O95784	Frame_Shift_Ins	INS	ENST00000221347.6	37	CCDS12546.1																																																																																				0.678	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZNF625	90589	broad.mit.edu	37	19	12258262	12258263	+	De_novo_Start_OutOfFrame	INS	-	-	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:12258262_12258263insT	ENST00000355738.1	-	0	289_290				ZNF625_ENST00000542938.1_De_novo_Start_OutOfFrame|ZNF625_ENST00000455799.1_Frame_Shift_Ins_p.N45fs|ZNF625-ZNF20_ENST00000430024.1_Frame_Shift_Ins_p.W47fs|ZNF625_ENST00000439556.2_Frame_Shift_Ins_p.W47fs			Q96I27	ZN625_HUMAN	zinc finger protein 625						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.W47fs*7(1)		breast(1)|kidney(1)|large_intestine(6)|lung(4)|skin(2)	14						TGATCTTTCCATTTTTTTCCTA	0.347																																					.												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	.	19						.																																			12119263			7568	.			BC007868	CCDS12269.1, CCDS12269.2	19p13.2	2013-01-08			ENSG00000257591	ENSG00000257591		"""Zinc fingers, C2H2-type"", ""-"""	30571	protein-coding gene	gene with protein product						12477932	Standard	NM_145233		Approved		uc010dyo.2	Q96I27	OTTHUMG00000156407	ENST00000355738.1:c.-61->A	19.37:g.12258269_12258269dupT		Somatic		Capture	Illumina HiSeq	Phase_I	12119262	.	A4FU45|I3L0E9	De_novo_Start_OutOfFrame	INS	ENST00000355738.1	37																																																																																					0.347	ZNF625-201	KNOWN	basic	protein_coding	protein_coding		NM_145233	
PRR22	163154	broad.mit.edu	37	19	5784177	5784178	+	Intron	INS	-	-	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:5784177_5784178insG	ENST00000419421.2	-	3	298				CTB-54O9.9_ENST00000586012.1_3'UTR	NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22									p.P28fs*67(1)		endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						GGGGCCCCTTTGGGGGACGACA	0.624																																					.												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	.	19						.			49,4131		4,41,2045						0.5	0.0			137	48,8128		2,44,4042	no	intron	PRR22	NM_001134316.1		6,85,6087	A1A1,A1R,RR		0.5871,1.1722,0.785				97,12259				5735178	SO:0001627	intron_variant	163154	.			BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.194-113->C	19.37:g.5784182_5784182dupG		Somatic		Capture	Illumina HiSeq	Phase_I	5735177	.	E9PB31	Frame_Shift_Ins	INS	ENST00000419421.2	37	CCDS45933.1																																																																																				0.624	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
DNMT1	1786	broad.mit.edu	37	19	10267124	10267124	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:10267124C>T	ENST00000340748.4	-	17	1529	c.1294G>A	c.(1294-1296)Gaa>Aaa	p.E432K	DNMT1_ENST00000359526.4_Missense_Mutation_p.E448K|DNMT1_ENST00000540357.1_Missense_Mutation_p.E432K			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	432	DNA replication foci-targeting sequence. {ECO:0000250}.|Homodimerization.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.E432K(3)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	AAGAAGAGTTCGATATTCTTC	0.453																																					p.E448K												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G1342A	19						.						127.0	111.0	116.0					19																	10267124		2203	4300	6503	10128124	SO:0001583	missense	1786	exon18			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.1294G>A	19.37:g.10267124C>T	ENSP00000345739:p.Glu432Lys	Somatic		Capture	Illumina HiSeq	Phase_I	10128124	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.535860	0.27475	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	T;T;T	0.77620	-1.11;-1.11;-1.11	5.65	3.53	0.40419	DNA (cytosine-5)-methyltransferase 1, replication foci domain (1);	0.051080	0.85682	N	0.000000	T	0.76564	0.4005	M	0.80982	2.52	0.53688	D	0.999976	B;B;B	0.25351	0.102;0.102;0.124	B;B;B	0.24269	0.031;0.031;0.052	T	0.73792	-0.3871	10	0.45353	T	0.12	.	10.6514	0.45651	0.0:0.7946:0.1332:0.0722	.	432;448;432	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	K	448;432;432;300	ENSP00000352516:E448K;ENSP00000440457:E432K;ENSP00000345739:E432K	ENSP00000345739:E432K	E	-	1	0	DNMT1	10128124	1.000000	0.71417	0.043000	0.18650	0.281000	0.26958	4.721000	0.61951	0.933000	0.37291	0.655000	0.94253	GAA		0.453	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	
ATG4D	84971	broad.mit.edu	37	19	10664956	10664956	+	IGR	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:10664956C>T	ENST00000309469.4	+	0	1949				MIR1238_ENST00000408483.1_RNA|KRI1_ENST00000312962.6_Splice_Site_p.A601T|KRI1_ENST00000361821.5_Splice_Site_p.A597T	NM_032885.4	NP_116274.3	Q86TL0	ATG4D_HUMAN	autophagy related 4D, cysteine peptidase						apoptotic process (GO:0006915)|autophagy (GO:0006914)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)	p.A601T(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	19			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			GGTGTCTCTGCCCTGAGGGAG	0.602																																					p.A601T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1801A	19						.						24.0	28.0	27.0					19																	10664956		2187	4285	6472	10525956	SO:0001628	intergenic_variant	65095	exon19			AJ312332	CCDS12241.1	19p13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000130734	ENSG00000130734			20789	protein-coding gene	gene with protein product		611340	"""AUT-like 4, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog D (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog D (S. cerevisiae)"""	AUTL4, APG4D		12446702	Standard	NM_032885		Approved	APG4-D	uc002mov.3	Q86TL0	OTTHUMG00000180582		19.37:g.10664956C>T		Somatic		Capture	Illumina HiSeq	Phase_I	10525956	NM_023008	Q969K0	Missense_Mutation	SNP	ENST00000309469.4	37	CCDS12241.1	.	.	.	.	.	.	.	.	.	.	C	5.363	0.252285	0.10185	.	.	ENSG00000129347	ENST00000312962;ENST00000361821	T;T	0.08546	3.25;3.08	4.22	0.625	0.17665	.	0.622148	0.16025	N	0.233133	T	0.02304	0.0071	N	0.01267	-0.92	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47302	-0.9128	10	0.15066	T	0.55	-1.5625	6.76	0.23536	0.0:0.3369:0.0:0.6631	.	601;597	Q8N9T8;D3YTE0	KRI1_HUMAN;.	T	601;597	ENSP00000320917:A601T;ENSP00000355366:A597T	ENSP00000320917:A601T	A	-	1	0	KRI1	10525956	0.107000	0.21998	0.115000	0.21578	0.046000	0.14306	0.537000	0.23144	0.139000	0.18822	-0.440000	0.05779	GCA		0.602	ATG4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452022.1	NM_032885	
QTRT1	81890	broad.mit.edu	37	19	10823637	10823637	+	Missense_Mutation	SNP	G	G	A	rs562572604		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:10823637G>A	ENST00000250237.5	+	9	990	c.980G>A	c.(979-981)cGc>cAc	p.R327H		NM_031209.2	NP_112486.1	Q9BXR0	TGT_HUMAN	queuine tRNA-ribosyltransferase 1	327					queuosine biosynthetic process (GO:0008616)|tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|queuine tRNA-ribosyltransferase activity (GO:0008479)	p.R327H(1)		large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	12			Epithelial(33;1.55e-05)|all cancers(31;3.42e-05)			AGGCACAGCCGCGCCTTCCTG	0.672													G|||	1	0.000199681	0.0	0.0	5008	,	,		14388	0.0		0.0	False		,,,				2504	0.001				p.R327H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G980A	19						.						37.0	31.0	33.0					19																	10823637		2202	4296	6498	10684637	SO:0001583	missense	81890	exon9			AF302783	CCDS12248.1	19p13.3	2014-06-11	2008-07-31		ENSG00000213339	ENSG00000213339	2.4.2.29		23797	protein-coding gene	gene with protein product	"""tRNA-guanine transglycosylase"""	609615				20354154	Standard	NM_031209		Approved	TGT	uc002mpr.3	Q9BXR0		ENST00000250237.5:c.980G>A	19.37:g.10823637G>A	ENSP00000250237:p.Arg327His	Somatic		Capture	Illumina HiSeq	Phase_I	10684637	NM_031209	B4DFM7|Q96BQ4|Q9BXQ9	Missense_Mutation	SNP	ENST00000250237.5	37	CCDS12248.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.518616	0.64634	.	.	ENSG00000213339	ENST00000250237	.	.	.	4.33	4.33	0.51752	.	0.000000	0.64402	U	0.000003	D	0.90954	0.7156	H	0.99487	4.59	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.95012	0.8152	9	0.87932	D	0	-16.4124	15.5854	0.76479	0.0:0.0:1.0:0.0	.	327	Q9BXR0	TGT_HUMAN	H	327	.	ENSP00000250237:R327H	R	+	2	0	QTRT1	10684637	1.000000	0.71417	1.000000	0.80357	0.138000	0.21146	6.956000	0.76013	1.967000	0.57214	0.491000	0.48974	CGC		0.672	QTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452086.1	NM_031209	
ZNF44	51710	broad.mit.edu	37	19	12383978	12383978	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:12383978G>T	ENST00000356109.5	-	5	1354	c.1236C>A	c.(1234-1236)ccC>ccA	p.P412P	ZNF44_ENST00000355684.5_Silent_p.P364P	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		TACATTCATAGGGTTTCTCTA	0.423																																					p.P364P												.	.	0			c.C1092A	19						.						103.0	107.0	106.0					19																	12383978		2203	4300	6503	12244978	SO:0001819	synonymous_variant	51710	exon4			X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"""Zinc fingers, C2H2-type"", ""-"""	13110	protein-coding gene	gene with protein product		194542	"""zinc finger protein 58"", ""zinc finger protein 44 (KOX 7)"", ""zinc finger protein 55"""	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.1236C>A	19.37:g.12383978G>T		Somatic		Capture	Illumina HiSeq	Phase_I	12244978	NM_016264	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Silent	SNP	ENST00000356109.5	37	CCDS54223.1																																																																																				0.423	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264	
MAN2B1	4125	broad.mit.edu	37	19	12760201	12760201	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:12760201G>A	ENST00000456935.2	-	19	2349	c.2309C>T	c.(2308-2310)cCc>cTc	p.P770L	CTD-2192J16.22_ENST00000597692.1_5'Flank|MAN2B1_ENST00000221363.4_Missense_Mutation_p.P769L	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	770					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.P770L(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						TCCTGCCACGGGCTCCGTCTG	0.552																																					p.P770L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2309T	19						.						83.0	59.0	67.0					19																	12760201		2203	4300	6503	12621201	SO:0001583	missense	4125	exon19				CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.2309C>T	19.37:g.12760201G>A	ENSP00000395473:p.Pro770Leu	Somatic		Capture	Illumina HiSeq	Phase_I	12621201	NM_000528	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.182619	0.38511	.	.	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	D;D	0.86769	-2.17;-2.17	4.55	2.38	0.29361	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.406771	0.18283	N	0.145956	D	0.93844	0.8031	H	0.94542	3.55	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.70487	0.969;0.969	D	0.92058	0.5654	10	0.87932	D	0	-7.6836	7.0656	0.25149	0.093:0.0:0.7354:0.1716	.	769;770	G5E928;O00754	.;MA2B1_HUMAN	L	770;709;769	ENSP00000395473:P770L;ENSP00000221363:P769L	ENSP00000221363:P769L	P	-	2	0	MAN2B1	12621201	1.000000	0.71417	0.001000	0.08648	0.036000	0.12997	7.001000	0.76297	0.532000	0.28657	-0.314000	0.08810	CCC		0.552	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
MAN2B1	4125	broad.mit.edu	37	19	12760969	12760969	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:12760969G>T	ENST00000456935.2	-	17	2154	c.2114C>A	c.(2113-2115)cCa>cAa	p.P705Q	CTD-2192J16.22_ENST00000597692.1_5'Flank|MAN2B1_ENST00000221363.4_Missense_Mutation_p.P704Q	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	705					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.P705Q(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CCGCTGTCCTGGGTACAGGCG	0.632																																					p.P705Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2114A	19						.						128.0	108.0	115.0					19																	12760969		2203	4300	6503	12621969	SO:0001583	missense	4125	exon17				CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.2114C>A	19.37:g.12760969G>T	ENSP00000395473:p.Pro705Gln	Somatic		Capture	Illumina HiSeq	Phase_I	12621969	NM_000528	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	.	.	.	.	.	.	.	.	.	.	G	5.594	0.294388	0.10567	.	.	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	D;D	0.82803	-1.65;-1.65	4.91	-1.57	0.08506	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.721236	0.12009	N	0.508032	T	0.67664	0.2917	L	0.39898	1.24	0.09310	N	1	B;P	0.36874	0.199;0.572	B;B	0.32864	0.095;0.154	T	0.55108	-0.8192	10	0.25106	T	0.35	-1.4886	3.8472	0.08940	0.0834:0.3988:0.2768:0.241	.	704;705	G5E928;O00754	.;MA2B1_HUMAN	Q	705;644;704	ENSP00000395473:P705Q;ENSP00000221363:P704Q	ENSP00000221363:P704Q	P	-	2	0	MAN2B1	12621969	0.000000	0.05858	0.001000	0.08648	0.697000	0.40408	0.459000	0.21908	-0.287000	0.09064	0.555000	0.69702	CCA		0.632	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
C19orf43	79002	broad.mit.edu	37	19	12842219	12842219	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:12842219C>T	ENST00000242784.4	-	2	479	c.362G>A	c.(361-363)gGc>gAc	p.G121D	C19orf43_ENST00000592273.1_Intron|C19orf43_ENST00000588213.1_Silent_p.R113R	NM_024038.2	NP_076943.1	Q9BQ61	CS043_HUMAN	chromosome 19 open reading frame 43	121								p.G121D(1)		endometrium(2)|large_intestine(2)	4						TTTGTTCCCGCCTCTGCGTTT	0.607																																					p.G121D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G362A	19						.						146.0	120.0	128.0					19																	12842219		2203	4300	6503	12703219	SO:0001583	missense	79002	exon2			AK027588	CCDS12279.1	19p13.2	2011-11-24			ENSG00000123144	ENSG00000123144			28424	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 18"""					12477932	Standard	NM_024038		Approved	MGC2803, fSAP18	uc002muu.3	Q9BQ61		ENST00000242784.4:c.362G>A	19.37:g.12842219C>T	ENSP00000242784:p.Gly121Asp	Somatic		Capture	Illumina HiSeq	Phase_I	12703219	NM_024038		Missense_Mutation	SNP	ENST00000242784.4	37	CCDS12279.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.807575	0.90623	.	.	ENSG00000123144	ENST00000242784	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.78597	0.4308	M	0.66297	2.02	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80520	-0.1346	9	0.87932	D	0	-7.9609	18.0139	0.89232	0.0:1.0:0.0:0.0	.	121	Q9BQ61	CS043_HUMAN	D	121	.	ENSP00000242784:G121D	G	-	2	0	C19orf43	12703219	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.365000	0.66116	2.534000	0.85438	0.655000	0.94253	GGC		0.607	C19orf43-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450856.1	NM_024038	
RTBDN	83546	broad.mit.edu	37	19	12940786	12940786	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:12940786C>T	ENST00000458671.2	-	2	160	c.8G>A	c.(7-9)tGc>tAc	p.C3Y	RTBDN_ENST00000322912.5_Missense_Mutation_p.C35Y|RTBDN_ENST00000589272.1_Missense_Mutation_p.C35Y|CTD-2265O21.3_ENST00000588469.1_RNA|RTBDN_ENST00000592204.1_Missense_Mutation_p.C13Y|RTBDN_ENST00000393233.2_5'UTR	NM_001080997.2	NP_001074466.1	Q9BSG5	RTBDN_HUMAN	retbindin	3						extracellular region (GO:0005576)		p.C35Y(1)		kidney(1)|large_intestine(5)|liver(1)|lung(4)|prostate(1)	12						GTGGACCCTGCAGTCCATGTC	0.607																																					p.C35Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G104A	19						.						69.0	57.0	61.0					19																	12940786		2203	4300	6503	12801786	SO:0001583	missense	83546	exon3			AY028917	CCDS12283.1, CCDS45994.1, CCDS59355.1, CCDS59356.1	19p13	2006-03-22				ENSG00000132026			30310	protein-coding gene	gene with protein product		609553				12107411	Standard	NM_001080997		Approved	FLJ36353	uc002mvj.4	Q9BSG5		ENST00000458671.2:c.8G>A	19.37:g.12940786C>T	ENSP00000416375:p.Cys3Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	12801786	NM_031429	F1T0I8|Q9BWT5	Missense_Mutation	SNP	ENST00000458671.2	37	CCDS45994.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.814515	0.32053	.	.	ENSG00000132026	ENST00000322912;ENST00000458671	T;T	0.52983	0.64;0.77	3.74	0.431	0.16523	.	0.787760	0.11181	N	0.590965	T	0.31071	0.0785	L	0.29908	0.895	0.58432	D	0.999999	B;B;B	0.26744	0.037;0.022;0.158	B;B;B	0.23275	0.045;0.02;0.035	T	0.11227	-1.0596	10	0.51188	T	0.08	-3.0078	5.376	0.16166	0.0:0.6097:0.0:0.3903	.	35;3;13	Q9BSG5-2;Q9BSG5;F1T0I8	.;RTBDN_HUMAN;.	Y	35;3	ENSP00000326253:C35Y;ENSP00000416375:C3Y	ENSP00000326253:C35Y	C	-	2	0	RTBDN	12801786	0.442000	0.25633	0.736000	0.30914	0.512000	0.34134	-0.080000	0.11339	0.181000	0.19994	0.561000	0.74099	TGC		0.607	RTBDN-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451513.1	NM_031429	
ASF1B	55723	broad.mit.edu	37	19	14231404	14231404	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:14231404C>A	ENST00000263382.3	-	4	975	c.476G>T	c.(475-477)aGg>aTg	p.R159M	ASF1B_ENST00000592798.1_Missense_Mutation_p.R100M|PRKACA_ENST00000590853.1_5'Flank|PRKACA_ENST00000308677.4_5'Flank|CTB-55O6.10_ENST00000590715.1_RNA	NM_018154.2	NP_060624.1	Q9NVP2	ASF1B_HUMAN	anti-silencing function 1B histone chaperone	159					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)		p.R159M(1)		endometrium(2)|large_intestine(2)|lung(2)|ovary(1)	7						GGCCTCCAGCCTGTCCATGTT	0.632																																					p.R159M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G476T	19						.						72.0	63.0	66.0					19																	14231404		2203	4300	6503	14092404	SO:0001583	missense	55723	exon4			AF279307	CCDS12306.1	19p13.12	2013-05-01	2013-05-01		ENSG00000105011	ENSG00000105011			20996	protein-coding gene	gene with protein product		609190	"""ASF1 anti-silencing function 1 homolog B (S. cerevisiae)"""			11897662, 11470414	Standard	NM_018154		Approved	FLJ10604	uc002mye.3	Q9NVP2	OTTHUMG00000150401	ENST00000263382.3:c.476G>T	19.37:g.14231404C>A	ENSP00000263382:p.Arg159Met	Somatic		Capture	Illumina HiSeq	Phase_I	14092404	NM_018154	Q53G51|Q9NVZ0	Missense_Mutation	SNP	ENST00000263382.3	37	CCDS12306.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.033085	0.35893	.	.	ENSG00000105011	ENST00000263382	.	.	.	5.8	-0.214	0.13161	.	0.421246	0.26275	N	0.025315	T	0.17450	0.0419	N	0.14661	0.345	0.18873	N	0.999986	B	0.27732	0.187	B	0.27262	0.078	T	0.11275	-1.0594	9	0.48119	T	0.1	.	5.4134	0.16360	0.0:0.2916:0.1477:0.5607	.	159	Q9NVP2	ASF1B_HUMAN	M	159	.	ENSP00000263382:R159M	R	-	2	0	ASF1B	14092404	0.008000	0.16893	0.008000	0.14137	0.861000	0.49209	0.398000	0.20899	-0.239000	0.09710	-0.127000	0.14921	AGG		0.632	ASF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317946.1	NM_018154	
LPHN1	22859	broad.mit.edu	37	19	14274139	14274139	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:14274139C>T	ENST00000340736.6	-	6	786	c.489G>A	c.(487-489)tgG>tgA	p.W163*	CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000592086.1_RNA|LPHN1_ENST00000361434.3_Nonsense_Mutation_p.W158*|LPHN1_ENST00000591528.1_5'UTR	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	163	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)	p.W163*(1)		central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GGTCCTTGCACCATGCGCCAG	0.647																																					p.W158X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G474A	19						.						39.0	31.0	34.0					19																	14274139		2203	4300	6503	14135139	SO:0001587	stop_gained	22859	exon5			AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"""-"", ""GPCR / Class B : Orphans"""	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.489G>A	19.37:g.14274139C>T	ENSP00000340688:p.Trp163*	Somatic		Capture	Illumina HiSeq	Phase_I	14135139	NM_014921	Q96IE7|Q9BU07|Q9HAR3	Nonsense_Mutation	SNP	ENST00000340736.6	37	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	C	38	6.756508	0.97817	.	.	ENSG00000072071	ENST00000340736;ENST00000361434	.	.	.	4.91	3.87	0.44632	.	0.144525	0.49916	D	0.000122	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.379	0.55295	0.1698:0.8302:0.0:0.0	.	.	.	.	X	163;158	.	ENSP00000340688:W163X	W	-	3	0	LPHN1	14135139	1.000000	0.71417	0.978000	0.43139	0.884000	0.51177	6.026000	0.70873	1.042000	0.40150	0.655000	0.94253	TGG		0.647	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921	
EMR2	30817	broad.mit.edu	37	19	14876163	14876163	+	Missense_Mutation	SNP	T	T	G	rs112610420	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:14876163T>G	ENST00000315576.3	-	10	1326	c.875A>C	c.(874-876)tAc>tCc	p.Y292S	EMR2_ENST00000346057.1_Missense_Mutation_p.Y243S|EMR2_ENST00000595839.1_Missense_Mutation_p.Y150S|EMR2_ENST00000392964.3_Missense_Mutation_p.Y31S|EMR2_ENST00000594076.1_Missense_Mutation_p.Y199S|EMR2_ENST00000392967.2_Missense_Mutation_p.Y292S|EMR2_ENST00000353005.1_Missense_Mutation_p.Y150S|EMR2_ENST00000596991.2_Missense_Mutation_p.Y292S|EMR2_ENST00000601345.1_Missense_Mutation_p.Y292S|EMR2_ENST00000353876.1_Missense_Mutation_p.Y199S|EMR2_ENST00000392965.3_Missense_Mutation_p.Y292S|EMR2_ENST00000594294.1_Missense_Mutation_p.Y243S	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	292					cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						GCCTGGCTTGTAGTCTCTGCC	0.612													T|||	11	0.00219649	0.0061	0.0014	5008	,	,		18411	0.0		0.002	False		,,,				2504	0.0				p.Y243S												.	.	0			c.A728C	19						.	T	SER/TYR,SER/TYR,SER/TYR,SER/TYR,SER/TYR,SER/TYR,SER/TYR	29,4377	35.2+/-66.4	1,27,2175	132.0	117.0	122.0		875,728,596,449,875,728,596	1.3	0.0	19	dbSNP_132	122	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense,missense,missense,missense,missense,missense	EMR2	NM_013447.2,NM_152916.1,NM_152917.1,NM_152918.1,NM_152919.1,NM_152920.1,NM_152921.1	144,144,144,144,144,144,144	1,34,6468	GG,GT,TT		0.0814,0.6582,0.2768	benign,benign,benign,benign,benign,benign,benign	292/824,243/775,199/731,150/682,292/813,243/764,199/720	14876163	36,12970	2203	4300	6503	14737163	SO:0001583	missense	30817	exon9			AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	3337	protein-coding gene	gene with protein product		606100	"""egf-like module containing, mucin-like, hormone receptor-like sequence 2"""				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.875A>C	19.37:g.14876163T>G	ENSP00000319883:p.Tyr292Ser	None		Capture	Illumina HiSeq	Phase_I	14737163	NM_152920	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	.	.	.	.	.	.	.	.	.	.	T	10.19	1.283366	0.23392	0.006582	8.14E-4	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000392965;ENST00000392964;ENST00000392962	T;T;T;T;T;T;T;T	0.77877	-0.82;-0.94;-0.37;0.42;1.18;-1.13;1.43;-1.07	3.57	1.3	0.21679	.	.	.	.	.	T	0.37265	0.0997	N	0.02539	-0.55	0.09310	N	0.999997	B;B;B;P;B;B;B;B	0.47106	0.0;0.001;0.0;0.89;0.001;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.37267	0.001;0.0;0.002;0.245;0.005;0.0;0.0;0.0	T	0.34875	-0.9811	9	0.18276	T	0.48	.	6.3718	0.21485	0.5996:0.0:0.0:0.4004	.	292;199;292;150;243;292;292;292	E7ESD7;Q9UHX3-4;A0JNV7;Q9UHX3-5;Q9UHX3-3;A8K6W1;Q9UHX3;Q9UHX3-2	.;.;.;.;.;.;EMR2_HUMAN;.	S	292;292;243;199;150;292;31;243	ENSP00000319883:Y292S;ENSP00000376694:Y292S;ENSP00000263380:Y243S;ENSP00000319454:Y199S;ENSP00000319838:Y150S;ENSP00000376692:Y292S;ENSP00000376691:Y31S;ENSP00000376689:Y243S	ENSP00000319883:Y292S	Y	-	2	0	EMR2	14737163	0.107000	0.21998	0.003000	0.11579	0.001000	0.01503	1.012000	0.29924	0.065000	0.16485	-1.057000	0.02308	TAC		0.612	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2		
NOTCH3	4854	broad.mit.edu	37	19	15272459	15272459	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:15272459G>T	ENST00000263388.2	-	33	6055	c.5980C>A	c.(5980-5982)Cac>Aac	p.H1994N		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1994					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.H1994N(1)		breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TTGGCAAAGTGGTCCAACAGC	0.642																																					p.H1994N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5980A	19						.						35.0	32.0	33.0					19																	15272459		2201	4300	6501	15133459	SO:0001583	missense	4854	exon33			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.5980C>A	19.37:g.15272459G>T	ENSP00000263388:p.His1994Asn	Somatic		Capture	Illumina HiSeq	Phase_I	15133459	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812234	0.70797	.	.	ENSG00000074181	ENST00000263388	T	0.66460	-0.21	4.03	4.03	0.46877	Ankyrin repeat-containing domain (4);	0.000000	0.33691	N	0.004643	T	0.75917	0.3915	L	0.46670	1.46	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	T	0.76280	-0.3017	10	0.44086	T	0.13	.	15.5047	0.75728	0.0:0.0:1.0:0.0	.	1994	Q9UM47	NOTC3_HUMAN	N	1994	ENSP00000263388:H1994N	ENSP00000263388:H1994N	H	-	1	0	NOTCH3	15133459	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	9.657000	0.98554	2.260000	0.74910	0.650000	0.86243	CAC		0.642	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
CYP4F22	126410	broad.mit.edu	37	19	15640597	15640597	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:15640597G>T	ENST00000269703.3	+	4	499	c.300G>T	c.(298-300)atG>atT	p.M100I	CYP4F22_ENST00000601005.2_Missense_Mutation_p.M100I	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22	100						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.M100I(1)		endometrium(6)|large_intestine(9)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	37						TGGTATGGATGGGACCTGTCC	0.537																																					p.M100I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G300T	19						.						196.0	142.0	160.0					19																	15640597		2203	4300	6503	15501597	SO:0001583	missense	126410	exon4				CCDS12331.1	19p13.12	2013-11-11			ENSG00000171954	ENSG00000171954		"""Cytochrome P450s"""	26820	protein-coding gene	gene with protein product		611495				16436457	Standard	NM_173483		Approved	FLJ39501	uc002nbh.4	Q6NT55	OTTHUMG00000182451	ENST00000269703.3:c.300G>T	19.37:g.15640597G>T	ENSP00000269703:p.Met100Ile	Somatic		Capture	Illumina HiSeq	Phase_I	15501597	NM_173483	Q8N8H4	Missense_Mutation	SNP	ENST00000269703.3	37	CCDS12331.1	.	.	.	.	.	.	.	.	.	.	G	9.267	1.044755	0.19748	.	.	ENSG00000171954	ENST00000269703	D	0.87571	-2.27	5.03	-10.1	0.00402	.	0.669125	0.14354	N	0.324868	T	0.53594	0.1806	N	0.02142	-0.665	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.55173	-0.8182	10	0.10902	T	0.67	.	1.5681	0.02608	0.1719:0.3021:0.2282:0.2977	.	100	Q6NT55	CP4FN_HUMAN	I	100	ENSP00000269703:M100I	ENSP00000269703:M100I	M	+	3	0	CYP4F22	15501597	0.000000	0.05858	0.003000	0.11579	0.585000	0.36419	-4.330000	0.00252	-5.130000	0.00021	0.462000	0.41574	ATG		0.537	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	NM_173483	
CYP4F12	66002	broad.mit.edu	37	19	15789169	15789169	+	Silent	SNP	C	C	T	rs369774036		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:15789169C>T	ENST00000550308.1	+	3	677	c.297C>T	c.(295-297)atC>atT	p.I99I	CYP4F12_ENST00000324632.10_Silent_p.I99I	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	99					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)	p.I99I(1)		NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	TCCCCTTCATCGTTTTATGCC	0.547																																					p.I99I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C297T	19						.	C		1,4391		0,1,2195	137.0	134.0	135.0		297	0.8	0.0	19		135	0,8596		0,0,4298	no	coding-synonymous	CYP4F12	NM_023944.3		0,1,6493	TT,TC,CC		0.0,0.0228,0.0077		99/525	15789169	1,12987	2196	4298	6494	15650169	SO:0001819	synonymous_variant	66002	exon3			AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.297C>T	19.37:g.15789169C>T		Somatic		Capture	Illumina HiSeq	Phase_I	15650169	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																				0.547	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
CYP4F12	66002	broad.mit.edu	37	19	15807285	15807285	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:15807285T>C	ENST00000550308.1	+	12	1740	c.1360T>C	c.(1360-1362)Tca>Cca	p.S454P	CYP4F12_ENST00000324632.10_Missense_Mutation_p.S454P	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	454					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)	p.S454P(1)		NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CAAGGGGAGGTCACCTCTGGC	0.557																																					p.S454P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1360C	19						.						129.0	122.0	125.0					19																	15807285		2202	4300	6502	15668285	SO:0001583	missense	66002	exon12			AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.1360T>C	19.37:g.15807285T>C	ENSP00000448998:p.Ser454Pro	Somatic		Capture	Illumina HiSeq	Phase_I	15668285	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	.	.	.	.	.	.	.	.	.	.	.	9.271	1.045628	0.19748	.	.	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.68479	-0.33;-0.33	2.31	2.31	0.28768	.	0.085006	0.48767	U	0.000162	T	0.63954	0.2555	L	0.38175	1.15	0.46586	D	0.999114	B	0.31989	0.35	P	0.46585	0.521	T	0.65059	-0.6260	10	0.56958	D	0.05	.	8.4933	0.33112	0.0:0.0:0.0:1.0	.	454	Q9HCS2	CP4FC_HUMAN	P	454	ENSP00000448998:S454P;ENSP00000321821:S454P	ENSP00000321821:S454P	S	+	1	0	CYP4F12	15668285	0.971000	0.33674	0.610000	0.28997	0.222000	0.24845	1.484000	0.35508	1.308000	0.44962	0.260000	0.18958	TCA		0.557	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
CYP4F2	8529	broad.mit.edu	37	19	16008283	16008283	+	Missense_Mutation	SNP	G	G	A	rs115517770	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:16008283G>A	ENST00000221700.6	-	2	234	c.139C>T	c.(139-141)Cgc>Tgc	p.R47C	CYP4F2_ENST00000011989.7_5'UTR	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2									p.R47C(1)		NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CACCGAAGGCGGCGGCAGTTG	0.622													.|||	4	0.000798722	0.0	0.0	5008	,	,		16598	0.004		0.0	False		,,,				2504	0.0				p.R47C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C139T	19						.						97.0	94.0	95.0					19																	16008283		2203	4300	6503	15869283	SO:0001583	missense	8529	exon2			U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.139C>T	19.37:g.16008283G>A	ENSP00000221700:p.Arg47Cys	Somatic		Capture	Illumina HiSeq	Phase_I	15869283	NM_001082		Missense_Mutation	SNP	ENST00000221700.6	37	CCDS12336.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	g	10.73	1.431948	0.25813	.	.	ENSG00000186115	ENST00000221700	D	0.91843	-2.92	2.99	1.8	0.24995	.	0.323656	0.22613	U	0.057806	D	0.84942	0.5584	M	0.66939	2.045	0.09310	N	0.999998	B	0.30793	0.295	B	0.24394	0.053	T	0.81267	-0.1010	10	0.62326	D	0.03	.	8.9254	0.35637	0.0:0.0:0.7784:0.2216	.	47	P78329	CP4F2_HUMAN	C	47	ENSP00000221700:R47C	ENSP00000221700:R47C	R	-	1	0	CYP4F2	15869283	0.001000	0.12720	0.002000	0.10522	0.178000	0.23041	0.529000	0.23019	1.655000	0.50712	0.479000	0.44913	CGC		0.622	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082	
CIB3	117286	broad.mit.edu	37	19	16279083	16279083	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:16279083G>T	ENST00000269878.4	-	4	260	c.211C>A	c.(211-213)Cgc>Agc	p.R71S	CIB3_ENST00000379859.3_Missense_Mutation_p.R22S|CIB3_ENST00000541493.1_Intron	NM_054113.2	NP_473454.1	Q96Q77	CIB3_HUMAN	calcium and integrin binding family member 3	71	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)	p.R71S(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	16						ATCCTCTGGCGGAAGGGGTTG	0.562																																					p.R71S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C211A	19						.						52.0	48.0	49.0					19																	16279083		2203	4300	6503	16140083	SO:0001583	missense	117286	exon4			AB050868	CCDS12340.1, CCDS74305.1	19p13.12	2013-01-10						"""EF-hand domain containing"""	24580	protein-coding gene	gene with protein product		610645					Standard	XM_005259728		Approved	KIP3	uc002nds.3	Q96Q77		ENST00000269878.4:c.211C>A	19.37:g.16279083G>T	ENSP00000269878:p.Arg71Ser	Somatic		Capture	Illumina HiSeq	Phase_I	16140083	NM_054113	E7EUX1|Q2M1W0|Q6ISP1	Missense_Mutation	SNP	ENST00000269878.4	37	CCDS12340.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.598011	0.46318	.	.	ENSG00000141977	ENST00000269878;ENST00000379859	T;T	0.66280	-0.2;3.02	4.83	3.75	0.43078	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.68796	0.3040	M	0.77616	2.38	0.80722	D	1	P;P	0.46784	0.884;0.884	B;P	0.48704	0.424;0.587	T	0.71596	-0.4545	10	0.39692	T	0.17	-28.6262	13.547	0.61709	0.0:0.0:0.8442:0.1558	.	22;71	E7EUX1;Q96Q77	.;CIB3_HUMAN	S	71;22	ENSP00000269878:R71S;ENSP00000369188:R22S	ENSP00000269878:R71S	R	-	1	0	CIB3	16140083	1.000000	0.71417	1.000000	0.80357	0.417000	0.31264	5.309000	0.65774	2.253000	0.74438	0.442000	0.29010	CGC		0.562	CIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460351.1	NM_054113	
MYO9B	4650	broad.mit.edu	37	19	17295791	17295791	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:17295791T>A	ENST00000594824.1	+	17	2638	c.2491T>A	c.(2491-2493)Ttc>Atc	p.F831I	MYO9B_ENST00000397274.2_Missense_Mutation_p.F831I|MYO9B_ENST00000595618.1_Missense_Mutation_p.F831I			Q13459	MYO9B_HUMAN	myosin IXB	831	Myosin motor.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.F831I(1)		breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						CAGCGCCCAGTTCCAGGTAGG	0.567																																					p.F831I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2491A	19						.						125.0	137.0	133.0					19																	17295791		2120	4240	6360	17156791	SO:0001583	missense	4650	exon17				CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.2491T>A	19.37:g.17295791T>A	ENSP00000471367:p.Phe831Ile	Somatic		Capture	Illumina HiSeq	Phase_I	17156791	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		.	.	.	.	.	.	.	.	.	.	T	27.8	4.865733	0.91511	.	.	ENSG00000099331	ENST00000397274	T	0.74421	-0.84	4.72	4.72	0.59763	Myosin head, motor domain (2);	0.000000	0.64402	D	0.000018	D	0.83580	0.5285	M	0.68593	2.085	0.51233	D	0.99991	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.99;0.99;0.999	D	0.83445	0.0045	10	0.40728	T	0.16	.	13.398	0.60865	0.0:0.0:0.0:1.0	.	831;831;837	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	I	831	ENSP00000380444:F831I	ENSP00000380444:F831I	F	+	1	0	MYO9B	17156791	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	7.888000	0.87302	1.768000	0.52137	0.459000	0.35465	TTC		0.567	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
LRRC25	126364	broad.mit.edu	37	19	18502854	18502854	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:18502854C>T	ENST00000339007.3	-	2	1514	c.861G>A	c.(859-861)ctG>ctA	p.L287L	LRRC25_ENST00000595840.1_Silent_p.L287L	NM_145256.2	NP_660299.2	Q8N386	LRC25_HUMAN	leucine rich repeat containing 25	287						integral component of membrane (GO:0016021)		p.L287L(1)		endometrium(1)|large_intestine(3)|lung(3)|skin(1)	8						CCAGTGACTGCAGGTTACAGT	0.562																																					p.L287L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G861A	19						.						131.0	96.0	108.0					19																	18502854		2203	4300	6503	18363854	SO:0001819	synonymous_variant	126364	exon2			AK095435	CCDS12377.1	19p13.11	2013-09-20			ENSG00000175489	ENSG00000175489			29806	protein-coding gene	gene with protein product		607518				12384430	Standard	NM_145256		Approved	MAPA, FLJ38116	uc002niw.3	Q8N386	OTTHUMG00000183361	ENST00000339007.3:c.861G>A	19.37:g.18502854C>T		Somatic		Capture	Illumina HiSeq	Phase_I	18363854	NM_145256	Q6IQ00|Q8N9A5	Silent	SNP	ENST00000339007.3	37	CCDS12377.1																																																																																				0.562	LRRC25-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466342.1	NM_145256	
TMEM59L	25789	broad.mit.edu	37	19	18727909	18727909	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:18727909G>A	ENST00000600490.1	+	6	846	c.661G>A	c.(661-663)Gtg>Atg	p.V221M	TMEM59L_ENST00000262817.3_Missense_Mutation_p.V221M			Q9UK28	TM59L_HUMAN	transmembrane protein 59-like	221						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.V221M(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|skin(2)	13						GGAGGTGCACGTGGGTAAGGT	0.632																																					p.V221M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G661A	19						.						49.0	48.0	49.0					19																	18727909		2203	4300	6503	18588909	SO:0001583	missense	25789	exon5			AF186264	CCDS12383.1	19p12	2008-02-05	2007-03-14	2007-03-14		ENSG00000105696			13237	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 4"""	C19orf4		10527841	Standard	NM_012109		Approved	BSMAP	uc002njy.4	Q9UK28		ENST00000600490.1:c.661G>A	19.37:g.18727909G>A	ENSP00000470879:p.Val221Met	Somatic		Capture	Illumina HiSeq	Phase_I	18588909	NM_012109		Missense_Mutation	SNP	ENST00000600490.1	37	CCDS12383.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.470362	0.26423	.	.	ENSG00000105696	ENST00000262817	T	0.46063	0.88	3.36	1.22	0.21188	.	0.853589	0.10235	N	0.699135	T	0.13372	0.0324	N	0.00926	-1.1	0.26510	N	0.974612	B	0.29936	0.262	B	0.22386	0.039	T	0.18241	-1.0343	10	0.30854	T	0.27	-11.9618	6.6718	0.23072	0.2538:0.0:0.7461:0.0	.	221	Q9UK28	TM59L_HUMAN	M	221	ENSP00000262817:V221M	ENSP00000262817:V221M	V	+	1	0	TMEM59L	18588909	0.750000	0.28316	0.995000	0.50966	0.947000	0.59692	0.721000	0.25911	0.422000	0.26005	0.462000	0.41574	GTG		0.632	TMEM59L-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465143.2		
NCAN	1463	broad.mit.edu	37	19	19329907	19329907	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:19329907G>A	ENST00000252575.6	+	3	356	c.257G>A	c.(256-258)gGc>gAc	p.G86D		NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	86	Ig-like V-type.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)	p.G100D(1)|p.G86D(1)		breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	ACTGCGTCGGGCCAGCGACAG	0.652																																					p.G86D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G257A	19						.						65.0	54.0	58.0					19																	19329907		2203	4300	6503	19190907	SO:0001583	missense	1463	exon3			AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.257G>A	19.37:g.19329907G>A	ENSP00000252575:p.Gly86Asp	Somatic		Capture	Illumina HiSeq	Phase_I	19190907	NM_004386	Q9UPK6	Missense_Mutation	SNP	ENST00000252575.6	37	CCDS12397.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.300308	0.81136	.	.	ENSG00000130287	ENST00000539499;ENST00000252575	T	0.67171	-0.25	4.55	4.55	0.56014	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.38837	N	0.001556	T	0.80008	0.4545	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77736	-0.2476	10	0.19590	T	0.45	.	14.8061	0.69956	0.0:0.0:1.0:0.0	.	86	O14594	NCAN_HUMAN	D	100;86	ENSP00000252575:G86D	ENSP00000252575:G86D	G	+	2	0	NCAN	19190907	1.000000	0.71417	0.997000	0.53966	0.755000	0.42902	7.389000	0.79806	2.060000	0.61445	0.491000	0.48974	GGC		0.652	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386	
DOT1L	84444	broad.mit.edu	37	19	2199922	2199922	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:2199922C>T	ENST00000398665.3	+	8	727	c.691C>T	c.(691-693)Cga>Tga	p.R231*		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	231	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)	p.R231*(1)		NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGGAGGGAGCGAATCGCCAA	0.677																																					p.R231X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C691T	19						.						48.0	55.0	53.0					19																	2199922		2112	4224	6336	2150922	SO:0001587	stop_gained	84444	exon8			AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.691C>T	19.37:g.2199922C>T	ENSP00000381657:p.Arg231*	Somatic		Capture	Illumina HiSeq	Phase_I	2150922	NM_032482	O60379|Q96JL1	Nonsense_Mutation	SNP	ENST00000398665.3	37	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	C	19.76	3.886675	0.72410	.	.	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000452696	.	.	.	4.05	2.95	0.34219	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-26.2334	8.7849	0.34814	0.3965:0.6035:0.0:0.0	.	.	.	.	X	231;231;207	.	ENSP00000221482:R231X	R	+	1	2	DOT1L	2150922	1.000000	0.71417	0.996000	0.52242	0.946000	0.59487	3.755000	0.55197	2.102000	0.63906	0.462000	0.41574	CGA		0.677	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482	
ZNF253	56242	broad.mit.edu	37	19	20002411	20002411	+	Missense_Mutation	SNP	G	G	A	rs200404486		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:20002411G>A	ENST00000589717.1	+	4	447	c.355G>A	c.(355-357)Gtg>Atg	p.V119M	ZNF253_ENST00000355650.4_Missense_Mutation_p.V43M|AC011477.1_ENST00000578823.1_RNA|CTC-559E9.8_ENST00000585571.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	119					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.V119M(2)		endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CTGTAAAAGCGTGGGTGAGCA	0.353													a|||	1	0.000199681	0.0	0.0	5008	,	,		18493	0.0		0.001	False		,,,				2504	0.0				p.V119M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G355A	19						.	G	MET/VAL	0,4294		0,0,2147	58.0	60.0	59.0		355	0.1	0.0	19		59	1,8551		0,1,4275	no	missense	ZNF253	NM_021047.2	21	0,1,6422	AA,AG,GG		0.0117,0.0,0.0078	benign	119/500	20002411	1,12845	2147	4276	6423	19863411	SO:0001583	missense	56242	exon4			AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"""Zinc fingers, C2H2-type"", ""-"""	13497	protein-coding gene	gene with protein product		606954	"""zinc finger protein 411"""	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.355G>A	19.37:g.20002411G>A	ENSP00000468720:p.Val119Met	Somatic		Capture	Illumina HiSeq	Phase_I	19863411	NM_021047	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Missense_Mutation	SNP	ENST00000589717.1	37	CCDS42532.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	a	8.774	0.926620	0.18056	0.0	1.17E-4	ENSG00000256771	ENST00000355650	.	.	.	1.4	0.105	0.14535	.	.	.	.	.	T	0.18467	0.0443	L	0.31526	0.94	0.09310	N	1	P	0.36315	0.547	B	0.20955	0.032	T	0.08994	-1.0695	7	.	.	.	.	6.5603	0.22483	0.1932:0.0:0.8068:0.0	.	119	O75346	ZN253_HUMAN	M	119	.	.	V	+	1	0	ZNF253	19863411	0.000000	0.05858	0.009000	0.14445	0.009000	0.06853	-3.077000	0.00615	-1.241000	0.02526	-1.261000	0.01458	GTG		0.353	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047	
ZNF43	7594	broad.mit.edu	37	19	21991188	21991188	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:21991188A>C	ENST00000354959.4	-	4	1820	c.1651T>G	c.(1651-1653)Tca>Gca	p.S551A	ZNF43_ENST00000598381.1_Missense_Mutation_p.S545A|ZNF43_ENST00000594012.1_Missense_Mutation_p.S545A|ZNF43_ENST00000595461.1_Missense_Mutation_p.S545A	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	551					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S551A(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		GTAAGGATTGAGAAATGGTTA	0.383																																					p.S551A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1651G	19						.						50.0	53.0	52.0					19																	21991188		2173	4281	6454	21783028	SO:0001583	missense	7594	exon4			X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"""Zinc fingers, C2H2-type"", ""-"""	13109	protein-coding gene	gene with protein product		603972	"""zinc finger protein 39-like 1 (KOX 27)"", ""zinc finger protein 43 (HTF6)"""	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.1651T>G	19.37:g.21991188A>C	ENSP00000347045:p.Ser551Ala	Somatic		Capture	Illumina HiSeq	Phase_I	21783028	NM_003423	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Missense_Mutation	SNP	ENST00000354959.4	37	CCDS12413.2	.	.	.	.	.	.	.	.	.	.	a	10.80	1.451907	0.26074	.	.	ENSG00000198521	ENST00000397148;ENST00000354959	T	0.35605	1.3	1.76	1.76	0.24704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.28995	0.0720	L	0.39397	1.21	0.09310	N	1	B	0.32939	0.391	B	0.37650	0.255	T	0.23619	-1.0183	9	0.44086	T	0.13	.	4.8818	0.13683	0.7275:0.0:0.0:0.2725	.	551	P17038	ZNF43_HUMAN	A	550;551	ENSP00000347045:S551A	ENSP00000347045:S551A	S	-	1	0	ZNF43	21783028	0.000000	0.05858	0.015000	0.15790	0.948000	0.59901	-0.875000	0.04205	0.808000	0.34231	0.254000	0.18369	TCA		0.383	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423	
ZNF681	148213	broad.mit.edu	37	19	23926704	23926704	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:23926704C>T	ENST00000402377.3	-	4	1789	c.1648G>A	c.(1648-1650)Gct>Act	p.A550T	ZNF681_ENST00000395385.3_Missense_Mutation_p.A481T	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	550					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A550T(1)|p.A481T(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TTATGTGTAGCAAGATGTGAG	0.388																																					p.A550T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1648A	19						.						48.0	51.0	50.0					19																	23926704		2202	4298	6500	23718544	SO:0001583	missense	148213	exon4			AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"""Zinc fingers, C2H2-type"", ""-"""	26457	protein-coding gene	gene with protein product	"""hypothetical protein FLJ31526"""						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.1648G>A	19.37:g.23926704C>T	ENSP00000384000:p.Ala550Thr	Somatic		Capture	Illumina HiSeq	Phase_I	23718544	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	37	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.081671	0.00371	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.08008	3.14;3.14	1.51	0.391	0.16282	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03178	0.0093	N	0.11313	0.125	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45877	-0.9231	9	0.02654	T	1	.	5.2472	0.15502	0.0:0.3847:0.0:0.6153	.	550	Q96N22	ZN681_HUMAN	T	550;481	ENSP00000384000:A550T;ENSP00000378783:A481T	ENSP00000378783:A481T	A	-	1	0	ZNF681	23718544	0.000000	0.05858	0.004000	0.12327	0.002000	0.02628	-2.714000	0.00815	-0.146000	0.11274	-0.817000	0.03123	GCT		0.388	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	
ZNF254	9534	broad.mit.edu	37	19	24310224	24310224	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:24310224C>A	ENST00000357002.4	+	4	1537	c.1422C>A	c.(1420-1422)tcC>tcA	p.S474S	ZNF254_ENST00000342944.6_Silent_p.S389S	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	474					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S474S(1)					all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				TTATATGGTCCTCAACCCTAA	0.398																																					p.S474S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1422A	19						.						60.0	60.0	60.0					19																	24310224		2203	4299	6502	24102064	SO:0001819	synonymous_variant	9534	exon4			AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"""Zinc fingers, C2H2-type"", ""-"""	13047	protein-coding gene	gene with protein product		604768	"""zinc finger protein 539"""	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.1422C>A	19.37:g.24310224C>A		Somatic		Capture	Illumina HiSeq	Phase_I	24102064	NM_203282	A4QPC0|Q86XL7	Silent	SNP	ENST00000357002.4	37	CCDS32983.1																																																																																				0.398	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876	
ZNF536	9745	broad.mit.edu	37	19	30935404	30935404	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:30935404A>C	ENST00000355537.3	+	2	1082	c.935A>C	c.(934-936)gAg>gCg	p.E312A		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	312					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)	p.E312A(1)		NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GCTTCGCAGGAGGAGGAGCTC	0.642																																					p.E312A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A935C	19						.						81.0	89.0	86.0					19																	30935404		2203	4300	6503	35627244	SO:0001583	missense	9745	exon2				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.935A>C	19.37:g.30935404A>C	ENSP00000347730:p.Glu312Ala	Somatic		Capture	Illumina HiSeq	Phase_I	35627244	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	A	13.18	2.159695	0.38119	.	.	ENSG00000198597	ENST00000355537	T	0.27256	1.68	5.59	5.59	0.84812	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.31575	0.0801	N	0.11000	0.08	0.58432	D	0.999998	D;D	0.89917	0.999;1.0	D;D	0.91635	0.989;0.999	T	0.25467	-1.0131	10	0.27082	T	0.32	-37.5138	15.7424	0.77910	1.0:0.0:0.0:0.0	.	312;312	A7E228;O15090	.;ZN536_HUMAN	A	312	ENSP00000347730:E312A	ENSP00000347730:E312A	E	+	2	0	ZNF536	35627244	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	9.302000	0.96175	2.125000	0.65367	0.402000	0.26972	GAG		0.642	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
PDCD5	9141	broad.mit.edu	37	19	33075873	33075873	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:33075873A>G	ENST00000590247.2	+	3	316	c.122A>G	c.(121-123)aAc>aGc	p.N41S	PDCD5_ENST00000586035.1_Missense_Mutation_p.N3S|PDCD5_ENST00000379316.3_Intron|PDCD5_ENST00000419343.3_Missense_Mutation_p.N41S|PDCD5_ENST00000592786.1_Missense_Mutation_p.N41S	NM_004708.3	NP_004699.1	O14737	PDCD5_HUMAN	programmed cell death 5	41					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.N41S(1)		breast(1)|large_intestine(2)|lung(1)|ovary(1)	5	Esophageal squamous(110;0.137)					GAAATGAGAAACAGTATCTTA	0.433																																					p.N41S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A122G	19						.						172.0	164.0	167.0					19																	33075873		2203	4300	6503	37767713	SO:0001583	missense	9141	exon3			AF014955	CCDS12423.1	19q13.11	2012-10-15			ENSG00000105185	ENSG00000105185			8764	protein-coding gene	gene with protein product	"""TFAR19 novel apoptosis-related"", ""TF1 cell apoptosis-related gene 19"""	604583				9920759	Standard	NM_004708		Approved	TFAR19, MGC9294	uc002ntm.3	O14737	OTTHUMG00000180224	ENST00000590247.2:c.122A>G	19.37:g.33075873A>G	ENSP00000466214:p.Asn41Ser	Somatic		Capture	Illumina HiSeq	Phase_I	37767713	NM_004708	B4DE64|Q53YC9|Q6IB70	Missense_Mutation	SNP	ENST00000590247.2	37	CCDS12423.1	.	.	.	.	.	.	.	.	.	.	A	18.80	3.701076	0.68501	.	.	ENSG00000105185	ENST00000419343;ENST00000221784	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.60766	0.2294	M	0.64404	1.975	0.80722	D	1	P;P	0.41420	0.657;0.749	B;P	0.44732	0.215;0.459	T	0.58775	-0.7577	9	0.27082	T	0.32	-12.5088	15.5112	0.75782	1.0:0.0:0.0:0.0	.	41;41	O14737;B4DE64	PDCD5_HUMAN;.	S	41	.	ENSP00000221784:N41S	N	+	2	0	PDCD5	37767713	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.785000	0.85724	2.157000	0.67596	0.533000	0.62120	AAC		0.433	PDCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450320.2	NM_004708	
SLC7A9	11136	broad.mit.edu	37	19	33334775	33334775	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:33334775C>T	ENST00000023064.4	-	10	1251	c.1060G>A	c.(1060-1062)Gcc>Acc	p.A354T	SLC7A9_ENST00000587772.1_Missense_Mutation_p.A354T|SLC7A9_ENST00000590341.1_Missense_Mutation_p.A354T	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	354			A -> T (in CSNU; type III; severe loss of amino acid transport activity). {ECO:0000269|PubMed:11157794, ECO:0000269|PubMed:12371955}.		amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)	p.A354T(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	AAGATGATGGCGGGGGCTGGA	0.557																																					p.A354T	GBM(181;1335 2108 9644 44178 46689)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1060A	19	GRCh37	CM010450	SLC7A9	M		.						50.0	46.0	47.0					19																	33334775		2203	4300	6503	38026615	SO:0001583	missense	11136	exon10			AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"""Solute carriers"""	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.1060G>A	19.37:g.33334775C>T	ENSP00000023064:p.Ala354Thr	Somatic		Capture	Illumina HiSeq	Phase_I	38026615	NM_001126335	B2R9A6	Missense_Mutation	SNP	ENST00000023064.4	37	CCDS12425.1	.	.	.	.	.	.	.	.	.	.	C	19.68	3.873067	0.72180	.	.	ENSG00000021488	ENST00000023064	D	0.91843	-2.92	5.37	4.32	0.51571	Amino acid permease domain (1);	0.048666	0.85682	D	0.000000	D	0.97377	0.9142	H	0.98005	4.125	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.65010	0.931;0.931	D	0.98563	1.0642	10	0.87932	D	0	.	14.9444	0.71020	0.1442:0.8558:0.0:0.0	.	354;354	Q53FY4;P82251	.;BAT1_HUMAN	T	354	ENSP00000023064:A354T	ENSP00000023064:A354T	A	-	1	0	SLC7A9	38026615	1.000000	0.71417	0.974000	0.42286	0.374000	0.29953	4.705000	0.61838	1.223000	0.43536	0.655000	0.94253	GCC		0.557	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1		
WDR88	126248	broad.mit.edu	37	19	33666304	33666304	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:33666304C>T	ENST00000355868.3	+	11	1321	c.1245C>T	c.(1243-1245)tgC>tgT	p.C415C	WDR88_ENST00000361680.2_3'UTR|CTD-2540B15.10_ENST00000590117.1_RNA|AC008738.2_ENST00000577275.1_RNA	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	415								p.C415C(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					CATGTCAGTGCGAAAGATGTG	0.493																																					p.C415C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1245T	19						.						148.0	144.0	145.0					19																	33666304		2203	4300	6503	38358144	SO:0001819	synonymous_variant	126248	exon11			BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"""WD repeat domain containing"""	26999	protein-coding gene	gene with protein product			"""PQQ repeat and WD repeat domain containing"""	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.1245C>T	19.37:g.33666304C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38358144	NM_173479	Q8NEF8	Silent	SNP	ENST00000355868.3	37	CCDS12429.1																																																																																				0.493	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479	
CEBPG	1054	broad.mit.edu	37	19	33870313	33870313	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:33870313G>A	ENST00000284000.4	+	2	830	c.168G>A	c.(166-168)tcG>tcA	p.S56S	CEBPG_ENST00000585933.2_Silent_p.S56S	NM_001806.3	NP_001797.1	P53567	CEBPG_HUMAN	CCAAT/enhancer binding protein (C/EBP), gamma	56					B cell differentiation (GO:0030183)|enucleate erythrocyte differentiation (GO:0043353)|immune response (GO:0006955)|liver development (GO:0001889)|mRNA metabolic process (GO:0016071)|natural killer cell mediated cytotoxicity (GO:0042267)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of DNA binding (GO:0043388)|positive regulation of DNA repair (GO:0045739)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.S56S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)	7	Esophageal squamous(110;0.137)					AAAAGAGTTCGCCCATGGATC	0.557																																					p.S56S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G168A	19						.						62.0	55.0	57.0					19																	33870313		2203	4300	6503	38562153	SO:0001819	synonymous_variant	1054	exon2			U20240	CCDS12432.1	19q13.2	2013-01-10				ENSG00000153879		"""basic leucine zipper proteins"""	1837	protein-coding gene	gene with protein product		138972				1884998	Standard	NM_001806		Approved	GPE1BP, IG/EBP-1	uc021usd.1	P53567		ENST00000284000.4:c.168G>A	19.37:g.33870313G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38562153	NM_001806	B2R946|Q5U052	Silent	SNP	ENST00000284000.4	37	CCDS12432.1																																																																																				0.557	CEBPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451427.2	NM_001806	
ZNF792	126375	broad.mit.edu	37	19	35449752	35449752	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:35449752C>T	ENST00000404801.1	-	4	1393	c.1007G>A	c.(1006-1008)aGc>aAc	p.S336N	ZNF792_ENST00000605484.1_Missense_Mutation_p.S269N	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	336					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S257N(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CACGTGAGGGCTTTCACCGGT	0.488																																					p.S336N	GBM(1;7 183 21053 22581 22847)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1007A	19						.						61.0	57.0	58.0					19																	35449752		2203	4300	6503	40141592	SO:0001583	missense	126375	exon4			AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"""Zinc fingers, C2H2-type"", ""-"""	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.1007G>A	19.37:g.35449752C>T	ENSP00000385099:p.Ser336Asn	Somatic		Capture	Illumina HiSeq	Phase_I	40141592	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Missense_Mutation	SNP	ENST00000404801.1	37	CCDS12440.2	.	.	.	.	.	.	.	.	.	.	c	15.33	2.801025	0.50315	.	.	ENSG00000180884	ENST00000404801;ENST00000379189	T	0.17213	2.29	2.75	0.567	0.17325	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09512	0.0234	N	0.17631	0.505	0.23559	N	0.997413	P	0.43287	0.802	B	0.38156	0.266	T	0.21075	-1.0256	9	0.72032	D	0.01	.	5.1241	0.14875	0.0:0.5796:0.0:0.4204	.	336	Q3KQV3	ZN792_HUMAN	N	336;96	ENSP00000385099:S336N	ENSP00000368487:S96N	S	-	2	0	ZNF792	40141592	0.001000	0.12720	0.193000	0.23327	0.893000	0.52053	0.383000	0.20651	0.238000	0.21222	0.563000	0.77884	AGC		0.488	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872	
MAG	4099	broad.mit.edu	37	19	35786738	35786738	+	Missense_Mutation	SNP	G	G	A	rs201990546		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:35786738G>A	ENST00000392213.3	+	4	428	c.269G>A	c.(268-270)cGc>cAc	p.R90H	MAG_ENST00000597035.1_Intron|MAG_ENST00000537831.2_Missense_Mutation_p.R65H|MAG_ENST00000361922.4_Missense_Mutation_p.R90H	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	90	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)	p.R90H(2)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GGCCGCAGCCGCCTCCTGGGG	0.652																																					p.R65H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G194A	19						.	G	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	82.0	94.0	90.0		194,269,269	5.3	1.0	19		90	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	MAG	NM_001199216.1,NM_002361.3,NM_080600.2	29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	65/602,90/627,90/583	35786738	1,13005	2203	4300	6503	40478578	SO:0001583	missense	4099	exon4			M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6783	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 4A"""	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.269G>A	19.37:g.35786738G>A	ENSP00000376048:p.Arg90His	Somatic		Capture	Illumina HiSeq	Phase_I	40478578	NM_001199216	B7Z2E5|F5GYC0|Q567S4	Missense_Mutation	SNP	ENST00000392213.3	37	CCDS12455.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.732752	0.89482	0.0	1.16E-4	ENSG00000105695	ENST00000262624;ENST00000361922;ENST00000392213;ENST00000537831	T;T;T	0.45668	0.89;0.89;0.89	5.31	5.31	0.75309	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.238219	0.41605	D	0.000855	T	0.32133	0.0819	N	0.11201	0.11	0.35842	D	0.826114	D;D;D	0.76494	0.996;0.999;0.998	P;P;P	0.57101	0.662;0.813;0.813	T	0.18304	-1.0341	10	0.06891	T	0.86	.	10.3226	0.43775	0.0907:0.0:0.9093:0.0	.	127;90;90	Q59GD9;P20916;Q567S4	.;MAG_HUMAN;.	H	127;90;90;65	ENSP00000355234:R90H;ENSP00000376048:R90H;ENSP00000440695:R65H	ENSP00000262624:R127H	R	+	2	0	MAG	40478578	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.042000	0.49815	2.650000	0.89964	0.442000	0.29010	CGC		0.652	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600	
KMT2B	9757	broad.mit.edu	37	19	36218613	36218613	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:36218613G>A	ENST00000222270.7	+	17	4317	c.4317G>A	c.(4315-4317)ggG>ggA	p.G1439G	KMT2B_ENST00000420124.1_Silent_p.G1439G|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1439					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G1441G(1)									GGCCAGATGGGAAGCAACTGC	0.647																																					p.G1439G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4317A	19						.						52.0	60.0	57.0					19																	36218613		2195	4289	6484	40910453	SO:0001819	synonymous_variant	9757	exon17			AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.4317G>A	19.37:g.36218613G>A		Somatic		Capture	Illumina HiSeq	Phase_I	40910453	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	37	CCDS46055.1																																																																																				0.647	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
ARHGAP33	115703	broad.mit.edu	37	19	36269374	36269374	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:36269374C>A	ENST00000007510.4	+	5	423	c.279C>A	c.(277-279)tcC>tcA	p.S93S	ARHGAP33_ENST00000314737.5_Silent_p.S93S|ARHGAP33_ENST00000221905.1_3'UTR|ARHGAP33_ENST00000378944.5_5'UTR			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	93	PX; atypical.				protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)	p.S93S(1)		endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						AGGGCCGTTCCTGGCCGGTTC	0.617																																					p.S93S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C279A	19						.						99.0	99.0	99.0					19																	36269374		2203	4300	6503	40961214	SO:0001819	synonymous_variant	115703	exon5			AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"""Rho GTPase activating proteins"""	23085	protein-coding gene	gene with protein product		614902	"""sorting nexin 26"""	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.279C>A	19.37:g.36269374C>A		Somatic		Capture	Illumina HiSeq	Phase_I	40961214	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	De_novo_Start_OutOfFrame	SNP	ENST00000007510.4	37																																																																																					0.617	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948	
POLR2I	5438	broad.mit.edu	37	19	36604927	36604927	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:36604927G>A	ENST00000221859.4	-	5	794	c.305C>T	c.(304-306)gCg>gTg	p.A102V	TBCB_ENST00000585746.1_5'Flank|TBCB_ENST00000221855.3_5'Flank|TBCB_ENST00000589996.1_5'Flank|TBCB_ENST00000586868.1_5'Flank	NM_006233.4	NP_006224.1	P36954	RPB9_HUMAN	polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa	102					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter (GO:0001193)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)	p.A102V(1)		kidney(1)|large_intestine(1)|ovary(1)	3	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CTCGGCCCGCGCACTGTGTGA	0.617											OREG0025437	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A102V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C305T	19						.						98.0	102.0	101.0					19																	36604927		2203	4300	6503	41296767	SO:0001583	missense	5438	exon5				CCDS12487.1	19q13.12	2013-10-17	2002-08-29		ENSG00000105258	ENSG00000105258	2.7.7.6	"""RNA polymerase subunits"""	9196	protein-coding gene	gene with protein product		180662	"""polymerase (RNA) II (DNA directed) polypeptide I (14.5kD)"""			8034326	Standard	NM_006233		Approved	RPB9, hRPB14.5	uc002ode.3	P36954	OTTHUMG00000181749	ENST00000221859.4:c.305C>T	19.37:g.36604927G>A	ENSP00000221859:p.Ala102Val	Somatic	864	Capture	Illumina HiSeq	Phase_I	41296767	NM_006233	B2R5J2|Q6NW05	Missense_Mutation	SNP	ENST00000221859.4	37	CCDS12487.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990806	0.35131	.	.	ENSG00000105258	ENST00000221859	T	0.43688	0.94	5.0	3.96	0.45880	Zinc finger, TFIIS-type (4);	0.094146	0.64402	D	0.000001	T	0.31295	0.0792	L	0.29908	0.895	0.40201	D	0.977519	B	0.19445	0.036	B	0.18263	0.021	T	0.17410	-1.0370	10	0.56958	D	0.05	-13.3781	11.5104	0.50490	0.0876:0.0:0.9124:0.0	.	102	P36954	RPB9_HUMAN	V	102	ENSP00000221859:A102V	ENSP00000221859:A102V	A	-	2	0	POLR2I	41296767	1.000000	0.71417	0.994000	0.49952	0.086000	0.17979	5.920000	0.70017	1.474000	0.48178	-0.140000	0.14226	GCG		0.617	POLR2I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457442.1	NM_006233	
SHD	56961	broad.mit.edu	37	19	4284783	4284783	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:4284783T>C	ENST00000543264.2	+	4	2061	c.598T>C	c.(598-600)Ttt>Ctt	p.F200L	SHD_ENST00000600475.1_3'UTR|SHD_ENST00000599689.1_Missense_Mutation_p.F200L	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	200								p.F200L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|stomach(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCAGTGCAGTTTGACAGTCC	0.617																																					p.F200L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T598C	19						.						51.0	55.0	53.0					19																	4284783		2203	4300	6503	4235783	SO:0001583	missense	56961	exon4			BC007206	CCDS12125.1	19p13.3	2013-02-14				ENSG00000105251		"""SH2 domain containing"""	30633	protein-coding gene	gene with protein product		610481				9315092	Standard	NM_020209		Approved		uc002lzw.2	Q96IW2		ENST00000543264.2:c.598T>C	19.37:g.4284783T>C	ENSP00000446058:p.Phe200Leu	Somatic		Capture	Illumina HiSeq	Phase_I	4235783	NM_020209	Q96NC2	Missense_Mutation	SNP	ENST00000543264.2	37	CCDS12125.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.381520	0.82792	.	.	ENSG00000105251	ENST00000543264;ENST00000221852	T	0.29397	1.57	4.44	4.44	0.53790	.	0.174039	0.51477	D	0.000089	T	0.46347	0.1388	M	0.62088	1.915	0.35704	D	0.815884	D;P	0.55605	0.972;0.879	P;P	0.60117	0.869;0.596	T	0.57254	-0.7843	10	0.42905	T	0.14	-9.0958	11.6784	0.51442	0.0:0.0:0.0:1.0	.	107;200	Q9NPN8;Q96IW2	.;SHD_HUMAN	L	200;115	ENSP00000446058:F200L	ENSP00000221852:F115L	F	+	1	0	SHD	4235783	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	6.610000	0.74178	1.868000	0.54150	0.402000	0.26972	TTT		0.617	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209	
ZNF529	57711	broad.mit.edu	37	19	37037948	37037948	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:37037948T>C	ENST00000591340.1	-	5	1670	c.1512A>G	c.(1510-1512)aaA>aaG	p.K504K	ZNF529_ENST00000334116.7_Silent_p.K399K	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	504					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K504K(1)|p.K503K(1)		breast(1)	1	Esophageal squamous(110;0.198)					ATTCATAGGGTTTTTCTCCAG	0.403																																					p.K504K												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A1512G	19						.						65.0	70.0	69.0					19																	37037948		2196	4298	6494	41729788	SO:0001819	synonymous_variant	57711	exon6			AK025110	CCDS54256.1	19q13.13	2014-08-22			ENSG00000186020	ENSG00000186020		"""Zinc fingers, C2H2-type"", ""-"""	29328	protein-coding gene	gene with protein product						10997877	Standard	NM_020951		Approved	KIAA1615	uc002oeh.4	Q6P280	OTTHUMG00000180714	ENST00000591340.1:c.1512A>G	19.37:g.37037948T>C		Somatic		Capture	Illumina HiSeq	Phase_I	41729788	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Silent	SNP	ENST00000591340.1	37	CCDS54256.1																																																																																				0.403	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951	
SIPA1L3	23094	broad.mit.edu	37	19	38692606	38692606	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:38692606C>T	ENST00000222345.6	+	20	5598	c.5089C>T	c.(5089-5091)Ccc>Tcc	p.P1697S	CTB-102L5.8_ENST00000598146.1_RNA|RN7SL663P_ENST00000578592.1_RNA	NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1697					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)	p.P1697S(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GGAGAGGGGACCCCCGACCCC	0.642																																					p.P1697S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5089T	19						.						58.0	62.0	61.0					19																	38692606		2203	4300	6503	43384446	SO:0001583	missense	23094	exon20			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.5089C>T	19.37:g.38692606C>T	ENSP00000222345:p.Pro1697Ser	Somatic		Capture	Illumina HiSeq	Phase_I	43384446	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.004108	0.74932	.	.	ENSG00000105738	ENST00000222345	T	0.30714	1.52	4.82	4.82	0.62117	.	0.137276	0.49916	D	0.000131	T	0.24774	0.0601	N	0.22421	0.69	0.47407	D	0.999417	P	0.39737	0.685	B	0.41412	0.356	T	0.03259	-1.1055	10	0.18710	T	0.47	-31.9995	16.6859	0.85306	0.0:1.0:0.0:0.0	.	1697	O60292	SI1L3_HUMAN	S	1697	ENSP00000222345:P1697S	ENSP00000222345:P1697S	P	+	1	0	SIPA1L3	43384446	0.987000	0.35691	0.999000	0.59377	0.908000	0.53690	2.065000	0.41442	2.217000	0.71921	0.561000	0.74099	CCC		0.642	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
KCNK6	9424	broad.mit.edu	37	19	38817249	38817249	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:38817249G>A	ENST00000263372.3	+	2	446	c.339G>A	c.(337-339)acG>acA	p.T113T		NM_004823.1	NP_004814.1	Q9Y257	KCNK6_HUMAN	potassium channel, subfamily K, member 6	113					negative regulation of systemic arterial blood pressure (GO:0003085)|potassium ion transport (GO:0006813)|regulation of resting membrane potential (GO:0060075)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)	p.T113T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)	17	all_cancers(60;5.83e-07)		Lung(45;0.00047)|LUSC - Lung squamous cell carcinoma(53;0.000613)		Ibutilide(DB00308)|Quinidine(DB00908)	GGTACACAACGCCACTGACTG	0.587																																					p.T113T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G339A	19						.						102.0	101.0	101.0					19																	38817249		2203	4300	6503	43509089	SO:0001819	synonymous_variant	9424	exon2			AF117708	CCDS12513.1	19q13.1	2012-03-07				ENSG00000099337		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6281	protein-coding gene	gene with protein product		603939				10075682, 10393428, 16382106	Standard	NM_004823		Approved	K2p6.1, TWIK-2	uc002oic.3	Q9Y257		ENST00000263372.3:c.339G>A	19.37:g.38817249G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43509089	NM_004823	Q9HB47	Silent	SNP	ENST00000263372.3	37	CCDS12513.1																																																																																				0.587	KCNK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460524.1	NM_004823	
KCNK6	9424	broad.mit.edu	37	19	38817447	38817447	+	Silent	SNP	C	C	T	rs368336056		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:38817447C>T	ENST00000263372.3	+	2	644	c.537C>T	c.(535-537)gtC>gtT	p.V179V		NM_004823.1	NP_004814.1	Q9Y257	KCNK6_HUMAN	potassium channel, subfamily K, member 6	179					negative regulation of systemic arterial blood pressure (GO:0003085)|potassium ion transport (GO:0006813)|regulation of resting membrane potential (GO:0060075)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)	p.V179V(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)	17	all_cancers(60;5.83e-07)		Lung(45;0.00047)|LUSC - Lung squamous cell carcinoma(53;0.000613)		Ibutilide(DB00308)|Quinidine(DB00908)	TGTTGGGGGTCGTAGTGACCG	0.622																																					p.V179V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C537T	19						.	C		0,4406		0,0,2203	100.0	97.0	98.0		537	-2.5	0.0	19		98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KCNK6	NM_004823.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		179/314	38817447	1,13005	2203	4300	6503	43509287	SO:0001819	synonymous_variant	9424	exon2			AF117708	CCDS12513.1	19q13.1	2012-03-07				ENSG00000099337		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6281	protein-coding gene	gene with protein product		603939				10075682, 10393428, 16382106	Standard	NM_004823		Approved	K2p6.1, TWIK-2	uc002oic.3	Q9Y257		ENST00000263372.3:c.537C>T	19.37:g.38817447C>T		Somatic		Capture	Illumina HiSeq	Phase_I	43509287	NM_004823	Q9HB47	Silent	SNP	ENST00000263372.3	37	CCDS12513.1																																																																																				0.622	KCNK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460524.1	NM_004823	
RINL	126432	broad.mit.edu	37	19	39361446	39361446	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:39361446A>G	ENST00000591812.1	-	8	874	c.788T>C	c.(787-789)gTc>gCc	p.V263A	RINL_ENST00000598904.1_Missense_Mutation_p.V149A|RINL_ENST00000602238.1_5'UTR|RINL_ENST00000340740.3_Missense_Mutation_p.V149A|CTC-360G5.6_ENST00000593830.1_RNA			Q6ZS11	RINL_HUMAN	Ras and Rab interactor-like	263					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|ruffle (GO:0001726)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.V149A(1)		endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|urinary_tract(2)	17						CAGAGACTGGACGTGAATGGT	0.622																																					p.V149A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T446C	19						.						68.0	59.0	62.0					19																	39361446		2203	4300	6503	44053286	SO:0001583	missense	126432	exon8			AK127808	CCDS12522.1, CCDS59386.1	19q13.2	2010-07-13			ENSG00000187994	ENSG00000187994			24795	protein-coding gene	gene with protein product							Standard	NM_001195833		Approved	FLJ45909	uc010xuo.2	Q6ZS11		ENST00000591812.1:c.788T>C	19.37:g.39361446A>G	ENSP00000467107:p.Val263Ala	Somatic		Capture	Illumina HiSeq	Phase_I	44053286	NM_198445	B4DPG5	Missense_Mutation	SNP	ENST00000591812.1	37	CCDS59386.1	.	.	.	.	.	.	.	.	.	.	A	12.06	1.824405	0.32237	.	.	ENSG00000187994	ENST00000340740;ENST00000536520	T	0.38722	1.12	5.22	5.22	0.72569	.	0.555435	0.16821	N	0.198148	T	0.27278	0.0669	N	0.24115	0.695	0.09310	N	1	P;P	0.40970	0.734;0.598	B;B	0.34824	0.185;0.19	T	0.13072	-1.0523	10	0.37606	T	0.19	-6.56	11.4003	0.49866	1.0:0.0:0.0:0.0	.	263;149	B4DPG5;Q6ZS11	.;RINL_HUMAN	A	149	ENSP00000340369:V149A	ENSP00000340369:V149A	V	-	2	0	RINL	44053286	0.401000	0.25303	0.331000	0.25455	0.100000	0.18952	3.944000	0.56629	2.197000	0.70478	0.402000	0.26972	GTC		0.622	RINL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460433.1	NM_198445	
PLIN4	729359	broad.mit.edu	37	19	4512415	4512415	+	Silent	SNP	G	G	A	rs374096913		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:4512415G>A	ENST00000301286.3	-	3	1514	c.1515C>T	c.(1513-1515)acC>acT	p.T505T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	505	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)		p.T433T(1)		NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						TGTCTACGCCGGTCTGGACGG	0.617													g|||	1	0.000199681	0.0008	0.0	5008	,	,		21873	0.0		0.0	False		,,,				2504	0.0				p.T505T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1515T	19						.	G		0,4056		0,0,2028	108.0	115.0	113.0		1515	-10.9	0.0	19		113	2,8360		0,2,4179	no	coding-synonymous	PLIN4	NM_001080400.1		0,2,6207	AA,AG,GG		0.0239,0.0,0.0161		505/1358	4512415	2,12416	2028	4181	6209	4463415	SO:0001819	synonymous_variant	729359	exon3			AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1515C>T	19.37:g.4512415G>A		Somatic		Capture	Illumina HiSeq	Phase_I	4463415	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																				0.617	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
FBXO17	115290	broad.mit.edu	37	19	39435738	39435738	+	Silent	SNP	G	G	A	rs138216167		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:39435738G>A	ENST00000292852.4	-	5	905	c.564C>T	c.(562-564)ggC>ggT	p.G188G	FBXO17_ENST00000595329.1_Silent_p.G188G|SARS2_ENST00000448145.2_Silent_p.G23G|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.R93C	NM_024907.5	NP_079183.4	Q96EF6	FBX17_HUMAN	F-box protein 17	188	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)	glycoprotein binding (GO:0001948)	p.G197G(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	7	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			TCTCTCGAGCGCCCCACCTGC	0.627																																					p.G197G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C591T	19						.	G	,	4,4402	6.2+/-15.9	0,4,2199	50.0	48.0	49.0		564,591	-9.1	0.3	19	dbSNP_134	49	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FBXO17	NM_024907.5,NM_148169.1	,	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	,	188/279,197/288	39435738	4,13002	2203	4300	6503	44127578	SO:0001819	synonymous_variant	115290	exon5			AF386743	CCDS12526.1	19q13.2	2010-07-02	2004-06-15	2004-06-16		ENSG00000269190		"""F-boxes /  ""other"""""	18754	protein-coding gene	gene with protein product	"""F-box only protein 26"""	609094	"""F-box only protein 17"""	FBXO26			Standard	NM_148169		Approved	FBG4, FLJ25205, MGC9379, FLJ11798, Fbx17		Q96EF6		ENST00000292852.4:c.564C>T	19.37:g.39435738G>A		Somatic		Capture	Illumina HiSeq	Phase_I	44127578	NM_148169	Q96LQ4	Silent	SNP	ENST00000292852.4	37	CCDS12526.1																																																																																				0.627	FBXO17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463273.1	NM_024907	
FBL	2091	broad.mit.edu	37	19	40331131	40331131	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:40331131T>A	ENST00000221801.3	-	3	319	c.206A>T	c.(205-207)aAc>aTc	p.N69I	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	69	DMA/Gly-rich.				histone glutamine methylation (GO:1990258)|osteoblast differentiation (GO:0001649)|rRNA processing (GO:0006364)|snoRNA metabolic process (GO:0016074)|tRNA processing (GO:0008033)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone-glutamine methyltransferase activity (GO:1990259)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.N69I(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)	9	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)	Renal(1328;0.000518)|Hepatocellular(1079;0.0893)	Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)	GBM - Glioblastoma multiforme(1328;0.000826)|STAD - Stomach adenocarcinoma(1328;0.138)		ACGACCCCGGTTGCCACCAGA	0.587																																					p.N69I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A206T	19						.						193.0	175.0	181.0					19																	40331131		2203	4300	6503	45022971	SO:0001583	missense	2091	exon3			AC005393	CCDS12545.1	19q13.1	2010-02-17			ENSG00000105202	ENSG00000105202			3599	protein-coding gene	gene with protein product		134795				1846968, 2026646	Standard	NM_001436		Approved	RNU3IP1, FLRN, FIB	uc002omn.3	P22087		ENST00000221801.3:c.206A>T	19.37:g.40331131T>A	ENSP00000221801:p.Asn69Ile	Somatic		Capture	Illumina HiSeq	Phase_I	45022971	NM_001436	B5BUE8|O75259|Q6IAT5|Q9UPI6	Missense_Mutation	SNP	ENST00000221801.3	37	CCDS12545.1	.	.	.	.	.	.	.	.	.	.	T	15.01	2.706464	0.48412	.	.	ENSG00000105202	ENST00000221801	.	.	.	4.79	-8.59	0.00893	.	4.639020	0.02733	N	0.115341	T	0.24044	0.0582	N	0.14661	0.345	0.23361	N	0.997839	B;B;B	0.18968	0.01;0.032;0.032	B;B;B	0.09377	0.004;0.002;0.002	T	0.30650	-0.9971	9	0.62326	D	0.03	-1.6229	9.8245	0.40903	0.0:0.4748:0.3542:0.171	.	69;8;69	B4DLD4;Q96BS4;P22087	.;.;FBRL_HUMAN	I	69	.	ENSP00000221801:N69I	N	-	2	0	FBL	45022971	0.001000	0.12720	0.454000	0.27019	0.870000	0.49936	-0.958000	0.03857	-1.392000	0.02082	0.418000	0.28097	AAC		0.587	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436	
FCGBP	8857	broad.mit.edu	37	19	40433093	40433093	+	Silent	SNP	C	C	T	rs148301068	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:40433093C>T	ENST00000221347.6	-	2	1183	c.1176G>A	c.(1174-1176)tcG>tcA	p.S392S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	392	IgGFc-binding.					extracellular vesicular exosome (GO:0070062)		p.S392S(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CTTCAGCATACGAGAACTCAC	0.607													C|||	2	0.000399361	0.0	0.0	5008	,	,		19193	0.001		0.0	False		,,,				2504	0.001				p.S392S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1176A	19						.						120.0	92.0	101.0					19																	40433093		2203	4300	6503	45124933	SO:0001819	synonymous_variant	8857	exon2			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.1176G>A	19.37:g.40433093C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45124933	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.607	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
SERTAD3	29946	broad.mit.edu	37	19	40947569	40947569	+	Missense_Mutation	SNP	C	C	T	rs369267116		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:40947569C>T	ENST00000322354.3	-	2	915	c.419G>A	c.(418-420)cGg>cAg	p.R140Q	CTC-492K19.4_ENST00000599050.1_RNA|SERTAD3_ENST00000392028.4_Missense_Mutation_p.R140Q|SERTAD3_ENST00000601217.1_5'Flank	NM_203344.2	NP_976219.1	Q9UJW9	SRTD3_HUMAN	SERTA domain containing 3	140					negative regulation of cell growth (GO:0030308)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.R140Q(1)		kidney(1)|large_intestine(4)|lung(2)	7			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CCCCAAGTACCGGGAGCTCAG	0.577																																					p.R140Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G419A	19						.	C	GLN/ARG,GLN/ARG	0,4406		0,0,2203	69.0	74.0	72.0		419,419	3.8	0.9	19		72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SERTAD3	NM_013368.3,NM_203344.2	43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	140/197,140/197	40947569	1,13005	2203	4300	6503	45639409	SO:0001583	missense	29946	exon2			AF192529	CCDS12558.1	19q13.2	2008-02-05				ENSG00000167565			17931	protein-coding gene	gene with protein product	"""RPA-binding trans-activator"""	612125				10982866, 11331592	Standard	NM_013368		Approved	RBT1	uc002onv.4	Q9UJW9		ENST00000322354.3:c.419G>A	19.37:g.40947569C>T	ENSP00000325414:p.Arg140Gln	Somatic		Capture	Illumina HiSeq	Phase_I	45639409	NM_203344	B3KQB3|Q96CQ2	Missense_Mutation	SNP	ENST00000322354.3	37	CCDS12558.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.497554	0.44455	0.0	1.16E-4	ENSG00000167565	ENST00000322354;ENST00000392028	.	.	.	5.89	3.78	0.43462	.	0.105878	0.37393	N	0.002118	T	0.21962	0.0529	N	0.08118	0	0.27726	N	0.944979	B	0.16802	0.019	B	0.06405	0.002	T	0.12630	-1.0540	9	0.45353	T	0.12	0.0043	9.169	0.37069	0.0:0.8327:0.0:0.1673	.	140	Q9UJW9	SRTD3_HUMAN	Q	140	.	ENSP00000325414:R140Q	R	-	2	0	SERTAD3	45639409	1.000000	0.71417	0.942000	0.38095	0.696000	0.40369	1.268000	0.33062	0.840000	0.34995	-0.150000	0.13652	CGG		0.577	SERTAD3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462573.1	NM_013368	
TGFB1	7040	broad.mit.edu	37	19	41848076	41848076	+	Splice_Site	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:41848076G>A	ENST00000221930.5	-	4	1577	c.711C>T	c.(709-711)aaC>aaT	p.N237N		NM_000660.4	NP_000651.3	P01137	TGFB1_HUMAN	transforming growth factor, beta 1	237	Arm domain. {ECO:0000250}.				active induction of host immune response by virus (GO:0046732)|adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains (GO:0002460)|aging (GO:0007568)|ATP biosynthetic process (GO:0006754)|blood coagulation (GO:0007596)|branch elongation involved in mammary gland duct branching (GO:0060751)|cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cell-cell junction organization (GO:0045216)|cellular calcium ion homeostasis (GO:0006874)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation (GO:0002062)|common-partner SMAD protein phosphorylation (GO:0007182)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|defense response to fungus, incompatible interaction (GO:0009817)|digestive tract development (GO:0048565)|embryo development (GO:0009790)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|evasion or tolerance of host defenses by virus (GO:0019049)|extracellular matrix assembly (GO:0085029)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|face morphogenesis (GO:0060325)|female pregnancy (GO:0007565)|frontal suture morphogenesis (GO:0060364)|germ cell migration (GO:0008354)|hematopoietic progenitor cell differentiation (GO:0002244)|hyaluronan catabolic process (GO:0030214)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|lens fiber cell differentiation (GO:0070306)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymph node development (GO:0048535)|macrophage derived foam cell differentiation (GO:0010742)|mammary gland branching involved in thelarche (GO:0060744)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|modulation by virus of host morphology or physiology (GO:0019048)|mononuclear cell proliferation (GO:0032943)|myelination (GO:0042552)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA replication (GO:0008156)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of extracellular matrix disassembly (GO:0010716)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of ossification (GO:0030279)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|ossification involved in bone remodeling (GO:0043932)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|phosphate-containing compound metabolic process (GO:0006796)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NAD+ ADP-ribosyltransferase activity (GO:1901666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of odontogenesis (GO:0042482)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to nucleus (GO:1900182)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein secretion (GO:0050714)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein export from nucleus (GO:0006611)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|receptor catabolic process (GO:0032801)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of binding (GO:0051098)|regulation of blood vessel remodeling (GO:0060312)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of cartilage development (GO:0061035)|regulation of cell migration (GO:0030334)|regulation of DNA binding (GO:0051101)|regulation of miRNA metabolic process (GO:2000628)|regulation of protein import into nucleus (GO:0042306)|regulation of sodium ion transport (GO:0002028)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulatory T cell differentiation (GO:0045066)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to laminar fluid shear stress (GO:0034616)|response to progesterone (GO:0032570)|response to radiation (GO:0009314)|response to vitamin D (GO:0033280)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|T cell homeostasis (GO:0043029)|tolerance induction to self antigen (GO:0002513)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|viral life cycle (GO:0019058)	axon (GO:0030424)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	antigen binding (GO:0003823)|cytokine activity (GO:0005125)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|type II transforming growth factor beta receptor binding (GO:0005114)	p.N237N(1)		endometrium(1)|large_intestine(2)|lung(4)|skin(1)	8					Hyaluronidase(DB00070)	AGGCCTCACCGTTGATGTCCA	0.587																																					p.N237N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C711T	19						.						77.0	67.0	70.0					19																	41848076		2203	4300	6503	46539916	SO:0001630	splice_region_variant	7040	exon4			X02812	CCDS33031.1	19q13.1	2014-01-30	2007-02-16			ENSG00000105329		"""Endogenous ligands"""	11766	protein-coding gene	gene with protein product	"""Camurati-Engelmann disease"", ""prepro-transforming growth factor beta-1"""	190180		TGFB, DPD1		10631145, 10843814	Standard	NM_000660		Approved	CED, TGFbeta	uc002oqh.2	P01137		ENST00000221930.5:c.712+1C>T	19.37:g.41848076G>A		Somatic		Capture	Illumina HiSeq	Phase_I	46539916	NM_000660	A8K792|Q9UCG4	Silent	SNP	ENST00000221930.5	37	CCDS33031.1																																																																																				0.587	TGFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463500.2		Silent
ATP1A3	478	broad.mit.edu	37	19	42489085	42489085	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:42489085C>A	ENST00000302102.5	-	8	1128	c.978G>T	c.(976-978)ctG>ctT	p.L326L	ATP1A3_ENST00000545399.1_Silent_p.L339L|ATP1A3_ENST00000602133.1_Silent_p.L296L|ATP1A3_ENST00000543770.1_Silent_p.L337L	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	326					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.L326L(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						CAGTGGCCAGCAGACCCTCTG	0.617																																					p.L326L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G978T	19						.						52.0	44.0	46.0					19																	42489085		2203	4300	6503	47180925	SO:0001819	synonymous_variant	478	exon8				CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"""ATPases / P-type"""	801	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-3"", ""sodium pump subunit alpha-3"", ""sodium-potassium ATPase catalytic subunit alpha-3"""	182350	"""dystonia 12"""	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.978G>T	19.37:g.42489085C>A		Somatic		Capture	Illumina HiSeq	Phase_I	47180925	NM_152296	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Silent	SNP	ENST00000302102.5	37	CCDS12594.1																																																																																				0.617	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296	
PSG1	5669	broad.mit.edu	37	19	43372995	43372995	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:43372995T>C	ENST00000436291.2	-	4	1017	c.901A>G	c.(901-903)Acg>Gcg	p.T301A	PSG1_ENST00000595356.1_Missense_Mutation_p.T301A|PSG1_ENST00000595124.1_Missense_Mutation_p.T208A|PSG1_ENST00000244296.2_Missense_Mutation_p.T301A|PSG1_ENST00000312439.6_Missense_Mutation_p.T301A|PSG1_ENST00000403380.3_Missense_Mutation_p.T208A	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	301	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.T301A(3)		breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				TCATTTCTCGTGACACTGGGT	0.493																																					p.T301A												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.A901G	19						.						35.0	42.0	39.0					19																	43372995		1501	2700	4201	48064835	SO:0001583	missense	5669	exon4				CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.901A>G	19.37:g.43372995T>C	ENSP00000413041:p.Thr301Ala	Somatic		Capture	Illumina HiSeq	Phase_I	48064835	NM_006905	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	37	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	11.29	1.594175	0.28445	.	.	ENSG00000231924	ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.14766	2.48;2.48;2.48;2.48	1.63	1.63	0.23807	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.41465	0.1160	H	0.96460	3.825	0.20926	N	0.999821	B;P;P;P;B;P;P	0.51147	0.063;0.914;0.787;0.788;0.407;0.942;0.841	B;P;P;P;B;P;P	0.60068	0.198;0.77;0.644;0.852;0.358;0.868;0.615	T	0.22382	-1.0218	9	0.87932	D	0	.	5.2049	0.15285	0.0:0.0:0.0:1.0	.	301;208;301;208;301;173;301	P11464-4;G5E9F7;P11464;Q8NBY8;P11464-3;B4DTG5;P11464-2	.;.;PSG1_HUMAN;.;.;.;.	A	301;208;301;301	ENSP00000413041:T301A;ENSP00000385386:T208A;ENSP00000308970:T301A;ENSP00000244296:T301A	ENSP00000244296:T301A	T	-	1	0	PSG1	48064835	0.007000	0.16637	0.576000	0.28549	0.007000	0.05969	2.071000	0.41500	0.715000	0.32103	0.164000	0.16699	ACG		0.493	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
IRGQ	126298	broad.mit.edu	37	19	44097155	44097155	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:44097155C>T	ENST00000602269.1	-	2	1080	c.895G>A	c.(895-897)Gcc>Acc	p.A299T	L34079.2_ENST00000594374.1_Missense_Mutation_p.A12T|IRGQ_ENST00000601520.1_5'UTR|IRGQ_ENST00000422989.1_Missense_Mutation_p.A299T			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	299	IRG-type G.							p.A299T(1)		endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				AGGATGAGGGCGTCGTAGTGC	0.687																																					p.A299T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G895A	19						.						43.0	42.0	42.0					19																	44097155		2203	4300	6503	48788995	SO:0001583	missense	126298	exon3			AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"""immunity-related GTPase family, Q1"""	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.895G>A	19.37:g.44097155C>T	ENSP00000472250:p.Ala299Thr	Somatic		Capture	Illumina HiSeq	Phase_I	48788995	NM_001007561	B2RNP3	Missense_Mutation	SNP	ENST00000602269.1	37	CCDS33040.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.089026	0.76756	.	.	ENSG00000167378	ENST00000422989	T	0.50813	0.73	4.5	4.5	0.54988	.	0.233723	0.32655	N	0.005816	T	0.55049	0.1896	L	0.57536	1.79	0.32558	N	0.53152	D	0.64830	0.994	P	0.54174	0.744	T	0.64287	-0.6443	10	0.45353	T	0.12	-17.3847	13.0111	0.58731	0.0:1.0:0.0:0.0	.	299	Q8WZA9	IRGQ_HUMAN	T	299	ENSP00000387535:A299T	ENSP00000387535:A299T	A	-	1	0	IRGQ	48788995	0.954000	0.32549	1.000000	0.80357	0.956000	0.61745	1.150000	0.31639	2.782000	0.95742	0.655000	0.94253	GCC		0.687	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561	
IRGC	56269	broad.mit.edu	37	19	44222974	44222974	+	Silent	SNP	C	C	T	rs541211616		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:44222974C>T	ENST00000244314.5	+	2	463	c.264C>T	c.(262-264)ggC>ggT	p.G88G		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	88	IRG-type G.					membrane (GO:0016020)	GTP binding (GO:0005525)|hydrolase activity, acting on acid anhydrides (GO:0016817)	p.G88G(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(2)	25		Prostate(69;0.0435)				CTCTCACGGGCGTCATGGAGA	0.697													C|||	1	0.000199681	0.0	0.0	5008	,	,		14516	0.0		0.0	False		,,,				2504	0.001				p.G88G	Colon(189;350 2037 11447 13433 38914)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C264T	19						.						39.0	38.0	39.0					19																	44222974		2203	4300	6503	48914814	SO:0001819	synonymous_variant	56269	exon2			BC066939	CCDS12629.1	19q13.32	2008-02-05	2005-10-31	2005-10-31	ENSG00000124449	ENSG00000124449			28835	protein-coding gene	gene with protein product			"""immunity-related GTPase family, cinema 1"""	IRGC1		12477932	Standard	NM_019612		Approved	Iigp5, CINEMA	uc002oxh.3	Q6NXR0	OTTHUMG00000154587	ENST00000244314.5:c.264C>T	19.37:g.44222974C>T		Somatic		Capture	Illumina HiSeq	Phase_I	48914814	NM_019612	Q05BR8	Silent	SNP	ENST00000244314.5	37	CCDS12629.1																																																																																				0.697	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612	
CEACAM20	125931	broad.mit.edu	37	19	45029253	45029253	+	RNA	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:45029253G>T	ENST00000454753.1	-	0	355							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				TGCAGCTGGAGGACTCCATAC	0.587																																					p.P26H												.	.	0			c.C77A	19						.						107.0	114.0	112.0					19																	45029253		2098	4217	6315	49721093			125931	exon2			AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45029253G>T		Somatic		Capture	Illumina HiSeq	Phase_I	49721093	NM_001102597		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																					0.587	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
PVRL2	5819	broad.mit.edu	37	19	45375403	45375403	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:45375403C>T	ENST00000252483.5	+	3	772	c.772C>T	c.(772-774)Cgc>Tgc	p.R258C	PVRL2_ENST00000252485.4_Missense_Mutation_p.R258C	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	258					acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)	p.R258C(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		CCTCTCTGTACGCTGTGAGTG	0.557																																					p.R258C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C772T	19						.						160.0	118.0	132.0					19																	45375403		2203	4300	6503	50067243	SO:0001583	missense	5819	exon3			X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.772C>T	19.37:g.45375403C>T	ENSP00000252483:p.Arg258Cys	Somatic		Capture	Illumina HiSeq	Phase_I	50067243	NM_002856	A8K5L5|O75455|Q6IBI6|Q96J29	Missense_Mutation	SNP	ENST00000252483.5	37	CCDS42576.1	.	.	.	.	.	.	.	.	.	.	C	16.62	3.172643	0.57584	.	.	ENSG00000130202	ENST00000252483;ENST00000252485	T;T	0.15487	2.42;2.42	4.25	3.15	0.36227	Immunoglobulin-like fold (1);	0.000000	0.49305	D	0.000142	T	0.36138	0.0956	M	0.79475	2.455	0.47441	D	0.999425	D;D	0.89917	1.0;1.0	P;D	0.65987	0.872;0.94	T	0.14643	-1.0465	10	0.72032	D	0.01	.	8.3414	0.32245	0.254:0.746:0.0:0.0	.	258;258	Q92692;Q92692-2	PVRL2_HUMAN;.	C	258	ENSP00000252483:R258C;ENSP00000252485:R258C	ENSP00000252483:R258C	R	+	1	0	PVRL2	50067243	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	2.396000	0.44468	2.190000	0.69967	0.561000	0.74099	CGC		0.557	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856	
RSPH6A	81492	broad.mit.edu	37	19	46308030	46308030	+	Missense_Mutation	SNP	G	G	A	rs138038020		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:46308030G>A	ENST00000221538.3	-	3	1275	c.1133C>T	c.(1132-1134)aCg>aTg	p.T378M	RSPH6A_ENST00000600188.1_Missense_Mutation_p.T114M|RSPH6A_ENST00000597055.1_Missense_Mutation_p.T378M	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	378	Glu-rich.					intracellular (GO:0005622)		p.T378M(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						GCCACCTTCCGTCATctcctc	0.647																																					p.T378M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1133T	19						.	G	MET/THR	0,4406		0,0,2203	83.0	68.0	73.0		1133	-1.6	0.0	19	dbSNP_134	73	7,8593	5.7+/-21.5	0,7,4293	no	missense	RSPH6A	NM_030785.3	81	0,7,6496	AA,AG,GG		0.0814,0.0,0.0538	benign	378/718	46308030	7,12999	2203	4300	6503	50999870	SO:0001583	missense	81492	exon3			AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"""radial spokehead-like 1"""	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.1133C>T	19.37:g.46308030G>A	ENSP00000221538:p.Thr378Met	Somatic		Capture	Illumina HiSeq	Phase_I	50999870	NM_030785	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	37	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	G	1.086	-0.665439	0.03428	0.0	8.14E-4	ENSG00000104941	ENST00000221538	T	0.17854	2.25	3.82	-1.63	0.08345	.	1.476590	0.04037	N	0.302425	T	0.09024	0.0223	N	0.12182	0.205	0.09310	N	1	B	0.13145	0.007	B	0.08055	0.003	T	0.30268	-0.9984	10	0.42905	T	0.14	-0.4287	3.1224	0.06396	0.4249:0.0:0.3384:0.2367	.	378	Q9H0K4	RSH6A_HUMAN	M	378	ENSP00000221538:T378M	ENSP00000221538:T378M	T	-	2	0	RSPH6A	50999870	0.000000	0.05858	0.013000	0.15412	0.044000	0.14063	-2.626000	0.00874	-0.369000	0.08028	-0.696000	0.03686	ACG		0.647	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1		
PRKD2	25865	broad.mit.edu	37	19	47181698	47181698	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:47181698C>T	ENST00000291281.4	-	16	2518	c.2293G>A	c.(2293-2295)Gcc>Acc	p.A765T	DACT3-AS1_ENST00000525008.1_RNA|PRKD2_ENST00000433867.1_Missense_Mutation_p.A765T|PRKD2_ENST00000593492.1_5'Flank|PRKD2_ENST00000595515.1_Missense_Mutation_p.A765T|PRKD2_ENST00000600194.1_Missense_Mutation_p.A608T|PRKD2_ENST00000601806.1_Missense_Mutation_p.A608T			Q9BZL6	KPCD2_HUMAN	protein kinase D2	765	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.A765T(1)		central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		TACATGAAGGCGGCGTTCTGG	0.632																																					p.A765T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2293A	19						.						113.0	91.0	99.0					19																	47181698		2203	4300	6503	51873538	SO:0001583	missense	25865	exon17			AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"""Pleckstrin homology (PH) domain containing"""	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.2293G>A	19.37:g.47181698C>T	ENSP00000291281:p.Ala765Thr	Somatic		Capture	Illumina HiSeq	Phase_I	51873538	NM_001079881	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000291281.4	37	CCDS12689.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.737957	0.89573	.	.	ENSG00000105287	ENST00000291281;ENST00000433867	T;T	0.65178	-0.14;-0.14	4.65	4.65	0.58169	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	U	0.000006	T	0.59729	0.2215	N	0.16602	0.42	0.80722	D	1	P;B;D	0.67145	0.803;0.35;0.996	B;B;P	0.54238	0.232;0.166;0.746	T	0.66048	-0.6020	10	0.56958	D	0.05	-34.6548	16.7079	0.85377	0.0:1.0:0.0:0.0	.	765;250;765	E7ER94;A0JLT6;Q9BZL6	.;.;KPCD2_HUMAN	T	765	ENSP00000291281:A765T;ENSP00000393978:A765T	ENSP00000291281:A765T	A	-	1	0	PRKD2	51873538	1.000000	0.71417	0.935000	0.37517	0.909000	0.53808	7.736000	0.84948	2.308000	0.77769	0.563000	0.77884	GCC		0.632	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457	
ARHGAP35	2909	broad.mit.edu	37	19	47422911	47422911	+	Missense_Mutation	SNP	C	C	T	rs199897795		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:47422911C>T	ENST00000404338.3	+	1	979	c.979C>T	c.(979-981)Cgc>Tgc	p.R327C		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	327	FF 1.				axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)	p.R327C(1)									GCACATCCACCGCCTCAAGCA	0.488																																					p.R327C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C979T	19						.						33.0	34.0	33.0					19																	47422911		1959	4147	6106	52114751	SO:0001583	missense	2909	exon1			M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"""Rho GTPase activating proteins"""	4591	protein-coding gene	gene with protein product		605277	"""glucocorticoid receptor DNA binding factor 1"""	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.979C>T	19.37:g.47422911C>T	ENSP00000385720:p.Arg327Cys	Somatic		Capture	Illumina HiSeq	Phase_I	52114751	NM_004491	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	37	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	C	15.30	2.791462	0.50102	.	.	ENSG00000160007	ENST00000317082;ENST00000501576;ENST00000404338	T	0.08720	3.06	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.24699	0.0599	L	0.48642	1.525	0.80722	D	1	D	0.89917	1.0	D	0.69142	0.962	T	0.00024	-1.2327	10	0.87932	D	0	-27.8494	19.2296	0.93833	0.0:1.0:0.0:0.0	.	327	Q9NRY4-2	.	C	327	ENSP00000385720:R327C	ENSP00000324820:R327C	R	+	1	0	ARHGAP35	52114751	0.977000	0.34250	1.000000	0.80357	0.998000	0.95712	2.458000	0.45014	2.835000	0.97688	0.650000	0.86243	CGC		0.488	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491	
PLA2G4C	8605	broad.mit.edu	37	19	48565307	48565307	+	Missense_Mutation	SNP	C	C	T	rs141101537	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:48565307C>T	ENST00000599921.1	-	14	1562	c.1205G>A	c.(1204-1206)cGg>cAg	p.R402Q	PLA2G4C_ENST00000413144.2_Missense_Mutation_p.R402Q|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.R402Q|CTD-2265M8.2_ENST00000601548.1_RNA|PLA2G4C_ENST00000596510.1_5'UTR|CTD-2265M8.2_ENST00000596552.1_RNA|CTD-2265M8.2_ENST00000601950.1_RNA|PLA2G4C_ENST00000599111.1_Missense_Mutation_p.R412Q			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	402	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)	p.R402Q(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		GTGAACCTCCCGCGTCGGGGG	0.612													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18117	0.0		0.0	False		,,,				2504	0.0				p.R402Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1205A	19						.	C	GLN/ARG,GLN/ARG,GLN/ARG	4,4402	8.1+/-20.4	0,4,2199	90.0	80.0	84.0		1235,1205,1205	2.8	0.0	19	dbSNP_134	84	0,8600		0,0,4300	no	missense,missense,missense	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	43,43,43	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	probably-damaging,probably-damaging,probably-damaging	412/552,402/528,402/542	48565307	4,13002	2203	4300	6503	53257119	SO:0001583	missense	8605	exon14			AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.1205G>A	19.37:g.48565307C>T	ENSP00000469473:p.Arg402Gln	Somatic		Capture	Illumina HiSeq	Phase_I	53257119	NM_001159323	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.944690	0.73672	9.08E-4	0.0	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.27256	1.68;1.68	2.79	2.79	0.32731	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.245612	0.30347	U	0.009832	T	0.49983	0.1589	M	0.84511	2.7	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.74348	0.983;0.925	T	0.35895	-0.9770	10	0.72032	D	0.01	-6.552	9.3872	0.38349	0.0:1.0:0.0:0.0	.	412;402	B4DI40;Q9UP65	.;PA24C_HUMAN	Q	402	ENSP00000346228:R402Q;ENSP00000400036:R402Q	ENSP00000346228:R402Q	R	-	2	0	PLA2G4C	53257119	0.013000	0.17824	0.005000	0.12908	0.455000	0.32408	1.903000	0.39858	1.270000	0.44297	0.405000	0.27470	CGG		0.612	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
GRIN2D	2906	broad.mit.edu	37	19	48945116	48945116	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:48945116C>T	ENST00000263269.3	+	11	2431	c.2343C>T	c.(2341-2343)ggC>ggT	p.G781G		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	781					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)	p.G781G(1)		autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TCGGCTCCGGCAAGGTCTTCG	0.632																																					p.G781G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2343T	19						.						62.0	49.0	53.0					19																	48945116		2203	4300	6503	53636928	SO:0001819	synonymous_variant	2906	exon11			U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4588	protein-coding gene	gene with protein product	"""N-methyl-d-aspartate receptor subunit 2D"""	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.2343C>T	19.37:g.48945116C>T		Somatic		Capture	Illumina HiSeq	Phase_I	53636928	NM_000836		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																				0.632	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1		
SPHK2	56848	broad.mit.edu	37	19	49129347	49129347	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:49129347G>A	ENST00000245222.4	+	3	605	c.239G>A	c.(238-240)cGc>cAc	p.R80H	AC022154.7_ENST00000594850.1_RNA|SPHK2_ENST00000600537.1_Missense_Mutation_p.R21H|AC022154.7_ENST00000598735.1_RNA|SPHK2_ENST00000599029.1_Missense_Mutation_p.R44H|SPHK2_ENST00000340932.3_Missense_Mutation_p.R44H|SPHK2_ENST00000601712.1_Missense_Mutation_p.R44H|SPHK2_ENST00000599033.1_3'UTR|AC022154.7_ENST00000600303.1_RNA|SPHK2_ENST00000598088.1_Missense_Mutation_p.R80H|SPHK2_ENST00000443164.1_Missense_Mutation_p.R142H|SPHK2_ENST00000599748.1_Missense_Mutation_p.R44H	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	80	Required for binding to sulfatide and phosphoinositides and for membrane localization.				blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)	p.R80H(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		CAGCGGCTGCGCCCCAAACCT	0.692																																					p.R80H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G239A	19						.						29.0	31.0	30.0					19																	49129347		2200	4297	6497	53821159	SO:0001583	missense	56848	exon3			AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.239G>A	19.37:g.49129347G>A	ENSP00000245222:p.Arg80His	Somatic		Capture	Illumina HiSeq	Phase_I	53821159	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Missense_Mutation	SNP	ENST00000245222.4	37	CCDS12727.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.267150	0.59540	.	.	ENSG00000063176	ENST00000245222;ENST00000406269;ENST00000340932;ENST00000443164	T;T;T	0.25414	2.18;1.89;1.8	3.98	2.9	0.33743	.	0.521667	0.19794	N	0.105908	T	0.29061	0.0722	L	0.40543	1.245	0.31538	N	0.660273	D;D;D;D	0.67145	0.97;0.983;0.996;0.982	B;B;P;B	0.53549	0.27;0.353;0.729;0.27	T	0.21965	-1.0230	10	0.42905	T	0.14	-14.9543	8.9321	0.35677	0.0:0.0:0.5954:0.4046	.	21;142;44;80	B4DU87;A0T4C8;Q9NRA0-3;Q9NRA0	.;.;.;SPHK2_HUMAN	H	80;80;44;142	ENSP00000245222:R80H;ENSP00000341091:R44H;ENSP00000413369:R142H	ENSP00000245222:R80H	R	+	2	0	SPHK2	53821159	0.965000	0.33210	0.999000	0.59377	0.978000	0.69477	0.395000	0.20850	0.977000	0.38444	0.557000	0.71058	CGC		0.692	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
TULP2	7288	broad.mit.edu	37	19	49391389	49391389	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:49391389C>T	ENST00000221399.3	-	8	910	c.766G>A	c.(766-768)Gaa>Aaa	p.E256K		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	256					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)	p.E256K(1)		NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		AAGGAGGCTTCGTGCCTCATA	0.622																																					p.E256K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G766A	19						.						86.0	58.0	68.0					19																	49391389		2203	4300	6503	54083201	SO:0001583	missense	7288	exon8			U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"""cancer/testis antigen 65"""	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.766G>A	19.37:g.49391389C>T	ENSP00000221399:p.Glu256Lys	Somatic		Capture	Illumina HiSeq	Phase_I	54083201	NM_003323	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	37	CCDS12739.1	.	.	.	.	.	.	.	.	.	.	C	0.139	-1.103865	0.01828	.	.	ENSG00000104804	ENST00000221399;ENST00000518572	D;T	0.82803	-1.65;2.25	3.83	-7.67	0.01272	.	.	.	.	.	T	0.47710	0.1460	N	0.03608	-0.345	0.09310	N	1	B	0.34214	0.442	B	0.24541	0.054	T	0.50381	-0.8835	9	0.09084	T	0.74	7.3037	2.3181	0.04204	0.1828:0.1847:0.3936:0.2388	.	256	O00295	TULP2_HUMAN	K	256;210	ENSP00000221399:E256K;ENSP00000428420:E210K	ENSP00000221399:E256K	E	-	1	0	TULP2	54083201	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.540000	0.06106	-3.493000	0.00153	-1.113000	0.02065	GAA		0.622	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323	
SLC17A7	57030	broad.mit.edu	37	19	49933867	49933867	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:49933867G>A	ENST00000221485.3	-	12	1763	c.1592C>T	c.(1591-1593)cCg>cTg	p.P531L	SLC17A7_ENST00000600601.1_Missense_Mutation_p.P464L|SLC17A7_ENST00000543531.1_Missense_Mutation_p.P519L	NM_020309.3	NP_064705.1	Q9P2U7	VGLU1_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 7	531	Pro-rich.				glutamate secretion (GO:0014047)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|long-term memory (GO:0007616)|neurotransmitter secretion (GO:0007269)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sequestering of neurotransmitter (GO:0042137)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|synaptic vesicle membrane (GO:0030672)	inorganic phosphate transmembrane transporter activity (GO:0005315)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:inorganic phosphate symporter activity (GO:0015319)	p.P531L(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	26		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(486;0.0245)		GGGTGCCCCCGGGGGCTCAGC	0.662																																					p.P531L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1592T	19						.						28.0	27.0	27.0					19																	49933867		2203	4298	6501	54625679	SO:0001583	missense	57030	exon12			AB032436	CCDS12764.1	19q13.33	2013-07-18	2013-07-18		ENSG00000104888	ENSG00000104888		"""Solute carriers"""	16704	protein-coding gene	gene with protein product	"""vesicular glutamate transporter 1"""	605208	"""solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7"""			8632143, 10820226	Standard	NM_020309		Approved	BNPI, VGLUT1	uc002pnp.3	Q9P2U7		ENST00000221485.3:c.1592C>T	19.37:g.49933867G>A	ENSP00000221485:p.Pro531Leu	Somatic		Capture	Illumina HiSeq	Phase_I	54625679	NM_020309	B4DFR9|B4DG46|Q6PCD0	Missense_Mutation	SNP	ENST00000221485.3	37	CCDS12764.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.360742	0.24598	.	.	ENSG00000104888	ENST00000221485;ENST00000543531	T;T	0.62639	0.01;0.01	4.68	4.68	0.58851	.	0.099687	0.43416	D	0.000570	T	0.39436	0.1078	N	0.22421	0.69	0.47276	D	0.999374	B;P	0.39782	0.019;0.688	B;B	0.29942	0.007;0.109	T	0.28427	-1.0044	10	0.27785	T	0.31	.	8.9592	0.35836	0.0995:0.0:0.9005:0.0	.	531;373	Q9P2U7;A8K0Q7	VGLU1_HUMAN;.	L	531;519	ENSP00000221485:P531L;ENSP00000441767:P519L	ENSP00000221485:P531L	P	-	2	0	SLC17A7	54625679	0.945000	0.32115	0.842000	0.33263	0.734000	0.41952	1.641000	0.37197	2.614000	0.88457	0.585000	0.79938	CCG		0.662	SLC17A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465367.2		
SLC17A7	57030	broad.mit.edu	37	19	49936086	49936086	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:49936086G>A	ENST00000221485.3	-	8	1170	c.999C>T	c.(997-999)ttC>ttT	p.F333F	SLC17A7_ENST00000600601.1_Silent_p.F266F|SLC17A7_ENST00000543531.1_Silent_p.F321F	NM_020309.3	NP_064705.1	Q9P2U7	VGLU1_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 7	333					glutamate secretion (GO:0014047)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|long-term memory (GO:0007616)|neurotransmitter secretion (GO:0007269)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sequestering of neurotransmitter (GO:0042137)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|synaptic vesicle membrane (GO:0030672)	inorganic phosphate transmembrane transporter activity (GO:0005315)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:inorganic phosphate symporter activity (GO:0015319)	p.F333F(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	26		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(486;0.0245)		TCTCGAAGCCGAACACTTCTT	0.642																																					p.F333F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C999T	19						.						26.0	25.0	26.0					19																	49936086		2202	4298	6500	54627898	SO:0001819	synonymous_variant	57030	exon8			AB032436	CCDS12764.1	19q13.33	2013-07-18	2013-07-18		ENSG00000104888	ENSG00000104888		"""Solute carriers"""	16704	protein-coding gene	gene with protein product	"""vesicular glutamate transporter 1"""	605208	"""solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7"""			8632143, 10820226	Standard	NM_020309		Approved	BNPI, VGLUT1	uc002pnp.3	Q9P2U7		ENST00000221485.3:c.999C>T	19.37:g.49936086G>A		Somatic		Capture	Illumina HiSeq	Phase_I	54627898	NM_020309	B4DFR9|B4DG46|Q6PCD0	Silent	SNP	ENST00000221485.3	37	CCDS12764.1																																																																																				0.642	SLC17A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465367.2		
SCAF1	58506	broad.mit.edu	37	19	50156051	50156051	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:50156051C>T	ENST00000360565.3	+	7	2529	c.2405C>T	c.(2404-2406)gCg>gTg	p.A802V		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	802	Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)	p.A802V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		AAGGAGTCGGCGCCTTCCTCA	0.662																																					p.A802V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2405T	19						.						42.0	54.0	49.0					19																	50156051		2199	4300	6499	54847863	SO:0001583	missense	58506	exon7			AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.2405C>T	19.37:g.50156051C>T	ENSP00000353769:p.Ala802Val	Somatic		Capture	Illumina HiSeq	Phase_I	54847863	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	37	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	C	11.70	1.715408	0.30413	.	.	ENSG00000126461	ENST00000360565	T	0.33216	1.42	3.26	2.18	0.27775	.	.	.	.	.	T	0.13157	0.0319	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28964	-1.0027	8	.	.	.	-6.2048	5.0557	0.14531	0.2027:0.6732:0.0:0.1241	.	802	Q9H7N4	SFR19_HUMAN	V	802	ENSP00000353769:A802V	.	A	+	2	0	SCAF1	54847863	0.003000	0.15002	0.004000	0.12327	0.962000	0.63368	0.197000	0.17197	0.881000	0.35993	0.561000	0.74099	GCG		0.662	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
AKT1S1	84335	broad.mit.edu	37	19	50374943	50374943	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:50374943C>G	ENST00000391833.1	-	3	2477	c.488G>C	c.(487-489)gGc>gCc	p.G163A	AKT1S1_ENST00000391834.2_Missense_Mutation_p.G163A|AKT1S1_ENST00000391835.1_Missense_Mutation_p.G183A|AKT1S1_ENST00000391832.3_Missense_Mutation_p.G163A|AKT1S1_ENST00000344175.5_Missense_Mutation_p.G163A|AKT1S1_ENST00000391831.1_Missense_Mutation_p.G163A	NM_001278160.1	NP_001265089.1			AKT1 substrate 1 (proline-rich)									p.G163A(1)		kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		GGTGGGGGGGCCGGCGGGGGT	0.657																																					p.G163A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G488C	19						.						30.0	39.0	36.0					19																	50374943		2199	4293	6492	55066755	SO:0001583	missense	84335	exon4			BC022241	CCDS12784.1, CCDS59410.1	19q13.33	2008-02-05			ENSG00000204673	ENSG00000204673			28426	protein-coding gene	gene with protein product	"""proline-rich Akt substrate, 40 kDa"""	610221				12524439	Standard	NM_032375		Approved	PRAS40, MGC2865, Lobe	uc031rmg.1	Q96B36	OTTHUMG00000150246	ENST00000391833.1:c.488G>C	19.37:g.50374943C>G	ENSP00000375709:p.Gly163Ala	Somatic		Capture	Illumina HiSeq	Phase_I	55066755	NM_001098632		Missense_Mutation	SNP	ENST00000391833.1	37	CCDS12784.1	.	.	.	.	.	.	.	.	.	.	C	4.139	0.024141	0.08006	.	.	ENSG00000204673	ENST00000391833;ENST00000344175;ENST00000391832;ENST00000391834;ENST00000391835;ENST00000391831	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	4.14	3.08	0.35506	.	0.617992	0.15446	N	0.261908	T	0.21186	0.0510	N	0.08118	0	0.23872	N	0.996605	B	0.06786	0.001	B	0.08055	0.003	T	0.13308	-1.0514	10	0.62326	D	0.03	-18.3859	5.8353	0.18602	0.0:0.6941:0.1996:0.1063	.	163	Q96B36	AKTS1_HUMAN	A	163;163;163;163;183;163	ENSP00000375709:G163A;ENSP00000341698:G163A;ENSP00000375708:G163A;ENSP00000375710:G163A;ENSP00000375711:G183A;ENSP00000375707:G163A	ENSP00000341698:G163A	G	-	2	0	AKT1S1	55066755	0.950000	0.32346	0.221000	0.23827	0.081000	0.17604	1.815000	0.38981	1.068000	0.40764	-0.176000	0.13171	GGC		0.657	AKT1S1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317073.1	NM_032375	
TBC1D17	79735	broad.mit.edu	37	19	50383578	50383578	+	Missense_Mutation	SNP	A	A	G	rs572709837		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:50383578A>G	ENST00000221543.5	+	4	537	c.238A>G	c.(238-240)Acc>Gcc	p.T80A	AKT1S1_ENST00000391834.2_5'Flank|TBC1D17_ENST00000535102.2_Missense_Mutation_p.T47A|TBC1D17_ENST00000598789.1_3'UTR|AKT1S1_ENST00000391835.1_5'Flank|AKT1S1_ENST00000482622.1_5'Flank|AKT1S1_ENST00000344175.5_5'Flank	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	80					autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)	p.T80A(1)		NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		GGAGGAACCAACCTTTGACCC	0.582													A|||	1	0.000199681	0.0	0.0	5008	,	,		18889	0.0		0.0	False		,,,				2504	0.001				p.T47A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A139G	19						.						108.0	91.0	97.0					19																	50383578		2203	4300	6503	55075390	SO:0001583	missense	79735	exon3			AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.238A>G	19.37:g.50383578A>G	ENSP00000221543:p.Thr80Ala	Somatic		Capture	Illumina HiSeq	Phase_I	55075390	NM_001168222	B4DT12|B9A6L8|F5H1W7	Missense_Mutation	SNP	ENST00000221543.5	37	CCDS12785.1	.	.	.	.	.	.	.	.	.	.	A	10.31	1.314268	0.23908	.	.	ENSG00000104946	ENST00000221543;ENST00000535102	T;T	0.29397	1.57;1.57	4.68	4.68	0.58851	Domain of unknown function DUF3548 (1);	0.572855	0.16094	N	0.229910	T	0.17365	0.0417	N	0.14661	0.345	0.27630	N	0.948068	B;B	0.19200	0.027;0.034	B;B	0.26614	0.043;0.071	T	0.20605	-1.0270	10	0.08381	T	0.77	-35.7261	10.4385	0.44450	1.0:0.0:0.0:0.0	.	47;80	F5H1W7;Q9HA65	.;TBC17_HUMAN	A	80;47	ENSP00000221543:T80A;ENSP00000446323:T47A	ENSP00000221543:T80A	T	+	1	0	TBC1D17	55075390	0.998000	0.40836	0.896000	0.35187	0.325000	0.28411	4.353000	0.59411	1.954000	0.56735	0.459000	0.35465	ACC		0.582	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682	
POLD1	5424	broad.mit.edu	37	19	50917112	50917112	+	Silent	SNP	G	G	A	rs545962328		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:50917112G>A	ENST00000440232.2	+	19	2417	c.2364G>A	c.(2362-2364)tcG>tcA	p.S788S	POLD1_ENST00000595904.1_Silent_p.S814S|POLD1_ENST00000599857.1_Silent_p.S788S|CTD-2545M3.6_ENST00000599632.1_5'Flank	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	788					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.S788S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		ACTTCCCGTCGCCCATCCGGC	0.637								DNA polymerases (catalytic subunits)																													p.S788S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2364A	19						.						50.0	54.0	53.0					19																	50917112		2203	4300	6503	55608924	SO:0001819	synonymous_variant	5424	exon19				CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2364G>A	19.37:g.50917112G>A		Somatic		Capture	Illumina HiSeq	Phase_I	55608924	NM_002691	Q8NER3|Q96H98	Silent	SNP	ENST00000440232.2	37	CCDS12795.1																																																																																				0.637	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
SIGLEC10	89790	broad.mit.edu	37	19	51918312	51918312	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:51918312G>A	ENST00000339313.5	-	8	1497	c.1381C>T	c.(1381-1383)Cac>Tac	p.H461Y	CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.H461Y|SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000441969.3_Intron|SIGLEC10_ENST00000432469.2_Intron|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.H403Y|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000353836.5_Intron|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000436984.2_Intron			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	461					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.H461Y(1)|p.H403Y(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CAGCTGCAGTGCAGACCCTCA	0.692																																					p.H403Y												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1207T	19						.						11.0	13.0	12.0					19																	51918312		2189	4268	6457	56610124	SO:0001583	missense	89790	exon8			AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.1381C>T	19.37:g.51918312G>A	ENSP00000345243:p.His461Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	56610124	NM_001171156	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	4.280	0.051110	0.08243	.	.	ENSG00000142512	ENST00000356298;ENST00000439889;ENST00000339313	D;D;D	0.85955	-2.05;-2.05;-2.05	4.83	-2.15	0.07102	.	2.229260	0.01296	N	0.010170	D	0.88340	0.6410	M	0.80982	2.52	0.09310	N	1	D;P	0.55800	0.973;0.752	P;P	0.58873	0.847;0.555	T	0.71735	-0.4503	10	0.15499	T	0.54	.	1.7961	0.03062	0.1823:0.2914:0.3775:0.1489	.	403;461	Q96LC7-3;Q96LC7	.;SIG10_HUMAN	Y	461;403;461	ENSP00000348646:H461Y;ENSP00000389132:H403Y;ENSP00000345243:H461Y	ENSP00000345243:H461Y	H	-	1	0	SIGLEC10	56610124	0.000000	0.05858	0.038000	0.18304	0.210000	0.24377	-0.343000	0.07791	0.072000	0.16694	0.561000	0.74099	CAC		0.692	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
FPR2	2358	broad.mit.edu	37	19	52272916	52272916	+	Silent	SNP	G	G	A	rs140469815	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:52272916G>A	ENST00000598776.1	+	2	1777	c.1005G>A	c.(1003-1005)acG>acA	p.T335T	FPR2_ENST00000340023.6_Silent_p.T335T|FPR2_ENST00000598953.1_Silent_p.T335T	NM_001462.3	NP_001453.1	P25090	FPR2_HUMAN	formyl peptide receptor 2	335					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|N-formyl peptide receptor activity (GO:0004982)	p.T335T(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33						CTAATGACACGGCTGCCAATT	0.537													G|||	2	0.000399361	0.0008	0.0	5008	,	,		18502	0.0		0.0	False		,,,				2504	0.001				p.T335T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1005A	19						.	G	,	3,4403		0,3,2200	65.0	61.0	62.0		1005,1005	-2.4	0.0	19	dbSNP_134	62	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FPR2	NM_001005738.1,NM_001462.3	,	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	,	335/352,335/352	52272916	3,13003	2203	4300	6503	56964728	SO:0001819	synonymous_variant	2358	exon2			M88107	CCDS12840.1	19q13.3-q13.4	2012-08-10	2008-04-17	2008-04-17		ENSG00000171049		"""GPCR / Class A : Formyl peptide receptors"", ""GPCR / Class A : Leukotriene receptors"""	3827	protein-coding gene	gene with protein product		136538	"""formyl peptide receptor-like 1"""	FPRL1		9054386	Standard	NM_001462		Approved	LXA4R, HM63, FPRH2, FMLPX, FPR2A, FMLP-R-II, ALXR	uc002pxr.3	P25090		ENST00000598776.1:c.1005G>A	19.37:g.52272916G>A		Somatic		Capture	Illumina HiSeq	Phase_I	56964728	NM_001462	A8K3E2	Silent	SNP	ENST00000598776.1	37	CCDS12840.1																																																																																				0.537	FPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466912.2	NM_001005738	
POLRMT	5442	broad.mit.edu	37	19	630096	630096	+	Missense_Mutation	SNP	G	G	A	rs199640816		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:630096G>A	ENST00000588649.2	-	3	350	c.266C>T	c.(265-267)gCg>gTg	p.A89V		NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	89					gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)	p.A89V(1)		cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGGAGCCGCGCCACATCCAC	0.672																																					p.A89V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C266T	19						.	G	VAL/ALA	0,4406		0,0,2203	55.0	60.0	58.0		266	3.1	0.0	19		58	1,8599	1.2+/-3.3	0,1,4299	yes	missense	POLRMT	NM_005035.3	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	89/1231	630096	1,13005	2203	4300	6503	581096	SO:0001583	missense	5442	exon3				CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.266C>T	19.37:g.630096G>A	ENSP00000465759:p.Ala89Val	Somatic		Capture	Illumina HiSeq	Phase_I	581096	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	.	.	.	.	.	.	.	.	.	.	G	10.52	1.371930	0.24857	0.0	1.16E-4	ENSG00000099821	ENST00000215591	T	0.42131	0.98	4.14	3.06	0.35304	.	0.521601	0.19517	N	0.112366	T	0.28732	0.0712	L	0.29908	0.895	0.09310	N	1	B	0.29671	0.254	B	0.18561	0.022	T	0.11941	-1.0567	10	0.41790	T	0.15	-6.6222	12.0497	0.53500	0.0:0.0:0.8199:0.1801	.	89	O00411	RPOM_HUMAN	V	89	ENSP00000215591:A89V	ENSP00000215591:A89V	A	-	2	0	POLRMT	581096	0.444000	0.25649	0.005000	0.12908	0.455000	0.32408	2.592000	0.46171	0.799000	0.34018	0.491000	0.48974	GCG		0.672	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
ZNF350	59348	broad.mit.edu	37	19	52468975	52468975	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:52468975G>A	ENST00000243644.4	-	5	958	c.731C>T	c.(730-732)tCc>tTc	p.S244F	HCCAT3_ENST00000600253.1_RNA|HCCAT3_ENST00000595010.1_RNA|ZNF350_ENST00000600703.1_5'Flank	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	244					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S244F(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		GAACTTTCTGGAGAAGGCTTT	0.443																																					p.S244F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C731T	19						.						122.0	112.0	115.0					19																	52468975		2203	4300	6503	57160787	SO:0001583	missense	59348	exon5			AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"""Zinc fingers, C2H2-type"", ""-"""	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.731C>T	19.37:g.52468975G>A	ENSP00000243644:p.Ser244Phe	Somatic		Capture	Illumina HiSeq	Phase_I	57160787	NM_021632	Q96G73|Q9HAQ4	Missense_Mutation	SNP	ENST00000243644.4	37	CCDS12845.1	.	.	.	.	.	.	.	.	.	.	G	10.52	1.373402	0.24857	.	.	ENSG00000256683	ENST00000243644	T	0.08008	3.14	3.41	2.35	0.29111	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.697521	0.11902	N	0.518532	T	0.11067	0.0270	M	0.75085	2.285	0.09310	N	0.999997	B	0.21688	0.059	B	0.17098	0.017	T	0.22591	-1.0212	10	0.48119	T	0.1	.	5.6707	0.17721	0.1092:0.0:0.6927:0.198	.	244	Q9GZX5	ZN350_HUMAN	F	244	ENSP00000243644:S244F	ENSP00000243644:S244F	S	-	2	0	ZNF350	57160787	0.000000	0.05858	0.928000	0.36995	0.990000	0.78478	-3.077000	0.00615	0.621000	0.30232	0.591000	0.81541	TCC		0.443	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632	
ZNF816	125893	broad.mit.edu	37	19	53454614	53454614	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:53454614A>G	ENST00000357666.4	-	5	714	c.414T>C	c.(412-414)agT>agC	p.S138S	ZNF816_ENST00000434371.2_Intron|ZNF816_ENST00000444460.2_Silent_p.S138S|ZNF321P_ENST00000391777.3_Intron|ZNF816_ENST00000391786.2_3'UTR	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	138					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S138S(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						TTCGGTCTGTACTACCAGTCA	0.398																																					p.S138S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T414C	19						.						173.0	178.0	176.0					19																	53454614		2203	4300	6503	58146426	SO:0001819	synonymous_variant	125893	exon5			BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"""Zinc fingers, C2H2-type"", ""-"""	26995	protein-coding gene	gene with protein product			"""zinc finger protein 816A"""	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.414T>C	19.37:g.53454614A>G		Somatic		Capture	Illumina HiSeq	Phase_I	58146426	NM_001031665	A8K7H5|Q3KR39|Q659B3	Silent	SNP	ENST00000357666.4	37	CCDS33096.1																																																																																				0.398	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665	
PRKCG	5582	broad.mit.edu	37	19	54396277	54396277	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:54396277A>T	ENST00000263431.3	+	8	1139	c.857A>T	c.(856-858)tAc>tTc	p.Y286F	PRKCG_ENST00000536044.1_Intron|PRKCG_ENST00000540413.1_Missense_Mutation_p.Y286F|PRKCG_ENST00000542049.1_Missense_Mutation_p.Y173F	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	286					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)	p.Y286F(1)		large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	GGCGAGTATTACAATGTGCCG	0.607																																					p.Y286F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A857T	19						.						64.0	56.0	59.0					19																	54396277		2203	4300	6503	59088089	SO:0001583	missense	5582	exon8			M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"""PKC-gamma"""	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.857A>T	19.37:g.54396277A>T	ENSP00000263431:p.Tyr286Phe	Somatic		Capture	Illumina HiSeq	Phase_I	59088089	NM_002739	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	A	12.98	2.098996	0.37048	.	.	ENSG00000126583	ENST00000540413;ENST00000263431;ENST00000542049	T;T;T	0.70045	-0.45;-0.45;-0.43	4.14	4.14	0.48551	C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.55000	0.1893	L	0.35854	1.095	0.52099	D	0.999949	B;B;B;B	0.13145	0.007;0.001;0.001;0.001	B;B;B;B	0.12837	0.004;0.006;0.006;0.008	T	0.51865	-0.8651	9	0.32370	T	0.25	.	11.7292	0.51726	1.0:0.0:0.0:0.0	.	173;286;286;286	B7Z8Q0;F5H5C4;B7Z3W6;P05129	.;.;.;KPCG_HUMAN	F	286;286;173	ENSP00000443493:Y286F;ENSP00000263431:Y286F;ENSP00000438090:Y173F	ENSP00000263431:Y286F	Y	+	2	0	PRKCG	59088089	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.979000	0.49313	1.819000	0.53055	0.379000	0.24179	TAC		0.607	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739	
TMC4	147798	broad.mit.edu	37	19	54669197	54669197	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:54669197C>T	ENST00000376591.4	-	6	1050	c.919G>A	c.(919-921)Gtc>Atc	p.V307I	TMC4_ENST00000476013.2_Intron|TMC4_ENST00000416963.1_5'Flank|TMC4_ENST00000301187.4_Missense_Mutation_p.V301I	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	307					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.V301I(1)		breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CGCACGTGGACGTCCCCGCAG	0.632																																					p.V307I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G919A	19						.						45.0	37.0	40.0					19																	54669197		2203	4300	6503	59361009	SO:0001583	missense	147798	exon6			AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.919G>A	19.37:g.54669197C>T	ENSP00000365776:p.Val307Ile	Somatic		Capture	Illumina HiSeq	Phase_I	59361009	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Missense_Mutation	SNP	ENST00000376591.4	37	CCDS46174.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.847741	0.32606	.	.	ENSG00000167608	ENST00000301187;ENST00000376591	T;T	0.49139	0.79;0.79	4.8	1.39	0.22231	.	1.115900	0.06622	N	0.757541	T	0.40743	0.1129	M	0.67953	2.075	0.09310	N	1	P;B	0.34892	0.474;0.019	B;B	0.19946	0.026;0.027	T	0.30060	-0.9991	10	0.40728	T	0.16	-4.7612	6.8226	0.23864	0.0:0.7019:0.0:0.2981	.	307;301	Q7Z404;Q7Z404-1	TMC4_HUMAN;.	I	301;307	ENSP00000301187:V301I;ENSP00000365776:V307I	ENSP00000301187:V301I	V	-	1	0	TMC4	59361009	0.001000	0.12720	0.085000	0.20634	0.820000	0.46376	0.932000	0.28884	0.559000	0.29153	-0.156000	0.13503	GTC		0.632	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2		
TSEN34	79042	broad.mit.edu	37	19	54695454	54695454	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:54695454G>T	ENST00000396383.1	+	2	550	c.239G>T	c.(238-240)aGc>aTc	p.S80I	MBOAT7_ENST00000474910.1_5'Flank|MBOAT7_ENST00000338624.6_5'Flank|MBOAT7_ENST00000245615.1_5'Flank|MBOAT7_ENST00000431666.2_5'Flank|CTD-3093M3.1_ENST00000594382.1_lincRNA|MBOAT7_ENST00000391754.1_5'Flank|TSEN34_ENST00000396388.2_Missense_Mutation_p.S80I|TSEN34_ENST00000429671.2_Missense_Mutation_p.S80I|TSEN34_ENST00000302937.4_Missense_Mutation_p.S80I			Q9BSV6	SEN34_HUMAN	TSEN34 tRNA splicing endonuclease subunit	80					mRNA processing (GO:0006397)|tRNA-type intron splice site recognition and cleavage (GO:0000379)	tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)	p.S80I(1)		endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	10	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CGGCACCACAGCCTGGTAAGG	0.667																																					p.S80I	Esophageal Squamous(37;841 964 4869 42824)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G239T	19						.						28.0	29.0	29.0					19																	54695454		1821	3961	5782	59387266	SO:0001583	missense	79042	exon1			AF211970	CCDS42609.1, CCDS74446.1	19q13.4	2013-08-06	2013-08-06	2005-03-12	ENSG00000170892	ENSG00000170892		"""tRNA splicing endonuclease subunits"""	15506	protein-coding gene	gene with protein product		608754	"""leukocyte receptor cluster (LRC) member 5"", ""tRNA splicing endonuclease 34 homolog (SEN34, S. cerevisiae)"", ""tRNA splicing endonuclease 34 homolog (S. cerevisiae)"""	LENG5		10941842, 15109492	Standard	NM_024075		Approved	SEN34, SEN34L	uc002qdw.3	Q9BSV6	OTTHUMG00000066515	ENST00000396383.1:c.239G>T	19.37:g.54695454G>T	ENSP00000379667:p.Ser80Ile	Somatic		Capture	Illumina HiSeq	Phase_I	59387266	NM_001077446	A6NNB1|B0V3J1|Q9BVT1|Q9H6H5	Missense_Mutation	SNP	ENST00000396383.1	37	CCDS42609.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.093124	0.36952	.	.	ENSG00000170892	ENST00000455798;ENST00000456872;ENST00000302937;ENST00000429671;ENST00000396383;ENST00000396388	T;T;T;T;T;T	0.66280	-0.2;-0.19;-0.18;-0.19;-0.18;-0.18	4.0	0.0723	0.14386	.	0.924044	0.09002	N	0.862859	T	0.48223	0.1488	L	0.43152	1.355	0.09310	N	1	P;B	0.34780	0.468;0.257	B;B	0.30646	0.118;0.075	T	0.35101	-0.9802	10	0.41790	T	0.15	.	6.3491	0.21365	0.1117:0.3519:0.5364:0.0	.	80;80	E7EQB3;Q9BSV6	.;SEN34_HUMAN	I	80;83;80;80;80;80	ENSP00000400743:S80I;ENSP00000408689:S83I;ENSP00000305524:S80I;ENSP00000397402:S80I;ENSP00000379667:S80I;ENSP00000379671:S80I	ENSP00000305524:S80I	S	+	2	0	TSEN34	59387266	0.997000	0.39634	0.975000	0.42487	0.876000	0.50452	2.844000	0.48246	0.255000	0.21593	0.561000	0.74099	AGC		0.667	TSEN34-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142200.1	NM_024075	
LILRA3	11026	broad.mit.edu	37	19	54802510	54802510	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:54802510T>C	ENST00000251390.3	-	5	1022	c.931A>G	c.(931-933)Agc>Ggc	p.S311G	LILRA3_ENST00000391744.3_Missense_Mutation_p.S247G|LILRA3_ENST00000391745.1_Missense_Mutation_p.S328G	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	311	Ig-like C2-type 3.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)	p.S311G(1)		NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AGGGGGTCGCTGGGGGCCGAC	0.667																																					p.S311G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A931G	19						.						26.0	30.0	29.0					19																	54802510		2191	4172	6363	59494322	SO:0001583	missense	11026	exon5			U91926		19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.931A>G	19.37:g.54802510T>C	ENSP00000251390:p.Ser311Gly	Somatic		Capture	Illumina HiSeq	Phase_I	59494322	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	37	CCDS12887.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.435365	0.43224	.	.	ENSG00000170866	ENST00000251390;ENST00000391744;ENST00000391745	T;T;T	0.01406	4.93;4.93;4.93	2.21	2.21	0.28008	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.393563	0.18664	N	0.134625	T	0.15435	0.0372	H	0.99732	4.735	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.20140	-1.0284	10	0.87932	D	0	.	6.4222	0.21750	0.0:0.0:0.0:1.0	.	311;311	E7EU74;Q8N6C8	.;LIRA3_HUMAN	G	311;247;328	ENSP00000251390:S311G;ENSP00000375624:S247G;ENSP00000375625:S328G	ENSP00000251390:S311G	S	-	1	0	LILRA3	59494322	0.999000	0.42202	0.111000	0.21465	0.065000	0.16274	3.003000	0.49505	1.289000	0.44618	0.477000	0.44152	AGC		0.667	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1		
LILRA4	23547	broad.mit.edu	37	19	54848837	54848837	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:54848837G>A	ENST00000291759.4	-	5	842	c.786C>T	c.(784-786)ggC>ggT	p.G262G	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	262	Ig-like C2-type 3.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.G262G(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		GCTGGGGGAGGCCATCGGCCC	0.657																																					p.G262G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C786T	19						.						23.0	26.0	25.0					19																	54848837		2203	4299	6502	59540649	SO:0001819	synonymous_variant	23547	exon5			AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.786C>T	19.37:g.54848837G>A		Somatic		Capture	Illumina HiSeq	Phase_I	59540649	NM_012276	Q32MC4	Silent	SNP	ENST00000291759.4	37	CCDS12890.1																																																																																				0.657	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
LAIR1	3903	broad.mit.edu	37	19	54876409	54876409	+	Start_Codon_SNP	SNP	C	C	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:54876409C>G	ENST00000391742.2	-	1	155	c.3G>C	c.(1-3)atG>atC	p.M1I	LAIR1_ENST00000313038.6_Intron|LAIR1_ENST00000348231.4_Start_Codon_SNP_p.M1I|LAIR1_ENST00000463489.1_Intron|LAIR1_ENST00000434277.2_Start_Codon_SNP_p.M1I|LAIR1_ENST00000391743.3_Intron|LAIR1_ENST00000474878.1_Start_Codon_SNP_p.M1I			Q6GTX8	LAIR1_HUMAN	leukocyte-associated immunoglobulin-like receptor 1	1					immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.M1I(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(4)|prostate(1)|stomach(3)	26	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0573)		GGTGGGGAGACATGGCCCAGG	0.657																																					p.M1I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3C	19						.						45.0	45.0	45.0					19																	54876409		2203	4300	6503	59568221	SO:0001582	initiator_codon_variant	3903	exon1			AF013249	CCDS12891.1, CCDS12892.1, CCDS74448.1, CCDS74449.1, CCDS74450.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167613	ENSG00000167613		"""Leukocyte-associated Ig like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6477	protein-coding gene	gene with protein product		602992	"""leukocyte-associated Ig-like receptor 1"""			9285412	Standard	XM_005258924		Approved	CD305	uc002qfk.1	Q6GTX8	OTTHUMG00000065545	ENST00000391742.2:c.3G>C	19.37:g.54876409C>G	ENSP00000375622:p.Met1Ile	Somatic		Capture	Illumina HiSeq	Phase_I	59568221	NM_021706		Missense_Mutation	SNP	ENST00000391742.2	37	CCDS12891.1	.	.	.	.	.	.	.	.	.	.	.	19.21	3.783473	0.70222	.	.	ENSG00000167613	ENST00000391742;ENST00000434277;ENST00000348231;ENST00000474878	T;T;T;T	0.00525	6.84;6.82;6.92;6.81	4.43	4.43	0.53597	.	0.000000	0.52532	D	0.000074	T	0.00608	0.0020	.	.	.	0.80722	D	1	P;P;D;P	0.56035	0.473;0.73;0.974;0.73	B;B;P;B	0.53689	0.122;0.351;0.732;0.132	D	0.86626	0.1882	9	0.10377	T	0.69	.	12.736	0.57225	0.0:1.0:0.0:0.0	.	1;1;1;1	Q6GTX8-3;D3YTC8;Q6GTX8-2;Q6GTX8	.;.;.;LAIR1_HUMAN	I	1	ENSP00000375622:M1I;ENSP00000391003:M1I;ENSP00000301193:M1I;ENSP00000418998:M1I	ENSP00000301193:M1I	M	-	3	0	LAIR1	59568221	0.771000	0.28555	0.715000	0.30552	0.147000	0.21601	2.648000	0.46647	2.455000	0.83008	0.555000	0.69702	ATG		0.657	LAIR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140506.1		Missense_Mutation
TTYH1	57348	broad.mit.edu	37	19	54947028	54947028	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:54947028A>G	ENST00000376530.3	+	12	1392	c.1289A>G	c.(1288-1290)gAc>gGc	p.D430G	TTYH1_ENST00000391739.3_3'UTR|TTYH1_ENST00000376531.3_Intron|AC008746.3_ENST00000457113.1_RNA|CTD-2587H19.3_ENST00000597355.1_lincRNA|TTYH1_ENST00000301194.4_Missense_Mutation_p.D430G|CTD-2587H19.2_ENST00000596631.1_RNA|TTYH1_ENST00000489425.1_3'UTR|AC008746.12_ENST00000599382.1_lincRNA	NM_001201461.1|NM_020659.3	NP_001188390.1|NP_065710.1	Q9H313	TTYH1_HUMAN	tweety family member 1	430	Poly-Asp.				cell-substrate adhesion (GO:0031589)|chloride transport (GO:0006821)|filopodium assembly (GO:0046847)|ion transmembrane transport (GO:0034220)|iron ion transmembrane transport (GO:0034755)|iron ion transport (GO:0006826)|mitotic nuclear division (GO:0007067)|regulation of anion transport (GO:0044070)|single organismal cell-cell adhesion (GO:0016337)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|filopodium membrane (GO:0031527)|filopodium tip (GO:0032433)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum membrane (GO:0030868)	calcium ion binding (GO:0005509)|iron ion transmembrane transporter activity (GO:0005381)|volume-sensitive chloride channel activity (GO:0072320)	p.D430G(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		GATGACACAGACGATGACGAC	0.647																																					p.D430G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1289G	19						.						135.0	120.0	125.0					19																	54947028		2203	4300	6503	59638840	SO:0001583	missense	57348	exon12			AF177909	CCDS12893.1, CCDS33106.1, CCDS56102.1	19q13.4	2013-09-02	2013-09-02		ENSG00000167614	ENSG00000167614			13476	protein-coding gene	gene with protein product		605784	"""tweety (Drosophila) homolog 1"", ""tweety homolog 1 (Drosophila)"""			10950931	Standard	NM_020659		Approved		uc002qfr.3	Q9H313	OTTHUMG00000065544	ENST00000376530.3:c.1289A>G	19.37:g.54947028A>G	ENSP00000365713:p.Asp430Gly	Somatic		Capture	Illumina HiSeq	Phase_I	59638840	NM_020659	B0VJY3|B0VJY4|B0VJY5|B2VAL9|Q5U682|Q68A17|Q6L750|Q6ZTE5|Q8WUU2	Missense_Mutation	SNP	ENST00000376530.3	37	CCDS12893.1	.	.	.	.	.	.	.	.	.	.	A	14.29	2.492324	0.44352	.	.	ENSG00000167614	ENST00000301194;ENST00000376530	T;T	0.15017	2.46;2.46	3.98	3.98	0.46160	.	.	.	.	.	T	0.23886	0.0578	L	0.35593	1.075	0.80722	D	1	P;P	0.51240	0.57;0.943	B;P	0.56865	0.294;0.808	T	0.01195	-1.1422	9	0.51188	T	0.08	.	11.1392	0.48392	1.0:0.0:0.0:0.0	.	430;430	Q9H313-2;Q9H313	.;TTYH1_HUMAN	G	430	ENSP00000301194:D430G;ENSP00000365713:D430G	ENSP00000301194:D430G	D	+	2	0	TTYH1	59638840	0.995000	0.38212	0.481000	0.27354	0.599000	0.36880	4.097000	0.57741	1.586000	0.49944	0.459000	0.35465	GAC		0.647	TTYH1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140498.1		
TNNI3	7137	broad.mit.edu	37	19	55666173	55666173	+	Missense_Mutation	SNP	C	C	T	rs371000425		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:55666173C>T	ENST00000344887.5	-	6	450	c.308G>A	c.(307-309)cGt>cAt	p.R103H	CTD-2587H24.4_ENST00000587871.1_3'UTR|TNNI3_ENST00000588882.1_Missense_Mutation_p.R78H|TNNI3_ENST00000590463.1_5'UTR	NM_000363.4	NP_000354.4	P19429	TNNI3_HUMAN	troponin I type 3 (cardiac)	103					cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|heart contraction (GO:0060047)|heart development (GO:0007507)|muscle filament sliding (GO:0030049)|negative regulation of ATPase activity (GO:0032780)|regulation of smooth muscle contraction (GO:0006940)|regulation of systemic arterial blood pressure by ischemic conditions (GO:0001980)|vasculogenesis (GO:0001570)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytosol (GO:0005829)|sarcomere (GO:0030017)|troponin complex (GO:0005861)	actin binding (GO:0003779)|calcium channel inhibitor activity (GO:0019855)|calcium-dependent protein binding (GO:0048306)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|troponin C binding (GO:0030172)|troponin T binding (GO:0031014)	p.R103H(1)|p.R103L(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		CTTGTCCACACGGGCGTGGAG	0.572																																					p.R103H												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G308A	19						.						128.0	126.0	127.0					19																	55666173		2121	4234	6355	60357985	SO:0001583	missense	7137	exon6			M64247	CCDS42628.1	19q13.4	2014-09-17	2005-09-12			ENSG00000129991			11947	protein-coding gene	gene with protein product		191044	"""troponin I, cardiac"", ""cardiomyopathy, dilated 2A (autosomal recessive)"""	CMD2A		9605869, 9241277, 10806205	Standard	NM_000363		Approved	TNNC1, CMH7	uc002qjg.4	P19429		ENST00000344887.5:c.308G>A	19.37:g.55666173C>T	ENSP00000341838:p.Arg103His	Somatic		Capture	Illumina HiSeq	Phase_I	60357985	NM_000363		Missense_Mutation	SNP	ENST00000344887.5	37	CCDS42628.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.225579	0.58668	.	.	ENSG00000129991	ENST00000344887	D	0.94650	-3.48	4.41	3.38	0.38709	.	0.118259	0.32736	N	0.005703	D	0.90954	0.7156	L	0.51853	1.615	0.18873	N	0.999984	D	0.54964	0.969	B	0.42163	0.378	D	0.85034	0.0919	10	0.66056	D	0.02	-35.6176	8.5508	0.33451	0.0:0.8065:0.0:0.1935	.	103	P19429	TNNI3_HUMAN	H	103	ENSP00000341838:R103H	ENSP00000341838:R103H	R	-	2	0	TNNI3	60357985	0.000000	0.05858	0.516000	0.27786	0.971000	0.66376	0.214000	0.17541	0.999000	0.39023	0.484000	0.47621	CGT		0.572	TNNI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452098.1		
U2AF2	11338	broad.mit.edu	37	19	56180115	56180115	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:56180115G>A	ENST00000308924.4	+	9	942	c.902G>A	c.(901-903)gGc>gAc	p.G301D	U2AF2_ENST00000450554.2_Missense_Mutation_p.G301D|CTD-2537I9.12_ENST00000589456.1_RNA|CTD-2537I9.13_ENST00000592252.1_RNA|U2AF2_ENST00000590551.1_Missense_Mutation_p.G137D|CTD-2537I9.12_ENST00000585940.1_RNA			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	301	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G301D(1)		biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		CTCTCCAAGGGCTACGCCTTC	0.617																																					p.G301D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G902A	19						.						69.0	66.0	67.0					19																	56180115		2203	4300	6503	60871927	SO:0001583	missense	11338	exon9			BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"""RNA binding motif (RRM) containing"""	23156	protein-coding gene	gene with protein product	"""U2 small nuclear ribonucleoprotein auxiliary factor (65kD)"", ""splicing factor U2AF 65 kD subunit"", ""U2 snRNP auxiliary factor large subunit"""	191318	"""U2 (RNU2) small nuclear RNA auxiliary factor 2"""			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.902G>A	19.37:g.56180115G>A	ENSP00000307863:p.Gly301Asp	Somatic		Capture	Illumina HiSeq	Phase_I	60871927	NM_007279	Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	37	CCDS12933.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.572951	0.86542	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	D;T	0.83591	-1.74;0.09	4.4	3.34	0.38264	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.95408	0.8509	H	0.99935	4.985	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96405	0.9300	10	0.87932	D	0	-32.268	13.4116	0.60946	0.0:0.1596:0.8404:0.0	.	301;301	P26368;P26368-2	U2AF2_HUMAN;.	D	301	ENSP00000307863:G301D;ENSP00000388475:G301D	ENSP00000307863:G301D	G	+	2	0	U2AF2	60871927	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.145000	0.94634	0.968000	0.38212	0.655000	0.94253	GGC		0.617	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279	
NLRP11	204801	broad.mit.edu	37	19	56329312	56329312	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:56329312G>A	ENST00000589093.1	-	2	322	c.229C>T	c.(229-231)Cgt>Tgt	p.R77C	NLRP11_ENST00000360133.3_Missense_Mutation_p.R77C|NLRP11_ENST00000443188.1_Missense_Mutation_p.R77C|NLRP11_ENST00000589824.2_Missense_Mutation_p.R77C|NLRP11_ENST00000592953.1_Intron			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	77	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)	p.R77C(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		TCTTCCTTACGCATCATTGAA	0.448																																					p.R77C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C229T	19						.						129.0	117.0	121.0					19																	56329312		2203	4300	6503	61021124	SO:0001583	missense	204801	exon4			AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"""Nucleotide-binding domain and leucine rich repeat containing"""	22945	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"""	609664	"""NACHT, leucine rich repeat and PYD containing 11"""	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.229C>T	19.37:g.56329312G>A	ENSP00000466285:p.Arg77Cys	Somatic		Capture	Illumina HiSeq	Phase_I	61021124	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	37	CCDS12935.1	.	.	.	.	.	.	.	.	.	.	G	12.35	1.911594	0.33721	.	.	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.58652	0.32;0.32	2.84	-5.68	0.02436	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.54791	0.1880	L	0.36672	1.1	0.09310	N	1	D	0.71674	0.998	D	0.69479	0.964	T	0.51148	-0.8742	9	0.72032	D	0.01	.	1.4182	0.02306	0.1187:0.2578:0.2669:0.3566	.	77	P59045	NAL11_HUMAN	C	77	ENSP00000409898:R77C;ENSP00000353251:R77C	ENSP00000353251:R77C	R	-	1	0	NLRP11	61021124	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.161000	0.03144	-1.531000	0.01749	-0.219000	0.12488	CGT		0.448	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007	
NLRP4	147945	broad.mit.edu	37	19	56370503	56370503	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:56370503G>A	ENST00000301295.6	+	3	2166	c.1744G>A	c.(1744-1746)Gac>Aac	p.D582N	NLRP4_ENST00000346986.5_Missense_Mutation_p.D582N|NLRP4_ENST00000587891.1_Missense_Mutation_p.D507N	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	582					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.D582N(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TCATATTATTGACAACGTGGA	0.418																																					p.D582N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1744A	19						.						81.0	74.0	77.0					19																	56370503		2203	4300	6503	61062315	SO:0001583	missense	147945	exon3			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1744G>A	19.37:g.56370503G>A	ENSP00000301295:p.Asp582Asn	Somatic		Capture	Illumina HiSeq	Phase_I	61062315	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	G	5.686	0.311054	0.10733	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	D;D	0.89050	-2.46;-2.46	3.47	-2.63	0.06133	.	.	.	.	.	T	0.73999	0.3659	N	0.25957	0.775	0.09310	N	1	B;P;B	0.39624	0.285;0.681;0.299	B;B;B	0.38458	0.155;0.274;0.13	T	0.66023	-0.6026	9	0.11485	T	0.65	.	0.5938	0.00733	0.3289:0.1701:0.3274:0.1737	.	582;507;582	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	N	582	ENSP00000301295:D582N;ENSP00000344787:D582N	ENSP00000301295:D582N	D	+	1	0	NLRP4	61062315	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.859000	0.04277	-0.393000	0.07739	-0.218000	0.12543	GAC		0.418	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
ZFP28	140612	broad.mit.edu	37	19	57066589	57066589	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:57066589C>A	ENST00000301318.3	+	8	2506	c.2435C>A	c.(2434-2436)tCt>tAt	p.S812Y	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	812					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S812Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		GGAGAGAGATCTTATAACTAT	0.383																																					p.S812Y	Ovarian(124;554 1662 19430 21141 52494)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2435A	19						.						139.0	144.0	143.0					19																	57066589		2203	4300	6503	61758401	SO:0001583	missense	140612	exon8				CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"""Zinc fingers, C2H2-type"", ""-"""	17801	protein-coding gene	gene with protein product			"""zinc finger protein 28 homolog (mouse)"""				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.2435C>A	19.37:g.57066589C>A	ENSP00000301318:p.Ser812Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	61758401	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.260355	0.39995	.	.	ENSG00000196867	ENST00000301318	T	0.28454	1.61	4.32	4.32	0.51571	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.921406	0.09031	N	0.858781	T	0.37376	0.1001	L	0.60904	1.88	0.80722	D	1	P	0.46277	0.875	B	0.41723	0.365	T	0.46679	-0.9174	10	0.87932	D	0	.	16.0727	0.80946	0.0:1.0:0.0:0.0	.	812	Q8NHY6	ZFP28_HUMAN	Y	812	ENSP00000301318:S812Y	ENSP00000301318:S812Y	S	+	2	0	ZFP28	61758401	0.023000	0.18921	0.004000	0.12327	0.402000	0.30811	2.948000	0.49066	2.396000	0.81511	0.655000	0.94253	TCT		0.383	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828	
ZIM3	114026	broad.mit.edu	37	19	57647043	57647043	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:57647043C>A	ENST00000269834.1	-	5	1047	c.662G>T	c.(661-663)aGg>aTg	p.R221M	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	221					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R221M(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TTTATAGGGCCTTTCCTCTGC	0.418																																					p.R221M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G662T	19						.						158.0	154.0	155.0					19																	57647043		2203	4300	6503	62338855	SO:0001583	missense	114026	exon5			AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"""Zinc fingers, C2H2-type"", ""-"""	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.662G>T	19.37:g.57647043C>A	ENSP00000269834:p.Arg221Met	Somatic		Capture	Illumina HiSeq	Phase_I	62338855	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.091170	0.36855	.	.	ENSG00000141946	ENST00000269834	T	0.20332	2.08	1.97	-0.325	0.12702	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35653	0.0939	M	0.68952	2.095	0.09310	N	1	D	0.63880	0.993	D	0.65323	0.934	T	0.15122	-1.0448	9	0.87932	D	0	.	5.2505	0.15519	0.0:0.3471:0.0:0.6529	.	221	Q96PE6	ZIM3_HUMAN	M	221	ENSP00000269834:R221M	ENSP00000269834:R221M	R	-	2	0	ZIM3	62338855	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.293000	0.08320	-0.146000	0.11274	0.313000	0.20887	AGG		0.418	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1		
AURKC	6795	broad.mit.edu	37	19	57743926	57743926	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:57743926C>T	ENST00000302804.7	+	4	499	c.313C>T	c.(313-315)Cgc>Tgc	p.R105C	AURKC_ENST00000448930.1_Missense_Mutation_p.R71C|AURKC_ENST00000415300.2_Missense_Mutation_p.R86C|AURKC_ENST00000598785.1_Missense_Mutation_p.R71C|AURKC_ENST00000599062.1_Missense_Mutation_p.R102C	NM_001015878.1	NP_001015878.1	Q9UQB9	AURKC_HUMAN	aurora kinase C	105	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|cytokinesis (GO:0000910)|histone modification (GO:0016570)|meiotic nuclear division (GO:0007126)|positive regulation of cytokinesis (GO:0032467)|protein phosphorylation (GO:0006468)|spindle midzone assembly involved in mitosis (GO:0051256)	chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.R105C(1)|p.R71C(1)		breast(1)|endometrium(1)|large_intestine(9)|lung(9)|ovary(3)|prostate(1)|stomach(1)	25		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)		CAATATCCTGCGCCTGTATAA	0.488																																					p.R71C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C211T	19						.						101.0	94.0	96.0					19																	57743926		2203	4300	6503	62435738	SO:0001583	missense	6795	exon4				CCDS33128.1, CCDS46205.1, CCDS46206.1	19q13.43	2013-09-19	2003-07-21	2003-07-23	ENSG00000105146	ENSG00000105146			11391	protein-coding gene	gene with protein product		603495	"""serine/threonine kinase 13 (aurora/IPL1-like)"""	STK13		9799611	Standard	XR_430209		Approved	AurC, ARK3	uc002qoe.3	Q9UQB9	OTTHUMG00000183106	ENST00000302804.7:c.313C>T	19.37:g.57743926C>T	ENSP00000302898:p.Arg105Cys	Somatic		Capture	Illumina HiSeq	Phase_I	62435738	NM_003160	O60681|O75442|Q6AZY8|Q6DLZ0|Q9UPK5	Missense_Mutation	SNP	ENST00000302804.7	37	CCDS33128.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.412483	0.42817	.	.	ENSG00000105146	ENST00000415300;ENST00000448930;ENST00000302804	T;T;T	0.09723	2.95;2.95;2.95	3.6	2.54	0.30619	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.25717	0.0626	M	0.83312	2.635	0.80722	D	1	D;D;D	0.59357	0.985;0.96;0.981	P;P;P	0.54664	0.758;0.612;0.715	T	0.07829	-1.0752	10	0.87932	D	0	-12.1449	10.3481	0.43918	0.2165:0.7835:0.0:0.0	.	102;105;86	Q5Y191;Q9UQB9;Q9UQB9-3	.;AURKC_HUMAN;.	C	86;71;105	ENSP00000407162:R86C;ENSP00000406798:R71C;ENSP00000302898:R105C	ENSP00000302898:R105C	R	+	1	0	AURKC	62435738	0.992000	0.36948	0.960000	0.40013	0.234000	0.25298	2.946000	0.49050	1.047000	0.40274	-0.410000	0.06199	CGC		0.488	AURKC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465089.1	NM_003160	
ZNF154	7710	broad.mit.edu	37	19	58216322	58216322	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:58216322G>A	ENST00000512439.2	-	2	255	c.59C>T	c.(58-60)gCc>gTc	p.A20V	ZNF551_ENST00000596085.1_Intron|AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron|ZNF154_ENST00000426889.1_Missense_Mutation_p.A20V			Q13106	ZN154_HUMAN	zinc finger protein 154	20	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A20V(2)		endometrium(1)|kidney(1)|large_intestine(7)|lung(3)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		GAAGTGTACGGCCACATCTTC	0.512																																					p.A20V												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C59T	19						.						144.0	138.0	140.0					19																	58216322		2203	4300	6503	62908134	SO:0001583	missense	7710	exon2			U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"""Zinc fingers, C2H2-type"", ""-"""	12939	protein-coding gene	gene with protein product		604085	"""zinc finger protein 154 (pHZ-92)"""			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.59C>T	19.37:g.58216322G>A	ENSP00000421258:p.Ala20Val	Somatic		Capture	Illumina HiSeq	Phase_I	62908134	NM_001085384	A7MCY3|Q8IVG7|Q8NAR0	Missense_Mutation	SNP	ENST00000512439.2	37	CCDS42639.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.567615	0.45694	.	.	ENSG00000179909	ENST00000512439;ENST00000426889	T;T	0.03301	3.98;3.98	2.78	1.72	0.24424	Krueppel-associated box (4);	.	.	.	.	T	0.10294	0.0252	M	0.85373	2.75	0.19945	N	0.999944	P	0.35433	0.501	B	0.44315	0.446	T	0.12785	-1.0534	9	0.87932	D	0	.	5.5837	0.17264	0.1593:0.0:0.8407:0.0	.	20	Q13106	ZN154_HUMAN	V	20	ENSP00000421258:A20V;ENSP00000442370:A20V	ENSP00000442370:A20V	A	-	2	0	ZNF154	62908134	0.002000	0.14202	0.574000	0.28523	0.776000	0.43924	0.884000	0.28214	0.732000	0.32470	0.313000	0.20887	GCC		0.512	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2		
ZSCAN18	65982	broad.mit.edu	37	19	58601566	58601566	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:58601566C>A	ENST00000240727.6	-	2	468	c.69G>T	c.(67-69)ccG>ccT	p.P23P	ZSCAN18_ENST00000601144.1_Silent_p.P23P|ZSCAN18_ENST00000600404.1_Silent_p.P79P|ZSCAN18_ENST00000421612.2_Intron	NM_023926.4	NP_076415.3	Q8TBC5	ZSC18_HUMAN	zinc finger and SCAN domain containing 18	23					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.P23P(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|skin(3)	19		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.114)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		CTGCTGACCCCGGCGTGGGCA	0.612																																					p.P79P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G237T	19						.						35.0	42.0	40.0					19																	58601566		2201	4296	6497	63293378	SO:0001819	synonymous_variant	65982	exon2			AY280799, AY279352	CCDS12971.1, CCDS46214.1, CCDS46215.1	19q13.43	2013-01-09	2007-02-20	2007-02-20		ENSG00000121413		"""-"", ""Zinc fingers, C2H2-type"""	21037	protein-coding gene	gene with protein product			"""zinc finger protein 447"""	ZNF447			Standard	NM_001145542		Approved	FLJ12895	uc010yht.1	Q8TBC5		ENST00000240727.6:c.69G>T	19.37:g.58601566C>A		Somatic		Capture	Illumina HiSeq	Phase_I	63293378	NM_001145542	B4DG23|E9PBI0|Q9BRK7|Q9H9A0	Silent	SNP	ENST00000240727.6	37	CCDS12971.1																																																																																				0.612	ZSCAN18-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466706.1	NM_023926	
ZNF324B	388569	broad.mit.edu	37	19	58967481	58967481	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:58967481G>A	ENST00000336614.4	+	4	1277	c.1170G>A	c.(1168-1170)acG>acA	p.T390T	ZNF324B_ENST00000545523.1_Silent_p.T390T|ZNF324B_ENST00000391696.1_Silent_p.T380T	NM_207395.2	NP_997278.2	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	390					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T390T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		ACGAGCGTACGCACACAGGCG	0.652																																					p.T390T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1170A	19						.						49.0	47.0	47.0					19																	58967481		2203	4300	6503	63659293	SO:0001819	synonymous_variant	388569	exon4			AK127750	CCDS33138.1	19q13.43	2013-01-08				ENSG00000249471		"""Zinc fingers, C2H2-type"", ""-"""	33107	protein-coding gene	gene with protein product							Standard	NM_207395		Approved	FLJ45850	uc002qsv.1	Q6AW86		ENST00000336614.4:c.1170G>A	19.37:g.58967481G>A		Somatic		Capture	Illumina HiSeq	Phase_I	63659293	NM_207395	B2RTZ6|Q6ZMX8|Q6ZS42	Silent	SNP	ENST00000336614.4	37	CCDS33138.1																																																																																				0.652	ZNF324B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467038.1	NM_207395	
VAV1	7409	broad.mit.edu	37	19	6833931	6833931	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:6833931C>T	ENST00000602142.1	+	19	1826	c.1744C>T	c.(1744-1746)Cgc>Tgc	p.R582C	VAV1_ENST00000596764.1_Missense_Mutation_p.R550C|VAV1_ENST00000304076.2_Missense_Mutation_p.R582C|VAV1_ENST00000599806.1_Missense_Mutation_p.R527C|VAV1_ENST00000539284.1_Missense_Mutation_p.R485C	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	582					apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R582C(1)		biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						CAAACTACATCGCAGGGCTCA	0.537																																					p.R582C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1744T	19						.						99.0	102.0	101.0					19																	6833931		2203	4300	6503	6784931	SO:0001583	missense	7409	exon19				CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12657	protein-coding gene	gene with protein product		164875	"""vav 1 oncogene"""	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.1744C>T	19.37:g.6833931C>T	ENSP00000472929:p.Arg582Cys	Somatic		Capture	Illumina HiSeq	Phase_I	6784931	NM_005428	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	37	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.473389	0.26423	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	T;T	0.76186	-0.05;-1.0	3.95	2.88	0.33553	.	0.729753	0.12826	N	0.436012	T	0.69079	0.3071	L	0.52573	1.65	0.47698	D	0.999499	P;B;P;B	0.42692	0.653;0.389;0.787;0.001	B;B;B;B	0.41860	0.219;0.083;0.368;0.002	T	0.66634	-0.5874	10	0.59425	D	0.04	.	9.0458	0.36345	0.2204:0.7796:0.0:0.0	.	485;582;527;582	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	C	582;485	ENSP00000302269:R582C;ENSP00000443242:R485C	ENSP00000302269:R582C	R	+	1	0	VAV1	6784931	0.804000	0.28969	0.955000	0.39395	0.740000	0.42216	0.863000	0.27913	0.770000	0.33336	0.491000	0.48974	CGC		0.537	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1		
FBN3	84467	broad.mit.edu	37	19	8140180	8140180	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:8140180G>A	ENST00000600128.1	-	60	7983	c.7569C>T	c.(7567-7569)ggC>ggT	p.G2523G	FBN3_ENST00000601739.1_Silent_p.G2523G|FBN3_ENST00000270509.2_Silent_p.G2523G			Q75N90	FBN3_HUMAN	fibrillin 3	2523	EGF-like 41; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.G2523G(1)		NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CACAGCCATGGCCTGAGCTGA	0.617																																					p.G2523G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C7569T	19						.						52.0	46.0	48.0					19																	8140180		2203	4300	6503	8046180	SO:0001819	synonymous_variant	84467	exon59				CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.7569C>T	19.37:g.8140180G>A		Somatic		Capture	Illumina HiSeq	Phase_I	8046180	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																				0.617	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
HNRNPM	4670	broad.mit.edu	37	19	8532431	8532431	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:8532431G>A	ENST00000325495.4	+	8	838	c.797G>A	c.(796-798)gGc>gAc	p.G266D	HNRNPM_ENST00000348943.3_Missense_Mutation_p.G227D	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	266	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)	p.G266D(1)		endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						ATGTTCAATGGCCAGCTGCTA	0.348																																					p.G266D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G797A	19						.						127.0	114.0	118.0					19																	8532431		2203	4300	6503	8438431	SO:0001583	missense	4670	exon8			L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"""RNA binding motif (RRM) containing"""	5046	protein-coding gene	gene with protein product	"""CEA receptor"""	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.797G>A	19.37:g.8532431G>A	ENSP00000325376:p.Gly266Asp	Somatic		Capture	Illumina HiSeq	Phase_I	8438431	NM_005968	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Missense_Mutation	SNP	ENST00000325495.4	37	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.995266	0.93167	.	.	ENSG00000099783	ENST00000325495;ENST00000348943;ENST00000544159	T;T	0.51071	0.72;1.76	5.44	5.44	0.79542	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.65165	0.2665	L	0.51422	1.61	0.80722	D	1	D;P;D;D;D	0.89917	0.99;0.902;1.0;0.998;0.998	D;D;D;D;D	0.97110	0.989;0.949;1.0;0.977;0.993	T	0.66089	-0.6010	10	0.72032	D	0.01	.	18.1809	0.89777	0.0:0.0:1.0:0.0	.	106;266;227;227;166	Q7KYM9;P52272;P52272-2;B4DEG4;Q59ES8	.;HNRPM_HUMAN;.;.;.	D	266;227;166	ENSP00000325376:G266D;ENSP00000325732:G227D	ENSP00000325376:G266D	G	+	2	0	HNRNPM	8438431	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	7.904000	0.87408	2.709000	0.92574	0.655000	0.94253	GGC		0.348	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		
MUC16	94025	broad.mit.edu	37	19	9025653	9025653	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:9025653C>A	ENST00000397910.4	-	15	37004	c.36801G>T	c.(36799-36801)aaG>aaT	p.K12267N		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12269	SEA 2. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.K12267N(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGAACAAGGGCTTGAGCTGTG	0.562																																					p.K12267N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G36801T	19						.						121.0	112.0	115.0					19																	9025653		1996	4171	6167	8886653	SO:0001583	missense	94025	exon15			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.36801G>T	19.37:g.9025653C>A	ENSP00000381008:p.Lys12267Asn	Somatic		Capture	Illumina HiSeq	Phase_I	8886653	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	0.145	-1.097849	0.01843	.	.	ENSG00000181143	ENST00000397910	T	0.20463	2.07	2.81	-5.61	0.02489	.	.	.	.	.	T	0.12689	0.0308	L	0.36672	1.1	.	.	.	B	0.17667	0.023	B	0.22152	0.038	T	0.26155	-1.0111	8	0.87932	D	0	.	1.3654	0.02200	0.4814:0.1734:0.1196:0.2256	.	12267	B5ME49	.	N	12267	ENSP00000381008:K12267N	ENSP00000381008:K12267N	K	-	3	2	MUC16	8886653	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-7.365000	0.00038	-3.437000	0.00163	-2.883000	0.00097	AAG		0.562	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MUC16	94025	broad.mit.edu	37	19	9085411	9085411	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:9085411G>T	ENST00000397910.4	-	1	6607	c.6404C>A	c.(6403-6405)cCt>cAt	p.P2135H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2135	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.P2135H(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGCCCCCACAGGAGTCTCAGA	0.488																																					p.P2135H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C6404A	19						.						86.0	85.0	85.0					19																	9085411		1913	4122	6035	8946411	SO:0001583	missense	94025	exon1			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.6404C>A	19.37:g.9085411G>T	ENSP00000381008:p.Pro2135His	Somatic		Capture	Illumina HiSeq	Phase_I	8946411	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	0.619	-0.822045	0.02755	.	.	ENSG00000181143	ENST00000397910	T	0.03301	3.98	0.235	0.235	0.15431	.	.	.	.	.	T	0.02156	0.0067	N	0.08118	0	.	.	.	P	0.34977	0.478	B	0.34931	0.192	T	0.40194	-0.9576	7	0.87932	D	0	.	.	.	.	.	2135	B5ME49	.	H	2135	ENSP00000381008:P2135H	ENSP00000381008:P2135H	P	-	2	0	MUC16	8946411	0.003000	0.15002	0.020000	0.16555	0.021000	0.10359	0.792000	0.26929	0.308000	0.22923	0.313000	0.20887	CCT		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MUC16	94025	broad.mit.edu	37	19	9090013	9090013	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:9090013T>C	ENST00000397910.4	-	1	2005	c.1802A>G	c.(1801-1803)cAt>cGt	p.H601R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	601	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.H601R(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGCAAACTGATGGGTGGTTGG	0.547																																					p.H601R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A1802G	19						.						61.0	64.0	63.0					19																	9090013		2182	4282	6464	8951013	SO:0001583	missense	94025	exon1			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.1802A>G	19.37:g.9090013T>C	ENSP00000381008:p.His601Arg	Somatic		Capture	Illumina HiSeq	Phase_I	8951013	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	2.621	-0.288649	0.05605	.	.	ENSG00000181143	ENST00000397910	T	0.02472	4.28	1.68	0.59	0.17458	.	.	.	.	.	T	0.01627	0.0052	N	0.08118	0	.	.	.	B	0.18310	0.027	B	0.11329	0.006	T	0.41305	-0.9516	8	0.87932	D	0	.	3.6266	0.08116	0.0:0.2187:0.0:0.7813	.	601	B5ME49	.	R	601	ENSP00000381008:H601R	ENSP00000381008:H601R	H	-	2	0	MUC16	8951013	0.000000	0.05858	0.045000	0.18777	0.088000	0.18126	-1.183000	0.03079	0.106000	0.17784	0.172000	0.16884	CAT		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF559	84527	broad.mit.edu	37	19	9453569	9453569	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:9453569C>T	ENST00000393883.2	+	6	2090	c.1442C>T	c.(1441-1443)aCa>aTa	p.T481I	ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000603380.1_Missense_Mutation_p.T481I|CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF559_ENST00000586255.1_Intron|ZNF559_ENST00000538743.1_Missense_Mutation_p.T401I|ZNF177_ENST00000605471.1_Intron|ZNF177_ENST00000541595.2_Intron|ZNF177_ENST00000446085.4_Intron|ZNF559_ENST00000587557.1_Missense_Mutation_p.T545I|ZNF559_ENST00000317221.7_3'UTR|ZNF177_ENST00000602856.1_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	481					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T481I(1)		endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						TCAGGCCTTACAGTACACATG	0.438																																					p.T481I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1442T	19						.						84.0	75.0	78.0					19																	9453569		2203	4300	6503	9314569	SO:0001583	missense	84527	exon6			AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"""Zinc fingers, C2H2-type"", ""-"""	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.1442C>T	19.37:g.9453569C>T	ENSP00000377461:p.Thr481Ile	Somatic		Capture	Illumina HiSeq	Phase_I	9314569	NM_032497	K7EMG6	Missense_Mutation	SNP	ENST00000393883.2	37	CCDS12211.1	.	.	.	.	.	.	.	.	.	.	C	11.64	1.699541	0.30142	.	.	ENSG00000188321	ENST00000317221;ENST00000538743;ENST00000393883	T;T	0.07908	3.15;3.15	2.22	-4.44	0.03557	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02767	0.0083	N	0.03983	-0.305	0.09310	N	1	B;B;B	0.29766	0.051;0.256;0.051	B;B;B	0.33960	0.032;0.173;0.032	T	0.40961	-0.9535	9	0.18276	T	0.48	.	2.4924	0.04614	0.1381:0.1806:0.1371:0.5442	.	481;481;401	B3KPL8;Q9BR84;B4DP29	.;ZN559_HUMAN;.	I	481;401;481	ENSP00000442832:T401I;ENSP00000377461:T481I	ENSP00000325393:T481I	T	+	2	0	ZNF559	9314569	0.000000	0.05858	0.000000	0.03702	0.898000	0.52572	-9.063000	0.00014	-1.786000	0.01269	0.313000	0.20887	ACA		0.438	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497	
ATG4D	84971	broad.mit.edu	37	19	10657546	10657546	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:10657546delC	ENST00000309469.4	+	4	698	c.525delC	c.(523-525)ggcfs	p.G175fs	ATG4D_ENST00000540862.1_Intron	NM_032885.4	NP_116274.3	Q86TL0	ATG4D_HUMAN	autophagy related 4D, cysteine peptidase	175					apoptotic process (GO:0006915)|autophagy (GO:0006914)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)	p.P177fs*75(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	19			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			TGGGCCTGGGCCCCCCTGAGC	0.662																																					p.G175fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.525delC	19						.						33.0	31.0	32.0					19																	10657546		2186	4279	6465	10518546	SO:0001589	frameshift_variant	84971	exon4			AJ312332	CCDS12241.1	19p13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000130734	ENSG00000130734			20789	protein-coding gene	gene with protein product		611340	"""AUT-like 4, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog D (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog D (S. cerevisiae)"""	AUTL4, APG4D		12446702	Standard	NM_032885		Approved	APG4-D	uc002mov.3	Q86TL0	OTTHUMG00000180582	ENST00000309469.4:c.525delC	19.37:g.10657546delC	ENSP00000311318:p.Gly175fs	Somatic		Capture	Illumina HiSeq	Phase_I	10518546	NM_032885	Q969K0	Frame_Shift_Del	DEL	ENST00000309469.4	37	CCDS12241.1																																																																																				0.662	ATG4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452022.1	NM_032885	
ZNF793	390927	broad.mit.edu	37	19	38028415	38028415	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:38028415delT	ENST00000587143.1	+	6	1090	c.855delT	c.(853-855)tgtfs	p.C285fs	ZNF793_ENST00000542455.1_Frame_Shift_Del_p.C285fs|ZNF793_ENST00000445217.1_Frame_Shift_Del_p.C285fs|ZNF793_ENST00000589319.1_Intron|ZNF793_ENST00000588578.1_3'UTR			Q6ZN11	ZN793_HUMAN	zinc finger protein 793	285					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C288fs*113(1)		kidney(2)|lung(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCTTTGAATGTTTTTTTTGTG	0.463																																					p.C285fs	Melanoma(44;400 1431 1499 19093)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.855delT	19						.						60.0	69.0	66.0					19																	38028415		2142	4276	6418	42720255	SO:0001589	frameshift_variant	390927	exon8			AK131417	CCDS46062.1	19q13.12	2013-01-08				ENSG00000188227		"""Zinc fingers, C2H2-type"", ""-"""	33115	protein-coding gene	gene with protein product							Standard	NM_001013659		Approved		uc010efm.3	Q6ZN11		ENST00000587143.1:c.855delT	19.37:g.38028415delT	ENSP00000468605:p.Cys285fs	Somatic		Capture	Illumina HiSeq	Phase_I	42720255	NM_001013659	E9PGN4|Q7Z3Q9	Frame_Shift_Del	DEL	ENST00000587143.1	37	CCDS46062.1																																																																																				0.463	ZNF793-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458621.1	NM_001013659	
IRGQ	126298	broad.mit.edu	37	19	44096566	44096568	+	In_Frame_Del	DEL	GCC	GCC	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	GCC	GCC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:44096566_44096568delGCC	ENST00000602269.1	-	2	1667_1669	c.1482_1484delGGC	c.(1480-1485)gcggca>gca	p.494_495AA>A	L34079.2_ENST00000594374.1_Intron|IRGQ_ENST00000601520.1_Intron|IRGQ_ENST00000422989.1_In_Frame_Del_p.494_495AA>A			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	494	Ala-rich.							p.A495delA(1)		endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				TGGGAGTGGTGCCGCCGCCGCCG	0.729																																					p.494_495del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.1482_1484del	19						.			20,2370		4,12,1179						-8.0	0.1			4	37,5111		2,33,2539	no	coding	IRGQ	NM_001007561.2		6,45,3718	A1A1,A1R,RR		0.7187,0.8368,0.7562				57,7481				48788408	SO:0001651	inframe_deletion	126298	exon3			AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"""immunity-related GTPase family, Q1"""	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.1482_1484delGGC	19.37:g.44096575_44096577delGCC	ENSP00000472250:p.Ala495del	Somatic		Capture	Illumina HiSeq	Phase_I	48788406	NM_001007561	B2RNP3	In_Frame_Del	DEL	ENST00000602269.1	37	CCDS33040.1																																																																																				0.729	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561	
CEACAM16	388551	broad.mit.edu	37	19	45202702	45202702	+	Intron	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:45202702delT	ENST00000587331.1	+	1	119				CEACAM16_ENST00000405314.2_5'Flank|CTB-171A8.1_ENST00000590796.1_RNA	NM_001039213.2	NP_001034302.2	Q2WEN9	CEA16_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 16						sensory perception of sound (GO:0007605)	extracellular region (GO:0005576)|stereocilium bundle tip (GO:0032426)		p.L61fs*1(4)		endometrium(3)|large_intestine(2)|lung(3)|ovary(1)	9	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)				gagcctatacttttttTTTTT	0.468																																					.												.	.	4	Deletion - Frameshift(4)	large_intestine(4)	.	19						.			259,128,2691		23,1,212,14,99,1190	52.0	61.0	58.0			-1.6	0.0	19	dbSNP_130	66	438,337,6203		44,7,343,34,262,2799	no	intron	CEACAM16	NM_001039213.2		67,8,555,48,361,3989	A1A1,A1A2,A1R,A2A2,A2R,RR		11.1063,12.5731,11.5553			45202702	697,465,8894	953	2098	3051	49894542	SO:0001627	intron_variant	388551	.				CCDS54278.1	19q13.31	2014-01-27			ENSG00000213892	ENSG00000213892		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31948	protein-coding gene	gene with protein product		614591				21368133	Standard	NM_001039213		Approved	DFNA4B	uc010xxd.2	Q2WEN9	OTTHUMG00000151519	ENST00000587331.1:c.-97+163T>-	19.37:g.45202702delT		Somatic		Capture	Illumina HiSeq	Phase_I	49894542	.	A7LI12	Frame_Shift_Del	DEL	ENST00000587331.1	37	CCDS54278.1																																																																																				0.468	CEACAM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322986.2	XM_371177	
FBXO46	23403	broad.mit.edu	37	19	46216087	46216087	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:46216087delC	ENST00000317683.3	-	2	800	c.667delG	c.(667-669)gacfs	p.D223fs		NM_001080469.1	NP_001073938.1	Q6PJ61	FBX46_HUMAN	F-box protein 46	223								p.D223fs*5(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	15		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00568)|GBM - Glioblastoma multiforme(486;0.0844)|Epithelial(262;0.201)		CGGCTGCAGTCCCCACCACCG	0.697																																					p.D223fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.667delG	19						.						19.0	23.0	22.0					19																	46216087		2012	4150	6162	50907927	SO:0001589	frameshift_variant	23403	exon2			BC021978	CCDS46116.1	19q13.3	2008-02-05	2004-06-15	2004-06-16		ENSG00000177051		"""F-boxes /  ""other"""""	25069	protein-coding gene	gene with protein product		609117	"""F-box only protein 34-like"""	FBXO34L		9585442	Standard	NM_001080469		Approved	20D7-FC4, Fbx46	uc002pcz.3	Q6PJ61		ENST00000317683.3:c.667delG	19.37:g.46216087delC	ENSP00000410007:p.Asp223fs	Somatic		Capture	Illumina HiSeq	Phase_I	50907927	NM_001080469		Frame_Shift_Del	DEL	ENST00000317683.3	37	CCDS46116.1																																																																																				0.697	FBXO46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459661.1	XM_371179	
ZNF28	7576	broad.mit.edu	37	19	53304402	53304402	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:53304402delT	ENST00000457749.2	-	4	815	c.696delA	c.(694-696)aaafs	p.K232fs	ZNF28_ENST00000414252.2_Frame_Shift_Del_p.K179fs|ZNF28_ENST00000360272.4_Frame_Shift_Del_p.K179fs|ZNF28_ENST00000438150.2_Frame_Shift_Del_p.K179fs	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	232					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K179fs*4(2)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		TTATCTGATGTTTTTTTAAAA	0.348																																					p.K232fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.696delA	19						.						114.0	108.0	110.0					19																	53304402		2203	4300	6503	57996214	SO:0001589	frameshift_variant	7576	exon4			X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"""Zinc fingers, C2H2-type"", ""-"""	13073	protein-coding gene	gene with protein product			"""zinc finger protein 28 (KOX 24)"""				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.696delA	19.37:g.53304402delT	ENSP00000397693:p.Lys232fs	Somatic		Capture	Illumina HiSeq	Phase_I	57996214	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Frame_Shift_Del	DEL	ENST00000457749.2	37	CCDS33093.2																																																																																				0.348	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969	
PPP6R1	22870	broad.mit.edu	37	19	55748036	55748036	+	Frame_Shift_Del	DEL	G	G	-	rs201977593		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:55748036delG	ENST00000412770.2	-	17	2529	c.1963delC	c.(1963-1965)cgtfs	p.R655fs	AC010327.1_ENST00000581390.1_RNA|PPP6R1_ENST00000587283.1_Frame_Shift_Del_p.R655fs	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	655	Glu-rich.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)	p.R655fs*>227(1)		breast(1)	1						TGGCCCAGACGGGCCCCCCTG	0.652																																					p.R655fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1963delC	19						.						21.0	23.0	22.0					19																	55748036		1888	4106	5994	60439848	SO:0001589	frameshift_variant	22870	exon17			AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	29195	protein-coding gene	gene with protein product		610875	"""KIAA1115"", ""SAPS domain family, member 1"""	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.1963delC	19.37:g.55748036delG	ENSP00000414202:p.Arg655fs	Somatic		Capture	Illumina HiSeq	Phase_I	60439848	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Frame_Shift_Del	DEL	ENST00000412770.2	37	CCDS46186.1																																																																																				0.652	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931	
USP29	57663	broad.mit.edu	37	19	57640239	57640239	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:57640239delA	ENST00000254181.4	+	4	650	c.196delA	c.(196-198)aaafs	p.K67fs	USP29_ENST00000598197.1_Frame_Shift_Del_p.K67fs	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	67					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.R68fs*7(1)		breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TAGACATTGTAAAAAAAGACA	0.323																																					p.K66fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.196delA	19						.						56.0	56.0	56.0					19																	57640239		2202	4300	6502	62332051	SO:0001589	frameshift_variant	57663	exon4				CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"""Ubiquitin-specific peptidases"""	18563	protein-coding gene	gene with protein product		609546	"""ubiquitin specific protease 29"""			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.196delA	19.37:g.57640239delA	ENSP00000254181:p.Lys67fs	Somatic		Capture	Illumina HiSeq	Phase_I	62332051	NM_020903		Frame_Shift_Del	DEL	ENST00000254181.4	37	CCDS33124.1																																																																																				0.323	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1		
SLC27A5	10998	broad.mit.edu	37	19	59022763	59022763	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr19:59022763G>A	ENST00000263093.2	-	1	669	c.560C>T	c.(559-561)gCc>gTc	p.A187V	SLC27A5_ENST00000601355.1_Intron	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	187					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.A187V(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		CATACACAGGGCTGGAACGGC	0.682																																					p.A187V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C560T	19						.						12.0	12.0	12.0					19																	59022763		2164	4239	6403	63714575	SO:0001583	missense	10998	exon1			AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.560C>T	19.37:g.59022763G>A	ENSP00000263093:p.Ala187Val	Somatic		Capture	Illumina HiSeq	Phase_I	63714575	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	.	.	.	.	.	.	.	.	.	.	g	15.91	2.971720	0.53614	.	.	ENSG00000083807	ENST00000263093	T	0.41065	1.01	4.18	3.11	0.35812	AMP-dependent synthetase/ligase (1);	0.165035	0.28952	N	0.013616	T	0.48295	0.1492	L	0.59436	1.845	0.24045	N	0.996068	P	0.46064	0.872	P	0.51582	0.674	T	0.38802	-0.9644	10	0.72032	D	0.01	-15.9137	9.9389	0.41567	0.0:0.2072:0.7928:0.0	.	187	Q9Y2P5	S27A5_HUMAN	V	187	ENSP00000263093:A187V	ENSP00000263093:A187V	A	-	2	0	SLC27A5	63714575	0.367000	0.25023	0.097000	0.21041	0.019000	0.09904	1.509000	0.35780	1.070000	0.40811	0.455000	0.32223	GCC		0.682	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
NOTCH2	4853	broad.mit.edu	37	1	120464982	120464983	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:120464982_120464983insC	ENST00000256646.2	-	28	5308_5309	c.5089_5090insG	c.(5089-5091)gtafs	p.V1697fs	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1697					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.V1697fs*9(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGCCATGATTACCCCCAGCAGA	0.5			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																												p.V1697fs			Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.5090_5091insG	1						.																																			120266506	SO:0001589	frameshift_variant	4853	exon28	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.5090dupG	1.37:g.120464987_120464987dupC	ENSP00000256646:p.Val1697fs	Somatic		Capture	Illumina HiSeq	Phase_I	120266505	NM_024408	Q5T3X7|Q99734|Q9H240	Frame_Shift_Ins	INS	ENST00000256646.2	37	CCDS908.1																																																																																				0.500	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
PYGO2	90780	broad.mit.edu	37	1	154932027	154932028	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-	-	G	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:154932027_154932028insG	ENST00000368457.2	-	3	619_620	c.448_449insC	c.(448-450)cagfs	p.Q150fs	PYGO2_ENST00000483463.1_5'Flank|RP11-307C12.12_ENST00000605085.1_RNA|PYGO2_ENST00000368456.1_Frame_Shift_Ins_p.Q113fs	NM_138300.3	NP_612157.1	Q9BRQ0	PYGO2_HUMAN	pygopus family PHD finger 2	150	Pro-rich.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|developmental growth (GO:0048589)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mammary gland development (GO:0030879)|palate development (GO:0060021)|positive regulation of chromatin binding (GO:0035563)|post-embryonic development (GO:0009791)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|spermatid nucleus differentiation (GO:0007289)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase regulator activity (GO:0035034)|zinc ion binding (GO:0008270)	p.Q150fs*27(2)		endometrium(2)|large_intestine(2)|lung(3)|skin(2)|urinary_tract(1)	10	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GCCAGGACCCTGGGGGGGCATG	0.619																																					p.Q150fs	NSCLC(87;357 1460 1955 21029 23522)											.	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.449_450insC	1						.																																			153198652	SO:0001589	frameshift_variant	90780	exon3			BC006132	CCDS1075.1	1q22	2013-10-09	2013-10-09		ENSG00000163348	ENSG00000163348		"""Zinc fingers, PHD-type"""	30257	protein-coding gene	gene with protein product		606903	"""pygopus homolog 2 (Drosophila)"""			11988739	Standard	NM_138300		Approved		uc001fft.3	Q9BRQ0	OTTHUMG00000037370	ENST00000368457.2:c.449dupC	1.37:g.154932034_154932034dupG	ENSP00000357442:p.Gln150fs	Somatic		Capture	Illumina HiSeq	Phase_I	153198651	NM_138300	Q8WYZ4|Q96CY2	Frame_Shift_Ins	INS	ENST00000368457.2	37	CCDS1075.1																																																																																				0.619	PYGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090949.1	NM_138300	
IGSF8	93185	broad.mit.edu	37	1	160062431	160062432	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:160062431_160062432insC	ENST00000368086.1	-	5	1582_1583	c.1366_1367insG	c.(1366-1368)gagfs	p.E456fs	IGSF8_ENST00000314485.7_Frame_Shift_Ins_p.E456fs|IGSF8_ENST00000460351.1_5'Flank			Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	456	Ig-like C2-type 4.				cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|nervous system development (GO:0007399)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.E456fs*84(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(19)|pancreas(1)|prostate(1)|skin(1)	33	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			GGAGGCAGTCTCCCCGCGGTAC	0.668																																					p.E456fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1367_1368insG	1						.																																			158329056	SO:0001589	frameshift_variant	93185	exon5			AF407274	CCDS1195.1	1q23.1	2013-01-11			ENSG00000162729	ENSG00000162729		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	17813	protein-coding gene	gene with protein product		606644				11504738, 11673522	Standard	NM_001206665		Approved	CD81P3, EWI2, PGRL, CD316	uc009wtf.3	Q969P0	OTTHUMG00000024075	ENST00000368086.1:c.1367dupG	1.37:g.160062435_160062435dupC	ENSP00000357065:p.Glu456fs	Somatic		Capture	Illumina HiSeq	Phase_I	158329055	NM_052868	Q8NG09|Q96DP4|Q9BTG9	Frame_Shift_Ins	INS	ENST00000368086.1	37	CCDS1195.1																																																																																				0.668	IGSF8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060636.1	NM_052868	
CLCNKA	1187	broad.mit.edu	37	1	16356551	16356552	+	Frame_Shift_Ins	INS	-	-	G	rs141107527		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-	-	G	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:16356551_16356552insG	ENST00000331433.4	+	14	1408_1409	c.1389_1390insG	c.(1390-1392)gggfs	p.G464fs	CLCNKA_ENST00000375692.1_Frame_Shift_Ins_p.G464fs|CLCNKA_ENST00000420078.1_Frame_Shift_Ins_p.G464fs|CLCNKA_ENST00000439316.2_Frame_Shift_Ins_p.G421fs|CLCNKA_ENST00000464764.1_3'UTR			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	464					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)	p.Y466fs*25(1)		breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	CCATCATGCCCGGGGGGTATGC	0.653																																					p.P463fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1389_1390insG	1						.																																			16229139	SO:0001589	frameshift_variant	1187	exon14				CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.1395dupG	1.37:g.16356557_16356557dupG	ENSP00000332771:p.Gly464fs	Somatic		Capture	Illumina HiSeq	Phase_I	16229138	NM_001042704	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Frame_Shift_Ins	INS	ENST00000331433.4	37	CCDS167.1																																																																																				0.653	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
GPATCH2	55105	broad.mit.edu	37	1	217604495	217604496	+	Frame_Shift_Ins	INS	-	-	T	rs201350030		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:217604495_217604496insT	ENST00000366935.3	-	10	1688_1689	c.1578_1579insA	c.(1576-1581)aaatccfs	p.S527fs		NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	527					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)	p.S527fs*>3(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		TCTTAGGCGGATTTTCCTGCAT	0.391																																					p.S527fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1579_1580insA	1						.																																			215671119	SO:0001589	frameshift_variant	55105	exon10			AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""G patch domain containing"""	25499	protein-coding gene	gene with protein product	"""cancer/testis antigen 110"", ""protein phosphatase 1, regulatory subunit 30"""			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.1579dupA	1.37:g.217604499_217604499dupT	ENSP00000355902:p.Ser527fs	Somatic		Capture	Illumina HiSeq	Phase_I	215671118	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Frame_Shift_Ins	INS	ENST00000366935.3	37	CCDS1518.1																																																																																				0.391	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040	
WDR78	79819	broad.mit.edu	37	1	67371018	67371019	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:67371018_67371019insA	ENST00000371026.3	-	2	265_266	c.210_211insT	c.(208-213)tttgctfs	p.A71fs	WDR78_ENST00000371022.3_Frame_Shift_Ins_p.A71fs|WDR78_ENST00000431318.1_5'UTR|WDR78_ENST00000488333.1_5'UTR|WDR78_ENST00000371023.3_Frame_Shift_Ins_p.A71fs	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	71					hematopoietic progenitor cell differentiation (GO:0002244)			p.A71fs*30(1)		NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						TTCATTGTAGCAAAAAAGCTAA	0.342																																					p.A71fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.211_212insT	1						.																																			67143607	SO:0001589	frameshift_variant	79819	exon2			BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"""WD repeat domain containing"""	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.211dupT	1.37:g.67371024_67371024dupA	ENSP00000360065:p.Ala71fs	Somatic		Capture	Illumina HiSeq	Phase_I	67143606	NM_024763	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Frame_Shift_Ins	INS	ENST00000371026.3	37	CCDS635.1																																																																																				0.342	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	
PEX14	5195	broad.mit.edu	37	1	10678421	10678421	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:10678421G>A	ENST00000356607.4	+	5	411	c.331G>A	c.(331-333)Gcc>Acc	p.A111T	PEX14_ENST00000538836.1_Missense_Mutation_p.A47T|RN7SL614P_ENST00000461850.2_RNA	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	111					microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)	p.A111T(1)		breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		AGATTACGGCGCCCTGGCCAT	0.632																																					p.A111T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G331A	1						.						85.0	73.0	77.0					1																	10678421		2203	4300	6503	10601008	SO:0001583	missense	5195	exon5			AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655			8856	protein-coding gene	gene with protein product		601791				9653144	Standard	NM_004565		Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.331G>A	1.37:g.10678421G>A	ENSP00000349016:p.Ala111Thr	Somatic		Capture	Illumina HiSeq	Phase_I	10601008	NM_004565	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Missense_Mutation	SNP	ENST00000356607.4	37	CCDS30582.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.860236	0.91433	.	.	ENSG00000142655	ENST00000356607;ENST00000538836	T;T	0.31769	1.48;1.48	4.93	4.93	0.64822	Peroxisome membrane anchor protein Pex14p, N-terminal (1);	0.055751	0.64402	D	0.000001	T	0.51432	0.1674	L	0.60455	1.87	0.80722	D	1	D;D;D	0.89917	0.996;1.0;0.992	P;D;P	0.87578	0.777;0.998;0.789	T	0.40646	-0.9552	10	0.21540	T	0.41	.	18.1594	0.89703	0.0:0.0:1.0:0.0	.	68;47;111	O75381-2;B7Z4Z4;O75381	.;.;PEX14_HUMAN	T	111;47	ENSP00000349016:A111T;ENSP00000444877:A47T	ENSP00000349016:A111T	A	+	1	0	PEX14	10601008	1.000000	0.71417	0.948000	0.38648	0.991000	0.79684	7.541000	0.82084	2.272000	0.75746	0.650000	0.86243	GCC		0.632	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		
CASZ1	54897	broad.mit.edu	37	1	10706326	10706326	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:10706326G>A	ENST00000377022.3	-	17	3872	c.3555C>T	c.(3553-3555)ctC>ctT	p.L1185L	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1185					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L1185L(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		AGTTCCCAAAGAGACAGTGGA	0.547																																					p.L1185L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3555T	1						.						170.0	191.0	184.0					1																	10706326		2129	4224	6353	10628913	SO:0001819	synonymous_variant	54897	exon17			AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.3555C>T	1.37:g.10706326G>A		Somatic		Capture	Illumina HiSeq	Phase_I	10628913	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																				0.547	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
CASZ1	54897	broad.mit.edu	37	1	10713848	10713848	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:10713848C>T	ENST00000377022.3	-	11	2583	c.2266G>A	c.(2266-2268)Gcc>Acc	p.A756T	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Missense_Mutation_p.A756T	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	756					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A756T(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		TCGGTGGCGGCAGTGGCGGCA	0.682																																					p.A756T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2266A	1						.						32.0	41.0	38.0					1																	10713848		2202	4297	6499	10636435	SO:0001583	missense	54897	exon11			AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.2266G>A	1.37:g.10713848C>T	ENSP00000366221:p.Ala756Thr	Somatic		Capture	Illumina HiSeq	Phase_I	10636435	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	C	5.667	0.307673	0.10733	.	.	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.22	3.2	0.36748	.	0.482499	0.22556	N	0.058526	T	0.15046	0.0363	N	0.22421	0.69	0.22675	N	0.998864	B;P;B	0.41848	0.002;0.763;0.01	B;B;B	0.35770	0.003;0.21;0.003	T	0.09164	-1.0687	9	0.21014	T	0.42	-7.8838	6.4783	0.22049	0.3017:0.6089:0.0:0.0894	.	780;756;756	B7Z1S3;Q86V15-2;Q86V15	.;.;CASZ1_HUMAN	T	756	.	ENSP00000339445:A756T	A	-	1	0	CASZ1	10636435	0.000000	0.05858	0.164000	0.22755	0.153000	0.21895	-0.619000	0.05572	2.299000	0.77371	0.511000	0.50034	GCC		0.682	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
COL11A1	1301	broad.mit.edu	37	1	103352444	103352444	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:103352444T>G	ENST00000370096.3	-	63	5089	c.4777A>C	c.(4777-4779)Atg>Ctg	p.M1593L	COL11A1_ENST00000358392.2_Missense_Mutation_p.M1605L|COL11A1_ENST00000512756.1_Missense_Mutation_p.M1477L|COL11A1_ENST00000353414.4_Missense_Mutation_p.M1554L	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1593	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.M1605L(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GGAAATTTCATATGCTCAATG	0.408																																					p.M1593L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4777C	1						.						194.0	186.0	189.0					1																	103352444		2203	4300	6503	103125032	SO:0001583	missense	1301	exon63			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.4777A>C	1.37:g.103352444T>G	ENSP00000359114:p.Met1593Leu	Somatic		Capture	Illumina HiSeq	Phase_I	103125032	NM_001854	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.238367	0.39598	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37	5.53	5.53	0.82687	Fibrillar collagen, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.45756	0.1358	L	0.43757	1.38	0.80722	D	1	B;B;B;P;B	0.34934	0.062;0.22;0.42;0.476;0.05	B;B;B;B;B	0.33196	0.078;0.069;0.099;0.159;0.047	T	0.49513	-0.8932	10	0.30854	T	0.27	.	15.6535	0.77115	0.0:0.0:0.0:1.0	.	1477;1554;1605;1593;813	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	L	1593;1605;1554;813;1477	ENSP00000359114:M1593L;ENSP00000351163:M1605L;ENSP00000302551:M1554L;ENSP00000426533:M1477L	ENSP00000302551:M1554L	M	-	1	0	COL11A1	103125032	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	8.040000	0.89188	2.107000	0.64212	0.260000	0.18958	ATG		0.408	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
VAV3	10451	broad.mit.edu	37	1	108322074	108322074	+	Missense_Mutation	SNP	G	G	A	rs371203483		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:108322074G>A	ENST00000370056.4	-	3	636	c.362C>T	c.(361-363)gCa>gTa	p.A121V	VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000527011.1_Missense_Mutation_p.A121V|VAV3_ENST00000371846.4_Missense_Mutation_p.A56V	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	121					angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)	p.A121V(1)		NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TGTGGCCAATGCTATAGGTGT	0.328																																					p.A121V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C362T	1						.						120.0	113.0	115.0					1																	108322074		2203	4300	6503	108123597	SO:0001583	missense	10451	exon3			AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.362C>T	1.37:g.108322074G>A	ENSP00000359073:p.Ala121Val	Somatic		Capture	Illumina HiSeq	Phase_I	108123597	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.56|15.56	2.870059|2.870059	0.51588|0.51588	.|.	.|.	ENSG00000134215|ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000371846|ENST00000490388	T;T;T|.	0.61980|.	0.06;0.06;0.06|.	5.66|5.66	5.66|5.66	0.87406|0.87406	Calponin homology domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.68751|0.68751	0.3035|0.3035	M|M	0.72118|0.72118	2.19|2.19	0.58432|0.58432	D|D	0.999994|0.999994	B;B;B|.	0.19583|.	0.032;0.037;0.016|.	B;B;B|.	0.21917|.	0.037;0.028;0.034|.	T|T	0.67891|0.67891	-0.5553|-0.5553	10|5	0.39692|.	T|.	0.17|.	.|.	16.6629|16.6629	0.85245|0.85245	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	121;121;121|.	B7ZLR1;E9PQ97;Q9UKW4|.	.;.;VAV3_HUMAN|.	V|Y	121;121;56|116	ENSP00000359073:A121V;ENSP00000432540:A121V;ENSP00000360912:A56V|.	ENSP00000359073:A121V|.	A|H	-|-	2|1	0|0	VAV3|VAV3	108123597|108123597	1.000000|1.000000	0.71417|0.71417	0.884000|0.884000	0.34674|0.34674	0.382000|0.382000	0.30200|0.30200	5.471000|5.471000	0.66762|0.66762	2.645000|2.645000	0.89757|0.89757	0.650000|0.650000	0.86243|0.86243	GCA|CAT		0.328	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
FNDC7	163479	broad.mit.edu	37	1	109270671	109270671	+	Silent	SNP	C	C	A	rs61740850	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:109270671C>A	ENST00000370017.3	+	7	1630	c.1353C>A	c.(1351-1353)ccC>ccA	p.P451P	FNDC7_ENST00000271311.2_Silent_p.P452P	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	451	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)		p.P218P(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		CATGTACTCCCCAGTTCATAA	0.498																																					p.P451P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1353A	1						.						206.0	189.0	195.0					1																	109270671		2203	4300	6503	109072194	SO:0001819	synonymous_variant	163479	exon7				CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"""Fibronectin type III domain containing"""	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.1353C>A	1.37:g.109270671C>A		Somatic		Capture	Illumina HiSeq	Phase_I	109072194	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Silent	SNP	ENST00000370017.3	37	CCDS44185.1	.	.	.	.	.	.	.	.	.	.	C	6.013	0.370820	0.11409	.	.	ENSG00000143107	ENST00000445274	T	0.51071	0.72	5.34	1.29	0.21616	.	0.326738	0.37906	N	0.001899	T	0.09158	0.0226	.	.	.	0.58432	D	0.999996	.	.	.	.	.	.	T	0.15407	-1.0438	7	0.06891	T	0.86	-5.1558	3.9691	0.09446	0.3546:0.3594:0.0:0.286	.	.	.	.	T	227	ENSP00000405986:P227T	ENSP00000405986:P227T	P	+	1	0	FNDC7	109072194	0.000000	0.05858	0.054000	0.19295	0.295000	0.27426	-1.887000	0.01617	0.238000	0.21222	-0.448000	0.05591	CCA		0.498	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
WDR47	22911	broad.mit.edu	37	1	109525940	109525940	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:109525940C>T	ENST00000369962.3	-	11	2281	c.2059G>A	c.(2059-2061)Gtg>Atg	p.V687M	WDR47_ENST00000369965.4_Missense_Mutation_p.V688M|WDR47_ENST00000357672.3_Missense_Mutation_p.V659M|WDR47_ENST00000400794.3_Missense_Mutation_p.V695M|WDR47_ENST00000361054.3_Missense_Mutation_p.V659M			O94967	WDR47_HUMAN	WD repeat domain 47	687					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.V688M(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		AAGGGCAGCACTTTGACGTAT	0.408																																					p.V688M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2062A	1						.						133.0	108.0	117.0					1																	109525940		2203	4300	6503	109327463	SO:0001583	missense	22911	exon11			AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			ENSG00000085433	ENSG00000085433		"""WD repeat domain containing"""	29141	protein-coding gene	gene with protein product		615734				10048485	Standard	NM_014969		Approved	KIAA0893	uc001dwl.3	O94967	OTTHUMG00000011734	ENST00000369962.3:c.2059G>A	1.37:g.109525940C>T	ENSP00000358979:p.Val687Met	Somatic		Capture	Illumina HiSeq	Phase_I	109327463	NM_014969	A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	Missense_Mutation	SNP	ENST00000369962.3	37	CCDS44187.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.947309	0.92593	.	.	ENSG00000085433	ENST00000400794;ENST00000369962;ENST00000361054;ENST00000369965;ENST00000357672	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.46	5.46	0.80206	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.75889	0.3911	M	0.70787	2.145	0.80722	D	1	D;D;D;D	0.89917	0.997;0.999;1.0;0.994	D;D;D;D	0.78314	0.975;0.991;0.99;0.952	T	0.78275	-0.2267	10	0.87932	D	0	-22.2828	19.292	0.94103	0.0:1.0:0.0:0.0	.	659;695;687;688	O94967-2;A8MX09;O94967;O94967-3	.;.;WDR47_HUMAN;.	M	695;687;659;688;659	ENSP00000383599:V695M;ENSP00000358979:V687M;ENSP00000354339:V659M;ENSP00000358982:V688M;ENSP00000350301:V659M	ENSP00000350301:V659M	V	-	1	0	WDR47	109327463	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.559000	0.86315	0.563000	0.77884	GTG		0.408	WDR47-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032414.2	NM_014969	
CELSR2	1952	broad.mit.edu	37	1	109807188	109807188	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:109807188C>A	ENST00000271332.3	+	11	5463	c.5402C>A	c.(5401-5403)cCg>cAg	p.P1801Q		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1801	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.P1801Q(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GACTCAAACCCGTGTCCTGCT	0.572																																					p.P1801Q	NSCLC(158;1285 2011 34800 34852 42084)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5402A	1						.						203.0	187.0	192.0					1																	109807188		2203	4300	6503	109608711	SO:0001583	missense	1952	exon11			D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.5402C>A	1.37:g.109807188C>A	ENSP00000271332:p.Pro1801Gln	Somatic		Capture	Illumina HiSeq	Phase_I	109608711	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	37	CCDS796.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.279119	0.80692	.	.	ENSG00000143126	ENST00000271332	T	0.76060	-0.99	4.94	4.94	0.65067	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.87398	0.6167	M	0.90922	3.16	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	D	0.88685	0.3205	9	0.51188	T	0.08	.	18.3548	0.90353	0.0:1.0:0.0:0.0	.	1801	Q9HCU4	CELR2_HUMAN	Q	1801	ENSP00000271332:P1801Q	ENSP00000271332:P1801Q	P	+	2	0	CELSR2	109608711	0.995000	0.38212	0.879000	0.34478	0.953000	0.61014	3.520000	0.53465	2.580000	0.87095	0.561000	0.74099	CCG		0.572	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
CELSR2	1952	broad.mit.edu	37	1	109814295	109814295	+	Missense_Mutation	SNP	G	G	A	rs201030395		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:109814295G>A	ENST00000271332.3	+	28	7938	c.7877G>A	c.(7876-7878)cGc>cAc	p.R2626H	CELSR2_ENST00000498157.1_3'UTR	NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2626					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.R2626H(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GCCTGCAGCCGCAAGCCCAGC	0.632													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19119	0.0		0.0	False		,,,				2504	0.0				p.R2626H	NSCLC(158;1285 2011 34800 34852 42084)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G7877A	1						.						64.0	55.0	58.0					1																	109814295		2203	4300	6503	109615818	SO:0001583	missense	1952	exon28			D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.7877G>A	1.37:g.109814295G>A	ENSP00000271332:p.Arg2626His	Somatic		Capture	Illumina HiSeq	Phase_I	109615818	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	37	CCDS796.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	15.41	2.823920	0.50739	.	.	ENSG00000143126	ENST00000271332	T	0.71222	-0.55	4.81	3.82	0.43975	.	.	.	.	.	T	0.32526	0.0832	N	0.17082	0.46	0.37298	D	0.908575	B	0.06786	0.001	B	0.06405	0.002	T	0.43782	-0.9370	9	0.51188	T	0.08	.	2.1993	0.03919	0.2474:0.0:0.4742:0.2784	.	2626	Q9HCU4	CELR2_HUMAN	H	2626	ENSP00000271332:R2626H	ENSP00000271332:R2626H	R	+	2	0	CELSR2	109615818	0.995000	0.38212	1.000000	0.80357	0.994000	0.84299	1.800000	0.38833	2.504000	0.84457	0.561000	0.74099	CGC		0.632	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
RAP1A	5906	broad.mit.edu	37	1	112246984	112246984	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:112246984G>A	ENST00000369709.3	+	6	523	c.344G>A	c.(343-345)gGc>gAc	p.G115D	RAP1A_ENST00000494982.1_3'UTR|RAP1A_ENST00000436150.2_Missense_Mutation_p.G115D|RAP1A_ENST00000356415.1_Missense_Mutation_p.G115D|RAP1A_ENST00000545460.1_Missense_Mutation_p.G115D	NM_002884.2	NP_002875.1	P62834	RAP1A_HUMAN	RAP1A, member of RAS oncogene family	115					activation of MAPKK activity (GO:0000186)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of vasculogenesis (GO:2001214)|protein transport (GO:0015031)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|guanyl-nucleotide exchange factor complex (GO:0032045)|late endosome (GO:0005770)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)	p.G115D(2)		endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(81;6.79e-06)|all_epithelial(167;2.42e-05)|all_lung(203;0.000105)|Lung NSC(277;0.00021)		Lung(183;0.0183)|Colorectal(144;0.0418)|LUSC - Lung squamous cell carcinoma(189;0.0966)|all cancers(265;0.098)|Epithelial(280;0.0981)|COAD - Colon adenocarcinoma(174;0.141)		ATTTTGGTTGGCAATAAATGT	0.363																																					p.G115D												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G344A	1						.						94.0	90.0	91.0					1																	112246984		2203	4300	6503	112048507	SO:0001583	missense	5906	exon7			BC014086	CCDS840.1	1p13.3	2014-05-09			ENSG00000116473	ENSG00000116473			9855	protein-coding gene	gene with protein product		179520				3143720	Standard	XM_006710803		Approved	KREV-1, SMGP21	uc001ebl.3	P62834	OTTHUMG00000011959	ENST00000369709.3:c.344G>A	1.37:g.112246984G>A	ENSP00000358723:p.Gly115Asp	Somatic		Capture	Illumina HiSeq	Phase_I	112048507	NM_001010935	P10113	Missense_Mutation	SNP	ENST00000369709.3	37	CCDS840.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.865388	0.91511	.	.	ENSG00000116473	ENST00000356415;ENST00000433097;ENST00000369709;ENST00000436150;ENST00000545460	D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04	5.92	4.98	0.66077	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.96059	0.8716	H	0.99752	4.75	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97374	0.9978	10	0.87932	D	0	.	16.1948	0.82021	0.0:0.0:0.8664:0.1336	.	115	P62834	RAP1A_HUMAN	D	115	ENSP00000348786:G115D;ENSP00000396741:G115D;ENSP00000358723:G115D;ENSP00000394318:G115D;ENSP00000443009:G115D	ENSP00000348786:G115D	G	+	2	0	RAP1A	112048507	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.809000	0.96659	0.655000	0.94253	GGC		0.363	RAP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033071.1	NM_002884	
AMPD1	270	broad.mit.edu	37	1	115215875	115215875	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:115215875C>T	ENST00000520113.2	-	16	2218	c.2203G>A	c.(2203-2205)Ggc>Agc	p.G735S	AMPD1_ENST00000369538.3_Missense_Mutation_p.G731S|AMPD1_ENST00000353928.6_Missense_Mutation_p.G702S			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	735					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)	p.G702S(1)		NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	TAATTGTCGCCCAGAAACTTT	0.413																																					p.G735S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2203A	1						.						72.0	70.0	71.0					1																	115215875		2203	4300	6503	115017398	SO:0001583	missense	270	exon16			M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"""AMPD isoform M"", ""skeletal muscle AMPD"""	102770	"""adenosine monophosphate deaminase 1 (isoform M)"""			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.2203G>A	1.37:g.115215875C>T	ENSP00000430075:p.Gly735Ser	Somatic		Capture	Illumina HiSeq	Phase_I	115017398	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	37	CCDS876.2	.	.	.	.	.	.	.	.	.	.	C	33	5.247962	0.95305	.	.	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.85339	-1.97;-1.97;-1.97	5.62	5.62	0.85841	Adenosine/AMP deaminase (1);	0.000000	0.85682	D	0.000000	D	0.93976	0.8071	M	0.91038	3.17	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94231	0.7476	10	0.72032	D	0.01	-19.1786	20.024	0.97514	0.0:1.0:0.0:0.0	.	731;702	Q5TF02;P23109	.;AMPD1_HUMAN	S	735;731;702	ENSP00000430075:G735S;ENSP00000358551:G731S;ENSP00000316520:G702S	ENSP00000316520:G702S	G	-	1	0	AMPD1	115017398	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	7.776000	0.85560	2.809000	0.96659	0.655000	0.94253	GGC		0.413	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4		
UBE2J2	118424	broad.mit.edu	37	1	1190801	1190801	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:1190801C>A	ENST00000349431.6	-	7	781	c.562G>T	c.(562-564)Gac>Tac	p.D188Y	UBE2J2_ENST00000400929.2_Missense_Mutation_p.D136Y|UBE2J2_ENST00000360466.2_Missense_Mutation_p.D188Y|UBE2J2_ENST00000339385.6_Missense_Mutation_p.D153Y|UBE2J2_ENST00000400930.4_Missense_Mutation_p.D204Y|UBE2J2_ENST00000347370.2_Missense_Mutation_p.D136Y|UBE2J2_ENST00000348298.7_Missense_Mutation_p.D136Y|UBE2J2_ENST00000491779.1_5'Flank	NM_058167.2	NP_477515.2	Q8N2K1	UB2J2_HUMAN	ubiquitin-conjugating enzyme E2, J2	188					protein ubiquitination (GO:0016567)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)	p.D204Y(1)		cervix(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.66e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.53e-21)|Colorectal(212;0.00019)|COAD - Colon adenocarcinoma(227;0.000215)|Kidney(185;0.00255)|BRCA - Breast invasive adenocarcinoma(365;0.00266)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0371)|Lung(427;0.205)		GGAACCACGTCTGGCAAGGGG	0.567																																					p.D204Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G610T	1						.						117.0	132.0	127.0					1																	1190801		2203	4300	6503	1180664	SO:0001583	missense	118424	exon8			AF296658	CCDS14.1, CCDS15.1, CCDS16.1	1p36.33	2011-05-19	2011-05-19		ENSG00000160087	ENSG00000160087		"""Ubiquitin-conjugating enzymes E2"""	19268	protein-coding gene	gene with protein product			"""ubiquitin-conjugating enzyme E2, J2 (UBC6 homolog, yeast)"""			11278356	Standard	NM_058167		Approved	Ubc6p, NCUBE2	uc001ado.3	Q8N2K1	OTTHUMG00000001911	ENST00000349431.6:c.562G>T	1.37:g.1190801C>A	ENSP00000305826:p.Asp188Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	1180664	NM_194315	A8MYC7|Q504T9|Q96N26|Q96T84	Missense_Mutation	SNP	ENST00000349431.6	37	CCDS14.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.213233	0.79352	.	.	ENSG00000160087	ENST00000347370;ENST00000349431;ENST00000339385;ENST00000348298;ENST00000400929;ENST00000360466;ENST00000400930;ENST00000435198	T;T;T;T;T;T;T;T	0.73469	0.83;-0.16;0.84;0.83;0.83;-0.16;-0.75;-0.17	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	D	0.82609	0.5074	L	0.40543	1.245	0.80722	D	1	D;D;D;D	0.89917	1.0;0.978;0.979;0.994	D;P;P;P	0.85130	0.997;0.659;0.563;0.854	T	0.82494	-0.0429	10	0.59425	D	0.04	-16.9998	19.3852	0.94554	0.0:1.0:0.0:0.0	.	136;204;188;221	A6NGS0;A8MYC7;Q8N2K1;B1AME9	.;.;UB2J2_HUMAN;.	Y	136;188;153;136;136;188;204;188	ENSP00000344857:D136Y;ENSP00000305826:D188Y;ENSP00000340197:D153Y;ENSP00000342541:D136Y;ENSP00000383718:D136Y;ENSP00000353653:D188Y;ENSP00000383719:D204Y;ENSP00000393301:D188Y	ENSP00000340197:D153Y	D	-	1	0	UBE2J2	1180664	1.000000	0.71417	0.990000	0.47175	0.945000	0.59286	5.722000	0.68485	2.830000	0.97506	0.655000	0.94253	GAC		0.567	UBE2J2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000005430.1	NM_058167	
PLOD1	5351	broad.mit.edu	37	1	12017006	12017006	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:12017006G>A	ENST00000196061.4	+	7	703	c.676G>A	c.(676-678)Gtg>Atg	p.V226M	PLOD1_ENST00000376369.3_Missense_Mutation_p.V273M|PLOD1_ENST00000485046.1_3'UTR	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	226					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|extracellular matrix organization (GO:0030198)|hydroxylysine biosynthetic process (GO:0046947)|oxidation-reduction process (GO:0055114)|response to hypoxia (GO:0001666)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)|protein homodimerization activity (GO:0042803)	p.V226M(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Succinic acid(DB00139)|Vitamin C(DB00126)	AATGGGCCATGTGAGAGCGAG	0.617																																					p.V226M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G676A	1						.						160.0	132.0	142.0					1																	12017006		2203	4300	6503	11939593	SO:0001583	missense	5351	exon7			BC016657	CCDS142.1	1p36.22	2011-08-25	2011-08-24	2004-12-14	ENSG00000083444	ENSG00000083444	1.14.11.4		9081	protein-coding gene	gene with protein product	"""lysyl hydroxlase 1"""	153454	"""procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)"""	LLH, PLOD		1577494	Standard	NM_000302		Approved	LH1	uc001atm.3	Q02809	OTTHUMG00000002393	ENST00000196061.4:c.676G>A	1.37:g.12017006G>A	ENSP00000196061:p.Val226Met	Somatic		Capture	Illumina HiSeq	Phase_I	11939593	NM_000302	B4DR87|Q96AV9|Q9H132	Missense_Mutation	SNP	ENST00000196061.4	37	CCDS142.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.509118	0.85282	.	.	ENSG00000083444	ENST00000376369;ENST00000196061	T;T	0.21734	1.99;1.99	4.36	4.36	0.52297	.	0.000000	0.85682	D	0.000000	T	0.48021	0.1477	M	0.80422	2.495	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.71656	0.974;0.968	T	0.53244	-0.8466	10	0.52906	T	0.07	.	16.0751	0.80962	0.0:0.0:1.0:0.0	.	273;226	B4DR87;Q02809	.;PLOD1_HUMAN	M	273;226	ENSP00000365548:V273M;ENSP00000196061:V226M	ENSP00000196061:V226M	V	+	1	0	PLOD1	11939593	1.000000	0.71417	0.951000	0.38953	0.910000	0.53928	9.606000	0.98325	2.261000	0.74972	0.655000	0.94253	GTG		0.617	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	NM_000302	
PRAMEF1	65121	broad.mit.edu	37	1	12854349	12854349	+	Silent	SNP	G	G	A	rs1063766		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:12854349G>A	ENST00000332296.7	+	3	676	c.573G>A	c.(571-573)ccG>ccA	p.P191P	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	191					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.P191P(2)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATCTAACGCCGATTAAATATC	0.413													g|||	1	0.000199681	0.0	0.0	5008	,	,		28376	0.0		0.0	False		,,,				2504	0.001				p.P191P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G573A	1						.						206.0	219.0	215.0					1																	12854349		2203	4300	6503	12776936	SO:0001819	synonymous_variant	65121	exon3			AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"""-"""	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.573G>A	1.37:g.12854349G>A		Somatic		Capture	Illumina HiSeq	Phase_I	12776936	NM_023013	Q9UQP2	Silent	SNP	ENST00000332296.7	37	CCDS148.1																																																																																				0.413	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
PRDM2	7799	broad.mit.edu	37	1	14107016	14107016	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:14107016G>T	ENST00000235372.7	+	8	3582	c.2726G>T	c.(2725-2727)gGg>gTg	p.G909V	PRDM2_ENST00000413440.1_Missense_Mutation_p.G708V|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000343137.4_Missense_Mutation_p.G708V|PRDM2_ENST00000311066.5_Missense_Mutation_p.G909V|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	909					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G909V(1)		endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		CCTGCAGATGGGACCAGGAGC	0.502																																					p.G708V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2123T	1						.						72.0	72.0	72.0					1																	14107016		2203	4300	6503	13979603	SO:0001583	missense	7799	exon3			U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.2726G>T	1.37:g.14107016G>T	ENSP00000235372:p.Gly909Val	Somatic		Capture	Illumina HiSeq	Phase_I	13979603	NM_001007257	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.708879	0.00712	.	.	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.01548	4.91;4.78;4.81;4.81	5.7	-7.64	0.01286	.	0.753844	0.13041	N	0.418516	T	0.00666	0.0022	N	0.04880	-0.145	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45425	-0.9262	10	0.09084	T	0.74	.	4.1513	0.10238	0.0854:0.3345:0.3231:0.257	.	767;909;909	Q5THJ0;Q13029;Q13029-2	.;PRDM2_HUMAN;.	V	909;909;909;708;708	ENSP00000235372:G909V;ENSP00000312352:G909V;ENSP00000411103:G708V;ENSP00000341621:G708V	ENSP00000235372:G909V	G	+	2	0	PRDM2	13979603	0.000000	0.05858	0.000000	0.03702	0.397000	0.30659	-1.379000	0.02554	-0.815000	0.04346	-0.264000	0.10439	GGG		0.502	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
MAB21L3	126868	broad.mit.edu	37	1	116670230	116670230	+	Missense_Mutation	SNP	C	C	T	rs370568745		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:116670230C>T	ENST00000369500.3	+	5	890	c.625C>T	c.(625-627)Cgc>Tgc	p.R209C	MAB21L3_ENST00000464946.1_3'UTR	NM_152367.2	NP_689580.2	Q8N8X9	MB213_HUMAN	mab-21-like 3 (C. elegans)	209								p.R209C(1)		breast(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|urinary_tract(1)	19						ATGTCTGCAGCGCTGGCCTTC	0.577																																					p.R209C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C625T	1						.	C	CYS/ARG	0,4406		0,0,2203	61.0	54.0	57.0		625	5.0	1.0	1		57	1,8599	1.2+/-3.3	0,1,4299	no	missense	MAB21L3	NM_152367.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	209/363	116670230	1,13005	2203	4300	6503	116471753	SO:0001583	missense	126868	exon5			AK096035	CCDS886.1	1p13.1	2011-02-23	2011-02-23	2011-02-23	ENSG00000173212	ENSG00000173212			26787	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 161"""	C1orf161		14702039	Standard	NM_152367		Approved	FLJ38716	uc001egc.1	Q8N8X9	OTTHUMG00000012110	ENST00000369500.3:c.625C>T	1.37:g.116670230C>T	ENSP00000358512:p.Arg209Cys	Somatic		Capture	Illumina HiSeq	Phase_I	116471753	NM_152367	Q5TDL7	Missense_Mutation	SNP	ENST00000369500.3	37	CCDS886.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.273553	0.59649	0.0	1.16E-4	ENSG00000173212	ENST00000369500	T	0.09538	2.97	5.92	5.01	0.66863	.	0.000000	0.64402	D	0.000004	T	0.07818	0.0196	M	0.80028	2.48	0.80722	D	1	B	0.34255	0.445	B	0.30029	0.11	T	0.03051	-1.1078	10	0.37606	T	0.19	-18.0279	13.2228	0.59899	0.0:0.927:0.0:0.073	.	209	Q8N8X9	MB213_HUMAN	C	209	ENSP00000358512:R209C	ENSP00000358512:R209C	R	+	1	0	MAB21L3	116471753	0.987000	0.35691	1.000000	0.80357	0.932000	0.56968	1.699000	0.37804	1.517000	0.48917	0.650000	0.86243	CGC		0.577	MAB21L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033486.1	NM_152367	
NBPF15	284565	broad.mit.edu	37	1	148594554	148594554	+	Missense_Mutation	SNP	G	G	A	rs143319883	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:148594554G>A	ENST00000369187.3	+	19	2416	c.1927G>A	c.(1927-1929)Gcc>Acc	p.A643T	NBPF15_ENST00000442702.2_Missense_Mutation_p.A643T	NM_173638.3	NP_775909.2	Q8N660	NBPFF_HUMAN	neuroblastoma breakpoint family, member 15	643	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.A643T(1)		NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12	all_hematologic(923;0.032)					TATCAGCTTCGCCCTTTACGT	0.423													.|||	2	0.000399361	0.0	0.0014	5008	,	,		18101	0.0		0.001	False		,,,				2504	0.0				p.A643T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1927A	1						.	G	THR/ALA,THR/ALA	1,4341		0,1,2170	109.0	147.0	134.0		1927,1927	-1.0	0.0	1	dbSNP_134	134	1,8581		0,1,4290	no	missense,missense	NBPF15	NM_001170755.1,NM_173638.3	58,58	0,2,6460	AA,AG,GG		0.0117,0.023,0.0155	benign,benign	643/671,643/671	148594554	2,12922	2171	4291	6462	146861178	SO:0001583	missense	284565	exon16			BC023087	CCDS72852.1	1q21.1	2014-01-16			ENSG00000243452	ENSG00000266338		"""neuroblastoma breakpoint family"""	28791	protein-coding gene	gene with protein product		610414, 614005	"""neuroblastoma breakpoint family, member 16"""	NBPF16		16079250	Standard	NM_173638		Approved	MGC8902	uc001esc.2	Q8N660	OTTHUMG00000013634	ENST00000369187.3:c.1927G>A	1.37:g.148594554G>A	ENSP00000358188:p.Ala643Thr	Somatic		Capture	Illumina HiSeq	Phase_I	146861178	NM_001102663	Q3BBV9|Q8IX77	Missense_Mutation	SNP	ENST00000369187.3	37	CCDS932.1	.	.	.	.	.	.	.	.	.	.	.	9.390	1.075305	0.20227	2.3E-4	1.17E-4	ENSG00000243452	ENST00000442702;ENST00000369187	T;T	0.11495	2.77;2.77	0.502	-1.0	0.10196	DUF1220 (2);	.	.	.	.	T	0.06917	0.0176	L	0.39514	1.22	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.16600	-1.0397	8	0.48119	T	0.1	.	.	.	.	.	643	Q8N660	NBPFF_HUMAN	T	643	ENSP00000416864:A643T;ENSP00000358188:A643T	ENSP00000358188:A643T	A	+	1	0	NBPF15	146861178	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-2.487000	0.00977	-1.518000	0.01778	-2.159000	0.00328	GCC		0.423	NBPF15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038609.3	NM_173638	
SV2A	9900	broad.mit.edu	37	1	149881364	149881364	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:149881364G>A	ENST00000369146.3	-	6	1658	c.1168C>T	c.(1168-1170)Cga>Tga	p.R390*	SV2A_ENST00000369145.1_Nonsense_Mutation_p.R390*	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A	390					cellular calcium ion homeostasis (GO:0006874)|neurotransmitter transport (GO:0006836)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane transporter activity (GO:0022857)	p.R390*(1)		breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(6)|pancreas(1)|prostate(8)|skin(2)|urinary_tract(2)	55	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)	GAGAACACTCGCTCAGGATGT	0.587																																					p.R390X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1168T	1						.						209.0	164.0	179.0					1																	149881364		2203	4300	6503	148147988	SO:0001587	stop_gained	9900	exon6			AB018279	CCDS940.1	1q21.2	2008-02-05			ENSG00000159164	ENSG00000159164			20566	protein-coding gene	gene with protein product		185860				7681585, 10611374	Standard	NM_014849		Approved	SV2, KIAA0736	uc001etg.3	Q7L0J3	OTTHUMG00000012209	ENST00000369146.3:c.1168C>T	1.37:g.149881364G>A	ENSP00000358142:p.Arg390*	Somatic		Capture	Illumina HiSeq	Phase_I	148147988	NM_014849	D3DUZ7|O94841|Q5QNX8|Q7Z3L6|Q8NBJ6|Q9BVZ9	Nonsense_Mutation	SNP	ENST00000369146.3	37	CCDS940.1	.	.	.	.	.	.	.	.	.	.	G	41	8.689862	0.98916	.	.	ENSG00000159164	ENST00000369146;ENST00000369145	.	.	.	5.24	4.26	0.50523	.	0.187740	0.44688	D	0.000425	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	-1.0946	10.3463	0.43907	0.0:0.0:0.7153:0.2847	.	.	.	.	X	390	.	ENSP00000358141:R390X	R	-	1	2	SV2A	148147988	1.000000	0.71417	0.990000	0.47175	0.806000	0.45545	4.587000	0.60991	2.732000	0.93576	0.655000	0.94253	CGA		0.587	SV2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033754.1		
ARNT	405	broad.mit.edu	37	1	150789612	150789612	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:150789612A>T	ENST00000358595.5	-	17	1845	c.1645T>A	c.(1645-1647)Ttt>Att	p.F549I	ARNT_ENST00000515192.1_Missense_Mutation_p.F535I|ARNT_ENST00000354396.2_Missense_Mutation_p.F549I|ARNT_ENST00000505755.1_Missense_Mutation_p.F534I	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	549					cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.F549I(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCCTGGGCAAATAAACCATCT	0.383			T	ETV6	AML																																p.F534I			Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1600A	1						.						103.0	96.0	98.0					1																	150789612		2203	4300	6503	149056236	SO:0001583	missense	405	exon16			AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"""Basic helix-loop-helix proteins"""	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.1645T>A	1.37:g.150789612A>T	ENSP00000351407:p.Phe549Ile	Somatic		Capture	Illumina HiSeq	Phase_I	149056236	NM_001197325	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Missense_Mutation	SNP	ENST00000358595.5	37	CCDS970.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.422196	0.83559	.	.	ENSG00000143437	ENST00000358595;ENST00000354396;ENST00000515192;ENST00000394700;ENST00000505755	T;T;T;T	0.09073	3.13;3.29;3.13;3.02	5.9	5.9	0.94986	.	0.344922	0.31612	N	0.007360	T	0.15478	0.0373	M	0.65498	2.005	0.42127	D	0.991454	P;D;D;D;P	0.65815	0.835;0.986;0.986;0.995;0.835	P;D;P;D;B	0.66497	0.476;0.913;0.885;0.944;0.421	T	0.06607	-1.0817	10	0.21014	T	0.42	.	16.3155	0.82918	1.0:0.0:0.0:0.0	.	534;549;535;534;549	A8K6P0;F8WAP6;P27540-3;P27540-2;P27540	.;.;.;.;ARNT_HUMAN	I	549;549;535;501;534	ENSP00000351407:F549I;ENSP00000346372:F549I;ENSP00000423851:F535I;ENSP00000427571:F534I	ENSP00000346372:F549I	F	-	1	0	ARNT	149056236	0.999000	0.42202	0.946000	0.38457	0.993000	0.82548	4.238000	0.58688	2.260000	0.74910	0.528000	0.53228	TTT		0.383	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084741.2		
TMOD4	29765	broad.mit.edu	37	1	151146968	151146968	+	Missense_Mutation	SNP	G	G	A	rs145543554		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:151146968G>A	ENST00000416280.2	-	3	278	c.179C>T	c.(178-180)aCg>aTg	p.T60M	VPS72_ENST00000496809.1_5'Flank|TMOD4_ENST00000601585.1_5'Flank			Q9NZQ9	TMOD4_HUMAN	tropomodulin 4 (muscle)	0					muscle contraction (GO:0006936)	striated muscle thin filament (GO:0005865)	tropomyosin binding (GO:0005523)	p.T60M(1)		endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	7	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CAGTGGCCCCGTTGGGCTCTT	0.547																																					p.T60M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C179T	1						.	G	MET/THR	1,4405		0,1,2202	171.0	167.0	168.0		179	5.7	1.0	1	dbSNP_134	168	0,8600		0,0,4300	no	missense	TMOD4	NM_013353.2	81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	60/346	151146968	1,13005	2203	4300	6503	149413592	SO:0001583	missense	29765	exon3			AF177173	CCDS988.1	1q12	2008-05-23			ENSG00000163157	ENSG00000163157			11874	protein-coding gene	gene with protein product	"""actin-capping protein"""	605834				10662549, 10497209	Standard	NM_013353		Approved	Sk-Tmod	uc001exc.4	Q9NZQ9	OTTHUMG00000012350	ENST00000416280.2:c.179C>T	1.37:g.151146968G>A	ENSP00000414180:p.Thr60Met	Somatic		Capture	Illumina HiSeq	Phase_I	149413592	NM_013353	B7Z6N9|Q5JR83|Q8WVL3|Q9UKH2	Missense_Mutation	SNP	ENST00000416280.2	37		.	.	.	.	.	.	.	.	.	.	.	27.9	4.871142	0.91587	2.27E-4	0.0	ENSG00000163157	ENST00000295314;ENST00000416280;ENST00000441701	T;T;T	0.49139	0.79;0.79;0.79	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.72087	0.3417	M	0.90369	3.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.984;0.999	T	0.77718	-0.2483	10	0.87932	D	0	-15.7012	18.5767	0.91157	0.0:0.0:1.0:0.0	.	60;60	B7Z6N9;Q9NZQ9	.;TMOD4_HUMAN	M	60	ENSP00000295314:T60M;ENSP00000414180:T60M;ENSP00000406333:T60M	ENSP00000295314:T60M	T	-	2	0	TMOD4	149413592	1.000000	0.71417	0.990000	0.47175	0.996000	0.88848	9.605000	0.98321	2.688000	0.91661	0.561000	0.74099	ACG		0.547	TMOD4-201	KNOWN	basic	protein_coding	protein_coding			
POGZ	23126	broad.mit.edu	37	1	151380601	151380601	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:151380601G>A	ENST00000271715.2	-	15	2664	c.2350C>T	c.(2350-2352)Cga>Tga	p.R784*	POGZ_ENST00000540984.1_Nonsense_Mutation_p.R146*|POGZ_ENST00000368863.2_Nonsense_Mutation_p.R689*|POGZ_ENST00000531094.1_Nonsense_Mutation_p.R722*|POGZ_ENST00000392723.1_Nonsense_Mutation_p.R731*|POGZ_ENST00000361398.3_Nonsense_Mutation_p.R731*|POGZ_ENST00000491586.1_Nonsense_Mutation_p.R740*|POGZ_ENST00000409503.1_Nonsense_Mutation_p.R775*	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	784					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R740*(1)|p.R784*(1)		NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GCATAAGCTCGAGAACAGCAG	0.423																																					p.R689X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C2065T	1						.						132.0	118.0	123.0					1																	151380601		2203	4300	6503	149647225	SO:0001587	stop_gained	23126	exon13			AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"""zinc finger protein 280E"", ""putative protein product of Nbla00003"""	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.2350C>T	1.37:g.151380601G>A	ENSP00000271715:p.Arg784*	Somatic		Capture	Illumina HiSeq	Phase_I	149647225	NM_145796	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Nonsense_Mutation	SNP	ENST00000271715.2	37	CCDS997.1	.	.	.	.	.	.	.	.	.	.	G	39	7.526051	0.98339	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000540984;ENST00000491586;ENST00000529669	.	.	.	5.51	3.41	0.39046	.	0.000000	0.53938	D	0.000050	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.1652	15.0936	0.72217	0.0:0.0:0.7333:0.2667	.	.	.	.	X	731;784;731;689;775;722;146;740;184	.	ENSP00000271715:R784X	R	-	1	2	POGZ	149647225	0.994000	0.37717	0.998000	0.56505	0.993000	0.82548	0.266000	0.18534	1.300000	0.44818	0.655000	0.94253	CGA		0.423	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171	
CGN	57530	broad.mit.edu	37	1	151506582	151506582	+	Silent	SNP	C	C	T	rs371262483		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:151506582C>T	ENST00000271636.7	+	15	3007	c.2874C>T	c.(2872-2874)gaC>gaT	p.D958D		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	952					transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)	p.D958D(1)		NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GTTCCCAGGACGACAGGGCCC	0.617																																					p.D958D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2874T	1						.	C		1,4393		0,1,2196	34.0	26.0	29.0		2874	-0.9	1.0	1		29	1,8593		0,1,4296	no	coding-synonymous	CGN	NM_020770.2		0,2,6492	TT,TC,CC		0.0116,0.0228,0.0154		958/1204	151506582	2,12986	2197	4297	6494	149773206	SO:0001819	synonymous_variant	57530	exon15			AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.2874C>T	1.37:g.151506582C>T		Somatic		Capture	Illumina HiSeq	Phase_I	149773206	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Silent	SNP	ENST00000271636.7	37	CCDS999.1																																																																																				0.617	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770	
LINGO4	339398	broad.mit.edu	37	1	151774253	151774253	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:151774253C>T	ENST00000368820.3	-	2	1865	c.928G>A	c.(928-930)Gca>Aca	p.A310T		NM_001004432.2	NP_001004432.1	Q6UY18	LIGO4_HUMAN	leucine rich repeat and Ig domain containing 4	310						integral component of membrane (GO:0016021)		p.A310T(1)		breast(2)|cervix(1)|endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			GTGAGGCATGCCCCTGACAGG	0.607																																					p.A310T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G928A	1						.						73.0	73.0	73.0					1																	151774253		2203	4300	6503	150040877	SO:0001583	missense	339398	exon2				CCDS30855.1	1q21.3	2013-01-11	2007-02-01	2007-02-01	ENSG00000213171	ENSG00000213171		"""Immunoglobulin superfamily / I-set domain containing"""	31814	protein-coding gene	gene with protein product		609794	"""leucine rich repeat neuronal 6D"""	LRRN6D			Standard	NM_001004432		Approved		uc001ezf.1	Q6UY18	OTTHUMG00000013059	ENST00000368820.3:c.928G>A	1.37:g.151774253C>T	ENSP00000357810:p.Ala310Thr	Somatic		Capture	Illumina HiSeq	Phase_I	150040877	NM_001004432		Missense_Mutation	SNP	ENST00000368820.3	37	CCDS30855.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.251650	0.59212	.	.	ENSG00000213171	ENST00000368820	T	0.79247	-1.25	5.51	5.51	0.81932	.	0.000000	0.49916	D	0.000137	T	0.54679	0.1873	N	0.25380	0.74	0.47819	D	0.999526	P	0.37370	0.592	B	0.40329	0.326	T	0.58763	-0.7579	10	0.07175	T	0.84	.	16.9624	0.86275	0.0:1.0:0.0:0.0	.	310	Q6UY18	LIGO4_HUMAN	T	310	ENSP00000357810:A310T	ENSP00000357810:A310T	A	-	1	0	LINGO4	150040877	0.992000	0.36948	0.851000	0.33527	0.967000	0.64934	4.750000	0.62162	2.873000	0.98535	0.561000	0.74099	GCA		0.607	LINGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036639.1	XM_291387	
TCHH	7062	broad.mit.edu	37	1	152081217	152081217	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:152081217T>C	ENST00000368804.1	-	2	4475	c.4476A>G	c.(4474-4476)caA>caG	p.Q1492Q		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1492	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.Q1492Q(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGCGCAGCTGTTGTTCCTCCT	0.547																																					p.Q1492Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A4476G	1						.						98.0	97.0	97.0					1																	152081217		1893	4113	6006	150347841	SO:0001819	synonymous_variant	7062	exon2			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.4476A>G	1.37:g.152081217T>C		Somatic		Capture	Illumina HiSeq	Phase_I	150347841	NM_007113	Q5VUI3	Silent	SNP	ENST00000368804.1	37	CCDS41396.1																																																																																				0.547	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
KAZN	23254	broad.mit.edu	37	1	15428263	15428263	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:15428263G>A	ENST00000376030.2	+	11	2066	c.1772G>A	c.(1771-1773)aGc>aAc	p.S591N		NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	591					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)		p.S38N(1)|p.S591N(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						GTGAACTTCAGCAGGGAGGTG	0.592																																					p.S591N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1772A	1						.						57.0	38.0	44.0					1																	15428263		2201	4298	6499	15300850	SO:0001583	missense	23254	exon11			AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"""Sterile alpha motif (SAM) domain containing"""	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.1772G>A	1.37:g.15428263G>A	ENSP00000365198:p.Ser591Asn	Somatic		Capture	Illumina HiSeq	Phase_I	15300850	NM_201628	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	37	CCDS152.2	.	.	.	.	.	.	.	.	.	.	G	13.03	2.114668	0.37339	.	.	ENSG00000189337	ENST00000376030	T	0.15718	2.4	4.53	3.61	0.41365	Sterile alpha motif/pointed domain (1);	0.149487	0.44097	D	0.000492	T	0.05823	0.0152	N	0.01219	-0.95	0.80722	D	1	B	0.19583	0.037	B	0.14023	0.01	T	0.23940	-1.0174	10	0.46703	T	0.11	-11.8626	8.6826	0.34218	0.1094:0.0:0.8905:0.0	.	591	Q674X7	KAZRN_HUMAN	N	591	ENSP00000365198:S591N	ENSP00000365198:S591N	S	+	2	0	KAZN	15300850	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.363000	0.59473	0.896000	0.36366	0.467000	0.42956	AGC		0.592	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999	
UBAP2L	9898	broad.mit.edu	37	1	154223540	154223540	+	Missense_Mutation	SNP	G	G	A	rs528881045	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:154223540G>A	ENST00000361546.2	+	12	1279	c.1237G>A	c.(1237-1239)Gca>Aca	p.A413T	UBAP2L_ENST00000343815.6_Missense_Mutation_p.A413T|UBAP2L_ENST00000271877.7_Missense_Mutation_p.A424T|UBAP2L_ENST00000428931.1_Missense_Mutation_p.A413T			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	413					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)	p.A413T(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AAGTGATTCAGCAGTGCACAG	0.483													A|||	6	0.00119808	0.0	0.0	5008	,	,		17853	0.0		0.0	False		,,,				2504	0.0061				p.A413T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1237A	1						.						73.0	76.0	75.0					1																	154223540		2203	4300	6503	152490164	SO:0001583	missense	9898	exon13			BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.1237G>A	1.37:g.154223540G>A	ENSP00000355343:p.Ala413Thr	Somatic		Capture	Illumina HiSeq	Phase_I	152490164	NM_014847	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	37	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	A	9.454	1.091453	0.20471	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000271877;ENST00000361546	T;T;T;T	0.11277	2.79;2.79;2.79;2.79	5.1	-4.8	0.03190	.	0.758190	0.13205	N	0.405608	T	0.01387	0.0045	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.16802	0.0;0.019;0.0;0.0;0.0	B;B;B;B;B	0.18871	0.0;0.023;0.001;0.001;0.0	T	0.40869	-0.9540	10	0.19590	T	0.45	5.803	13.7895	0.63131	0.1753:0.0:0.7005:0.1241	.	327;424;406;413;413	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	T	413;413;424;413	ENSP00000345308:A413T;ENSP00000389445:A413T;ENSP00000271877:A424T;ENSP00000355343:A413T	ENSP00000271877:A424T	A	+	1	0	UBAP2L	152490164	0.004000	0.15560	0.149000	0.22428	0.950000	0.60333	-0.010000	0.12743	-1.244000	0.02516	-1.216000	0.01612	GCA		0.483	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847	
DCST2	127579	broad.mit.edu	37	1	154995674	154995674	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:154995674G>T	ENST00000368424.3	-	14	2082	c.2024C>A	c.(2023-2025)cCt>cAt	p.P675H		NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	675						integral component of membrane (GO:0016021)		p.P675H(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TGCCTGCTCAGGGTCCTTCCT	0.582																																					p.P675H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2024A	1						.						61.0	64.0	63.0					1																	154995674		2037	4183	6220	153262298	SO:0001583	missense	127579	exon14			AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.2024C>A	1.37:g.154995674G>T	ENSP00000357409:p.Pro675His	Somatic		Capture	Illumina HiSeq	Phase_I	153262298	NM_144622	Q2M2R2|Q8N810|Q96M03	Missense_Mutation	SNP	ENST00000368424.3	37	CCDS1082.2	.	.	.	.	.	.	.	.	.	.	G	14.42	2.530887	0.45073	.	.	ENSG00000163354	ENST00000368424	T	0.24908	1.83	4.31	2.23	0.28157	.	.	.	.	.	T	0.06142	0.0159	N	0.14661	0.345	0.09310	N	1	D	0.56746	0.977	B	0.43536	0.423	T	0.13926	-1.0491	9	0.46703	T	0.11	-6.2649	6.6652	0.23037	0.0:0.1999:0.5936:0.2065	.	675	Q5T1A1	DCST2_HUMAN	H	675	ENSP00000357409:P675H	ENSP00000357409:P675H	P	-	2	0	DCST2	153262298	0.121000	0.22262	0.007000	0.13788	0.489000	0.33432	1.710000	0.37920	1.112000	0.41740	0.655000	0.94253	CCT		0.582	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622	
DCST2	127579	broad.mit.edu	37	1	154997017	154997017	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:154997017A>G	ENST00000368424.3	-	11	1731	c.1673T>C	c.(1672-1674)cTg>cCg	p.L558P	DCST2_ENST00000295536.5_Missense_Mutation_p.L558P	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	558						integral component of membrane (GO:0016021)		p.L558P(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TGATCGGTGCAGGGCAGCCAA	0.612																																					p.L558P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1673C	1						.						71.0	64.0	66.0					1																	154997017		2203	4300	6503	153263641	SO:0001583	missense	127579	exon11			AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.1673T>C	1.37:g.154997017A>G	ENSP00000357409:p.Leu558Pro	Somatic		Capture	Illumina HiSeq	Phase_I	153263641	NM_144622	Q2M2R2|Q8N810|Q96M03	Missense_Mutation	SNP	ENST00000368424.3	37	CCDS1082.2	.	.	.	.	.	.	.	.	.	.	A	12.15	1.852311	0.32699	.	.	ENSG00000163354	ENST00000368424;ENST00000295536	T;T	0.28255	1.62;1.67	4.14	4.14	0.48551	.	0.214231	0.27539	N	0.018901	T	0.26484	0.0647	L	0.36672	1.1	0.23238	N	0.998068	D	0.71674	0.998	D	0.63488	0.915	T	0.03619	-1.1019	10	0.52906	T	0.07	-5.3063	10.772	0.46327	1.0:0.0:0.0:0.0	.	558	Q5T1A1	DCST2_HUMAN	P	558	ENSP00000357409:L558P;ENSP00000295536:L558P	ENSP00000295536:L558P	L	-	2	0	DCST2	153263641	0.982000	0.34865	0.183000	0.23137	0.244000	0.25665	5.498000	0.66931	1.742000	0.51746	0.379000	0.24179	CTG		0.612	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622	
FAM189B	10712	broad.mit.edu	37	1	155220403	155220403	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:155220403G>A	ENST00000361361.2	-	9	1683	c.1174C>T	c.(1174-1176)Cca>Tca	p.P392S	FAM189B_ENST00000472550.1_5'Flank|FAM189B_ENST00000368368.3_Missense_Mutation_p.P374S|FAM189B_ENST00000350210.2_Missense_Mutation_p.P296S	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	392						integral component of membrane (GO:0016021)	WW domain binding (GO:0050699)	p.P392S(1)		breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23						GGGCGCCGTGGCAGGGGGCTT	0.701																																					p.P296S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C886T	1						.						8.0	11.0	10.0					1																	155220403		2079	4119	6198	153487027	SO:0001583	missense	10712	exon6			AF070550	CCDS1103.1, CCDS1104.1, CCDS58035.1	1q21	2009-07-09	2009-07-09	2009-07-09	ENSG00000160767	ENSG00000160767			1233	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 2"""	C1orf2		9331372	Standard	NM_006589		Approved	cote1	uc001fjm.3	P81408	OTTHUMG00000035844	ENST00000361361.2:c.1174C>T	1.37:g.155220403G>A	ENSP00000354958:p.Pro392Ser	Somatic		Capture	Illumina HiSeq	Phase_I	153487027	NM_198264	B1AVS5|Q8IXL3|Q9BR66	Missense_Mutation	SNP	ENST00000361361.2	37	CCDS1103.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.914456	0.72983	.	.	ENSG00000160767	ENST00000350210;ENST00000368368;ENST00000361361;ENST00000323361	T;T;T	0.03358	3.96;3.96;3.96	4.27	4.27	0.50696	.	0.098809	0.41605	D	0.000852	T	0.01558	0.0050	N	0.08118	0	0.43160	D	0.994948	P;B;P;B	0.44521	0.837;0.19;0.573;0.19	P;B;B;B	0.44359	0.447;0.068;0.199;0.068	T	0.64037	-0.6501	10	0.59425	D	0.04	.	14.5634	0.68156	0.0:0.0:1.0:0.0	.	157;374;296;392	B1AVS2;B1AVS5;P81408-2;P81408	.;.;.;F189B_HUMAN	S	296;374;392;102	ENSP00000307128:P296S;ENSP00000357352:P374S;ENSP00000354958:P392S	ENSP00000323164:P102S	P	-	1	0	FAM189B	153487027	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.070000	0.64376	2.372000	0.80975	0.563000	0.77884	CCA		0.701	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589	
YY1AP1	55249	broad.mit.edu	37	1	155638479	155638479	+	Missense_Mutation	SNP	C	C	T	rs151172022		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:155638479C>T	ENST00000295566.4	-	9	979	c.956G>A	c.(955-957)cGc>cAc	p.R319H	YY1AP1_ENST00000347088.5_Missense_Mutation_p.R273H|YY1AP1_ENST00000404643.1_Missense_Mutation_p.R253H|YY1AP1_ENST00000368330.2_Missense_Mutation_p.R273H|YY1AP1_ENST00000407221.1_Missense_Mutation_p.R242H|YY1AP1_ENST00000361831.5_Missense_Mutation_p.R262H|YY1AP1_ENST00000535662.1_Missense_Mutation_p.R119H|YY1AP1_ENST00000368340.5_Missense_Mutation_p.R391H|YY1AP1_ENST00000355499.4_Missense_Mutation_p.R273H|YY1AP1_ENST00000405763.3_Missense_Mutation_p.R411H|YY1AP1_ENST00000311573.5_Missense_Mutation_p.R242H|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000359205.5_Missense_Mutation_p.R262H|YY1AP1_ENST00000476093.1_5'Flank|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000368339.5_Missense_Mutation_p.R411H	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	319					regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R319H(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					TGTCAGTTGGCGGGCAGTCTT	0.448																																					p.R339H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1016A	1						.						265.0	223.0	237.0					1																	155638479		2203	4300	6503	153905103	SO:0001583	missense	55249	exon9			BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.956G>A	1.37:g.155638479C>T	ENSP00000295566:p.Arg319His	Somatic		Capture	Illumina HiSeq	Phase_I	153905103	NM_001198906	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Missense_Mutation	SNP	ENST00000295566.4	37	CCDS1115.1	.	.	.	.	.	.	.	.	.	.	C	1.212	-0.629366	0.03610	.	.	ENSG00000163374	ENST00000359205;ENST00000355499;ENST00000311573;ENST00000347088;ENST00000361831;ENST00000368340;ENST00000295566;ENST00000368330;ENST00000407221;ENST00000404643;ENST00000368339;ENST00000535662;ENST00000405763	T;T;T;T;T;T;T;T;T;T;T;T	0.21031	2.09;2.09;2.08;2.09;2.09;2.03;2.05;2.09;2.08;2.06;2.05;2.07	3.4	2.12	0.27331	.	0.360038	0.26096	N	0.026365	T	0.01254	0.0041	N	0.00500	-1.43	0.80722	D	1	B;B;B;B;B;B;B	0.12013	0.001;0.0;0.0;0.005;0.0;0.0;0.003	B;B;B;B;B;B;B	0.06405	0.001;0.0;0.0;0.002;0.0;0.0;0.001	T	0.45175	-0.9279	10	0.06625	T	0.88	.	8.2661	0.31815	0.0:0.1013:0.0:0.8987	.	339;411;253;411;319;273;391	B4DQQ0;B4DMP2;Q9H869-4;B0QZ55;Q9H869;Q9H869-2;Q5VYZ1	.;.;.;.;YYAP1_HUMAN;.;.	H	262;273;242;273;262;391;319;273;242;253;411;119;411	ENSP00000352134:R262H;ENSP00000347686:R273H;ENSP00000311138:R242H;ENSP00000316079:R273H;ENSP00000355298:R262H;ENSP00000357324:R391H;ENSP00000295566:R319H;ENSP00000357314:R273H;ENSP00000385791:R242H;ENSP00000385390:R253H;ENSP00000357323:R411H;ENSP00000437926:R119H	ENSP00000295566:R319H	R	-	2	0	YY1AP1	153905103	1.000000	0.71417	0.978000	0.43139	0.881000	0.50899	1.908000	0.39907	0.474000	0.27392	-0.672000	0.03802	CGC		0.448	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118	
RXFP4	339403	broad.mit.edu	37	1	155912122	155912122	+	Silent	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:155912122A>C	ENST00000368318.3	+	1	643	c.622A>C	c.(622-624)Agg>Cgg	p.R208R		NM_181885.2	NP_871001.1	Q8TDU9	RL3R2_HUMAN	relaxin/insulin-like family peptide receptor 4	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)	p.R208R(1)		endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	13	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					CCAGCTGCAGAGGGTGGTGCT	0.667																																					p.R208R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A622C	1						.						58.0	62.0	60.0					1																	155912122		2203	4300	6503	154178746	SO:0001819	synonymous_variant	339403	exon1			AB065617	CCDS1124.1	1q22	2012-08-08	2006-05-09	2006-03-15	ENSG00000173080	ENSG00000173080		"""GPCR / Class A : Relaxin family peptide receptors"""	14666	protein-coding gene	gene with protein product		609043	"""G protein-coupled receptor 100"", ""relaxin 3 receptor 2"", ""relaxin family peptide receptor 4"""	GPR100, RLN3R2		15956688, 16507880	Standard	NM_181885		Approved	GPCR142, RXFPR4	uc010pgs.2	Q8TDU9	OTTHUMG00000017463	ENST00000368318.3:c.622A>C	1.37:g.155912122A>C		Somatic		Capture	Illumina HiSeq	Phase_I	154178746	NM_181885	B0M0L4|Q3MJB1|Q8NGZ8	Silent	SNP	ENST00000368318.3	37	CCDS1124.1																																																																																				0.667	RXFP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046203.1	NM_181885	
ARHGEF11	9826	broad.mit.edu	37	1	156939094	156939094	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:156939094G>A	ENST00000361409.2	-	9	1427	c.685C>T	c.(685-687)Cgc>Tgc	p.R229C	ARHGEF11_ENST00000368194.3_Missense_Mutation_p.R269C	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	229					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R269C(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GAAGGAAAGCGTTCTGTCCCA	0.562																																					p.R269C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C805T	1						.						45.0	37.0	40.0					1																	156939094		2203	4299	6502	155205718	SO:0001583	missense	9826	exon10			AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"""Rho guanine nucleotide exchange factors"""	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.685C>T	1.37:g.156939094G>A	ENSP00000354644:p.Arg229Cys	Somatic		Capture	Illumina HiSeq	Phase_I	155205718	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.916718	0.92249	.	.	ENSG00000132694	ENST00000368194;ENST00000361409	T;T	0.70282	-0.37;-0.47	4.89	4.89	0.63831	.	0.000000	0.51477	D	0.000081	T	0.70037	0.3178	L	0.32530	0.975	0.80722	D	1	D;D	0.76494	0.998;0.999	P;P	0.59424	0.72;0.857	T	0.73902	-0.3836	10	0.72032	D	0.01	-16.0265	18.1945	0.89817	0.0:0.0:1.0:0.0	.	229;269	O15085;O15085-2	ARHGB_HUMAN;.	C	269;229	ENSP00000357177:R269C;ENSP00000354644:R229C	ENSP00000354644:R229C	R	-	1	0	ARHGEF11	155205718	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	6.042000	0.70996	2.690000	0.91761	0.655000	0.94253	CGC		0.562	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	
KIRREL	55243	broad.mit.edu	37	1	158059508	158059508	+	Splice_Site	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:158059508G>T	ENST00000359209.6	+	10	1239	c.1172G>T	c.(1171-1173)gGg>gTg	p.G391V	KIRREL_ENST00000368173.3_Splice_Site_p.G407V|KIRREL_ENST00000360089.4_Splice_Site_p.G227V|KIRREL_ENST00000368172.1_Splice_Site_p.G205V|KIRREL_ENST00000416935.2_Splice_Site_p.G291V|KIRREL_ENST00000392272.2_Splice_Site_p.G288V			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	391					excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)	p.G227V(2)|p.G407V(2)|p.G391V(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					TTGCTTGCAGGGCCCCCCATC	0.582																																					p.G391V												.	.	5	Substitution - Missense(5)	lung(3)|large_intestine(2)	c.G1172T	1						.						132.0	122.0	125.0					1																	158059508		2203	4300	6503	156326132	SO:0001630	splice_region_variant	55243	exon10			AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15734	protein-coding gene	gene with protein product	"""nephrin-like protein 1"""	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.1172-1G>T	1.37:g.158059508G>T		Somatic		Capture	Illumina HiSeq	Phase_I	156326132	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Missense_Mutation	SNP	ENST00000359209.6	37	CCDS1172.2	.	.	.	.	.	.	.	.	.	.	G	20.4	3.978093	0.74360	.	.	ENSG00000183853	ENST00000360089;ENST00000368173;ENST00000392272;ENST00000359209;ENST00000416935;ENST00000368172	T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63	5.28	5.28	0.74379	Immunoglobulin-like fold (1);	0.000000	0.39834	N	0.001255	T	0.49712	0.1573	M	0.78637	2.42	0.80722	D	1	D;D;D;D	0.89917	0.992;1.0;1.0;1.0	D;D;D;D	0.97110	0.979;1.0;1.0;1.0	T	0.50338	-0.8840	9	.	.	.	.	16.3856	0.83503	0.0:0.0:1.0:0.0	.	291;227;205;391	B4DN67;Q5W0F9;Q5W0G0;Q96J84	.;.;.;KIRR1_HUMAN	V	227;407;288;391;291;205	ENSP00000353202:G227V;ENSP00000357155:G407V;ENSP00000376098:G288V;ENSP00000352138:G391V;ENSP00000389674:G291V;ENSP00000357154:G205V	.	G	+	2	0	KIRREL	156326132	1.000000	0.71417	1.000000	0.80357	0.503000	0.33858	9.552000	0.98115	2.463000	0.83235	0.460000	0.39030	GGG		0.582	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240	Missense_Mutation
IFI16	3428	broad.mit.edu	37	1	159023479	159023479	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:159023479G>T	ENST00000295809.7	+	11	2497	c.2242G>T	c.(2242-2244)Ggg>Tgg	p.G748W	IFI16_ENST00000430894.2_Missense_Mutation_p.G696W|IFI16_ENST00000448393.2_Missense_Mutation_p.G636W|IFI16_ENST00000359709.3_Missense_Mutation_p.G692W|IFI16_ENST00000368132.3_Missense_Mutation_p.G692W|IFI16_ENST00000368131.4_Missense_Mutation_p.G692W|IFI16_ENST00000340979.6_Missense_Mutation_p.G636W			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	748	HIN-200 2. {ECO:0000255|PROSITE- ProRule:PRU00106}.|Interaction with TP53 core domain.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)	p.G692W(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					TGGGAATACCGGGGAGTTGAG	0.413																																					p.G692W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2074T	1						.						129.0	127.0	128.0					1																	159023479		2203	4300	6503	157290103	SO:0001583	missense	3428	exon10			M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.2242G>T	1.37:g.159023479G>T	ENSP00000295809:p.Gly748Trp	Somatic		Capture	Illumina HiSeq	Phase_I	157290103	NM_005531	B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Missense_Mutation	SNP	ENST00000295809.7	37		.	.	.	.	.	.	.	.	.	.	G	13.36	2.212667	0.39102	.	.	ENSG00000163565	ENST00000359709;ENST00000295809;ENST00000340979;ENST00000368131;ENST00000368132;ENST00000430894	T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01	4.83	-9.66	0.00534	.	.	.	.	.	T	0.02342	0.0072	N	0.11427	0.14	0.09310	N	1	P;B;P	0.44090	0.826;0.036;0.602	B;B;B	0.43018	0.405;0.04;0.363	T	0.24870	-1.0148	9	0.36615	T	0.2	.	0.6372	0.00804	0.4249:0.2422:0.1789:0.154	.	696;636;692	E7EPR3;Q16666-3;Q16666-2	.;.;.	W	377;748;636;692;692;696	ENSP00000295809:G748W;ENSP00000342741:G636W;ENSP00000357113:G692W;ENSP00000357114:G692W;ENSP00000394935:G696W	ENSP00000295809:G748W	G	+	1	0	IFI16	157290103	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.907000	0.01589	-1.731000	0.01360	-1.140000	0.01884	GGG		0.413	IFI16-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000421720.1	NM_005531	
CADM3	57863	broad.mit.edu	37	1	159163754	159163754	+	Silent	SNP	G	G	A	rs367893559		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:159163754G>A	ENST00000368125.4	+	5	772	c.615G>A	c.(613-615)gcG>gcA	p.A205A	CADM3_ENST00000368124.4_Silent_p.A239A|CTA-134P22.2_ENST00000415675.2_RNA	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	205	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|protein localization (GO:0008104)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.A239A(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					ATGATGGGGCGAGCATCGTGT	0.502																																					p.A239A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G717A	1						.	G	,	0,4406		0,0,2203	122.0	108.0	113.0		615,717	-10.0	0.0	1		113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CADM3	NM_001127173.1,NM_021189.3	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	205/399,239/433	159163754	1,13005	2203	4300	6503	157430378	SO:0001819	synonymous_variant	57863	exon6			AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17601	protein-coding gene	gene with protein product	"""nectin-like 1"""	609743	"""immunoglobulin superfamily, member 4B"""	IGSF4B		11536053	Standard	NM_021189		Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.615G>A	1.37:g.159163754G>A		Somatic		Capture	Illumina HiSeq	Phase_I	157430378	NM_021189	Q8IZQ9|Q9NVJ5|Q9UJP1	Silent	SNP	ENST00000368125.4	37	CCDS44251.1																																																																																				0.502	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189	
OR10J3	441911	broad.mit.edu	37	1	159283606	159283606	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:159283606G>A	ENST00000332217.5	-	1	843	c.844C>T	c.(844-846)Cac>Tac	p.H282Y		NM_001004467.1	NP_001004467.1	Q5JRS4	O10J3_HUMAN	olfactory receptor, family 10, subfamily J, member 3	282						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H282Y(1)		breast(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(19)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	47	all_hematologic(112;0.0429)					GTAGGGGAGTGATGAGTGTAG	0.507																																					p.H282Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C844T	1						.						128.0	111.0	116.0					1																	159283606		2203	4300	6503	157550230	SO:0001583	missense	441911	exon1				CCDS30909.1	1q23.2	2012-08-09		2004-03-10	ENSG00000196266	ENSG00000196266		"""GPCR / Class A : Olfactory receptors"""	14992	protein-coding gene	gene with protein product				OR10J3P			Standard	NM_001004467		Approved		uc010piu.2	Q5JRS4	OTTHUMG00000037233	ENST00000332217.5:c.844C>T	1.37:g.159283606G>A	ENSP00000331789:p.His282Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	157550230	NM_001004467		Missense_Mutation	SNP	ENST00000332217.5	37	CCDS30909.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.060630	0.36373	.	.	ENSG00000196266	ENST00000332217	T	0.36699	1.24	5.34	2.35	0.29111	.	2587.430000	0.01146	U	0.006316	T	0.10208	0.0250	N	0.08118	0	0.22719	N	0.998818	B	0.22604	0.072	B	0.33121	0.158	T	0.35051	-0.9804	10	0.87932	D	0	.	5.2982	0.15764	0.2509:0.1484:0.6007:0.0	.	282	Q5JRS4	O10J3_HUMAN	Y	282	ENSP00000331789:H282Y	ENSP00000331789:H282Y	H	-	1	0	OR10J3	157550230	0.000000	0.05858	1.000000	0.80357	0.977000	0.68977	-0.628000	0.05515	0.786000	0.33708	0.655000	0.94253	CAC		0.507	OR10J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090629.1		
OR10J3	441911	broad.mit.edu	37	1	159283762	159283762	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:159283762C>T	ENST00000332217.5	-	1	687	c.688G>A	c.(688-690)Gcc>Acc	p.A230T		NM_001004467.1	NP_001004467.1	Q5JRS4	O10J3_HUMAN	olfactory receptor, family 10, subfamily J, member 3	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A230T(1)		breast(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(19)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	47	all_hematologic(112;0.0429)					TCAGCTGAGGCAATCTTAAGA	0.498																																					p.A230T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G688A	1						.						159.0	140.0	147.0					1																	159283762		2203	4300	6503	157550386	SO:0001583	missense	441911	exon1				CCDS30909.1	1q23.2	2012-08-09		2004-03-10	ENSG00000196266	ENSG00000196266		"""GPCR / Class A : Olfactory receptors"""	14992	protein-coding gene	gene with protein product				OR10J3P			Standard	NM_001004467		Approved		uc010piu.2	Q5JRS4	OTTHUMG00000037233	ENST00000332217.5:c.688G>A	1.37:g.159283762C>T	ENSP00000331789:p.Ala230Thr	Somatic		Capture	Illumina HiSeq	Phase_I	157550386	NM_001004467		Missense_Mutation	SNP	ENST00000332217.5	37	CCDS30909.1	.	.	.	.	.	.	.	.	.	.	C	11.31	1.601612	0.28534	.	.	ENSG00000196266	ENST00000332217	T	0.00348	8.0	5.34	0.15	0.14883	GPCR, rhodopsin-like superfamily (1);	1.371220	0.05739	N	0.601116	T	0.00039	0.0001	N	0.10945	0.07	0.09310	N	1	B	0.23185	0.081	B	0.33121	0.158	T	0.15694	-1.0428	10	0.56958	D	0.05	.	1.469	0.02411	0.2674:0.3198:0.2606:0.1522	.	230	Q5JRS4	O10J3_HUMAN	T	230	ENSP00000331789:A230T	ENSP00000331789:A230T	A	-	1	0	OR10J3	157550386	0.000000	0.05858	0.021000	0.16686	0.699000	0.40488	-0.710000	0.05024	-0.121000	0.11787	0.655000	0.94253	GCC		0.498	OR10J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090629.1		
OR10J5	127385	broad.mit.edu	37	1	159505500	159505500	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:159505500G>A	ENST00000334857.2	-	1	342	c.298C>T	c.(298-300)Caa>Taa	p.Q100*		NM_001004469.1	NP_001004469.1	Q8NHC4	O10J5_HUMAN	olfactory receptor, family 10, subfamily J, member 5	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q100*(1)		kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	22	all_hematologic(112;0.0429)					AAGAACATTTGTGTAGCACAG	0.463																																					p.Q100X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C298T	1						.						126.0	110.0	115.0					1																	159505500		2203	4300	6503	157772124	SO:0001587	stop_gained	127385	exon1				CCDS30910.1	1q23.2	2012-08-09			ENSG00000184155	ENSG00000184155		"""GPCR / Class A : Olfactory receptors"""	14993	protein-coding gene	gene with protein product							Standard	NM_001004469		Approved		uc010piw.2	Q8NHC4	OTTHUMG00000022738	ENST00000334857.2:c.298C>T	1.37:g.159505500G>A	ENSP00000334441:p.Gln100*	Somatic		Capture	Illumina HiSeq	Phase_I	157772124	NM_001004469	B9EH35|Q6IFH2	Nonsense_Mutation	SNP	ENST00000334857.2	37	CCDS30910.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.124144	0.56613	.	.	ENSG00000184155	ENST00000334857	.	.	.	4.32	3.37	0.38596	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	11.3528	0.49598	0.0:0.0:0.817:0.183	.	.	.	.	X	100	.	ENSP00000334441:Q100X	Q	-	1	0	OR10J5	157772124	1.000000	0.71417	0.745000	0.31077	0.300000	0.27592	7.499000	0.81566	1.108000	0.41662	0.467000	0.42956	CAA		0.463	OR10J5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059021.1	NM_001004469	
FCRL6	343413	broad.mit.edu	37	1	159784044	159784044	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:159784044T>C	ENST00000368106.3	+	8	1110	c.1109T>C	c.(1108-1110)gTc>gCc	p.V370A	FCRL6_ENST00000392235.3_Missense_Mutation_p.V275A|FCRL6_ENST00000339348.5_Missense_Mutation_p.V370A|FCRL6_ENST00000321935.6_Missense_Mutation_p.V377A	NM_001004310.2	NP_001004310.2	Q6DN72	FCRL6_HUMAN	Fc receptor-like 6	370						external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.V370A(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	24	all_hematologic(112;0.0597)					GAAGGTGTTGTCTACTCTGTG	0.458																																					p.V370A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1109C	1						.						203.0	180.0	187.0					1																	159784044		2203	4300	6503	158050668	SO:0001583	missense	343413	exon8			AK131201	CCDS30912.1, CCDS60312.1	1q23.2	2013-01-11			ENSG00000181036	ENSG00000181036		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31910	protein-coding gene	gene with protein product		613562					Standard	NM_001004310		Approved	IFGP6, FLJ16056, FcRH6	uc001fud.4	Q6DN72	OTTHUMG00000035351	ENST00000368106.3:c.1109T>C	1.37:g.159784044T>C	ENSP00000357086:p.Val370Ala	Somatic		Capture	Illumina HiSeq	Phase_I	158050668	NM_001004310	A1KXW6|A2A4D6|Q6DN73|Q6XRC3|Q6ZNI1	Missense_Mutation	SNP	ENST00000368106.3	37	CCDS30912.1	.	.	.	.	.	.	.	.	.	.	T	9.894	1.205063	0.22205	.	.	ENSG00000181036	ENST00000321935;ENST00000339348;ENST00000392235;ENST00000368106	T;T;T;T	0.01455	5.14;5.08;5.46;4.87	3.73	-2.21	0.06973	.	.	.	.	.	T	0.00440	0.0014	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.23806	0.015;0.091;0.055;0.091	B;B;B;B	0.19148	0.01;0.024;0.011;0.024	T	0.40308	-0.9570	9	0.49607	T	0.09	.	8.1122	0.30922	0.0:0.537:0.0:0.463	.	370;275;370;377	Q6DN72-3;Q6DN72-4;Q6DN72;Q6DN72-2	.;.;FCRL6_HUMAN;.	A	377;370;275;370	ENSP00000320625:V377A;ENSP00000340949:V370A;ENSP00000376068:V275A;ENSP00000357086:V370A	ENSP00000320625:V377A	V	+	2	0	FCRL6	158050668	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.596000	0.05720	-0.730000	0.04869	-0.419000	0.06015	GTC		0.458	FCRL6-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276853.1	NM_001004310	
IGSF9	57549	broad.mit.edu	37	1	159902400	159902400	+	Missense_Mutation	SNP	C	C	T	rs527258901		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:159902400C>T	ENST00000368094.1	-	10	1344	c.1147G>A	c.(1147-1149)Gcc>Acc	p.A383T	IGSF9_ENST00000493195.1_5'UTR|IGSF9_ENST00000361509.3_Missense_Mutation_p.A367T	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	383	Ig-like 4.				dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.A367T(2)		central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			TTCCCCAGGGCGATGATCAGT	0.607													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14747	0.0		0.0	False		,,,				2504	0.0				p.A383T												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1147A	1						.						55.0	49.0	51.0					1																	159902400		2203	4300	6503	158169024	SO:0001583	missense	57549	exon10			AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.1147G>A	1.37:g.159902400C>T	ENSP00000357073:p.Ala383Thr	Somatic		Capture	Illumina HiSeq	Phase_I	158169024	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	37	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.043191	0.36085	.	.	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.76709	-1.04;2.73	4.7	4.7	0.59300	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.38605	N	0.001623	T	0.49813	0.1579	N	0.11427	0.14	0.44685	D	0.997672	B;P	0.51537	0.386;0.946	B;B	0.43331	0.151;0.416	T	0.56232	-0.8013	9	.	.	.	-16.8899	15.1302	0.72517	0.0:1.0:0.0:0.0	.	383;383	Q9P2J2;C9JI81	TUTLA_HUMAN;.	T	367;383;383	ENSP00000355049:A367T;ENSP00000357073:A383T	.	A	-	1	0	IGSF9	158169024	0.370000	0.25047	1.000000	0.80357	0.593000	0.36681	1.241000	0.32743	2.154000	0.67381	0.561000	0.74099	GCC		0.607	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789	
ATP1A2	477	broad.mit.edu	37	1	160098554	160098554	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:160098554G>A	ENST00000361216.3	+	9	1219	c.1130G>A	c.(1129-1131)gGc>gAc	p.G377D	ATP1A2_ENST00000392233.3_Missense_Mutation_p.G377D	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	377					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.G377D(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			GACAAGACGGGCACCCTCACC	0.602																																					p.G377D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1130A	1						.						131.0	105.0	114.0					1																	160098554		2203	4300	6503	158365178	SO:0001583	missense	477	exon9			AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"""ATPases / P-type"""	800	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-2"", ""sodium pump subunit alpha-2"", ""sodium-potassium ATPase catalytic subunit alpha-2"""	182340	"""migraine, hemiplegic 2"", ""ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"""	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.1130G>A	1.37:g.160098554G>A	ENSP00000354490:p.Gly377Asp	Somatic		Capture	Illumina HiSeq	Phase_I	158365178	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	37	CCDS1196.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.136282|5.136282	0.94517|0.94517	.|.	.|.	ENSG00000018625|ENSG00000018625	ENST00000447527|ENST00000538123;ENST00000361216;ENST00000392233;ENST00000435866	.|D;D	.|0.99458	.|-5.93;-5.93	4.77|4.77	4.77|4.77	0.60923|0.60923	.|Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99816|0.99816	0.9919|0.9919	H|H	0.99286|0.99286	4.5|4.5	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|1.0;1.0;1.0;1.0	D|D	0.96574|0.96574	0.9425|0.9425	5|10	.|0.87932	.|D	.|0	.|.	16.9484|16.9484	0.86236|0.86236	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|222;377;277;377	.|B4DHD7;B1AKY9;F5GXJ7;P50993	.|.;.;.;AT1A2_HUMAN	T|D	88|222;377;377;80	.|ENSP00000354490:G377D;ENSP00000376066:G377D	.|ENSP00000354490:G377D	A|G	+|+	1|2	0|0	ATP1A2|ATP1A2	158365178|158365178	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.789000|9.789000	0.99068|0.99068	2.359000|2.359000	0.80004|0.80004	0.561000|0.561000	0.74099|0.74099	GCA|GGC		0.602	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702	
C1orf192	257177	broad.mit.edu	37	1	161336267	161336267	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:161336267A>G	ENST00000367974.1	-	2	57	c.52T>C	c.(52-54)Tat>Cat	p.Y18H	RP11-122G18.5_ENST00000437833.2_lincRNA	NM_001013625.2	NP_001013647.2	Q5VTH2	CA192_HUMAN	chromosome 1 open reading frame 192	18								p.Y18H(1)		endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10	all_cancers(52;4.64e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			TTCTGCAGATACTTGGATGAG	0.443																																					p.Y18H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T52C	1						.						258.0	230.0	239.0					1																	161336267		2203	4300	6503	159602891	SO:0001583	missense	257177	exon2				CCDS30921.1	1q23.3	2014-02-21			ENSG00000188931	ENSG00000188931			32325	protein-coding gene	gene with protein product							Standard	NM_001013625		Approved	Flattop, Fltp	uc001gal.4	Q5VTH2	OTTHUMG00000034462	ENST00000367974.1:c.52T>C	1.37:g.161336267A>G	ENSP00000356951:p.Tyr18His	Somatic		Capture	Illumina HiSeq	Phase_I	159602891	NM_001013625		Missense_Mutation	SNP	ENST00000367974.1	37	CCDS30921.1	.	.	.	.	.	.	.	.	.	.	A	16.40	3.112058	0.56398	.	.	ENSG00000188931	ENST00000367974	.	.	.	4.73	0.973	0.19710	.	0.761560	0.11835	N	0.524829	T	0.30854	0.0778	L	0.54323	1.7	0.28287	N	0.923724	D	0.64830	0.994	P	0.59643	0.861	T	0.06862	-1.0803	8	0.44086	T	0.13	-12.9291	2.7219	0.05203	0.4911:0.0:0.1805:0.3284	.	18	Q5VTH2	CA192_HUMAN	H	18	.	ENSP00000356951:Y18H	Y	-	1	0	C1orf192	159602891	0.876000	0.30132	0.912000	0.35992	0.832000	0.47134	1.114000	0.31196	0.056000	0.16144	0.383000	0.25322	TAT		0.443	C1orf192-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083309.1	NM_001013625	
SPEN	23013	broad.mit.edu	37	1	16261103	16261103	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:16261103A>G	ENST00000375759.3	+	11	8572	c.8368A>G	c.(8368-8370)Atg>Gtg	p.M2790V		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2790	Interaction with RBPSUH. {ECO:0000250}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.M2790V(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CCCAGGGTCCATGCCTGTGAT	0.582																																					p.M2790V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A8368G	1						.						59.0	57.0	58.0					1																	16261103		2203	4300	6503	16133690	SO:0001583	missense	23013	exon11				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.8368A>G	1.37:g.16261103A>G	ENSP00000364912:p.Met2790Val	Somatic		Capture	Illumina HiSeq	Phase_I	16133690	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	10.09	1.254470	0.22965	.	.	ENSG00000065526	ENST00000375759	T	0.09255	3.0	5.08	5.08	0.68730	.	.	.	.	.	T	0.14098	0.0341	L	0.38175	1.15	0.45662	D	0.998582	B	0.28933	0.228	B	0.40285	0.325	T	0.15896	-1.0421	9	0.24483	T	0.36	-23.6991	14.8403	0.70217	1.0:0.0:0.0:0.0	.	2790	Q96T58	MINT_HUMAN	V	2790	ENSP00000364912:M2790V	ENSP00000364912:M2790V	M	+	1	0	SPEN	16133690	1.000000	0.71417	0.944000	0.38274	0.101000	0.19017	6.355000	0.73041	1.913000	0.55393	0.459000	0.35465	ATG		0.582	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
FCGR3A	2214	broad.mit.edu	37	1	161599761	161599761	+	Intron	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:161599761A>G	ENST00000540048.1	-	2	94				FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000403078.3_Intron|FCGR2B_ENST00000367962.4_Intron|FCGR3B_ENST00000531221.1_Silent_p.S78S|FCGR3B_ENST00000294800.3_Silent_p.S42S|FCGR3B_ENST00000367964.2_Silent_p.S42S|FCGR2B_ENST00000367960.5_Intron			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S42S(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TCAGAGTCACACTGTCCTTCT	0.532																																					p.S42S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T126C	1						.						72.0	80.0	77.0					1																	161599761		2148	4290	6438	159866385	SO:0001627	intron_variant	2215	exon3			BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000540048.1:c.61+396T>C	1.37:g.161599761A>G		Somatic		Capture	Illumina HiSeq	Phase_I	159866385	NM_000570	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Silent	SNP	ENST00000540048.1	37		.	.	.	.	.	.	.	.	.	.	A	5.347	0.249283	0.10130	.	.	ENSG00000162747	ENST00000421702	.	.	.	2.79	-4.05	0.03998	.	.	.	.	.	T	0.07369	0.0186	.	.	.	0.25260	N	0.989603	.	.	.	.	.	.	T	0.33266	-0.9875	4	.	.	.	.	4.1257	0.10126	0.4271:0.194:0.3788:0.0	.	.	.	.	R	63	.	.	C	-	1	0	FCGR3B	159866385	0.000000	0.05858	0.011000	0.14972	0.201000	0.24016	-1.270000	0.02831	-1.021000	0.03350	-0.575000	0.04146	TGT		0.532	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569	
UCK2	7371	broad.mit.edu	37	1	165859446	165859446	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:165859446C>A	ENST00000367879.4	+	2	408	c.105C>A	c.(103-105)tcC>tcA	p.S35S	UCK2_ENST00000372212.4_Silent_p.S35S	NM_012474.4	NP_036606.2	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2	35					cellular response to oxygen levels (GO:0071453)|CTP salvage (GO:0044211)|feeding behavior (GO:0007631)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to axon injury (GO:0048678)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)	p.S35S(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					CACAGTCTTCCGTGTGTGCTA	0.537																																					p.S35S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C105A	1						.						132.0	115.0	121.0					1																	165859446		2203	4300	6503	164126070	SO:0001819	synonymous_variant	7371	exon2			AF236637	CCDS1252.1	1p32	2012-10-02	2004-07-13	2004-07-14	ENSG00000143179	ENSG00000143179	2.7.1.48		12562	protein-coding gene	gene with protein product		609329	"""uridine monophosphate kinase"""	UMPK			Standard	NM_012474		Approved		uc001gdp.3	Q9BZX2	OTTHUMG00000040117	ENST00000367879.4:c.105C>A	1.37:g.165859446C>A		Somatic		Capture	Illumina HiSeq	Phase_I	164126070	NM_012474	Q5VV91|Q7KZV3|Q92528|Q96KG5|Q9BU42	Silent	SNP	ENST00000367879.4	37	CCDS1252.1																																																																																				0.537	UCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096753.1	NM_012474	
DUSP27	92235	broad.mit.edu	37	1	167095353	167095353	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:167095353C>A	ENST00000361200.2	+	6	1151	c.985C>A	c.(985-987)Ctg>Atg	p.L329M	DUSP27_ENST00000485151.1_3'UTR|DUSP27_ENST00000271385.5_Missense_Mutation_p.L329M|DUSP27_ENST00000443333.1_Missense_Mutation_p.L329M			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	329					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.L329M(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						TGGCTCCTCCCTGGGGAAGGC	0.662																																					p.L329M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C985A	1						.						19.0	24.0	22.0					1																	167095353		2203	4299	6502	165361977	SO:0001583	missense	92235	exon5			AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.985C>A	1.37:g.167095353C>A	ENSP00000354483:p.Leu329Met	Somatic		Capture	Illumina HiSeq	Phase_I	165361977	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	C	7.680	0.688712	0.14973	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03441	3.93;3.93;3.93	4.6	-9.19	0.00685	.	11.461900	0.00166	N	0.000000	T	0.00724	0.0024	L	0.34521	1.04	0.09310	N	0.999993	B	0.16396	0.017	B	0.14023	0.01	T	0.43507	-0.9387	10	0.20046	T	0.44	-7.9638	5.1525	0.15017	0.1516:0.4231:0.3103:0.115	.	329	Q5VZP5	DUS27_HUMAN	M	329	ENSP00000354483:L329M;ENSP00000271385:L329M;ENSP00000404874:L329M	ENSP00000271385:L329M	L	+	1	2	DUSP27	165361977	0.000000	0.05858	0.360000	0.25837	0.975000	0.68041	-1.354000	0.02614	-1.868000	0.01142	-0.499000	0.04595	CTG		0.662	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
GPR161	23432	broad.mit.edu	37	1	168056933	168056933	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:168056933A>G	ENST00000367838.1	-	7	1527	c.1214T>C	c.(1213-1215)aTg>aCg	p.M405T	GPR161_ENST00000271357.5_Missense_Mutation_p.M405T|GPR161_ENST00000367836.1_Missense_Mutation_p.M273T|GPR161_ENST00000539777.1_Missense_Mutation_p.M327T|GPR161_ENST00000537209.1_Missense_Mutation_p.M425T|GPR161_ENST00000546300.1_Missense_Mutation_p.M291T|GPR161_ENST00000367835.1_Missense_Mutation_p.M405T|GPR161_ENST00000361697.2_Missense_Mutation_p.M405T	NM_001267611.1|NM_153832.2	NP_001254540.1|NP_722561.1	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161	405					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)	p.M405T(1)		breast(1)|endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	all_hematologic(923;0.215)					AAGCAGCATCATATCTGTCCC	0.507																																					p.M405T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1214C	1						.						167.0	149.0	155.0					1																	168056933		2203	4300	6503	166323557	SO:0001583	missense	23432	exon7			AF091890	CCDS1268.1, CCDS58042.1, CCDS58043.1, CCDS58044.1, CCDS58045.1, CCDS72978.1	1q23.3	2012-08-21			ENSG00000143147	ENSG00000143147		"""GPCR / Class A : Orphans"""	23694	protein-coding gene	gene with protein product		612250				11959142	Standard	NM_153832		Approved	RE2	uc009wvo.4	Q8N6U8	OTTHUMG00000034651	ENST00000367838.1:c.1214T>C	1.37:g.168056933A>G	ENSP00000356812:p.Met405Thr	Somatic		Capture	Illumina HiSeq	Phase_I	166323557	NM_153832	B3KV34|B7Z5D7|B7Z5E8|B7Z5Z6|F5GXD6|F5H6J7|O75963|Q5TGK0|Q5TGK1|Q5TGK2	Missense_Mutation	SNP	ENST00000367838.1	37	CCDS1268.1	.	.	.	.	.	.	.	.	.	.	A	10.04	1.242562	0.22796	.	.	ENSG00000143147	ENST00000367838;ENST00000271357;ENST00000367836;ENST00000367835;ENST00000546300;ENST00000539777;ENST00000537209;ENST00000361697	T;T;T;T;T;T;T;T	0.80214	0.14;0.14;-1.35;0.14;-0.88;-0.85;0.23;0.14	5.83	3.5	0.40072	.	0.440250	0.24018	N	0.042316	T	0.30417	0.0764	N	0.01352	-0.895	0.21915	N	0.999471	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.04140	-1.0974	9	0.31617	T	0.26	-4.9039	6.678	0.23106	0.7304:0.1309:0.1387:0.0	.	425;291;327;425;405	F5GXD6;B7Z5E8;F5H6J7;B7Z5Z6;Q8N6U8	.;.;.;.;GP161_HUMAN	T	405;405;273;405;291;327;425;405	ENSP00000356812:M405T;ENSP00000271357:M405T;ENSP00000356810:M273T;ENSP00000356809:M405T;ENSP00000444348:M291T;ENSP00000437576:M327T;ENSP00000441039:M425T;ENSP00000355194:M405T	ENSP00000271357:M405T	M	-	2	0	GPR161	166323557	1.000000	0.71417	0.544000	0.28141	0.744000	0.42396	5.649000	0.67936	0.457000	0.26962	0.459000	0.35465	ATG		0.507	GPR161-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083829.1	NM_007369	
F5	2153	broad.mit.edu	37	1	169483585	169483585	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:169483585A>G	ENST00000367797.3	-	25	6842	c.6641T>C	c.(6640-6642)cTt>cCt	p.L2214P	F5_ENST00000367796.3_Missense_Mutation_p.L2219P	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	2214	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)	p.L2214P(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	TTCCAGGCGAAGTGCAATACT	0.383																																					p.L2214P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T6641C	1						.						90.0	92.0	91.0					1																	169483585		2203	4300	6503	167750209	SO:0001583	missense	2153	exon25			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.6641T>C	1.37:g.169483585A>G	ENSP00000356771:p.Leu2214Pro	Somatic		Capture	Illumina HiSeq	Phase_I	167750209	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.227534	0.79576	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.85411	-1.98;-1.98	5.09	5.09	0.68999	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.060968	0.64402	D	0.000002	D	0.94231	0.8148	H	0.96889	3.9	0.39520	D	0.968496	D	0.89917	1.0	D	0.97110	1.0	D	0.96125	0.9088	9	0.87932	D	0	-16.2435	14.5117	0.67791	1.0:0.0:0.0:0.0	.	2214	P12259	FA5_HUMAN	P	2214;2219	ENSP00000356771:L2214P;ENSP00000356770:L2219P	ENSP00000356770:L2219P	L	-	2	0	F5	167750209	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.513000	0.81739	1.909000	0.55274	0.482000	0.46254	CTT		0.383	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
C1orf112	55732	broad.mit.edu	37	1	169798423	169798423	+	Missense_Mutation	SNP	G	G	A	rs199972566		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:169798423G>A	ENST00000286031.6	+	13	1847	c.1147G>A	c.(1147-1149)Gtt>Att	p.V383I	C1orf112_ENST00000413811.2_Silent_p.P310P|C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000359326.4_Missense_Mutation_p.V383I	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	383								p.V383I(1)		breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					ACTCAAAGCCGTTTTCTACAG	0.368																																					p.V383I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1147A	1						.	A	ILE/VAL	0,4406		0,0,2203	132.0	130.0	131.0		1147	0.3	1.0	1		131	1,8599	818.9+/-406.8	0,1,4299	yes	missense	C1orf112	NM_018186.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	383/854	169798423	1,13005	2203	4300	6503	168065047	SO:0001583	missense	55732	exon13			AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.1147G>A	1.37:g.169798423G>A	ENSP00000286031:p.Val383Ile	Somatic		Capture	Illumina HiSeq	Phase_I	168065047	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Missense_Mutation	SNP	ENST00000286031.6	37	CCDS1285.1	.	.	.	.	.	.	.	.	.	.	A	4.414	0.076588	0.08485	0.0	1.16E-4	ENSG00000000460	ENST00000359326;ENST00000286031	T;T	0.53423	0.62;0.62	5.65	0.327	0.15913	.	0.515352	0.22674	N	0.057038	T	0.02533	0.0077	N	0.00408	-1.53	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.43114	-0.9411	10	0.02654	T	1	-7.9543	1.5893	0.02650	0.4171:0.1406:0.3065:0.1358	.	325;383	B4DGF2;Q9NSG2	.;CA112_HUMAN	I	383	ENSP00000352276:V383I;ENSP00000286031:V383I	ENSP00000286031:V383I	V	+	1	0	C1orf112	168065047	0.698000	0.27777	0.999000	0.59377	0.957000	0.61999	0.011000	0.13264	0.093000	0.17368	-0.516000	0.04426	GTT		0.368	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	
SCYL3	57147	broad.mit.edu	37	1	169831881	169831881	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:169831881A>G	ENST00000367770.1	-	9	1060	c.1013T>C	c.(1012-1014)gTg>gCg	p.V338A	SCYL3_ENST00000470238.1_5'UTR|SCYL3_ENST00000367771.6_Missense_Mutation_p.V338A|RN7SL333P_ENST00000476398.2_RNA|SCYL3_ENST00000367772.4_Missense_Mutation_p.V338A			Q8IZE3	PACE1_HUMAN	SCY1-like 3 (S. cerevisiae)	338					cell migration (GO:0016477)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)	p.V338A(2)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CACGGGGATCACCCGTGACTG	0.498																																					p.V338A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1013C	1						.						154.0	144.0	148.0					1																	169831881		2203	4300	6503	168098505	SO:0001583	missense	57147	exon10			BC014662	CCDS1286.1, CCDS1287.1	1q24.2	2008-02-05			ENSG00000000457	ENSG00000000457			19285	protein-coding gene	gene with protein product	"""ezrin-binding partner PACE-1"""	608192				12651155	Standard	NM_020423		Approved	PACE-1, PACE1	uc001ggs.3	Q8IZE3	OTTHUMG00000035941	ENST00000367770.1:c.1013T>C	1.37:g.169831881A>G	ENSP00000356744:p.Val338Ala	Somatic		Capture	Illumina HiSeq	Phase_I	168098505	NM_181093	A8K8Z2|Q5THA6|Q5THA8|Q8IZN9|Q96C56|Q9UBK6	Missense_Mutation	SNP	ENST00000367770.1	37	CCDS1287.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.834291	0.91036	.	.	ENSG00000000457	ENST00000367772;ENST00000367771;ENST00000367770;ENST00000423670	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.54095	0.1837	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.987	T	0.61594	-0.7031	10	0.87932	D	0	-18.2751	15.4057	0.74874	1.0:0.0:0.0:0.0	.	338;338	Q8IZE3-2;Q8IZE3	.;PACE1_HUMAN	A	338	ENSP00000356746:V338A;ENSP00000356745:V338A;ENSP00000356744:V338A;ENSP00000407993:V338A	ENSP00000356744:V338A	V	-	2	0	SCYL3	168098505	1.000000	0.71417	0.996000	0.52242	0.848000	0.48234	8.857000	0.92250	2.116000	0.64780	0.496000	0.49642	GTG		0.498	SCYL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087550.4	NM_181093	
MROH9	80133	broad.mit.edu	37	1	170964586	170964586	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:170964586C>T	ENST00000367758.3	+	13	1350	c.1251C>T	c.(1249-1251)gcC>gcT	p.A417A	MROH9_ENST00000367759.4_Silent_p.A417A	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	417								p.A417A(1)									AAGCGGTGGCCCAGTATTTCC	0.468																																					p.A417A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1251T	1						.						105.0	102.0	103.0					1																	170964586		1912	4115	6027	169231210	SO:0001819	synonymous_variant	80133	exon13			AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.1251C>T	1.37:g.170964586C>T		Somatic		Capture	Illumina HiSeq	Phase_I	169231210	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Silent	SNP	ENST00000367758.3	37	CCDS41436.1	.	.	.	.	.	.	.	.	.	.	C	1.362	-0.588385	0.03799	.	.	ENSG00000117501	ENST00000426136	.	.	.	5.57	-0.173	0.13322	.	.	.	.	.	T	0.07954	0.0199	.	.	.	0.28718	N	0.90321	.	.	.	.	.	.	T	0.31586	-0.9938	4	.	.	.	-4.2041	1.517	0.02508	0.2881:0.4056:0.1404:0.1659	.	.	.	.	S	24	.	.	P	+	1	0	C1orf129	169231210	0.916000	0.31088	0.730000	0.30809	0.074000	0.17049	-0.025000	0.12413	0.268000	0.21939	-0.163000	0.13421	CCA		0.468	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
PRRC2C	23215	broad.mit.edu	37	1	171548526	171548526	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:171548526A>C	ENST00000338920.4	+	27	7424	c.7187A>C	c.(7186-7188)cAt>cCt	p.H2396P	PRRC2C_ENST00000426496.2_Missense_Mutation_p.H2331P|PRRC2C_ENST00000392078.3_Missense_Mutation_p.H2398P|PRRC2C_ENST00000367742.3_Missense_Mutation_p.H2398P	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2396	Gln-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.H2398P(1)									GACACAAGTCATTTATTCAAT	0.418																																					p.H2396P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A7187C	1						.						112.0	99.0	103.0					1																	171548526		2203	4300	6503	169815150	SO:0001583	missense	23215	exon27			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.7187A>C	1.37:g.171548526A>C	ENSP00000343629:p.His2396Pro	Somatic		Capture	Illumina HiSeq	Phase_I	169815150	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.70|17.70	3.453688|3.453688	0.63290|0.63290	.|.	.|.	ENSG00000117523|ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080;ENST00000412837|ENST00000495585	T;T;T;T|.	0.07216|.	3.21;3.26;3.25;3.25|.	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	0.000000|.	0.48767|.	D|.	0.000180|.	T|T	0.63896|0.63896	0.2550|0.2550	M|M	0.63843|0.63843	1.955|1.955	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	T|T	0.64219|0.64219	-0.6459|-0.6459	10|5	0.66056|.	D|.	0.02|.	.|.	15.5476|15.5476	0.76118|0.76118	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	2396|.	Q9Y520-4|.	.|.	P|L	2398;2350;2331;2398;2396;2153;233|879	ENSP00000375928:H2398P;ENSP00000410219:H2331P;ENSP00000356716:H2398P;ENSP00000343629:H2396P|.	ENSP00000343629:H2396P|.	H|I	+|+	2|1	0|0	PRRC2C|PRRC2C	169815150|169815150	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	8.807000|8.807000	0.91935|0.91935	2.128000|2.128000	0.65567|0.65567	0.528000|0.528000	0.53228|0.53228	CAT|ATT		0.418	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
PADI3	51702	broad.mit.edu	37	1	17586186	17586186	+	Missense_Mutation	SNP	G	G	A	rs150292444		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:17586186G>A	ENST00000375460.3	+	2	246	c.206G>A	c.(205-207)cGc>cAc	p.R69H		NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	69					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)	p.R69H(1)		breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	AGGCGGTGGCGCTTTGACGCG	0.592																																					p.R69H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G206A	1						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	77.0	66.0	70.0		206	-7.0	0.1	1	dbSNP_134	70	0,8600		0,0,4300	no	missense	PADI3	NM_016233.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	69/665	17586186	1,13005	2203	4300	6503	17458773	SO:0001583	missense	51702	exon2			AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"""Peptidyl arginine deiminases"""	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.206G>A	1.37:g.17586186G>A	ENSP00000364609:p.Arg69His	Somatic		Capture	Illumina HiSeq	Phase_I	17458773	NM_016233	Q58EY7|Q70SX5	Missense_Mutation	SNP	ENST00000375460.3	37	CCDS179.1	.	.	.	.	.	.	.	.	.	.	G	5.719	0.317219	0.10845	2.27E-4	0.0	ENSG00000142619	ENST00000375460	T	0.09255	3.0	5.2	-7.01	0.01594	Cupredoxin (1);Protein-arginine deiminase (PAD) N-terminal (1);	0.533866	0.19741	N	0.107104	T	0.03095	0.0091	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.29610	-1.0006	10	0.44086	T	0.13	-5.3922	6.7913	0.23701	0.2325:0.1122:0.5451:0.1102	.	69	Q9ULW8	PADI3_HUMAN	H	69	ENSP00000364609:R69H	ENSP00000364609:R69H	R	+	2	0	PADI3	17458773	0.531000	0.26338	0.098000	0.21074	0.041000	0.13682	-0.404000	0.07205	-0.890000	0.03945	-1.012000	0.02466	CGC		0.592	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1		
METTL13	51603	broad.mit.edu	37	1	171753044	171753044	+	Silent	SNP	G	G	A	rs201273694		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:171753044G>A	ENST00000361735.3	+	2	584	c.318G>A	c.(316-318)acG>acA	p.T106T	METTL13_ENST00000458517.1_Silent_p.T105T|METTL13_ENST00000362019.3_Silent_p.T20T|METTL13_ENST00000367737.5_Silent_p.T106T	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	106							methyltransferase activity (GO:0008168)	p.T106T(1)		breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						TGGACATGACGCAGATGGAGT	0.502													G|||	1	0.000199681	0.0	0.0014	5008	,	,		23401	0.0		0.0	False		,,,				2504	0.0				p.T20T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G60A	1						.						134.0	119.0	124.0					1																	171753044		2203	4300	6503	170019667	SO:0001819	synonymous_variant	51603	exon2			AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"""KIAA0859"""	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.318G>A	1.37:g.171753044G>A		Somatic		Capture	Illumina HiSeq	Phase_I	170019667	NM_014955	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Silent	SNP	ENST00000361735.3	37	CCDS1299.1																																																																																				0.502	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955	
PAPPA2	60676	broad.mit.edu	37	1	176525463	176525463	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:176525463T>G	ENST00000367662.3	+	2	1169	c.5T>G	c.(4-6)aTg>aGg	p.M2R	PAPPA2_ENST00000367661.3_Missense_Mutation_p.M2R	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	2					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.M2R(2)		NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						GGAGGTATGATGTGCTTAAAG	0.498																																					p.M2R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T5G	1						.						121.0	117.0	118.0					1																	176525463		1965	4159	6124	174792086	SO:0001583	missense	60676	exon2			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.5T>G	1.37:g.176525463T>G	ENSP00000356634:p.Met2Arg	Somatic		Capture	Illumina HiSeq	Phase_I	174792086	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	T	8.147	0.786437	0.16189	.	.	ENSG00000116183	ENST00000367662;ENST00000367661	T;T	0.34667	4.61;1.35	4.82	1.13	0.20643	.	0.391115	0.19560	U	0.111343	T	0.29945	0.0749	M	0.63428	1.95	0.32962	D	0.521196	B;B	0.26002	0.139;0.139	B;B	0.25140	0.018;0.058	T	0.28776	-1.0033	10	0.87932	D	0	-6.341	3.2217	0.06717	0.1728:0.1943:0.0:0.6328	.	2;2	Q9BXP8;A9Z1Y8	PAPP2_HUMAN;.	R	2	ENSP00000356634:M2R;ENSP00000356633:M2R	ENSP00000356633:M2R	M	+	2	0	PAPPA2	174792086	1.000000	0.71417	0.735000	0.30896	0.204000	0.24138	1.586000	0.36611	-0.059000	0.13154	-0.441000	0.05720	ATG		0.498	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		
ASTN1	460	broad.mit.edu	37	1	176903418	176903418	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:176903418C>T	ENST00000367654.3	-	16	2776	c.2565G>A	c.(2563-2565)gcG>gcA	p.A855A	ASTN1_ENST00000361833.2_Silent_p.A847A|ASTN1_ENST00000367657.3_Silent_p.A847A|ASTN1_ENST00000424564.2_Silent_p.A847A|ASTN1_ENST00000281881.3_5'Flank	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	855					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.A847A(1)		NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GGTCCAACAGCGCCACAAAAT	0.542																																					p.A847A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2541A	1						.						111.0	92.0	99.0					1																	176903418		2203	4300	6503	175170041	SO:0001819	synonymous_variant	460	exon16			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.2565G>A	1.37:g.176903418C>T		Somatic		Capture	Illumina HiSeq	Phase_I	175170041	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																					0.542	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
ASTN1	460	broad.mit.edu	37	1	177001946	177001946	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:177001946C>T	ENST00000367654.3	-	3	722	c.511G>A	c.(511-513)Gtg>Atg	p.V171M	ASTN1_ENST00000361833.2_Missense_Mutation_p.V171M|ASTN1_ENST00000367657.3_Missense_Mutation_p.V171M|ASTN1_ENST00000424564.2_Missense_Mutation_p.V171M|ASTN1_ENST00000281881.3_5'UTR	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	171					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.V171M(1)		NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						AGGATCATCACCAGGCACAAG	0.577																																					p.V171M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G511A	1						.						52.0	49.0	50.0					1																	177001946		2203	4300	6503	175268569	SO:0001583	missense	460	exon3			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.511G>A	1.37:g.177001946C>T	ENSP00000356626:p.Val171Met	Somatic		Capture	Illumina HiSeq	Phase_I	175268569	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		.	.	.	.	.	.	.	.	.	.	C	17.21	3.332284	0.60853	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.17528	2.27;2.68;2.69;2.27	5.42	5.42	0.78866	.	0.058018	0.64402	D	0.000002	T	0.17704	0.0425	L	0.29908	0.895	0.58432	D	0.999994	D;P;P	0.53462	0.96;0.835;0.835	P;B;B	0.46253	0.509;0.412;0.412	T	0.00728	-1.1591	10	0.51188	T	0.08	-15.4941	14.4316	0.67254	0.0:0.8525:0.1475:0.0	.	171;171;171	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	M	171	ENSP00000356629:V171M;ENSP00000354536:V171M;ENSP00000356626:V171M;ENSP00000395041:V171M	ENSP00000354536:V171M	V	-	1	0	ASTN1	175268569	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	2.605000	0.46283	2.509000	0.84616	0.655000	0.94253	GTG		0.577	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
BRINP2	57795	broad.mit.edu	37	1	177226448	177226448	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:177226448C>T	ENST00000361539.4	+	4	909	c.597C>T	c.(595-597)gcC>gcT	p.A199A	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	199	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)		p.A199A(1)									AGCTGGCCGCCTCCTACTTCA	0.582																																					p.A199A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C597T	1						.						48.0	48.0	48.0					1																	177226448		2203	4300	6503	175493071	SO:0001819	synonymous_variant	57795	exon4				CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.597C>T	1.37:g.177226448C>T		Somatic		Capture	Illumina HiSeq	Phase_I	175493071	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Silent	SNP	ENST00000361539.4	37	CCDS1320.1																																																																																				0.582	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165	
QSOX1	5768	broad.mit.edu	37	1	180165502	180165502	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:180165502A>G	ENST00000367602.3	+	12	1648	c.1574A>G	c.(1573-1575)gAa>gGa	p.E525G	QSOX1_ENST00000367600.5_Missense_Mutation_p.E525G			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	525					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)	p.E525G(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						TGGGACGTGGAAGCCACCCTC	0.612																																					p.E525G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1574G	1						.						153.0	152.0	152.0					1																	180165502		2203	4300	6503	178432125	SO:0001583	missense	5768	exon12			U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"""quiescin Q6"""	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.1574A>G	1.37:g.180165502A>G	ENSP00000356574:p.Glu525Gly	Somatic		Capture	Illumina HiSeq	Phase_I	178432125	NM_002826	Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Missense_Mutation	SNP	ENST00000367602.3	37	CCDS1337.1	.	.	.	.	.	.	.	.	.	.	A	4.978	0.181735	0.09495	.	.	ENSG00000116260	ENST00000367602;ENST00000367600	T;T	0.15372	3.59;2.43	5.35	-6.58	0.01836	.	1.870380	0.02156	N	0.058387	T	0.04815	0.0130	N	0.00960	-1.095	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.0;0.001	T	0.32719	-0.9896	10	0.15066	T	0.55	0.3323	7.5457	0.27766	0.4807:0.2686:0.2508:0.0	.	525;525;525;525	A8K4C2;A8K477;O00391;O00391-2	.;.;QSOX1_HUMAN;.	G	525	ENSP00000356574:E525G;ENSP00000356572:E525G	ENSP00000356572:E525G	E	+	2	0	QSOX1	178432125	0.000000	0.05858	0.008000	0.14137	0.367000	0.29736	-1.140000	0.03210	-1.822000	0.01211	-0.480000	0.04831	GAA		0.612	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1	NM_002826	
CACNA1E	777	broad.mit.edu	37	1	181702788	181702788	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:181702788G>A	ENST00000367573.2	+	21	3164	c.3164G>A	c.(3163-3165)tGc>tAc	p.C1055Y	CACNA1E_ENST00000357570.5_Missense_Mutation_p.C1006Y|CACNA1E_ENST00000367570.1_Missense_Mutation_p.C1055Y|CACNA1E_ENST00000526775.1_Missense_Mutation_p.C1036Y|CACNA1E_ENST00000360108.3_Missense_Mutation_p.C1036Y|CACNA1E_ENST00000358338.5_Missense_Mutation_p.C987Y|CACNA1E_ENST00000367567.4_Missense_Mutation_p.C662Y	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1055					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.C1055Y(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GACCTCTCCTGCATCACGGCC	0.647																																					p.C1055Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3164A	1						.						48.0	56.0	53.0					1																	181702788		2200	4287	6487	179969411	SO:0001583	missense	777	exon21			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3164G>A	1.37:g.181702788G>A	ENSP00000356545:p.Cys1055Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	179969411	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.425831	0.43020	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96041	-3.82;-3.83;-3.82;-3.83;-3.89;-3.83;-3.82	4.99	4.05	0.47172	.	4.055390	0.00531	N	0.000203	D	0.90504	0.7025	N	0.08118	0	0.28130	N	0.930239	B;B;B	0.26445	0.0;0.149;0.0	B;B;B	0.25614	0.001;0.062;0.001	T	0.78453	-0.2198	10	0.20519	T	0.43	.	13.3564	0.60631	0.0:0.2573:0.7427:0.0	.	1036;1055;1055	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	Y	1055;1036;1006;987;662;1036;1055	ENSP00000356542:C1055Y;ENSP00000434814:C1036Y;ENSP00000350183:C1006Y;ENSP00000351101:C987Y;ENSP00000356539:C662Y;ENSP00000353222:C1036Y;ENSP00000356545:C1055Y	ENSP00000350183:C1006Y	C	+	2	0	CACNA1E	179969411	0.995000	0.38212	1.000000	0.80357	0.970000	0.65996	2.926000	0.48892	2.313000	0.78055	0.561000	0.74099	TGC		0.647	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
HMCN1	83872	broad.mit.edu	37	1	186014823	186014823	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:186014823C>T	ENST00000271588.4	+	41	6537	c.6308C>T	c.(6307-6309)cCg>cTg	p.P2103L	HMCN1_ENST00000367492.2_Missense_Mutation_p.P2103L	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2103					response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.P2103L(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CATGTAGTTCCGCCAAATATT	0.388																																					p.P2103L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6308T	1						.						112.0	100.0	104.0					1																	186014823		2203	4300	6503	184281446	SO:0001583	missense	83872	exon41			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.6308C>T	1.37:g.186014823C>T	ENSP00000271588:p.Pro2103Leu	Somatic		Capture	Illumina HiSeq	Phase_I	184281446	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.278725	0.80692	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.51574	0.7;0.7	5.35	4.44	0.53790	Immunoglobulin-like fold (1);	0.099034	0.64402	D	0.000001	T	0.51007	0.1649	M	0.88775	2.98	0.80722	D	1	P	0.42692	0.787	B	0.30782	0.12	T	0.63989	-0.6512	10	0.54805	T	0.06	.	15.4358	0.75146	0.1401:0.8599:0.0:0.0	.	2103	Q96RW7	HMCN1_HUMAN	L	2103	ENSP00000271588:P2103L;ENSP00000356462:P2103L	ENSP00000271588:P2103L	P	+	2	0	HMCN1	184281446	1.000000	0.71417	0.998000	0.56505	0.893000	0.52053	7.294000	0.78760	1.239000	0.43787	0.650000	0.86243	CCG		0.388	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
KLHDC7A	127707	broad.mit.edu	37	1	18809496	18809496	+	Missense_Mutation	SNP	C	C	T	rs369329894		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:18809496C>T	ENST00000400664.1	+	1	2073	c.2021C>T	c.(2020-2022)gCg>gTg	p.A674V		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	674						integral component of membrane (GO:0016021)		p.A674V(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GAGATGGTGGCGGTCAACGGC	0.697																																					p.A674V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2021T	1						.						49.0	46.0	47.0					1																	18809496		2203	4300	6503	18682083	SO:0001583	missense	127707	exon1			AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.2021C>T	1.37:g.18809496C>T	ENSP00000383505:p.Ala674Val	Somatic		Capture	Illumina HiSeq	Phase_I	18682083	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	.	.	.	.	.	.	.	.	.	.	C	19.82	3.898837	0.72754	.	.	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.19532	2.14	4.68	4.68	0.58851	Kelch-type beta propeller (1);	0.311841	0.28647	N	0.014603	T	0.43277	0.1240	M	0.73962	2.25	0.39334	D	0.965478	D;D	0.89917	1.0;1.0	D;D	0.69307	0.95;0.963	T	0.36720	-0.9736	10	0.34782	T	0.22	.	12.9081	0.58164	0.0:0.8354:0.1646:0.0	.	611;674	A7E2V3;Q5VTJ3	.;KLD7A_HUMAN	V	674;611	ENSP00000383505:A674V	ENSP00000383505:A674V	A	+	2	0	KLHDC7A	18682083	0.996000	0.38824	0.978000	0.43139	0.857000	0.48899	3.367000	0.52350	2.123000	0.65237	0.561000	0.74099	GCG		0.697	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
HMCN1	83872	broad.mit.edu	37	1	186147591	186147591	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:186147591G>A	ENST00000271588.4	+	104	16216	c.15987G>A	c.(15985-15987)caG>caA	p.Q5329Q	HMCN1_ENST00000367492.2_Intron|GS1-174L6.4_ENST00000428391.1_RNA	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5329	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.Q5329Q(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GTGCACATCAGTGCTCCAACA	0.433																																					p.Q5329Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G15987A	1						.						90.0	93.0	92.0					1																	186147591		2203	4300	6503	184414214	SO:0001819	synonymous_variant	83872	exon104			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15987G>A	1.37:g.186147591G>A		Somatic		Capture	Illumina HiSeq	Phase_I	184414214	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																				0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
CFH	3075	broad.mit.edu	37	1	196712742	196712742	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:196712742A>G	ENST00000367429.4	+	20	3534	c.3294A>G	c.(3292-3294)gaA>gaG	p.E1098E		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	1098	Sushi 18. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)	p.E1098E(1)		NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						ACTGGACGGAACCACCTCAAT	0.348																																					p.E1098E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A3294G	1						.						239.0	231.0	234.0					1																	196712742		2203	4300	6503	194979365	SO:0001819	synonymous_variant	3075	exon20			Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.3294A>G	1.37:g.196712742A>G		Somatic		Capture	Illumina HiSeq	Phase_I	194979365	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000367429.4	37	CCDS1385.1																																																																																				0.348	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186	
CAPZB	832	broad.mit.edu	37	1	19684041	19684041	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:19684041C>T	ENST00000375142.1	-	5	392	c.346G>A	c.(346-348)Gtc>Atc	p.V116I	CAPZB_ENST00000264202.6_Missense_Mutation_p.V116I|CAPZB_ENST00000375144.1_Missense_Mutation_p.V104I|CAPZB_ENST00000433834.1_Missense_Mutation_p.V145I|CAPZB_ENST00000264203.3_Missense_Mutation_p.V142I|CAPZB_ENST00000401084.2_Missense_Mutation_p.V116I	NM_001206540.1	NP_001193469.1	P47756	CAPZB_HUMAN	capping protein (actin filament) muscle Z-line, beta	116					actin cytoskeleton organization (GO:0030036)|barbed-end actin filament capping (GO:0051016)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|muscle fiber development (GO:0048747)|negative regulation of microtubule polymerization (GO:0031115)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)|regulation of protein kinase C signaling (GO:0090036)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|membrane (GO:0016020)|WASH complex (GO:0071203)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.V116I(1)		endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	7		Colorectal(325;3.93e-05)|Renal(390;0.000147)|all_lung(284;0.000169)|Lung NSC(340;0.000202)|Breast(348;0.000496)|Ovarian(437;0.00428)|Myeloproliferative disorder(586;0.0262)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Kidney(64;8.63e-06)|BRCA - Breast invasive adenocarcinoma(304;4.06e-05)|KIRC - Kidney renal clear cell carcinoma(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000525)|STAD - Stomach adenocarcinoma(196;0.00779)|READ - Rectum adenocarcinoma(331;0.103)|Lung(427;0.173)		ACAGATGAGACGCCACCTTCA	0.498																																					p.V116I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G346A	1						.						77.0	74.0	75.0					1																	19684041		1985	4157	6142	19556628	SO:0001583	missense	832	exon5			U03271	CCDS41277.1, CCDS55579.1, CCDS72717.1, CCDS72718.1	1p36.1	2014-05-09			ENSG00000077549	ENSG00000077549			1491	protein-coding gene	gene with protein product		601572					Standard	NM_004930		Approved		uc021ohr.1	P47756	OTTHUMG00000002556	ENST00000375142.1:c.346G>A	1.37:g.19684041C>T	ENSP00000364284:p.Val116Ile	Somatic		Capture	Illumina HiSeq	Phase_I	19556628	NM_004930	Q32Q68|Q5U0L4|Q8TB49|Q9NUC4	Missense_Mutation	SNP	ENST00000375142.1	37	CCDS55579.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.304329	0.81136	.	.	ENSG00000077549	ENST00000401084;ENST00000264203;ENST00000375144;ENST00000375142;ENST00000433834;ENST00000375145;ENST00000264202;ENST00000413711;ENST00000457768	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.73560	0.3602	L	0.45581	1.43	0.80722	D	1	D;P;B;D	0.76494	0.999;0.862;0.032;0.999	D;P;B;D	0.83275	0.996;0.901;0.028;0.996	T	0.66176	-0.5989	9	0.20046	T	0.44	-10.6626	18.6724	0.91516	0.0:1.0:0.0:0.0	.	145;142;116;104	B1AK88;B1AK85;P47756-2;B1AK87	.;.;.;.	I	116;142;104;116;145;178;116;104;88	.	ENSP00000264202:V116I	V	-	1	0	CAPZB	19556628	1.000000	0.71417	0.974000	0.42286	0.990000	0.78478	7.298000	0.78815	2.756000	0.94617	0.563000	0.77884	GTC		0.498	CAPZB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007260.1		
CRB1	23418	broad.mit.edu	37	1	197297928	197297928	+	Silent	SNP	C	C	T	rs576678571		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:197297928C>T	ENST00000367400.3	+	2	582	c.447C>T	c.(445-447)caC>caT	p.H149H	CRB1_ENST00000538660.1_Silent_p.H149H|CRB1_ENST00000535699.1_Silent_p.H80H|CRB1_ENST00000367399.2_Silent_p.H149H	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	149	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.H149H(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						AGATAGATCACGATGAGTGTG	0.502													C|||	1	0.000199681	0.0	0.0	5008	,	,		21783	0.0		0.0	False		,,,				2504	0.001				p.H149H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C447T	1						.						94.0	77.0	83.0					1																	197297928		2203	4300	6503	195564551	SO:0001819	synonymous_variant	23418	exon2				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"""crumbs (Drosophila) homolog 1"", ""crumbs homolog 1 (Drosophila)"""	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.447C>T	1.37:g.197297928C>T		Somatic		Capture	Illumina HiSeq	Phase_I	195564551	NM_201253	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Silent	SNP	ENST00000367400.3	37	CCDS1390.1																																																																																				0.502	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253	
TNNI1	7135	broad.mit.edu	37	1	201380612	201380612	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:201380612C>T	ENST00000361379.4	-	7	421	c.329G>A	c.(328-330)cGc>cAc	p.R110H	TNNI1_ENST00000555948.1_Intron|TNNI1_ENST00000367312.1_Missense_Mutation_p.R110H|TNNI1_ENST00000336092.4_Missense_Mutation_p.R110H	NM_003281.3	NP_003272.3	P19237	TNNI1_HUMAN	troponin I type 1 (skeletal, slow)	110	Involved in binding TNC and actin.				muscle filament sliding (GO:0030049)|regulation of striated muscle contraction (GO:0006942)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytosol (GO:0005829)|troponin complex (GO:0005861)	metal ion binding (GO:0046872)	p.R110H(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	8						CAGGGGCGGGCGCTTGAACTT	0.632																																					p.R110H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G329A	1						.						51.0	50.0	50.0					1																	201380612		2203	4300	6503	199647235	SO:0001583	missense	7135	exon6			BC012600	CCDS1411.1	1q31.3	2008-02-05	2005-09-12		ENSG00000159173	ENSG00000159173			11945	protein-coding gene	gene with protein product		191042	"""troponin I, skeletal, slow"""			2365354, 8144655	Standard	NM_003281		Approved		uc021phd.1	P19237	OTTHUMG00000035736	ENST00000361379.4:c.329G>A	1.37:g.201380612C>T	ENSP00000354488:p.Arg110His	Somatic		Capture	Illumina HiSeq	Phase_I	199647235	NM_003281	A6NEH3|A8MSJ0|Q659A5|Q6FGS7|Q6FGW1|Q6ICU2|Q86T57|Q96DT9	Missense_Mutation	SNP	ENST00000361379.4	37	CCDS1411.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.755950	0.89843	.	.	ENSG00000159173	ENST00000358712;ENST00000361379;ENST00000336092;ENST00000413495;ENST00000367312;ENST00000555340;ENST00000556362	D;D;D;D;D	0.94613	-3.47;-3.47;-3.47;-3.47;-3.47	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	D	0.97120	0.9059	M	0.86651	2.83	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97453	1.0029	10	0.87932	D	0	-23.6196	11.142	0.48408	0.0:0.9142:0.0:0.0858	.	110	P19237	TNNI1_HUMAN	H	110;110;110;110;110;89;110	ENSP00000354488:R110H;ENSP00000337022:R110H;ENSP00000356281:R110H;ENSP00000451660:R89H;ENSP00000451776:R110H	ENSP00000337022:R110H	R	-	2	0	TNNI1	199647235	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	6.066000	0.71185	2.141000	0.66446	0.561000	0.74099	CGC		0.632	TNNI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087001.1	NM_003281	
LMOD1	25802	broad.mit.edu	37	1	201868646	201868646	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:201868646G>A	ENST00000367288.4	-	2	1741	c.1495C>T	c.(1495-1497)Ccc>Tcc	p.P499S	RP11-307B6.3_ENST00000458139.1_RNA|RP11-307B6.3_ENST00000414927.1_RNA	NM_012134.2	NP_036266.2	P29536	LMOD1_HUMAN	leiomodin 1 (smooth muscle)	499					muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)		p.P499S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						CCGGCCTTGGGTACCTCCAGC	0.577																																					p.P499S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1495T	1						.						49.0	52.0	51.0					1																	201868646		1989	4142	6131	200135269	SO:0001583	missense	25802	exon2			X54162	CCDS53457.1	1q32.1	2008-05-22			ENSG00000163431	ENSG00000163431			6647	protein-coding gene	gene with protein product		602715					Standard	NM_012134		Approved	64kD, D1, 1D	uc021phl.1	P29536	OTTHUMG00000035802	ENST00000367288.4:c.1495C>T	1.37:g.201868646G>A	ENSP00000356257:p.Pro499Ser	Somatic		Capture	Illumina HiSeq	Phase_I	200135269	NM_012134	B1APV6|C4AMB1|Q68EN2	Missense_Mutation	SNP	ENST00000367288.4	37	CCDS53457.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.960269	0.74016	.	.	ENSG00000163431	ENST00000367288;ENST00000400965;ENST00000412469	T	0.21191	2.02	4.52	4.52	0.55395	.	0.000000	0.39687	N	0.001281	T	0.46639	0.1403	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.48864	-0.8997	10	0.56958	D	0.05	-20.4171	15.0879	0.72170	0.0:0.0:1.0:0.0	.	448;499	B4E3S9;P29536	.;LMOD1_HUMAN	S	499;499;448	ENSP00000356257:P499S	ENSP00000356257:P499S	P	-	1	0	LMOD1	200135269	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	7.738000	0.84966	2.182000	0.69389	0.655000	0.94253	CCC		0.577	LMOD1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087085.2		
PPFIA4	8497	broad.mit.edu	37	1	203025570	203025570	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:203025570C>T	ENST00000447715.2	+	23	2549	c.2108C>T	c.(2107-2109)tCc>tTc	p.S703F	PPFIA4_ENST00000295706.4_Missense_Mutation_p.S219F|PPFIA4_ENST00000272198.6_Missense_Mutation_p.S219F|PPFIA4_ENST00000599966.1_Missense_Mutation_p.S219F|PPFIA4_ENST00000367240.2_Missense_Mutation_p.S704F|PPFIA4_ENST00000414050.2_Missense_Mutation_p.S432F			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	703					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)		p.S850F(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						TCTCCTCCTTCCTCACCCAGG	0.567																																					p.S219F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C656T	1						.						48.0	54.0	52.0					1																	203025570		2024	4168	6192	201292193	SO:0001583	missense	8497	exon5			AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.2108C>T	1.37:g.203025570C>T	ENSP00000402576:p.Ser703Phe	Somatic		Capture	Illumina HiSeq	Phase_I	201292193	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		.	.	.	.	.	.	.	.	.	.	c	28.0	4.882878	0.91740	.	.	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31	4.78	4.78	0.61160	.	0.000000	0.45126	D	0.000390	T	0.56470	0.1987	M	0.61703	1.905	0.80722	D	1	D;P;D;D	0.67145	0.985;0.911;0.996;0.993	P;P;D;P	0.66602	0.883;0.66;0.945;0.883	T	0.55566	-0.8121	10	0.42905	T	0.14	-19.7234	18.0072	0.89213	0.0:1.0:0.0:0.0	.	432;703;219;219	B4DIS5;B1N949;O75335-2;O75335	.;.;.;LIPA4_HUMAN	F	704;703;219;432;219	ENSP00000356209:S704F;ENSP00000402576:S703F;ENSP00000295706:S219F;ENSP00000400379:S432F;ENSP00000272198:S219F	ENSP00000272198:S219F	S	+	2	0	PPFIA4	201292193	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.259000	0.78381	2.489000	0.83994	0.457000	0.33378	TCC		0.567	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	
ADORA1	134	broad.mit.edu	37	1	203134611	203134611	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:203134611G>T	ENST00000367236.4	+	3	1485	c.564G>T	c.(562-564)tgG>tgT	p.W188C	ADORA1_ENST00000337894.4_Missense_Mutation_p.W188C|ADORA1_ENST00000309502.3_Missense_Mutation_p.W188C|ADORA1_ENST00000472535.1_3'UTR|ADORA1_ENST00000367235.1_3'UTR	NM_001048230.1	NP_001041695.1	P30542	AA1R_HUMAN	adenosine A1 receptor	188					activation of MAPKK activity (GO:0000186)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cognition (GO:0050890)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood pressure (GO:0045776)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heart contraction (GO:0045822)|negative regulation of hormone secretion (GO:0046888)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of mucus secretion (GO:0070256)|negative regulation of neurotrophin production (GO:0032900)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of vasodilation (GO:0045908)|nervous system development (GO:0007399)|phagocytosis (GO:0006909)|positive regulation of blood pressure (GO:0045777)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of nucleoside transport (GO:0032244)|positive regulation of peptide secretion (GO:0002793)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of protein dephosphorylation (GO:0035307)|protein targeting to membrane (GO:0006612)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of glomerular filtration (GO:0003093)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|relaxation of vascular smooth muscle (GO:0060087)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|temperature homeostasis (GO:0001659)	asymmetric synapse (GO:0032279)|axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled adenosine receptor activity (GO:0001609)|phospholipase C activity (GO:0004629)|purine nucleoside binding (GO:0001883)	p.W188C(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(9)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25					Adenosine(DB00640)|Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Gabapentin(DB00996)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Theobromine(DB01412)|Theophylline(DB00277)	TCTTTGTGTGGGTGCTGCCCC	0.577																																					p.W188C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G564T	1						.						163.0	168.0	166.0					1																	203134611		2203	4300	6503	201401234	SO:0001583	missense	134	exon3			BC026340	CCDS1434.1	1q32.1	2012-08-08			ENSG00000163485	ENSG00000163485		"""GPCR / Class A : Adenosine receptors"""	262	protein-coding gene	gene with protein product		102775				1662665, 2541503	Standard	NM_001048230		Approved	RDC7	uc001gzf.1	P30542	OTTHUMG00000042125	ENST00000367236.4:c.564G>T	1.37:g.203134611G>T	ENSP00000356205:p.Trp188Cys	Somatic		Capture	Illumina HiSeq	Phase_I	201401234	NM_001048230	A6NFY5|A6NGP4|A8K1L3|B3KXQ4|D2CGD0|Q6FHK3|Q8TAM8	Missense_Mutation	SNP	ENST00000367236.4	37	CCDS1434.1	.	.	.	.	.	.	.	.	.	.	G	9.302	1.053436	0.19907	.	.	ENSG00000163485	ENST00000309502;ENST00000367236;ENST00000337894	T;T;T	0.71817	-0.6;-0.6;-0.6	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.106329	0.64402	D	0.000001	T	0.75679	0.3882	N	0.21508	0.67	0.80722	D	1	D;D;B	0.89917	1.0;1.0;0.071	D;D;B	0.97110	0.995;1.0;0.168	T	0.74087	-0.3778	10	0.31617	T	0.26	-14.7387	19.0713	0.93138	0.0:0.0:1.0:0.0	.	221;120;188	B7Z379;B7Z1L9;P30542	.;.;AA1R_HUMAN	C	188	ENSP00000308549:W188C;ENSP00000356205:W188C;ENSP00000338435:W188C	ENSP00000308549:W188C	W	+	3	0	ADORA1	201401234	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.568000	0.67385	2.586000	0.87340	0.561000	0.74099	TGG		0.577	ADORA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100273.1	NM_000674	
PRELP	5549	broad.mit.edu	37	1	203452745	203452745	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:203452745G>A	ENST00000343110.2	+	2	560	c.433G>A	c.(433-435)Gtg>Atg	p.V145M		NM_002725.3|NM_201348.1	NP_002716.1|NP_958505.1	P51888	PRELP_HUMAN	proline/arginine-rich end leucine-rich repeat protein	145					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)	p.V145M(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			BRCA - Breast invasive adenocarcinoma(75;0.109)			AGACCAGAGGGTGCTGGAGAA	0.582																																					p.V145M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G433A	1						.						88.0	88.0	88.0					1																	203452745		2203	4300	6503	201719368	SO:0001583	missense	5549	exon2			BC032498	CCDS1438.1	1q32	2008-02-05	2005-07-24		ENSG00000188783	ENSG00000188783		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	9357	protein-coding gene	gene with protein product	"""prolargin proteoglycan"""	601914	"""proline arginine-rich end leucine-rich repeat protein"""				Standard	NM_002725		Approved	SLRR2A, prolargin	uc001gzt.3	P51888	OTTHUMG00000035911	ENST00000343110.2:c.433G>A	1.37:g.203452745G>A	ENSP00000343924:p.Val145Met	Somatic		Capture	Illumina HiSeq	Phase_I	201719368	NM_002725	Q6FG38	Missense_Mutation	SNP	ENST00000343110.2	37	CCDS1438.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.281772	0.59758	.	.	ENSG00000188783	ENST00000343110	T	0.58060	0.36	4.42	4.42	0.53409	.	0.000000	0.64402	D	0.000001	T	0.72045	0.3412	M	0.87900	2.915	0.42460	D	0.992784	D	0.63046	0.992	D	0.68353	0.957	T	0.76686	-0.2868	10	0.72032	D	0.01	-11.2757	9.4534	0.38741	0.0993:0.0:0.9007:0.0	.	145	P51888	PRELP_HUMAN	M	145	ENSP00000343924:V145M	ENSP00000343924:V145M	V	+	1	0	PRELP	201719368	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.280000	0.65603	2.025000	0.59659	0.462000	0.41574	GTG		0.582	PRELP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087474.1	NM_002725	
PLEKHA6	22874	broad.mit.edu	37	1	204198219	204198219	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:204198219C>T	ENST00000272203.3	-	19	2913	c.2597G>A	c.(2596-2598)cGc>cAc	p.R866H	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.R886H	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	866								p.R866H(1)		breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			ATGGATGCTGCGGTGGCGGCG	0.642																																					p.R866H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2597A	1						.						38.0	39.0	39.0					1																	204198219		2203	4300	6503	202464842	SO:0001583	missense	22874	exon19			AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"""Pleckstrin homology (PH) domain containing"""	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.2597G>A	1.37:g.204198219C>T	ENSP00000272203:p.Arg866His	Somatic		Capture	Illumina HiSeq	Phase_I	202464842	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.728117	0.89390	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.11495	2.77;3.23	5.59	5.59	0.84812	.	0.129644	0.49916	D	0.000138	T	0.33265	0.0857	M	0.68952	2.095	0.51767	D	0.999933	D	0.76494	0.999	D	0.74674	0.984	T	0.00670	-1.1617	10	0.46703	T	0.11	-23.2779	19.1923	0.93672	0.0:1.0:0.0:0.0	.	866	Q9Y2H5	PKHA6_HUMAN	H	866;886	ENSP00000272203:R866H;ENSP00000402046:R886H	ENSP00000272203:R866H	R	-	2	0	PLEKHA6	202464842	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.255000	0.58804	2.629000	0.89072	0.591000	0.81541	CGC		0.642	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935	
CNTN2	6900	broad.mit.edu	37	1	205033795	205033795	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:205033795G>A	ENST00000331830.4	+	12	1720	c.1436G>A	c.(1435-1437)aGc>aAc	p.S479N	AL583832.1_ENST00000515887.1_RNA	NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	479	Ig-like C2-type 5.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)	p.S479N(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			AGAAACATCAGCCGGTCAGAT	0.527																																					p.S479N	Melanoma(183;2548 2817 37099 41192)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1436A	1						.						151.0	129.0	136.0					1																	205033795		2203	4300	6503	203300418	SO:0001583	missense	6900	exon12			X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.1436G>A	1.37:g.205033795G>A	ENSP00000330633:p.Ser479Asn	Somatic		Capture	Illumina HiSeq	Phase_I	203300418	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	37	CCDS1449.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.638574	0.87760	.	.	ENSG00000184144	ENST00000331830	T	0.66815	-0.23	5.47	5.47	0.80525	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.193936	0.35870	N	0.002936	T	0.79094	0.4388	M	0.62016	1.91	0.50313	D	0.999861	D;D	0.76494	0.999;0.994	D;D	0.76575	0.988;0.971	T	0.79960	-0.1583	10	0.59425	D	0.04	.	14.5306	0.67923	0.0:0.1466:0.8534:0.0	.	479;370	Q02246;Q68DA2	CNTN2_HUMAN;.	N	479	ENSP00000330633:S479N	ENSP00000330633:S479N	S	+	2	0	CNTN2	203300418	1.000000	0.71417	0.972000	0.41901	0.978000	0.69477	5.141000	0.64814	2.577000	0.86979	0.561000	0.74099	AGC		0.527	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076	
PM20D1	148811	broad.mit.edu	37	1	205819094	205819094	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:205819094G>A	ENST00000367136.4	-	1	151	c.107C>T	c.(106-108)gCg>gTg	p.A36V	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	36					negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)	p.A36V(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			GATTCGCGACGCCCTTTGATG	0.597																																					p.A36V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C107T	1						.						89.0	90.0	90.0					1																	205819094		2203	4300	6503	204085717	SO:0001583	missense	148811	exon1				CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.107C>T	1.37:g.205819094G>A	ENSP00000356104:p.Ala36Val	Somatic		Capture	Illumina HiSeq	Phase_I	204085717	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476652	0.44044	.	.	ENSG00000162877	ENST00000367136	T	0.06933	3.24	5.17	0.875	0.19130	.	0.956528	0.08685	N	0.908907	T	0.04634	0.0126	L	0.36672	1.1	0.09310	N	1	P	0.39737	0.685	B	0.25405	0.06	T	0.39272	-0.9622	10	0.28530	T	0.3	.	2.778	0.05353	0.0889:0.2024:0.4105:0.2982	.	36	Q6GTS8	P20D1_HUMAN	V	36	ENSP00000356104:A36V	ENSP00000356104:A36V	A	-	2	0	PM20D1	204085717	0.000000	0.05858	0.001000	0.08648	0.390000	0.30446	0.158000	0.16422	-0.018000	0.14079	0.655000	0.94253	GCG		0.597	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
C1orf116	79098	broad.mit.edu	37	1	207196482	207196482	+	Silent	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:207196482T>G	ENST00000359470.5	-	4	876	c.627A>C	c.(625-627)ccA>ccC	p.P209P	C1orf116_ENST00000461135.2_5'UTR	NM_023938.5	NP_076427.2	Q9BW04	SARG_HUMAN	chromosome 1 open reading frame 116	209						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.P209P(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(4)|stomach(1)	29	Prostate(682;0.19)					TACACTGCTCTGGCTGGGTGT	0.662																																					p.P209P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A627C	1						.						101.0	111.0	107.0					1																	207196482		2203	4300	6503	205263105	SO:0001819	synonymous_variant	79098	exon4				CCDS1475.1, CCDS44306.1	1q32.1	2012-06-26			ENSG00000182795	ENSG00000182795			28667	protein-coding gene	gene with protein product	"""specifically androgen-regulated gene"""	611680				15525603, 9389513	Standard	NM_023938		Approved	SARG, FLJ36507, MGC2742, MGC4309	uc001hfd.2	Q9BW04	OTTHUMG00000036580	ENST00000359470.5:c.627A>C	1.37:g.207196482T>G		Somatic		Capture	Illumina HiSeq	Phase_I	205263105	NM_023938	C9JV41|Q658X3	Silent	SNP	ENST00000359470.5	37	CCDS1475.1																																																																																				0.662	C1orf116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088973.1	NM_024115	
CD55	1604	broad.mit.edu	37	1	207500131	207500131	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:207500131C>T	ENST00000367064.3	+	5	871	c.613C>T	c.(613-615)Ctt>Ttt	p.L205F	CD55_ENST00000367065.5_Missense_Mutation_p.L205F|CD55_ENST00000367063.2_Missense_Mutation_p.L205F|CD55_ENST00000391920.4_Missense_Mutation_p.L205F|CD55_ENST00000367062.4_Missense_Mutation_p.L205F|CD55_ENST00000314754.8_Missense_Mutation_p.L205F|CD55_ENST00000465534.1_3'UTR|CD55_ENST00000367067.4_3'UTR|CD55_ENST00000391921.4_Missense_Mutation_p.L141F	NM_000574.3	NP_000565.1	P08174	DAF_HUMAN	CD55 molecule, decay accelerating factor for complement (Cromer blood group)	205	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				CD4-positive, alpha-beta T cell cytokine production (GO:0035743)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|maternal process involved in parturition (GO:0060137)|negative regulation of complement activation (GO:0045916)|positive regulation of CD4-positive, alpha-beta T cell activation (GO:2000516)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of complement activation (GO:0030449)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|respiratory burst (GO:0045730)|response to peptide hormone (GO:0043434)|response to virus (GO:0009615)|spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	enzyme inhibitor activity (GO:0004857)|lipid binding (GO:0008289)|virus receptor activity (GO:0001618)	p.L205F(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16					Chloramphenicol(DB00446)	TAGTTTTTGTCTTATTTCAGG	0.398																																					p.L205F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C613T	1						.						216.0	210.0	212.0					1																	207500131		2203	4300	6503	205566754	SO:0001583	missense	1604	exon5			BC001288	CCDS31006.1, CCDS44307.1, CCDS73022.1	1q32	2014-09-17	2006-03-28	2006-02-23	ENSG00000196352	ENSG00000196352		"""CD molecules"", ""Blood group antigens"""	2665	protein-coding gene	gene with protein product		125240	"""decay accelerating factor for complement (CD55, Cromer blood group system)"""	DAF			Standard	XM_005273077		Approved	CR, TC, CROM	uc001hfr.4	P08174	OTTHUMG00000036255	ENST00000367064.3:c.613C>T	1.37:g.207500131C>T	ENSP00000356031:p.Leu205Phe	Somatic		Capture	Illumina HiSeq	Phase_I	205566754	NM_000574	B1AP14|D3DT83|D3DT84|E7ER69|P09679|P78361|Q14UF2|Q14UF3|Q14UF4|Q14UF5|Q14UF6	Missense_Mutation	SNP	ENST00000367064.3	37	CCDS31006.1	.	.	.	.	.	.	.	.	.	.	C	0.361	-0.939268	0.02322	.	.	ENSG00000196352	ENST00000367064;ENST00000367063;ENST00000391921;ENST00000536840;ENST00000314754;ENST00000367065;ENST00000391920;ENST00000367062	T;T;T;T;T;T;T	0.26660	1.72;1.72;1.72;1.72;1.72;1.72;1.72	4.97	-9.95	0.00446	Complement control module (2);Sushi/SCR/CCP (3);	5.000170	0.00166	N	0.000002	T	0.39253	0.1071	M	0.67625	2.065	0.21147	N	0.999779	D;D;B;D;P	0.76494	0.999;0.999;0.323;0.999;0.58	D;D;B;D;B	0.79784	0.993;0.993;0.062;0.993;0.156	T	0.64879	-0.6303	10	0.28530	T	0.3	.	2.7668	0.05322	0.1717:0.1427:0.3874:0.2982	.	141;205;205;205;205	B1AP15;Q14UF4;P08174-2;P08174;B1AP13	.;.;.;DAF_HUMAN;.	F	205;205;141;141;205;205;205;205	ENSP00000356031:L205F;ENSP00000356030:L205F;ENSP00000375788:L141F;ENSP00000316333:L205F;ENSP00000356032:L205F;ENSP00000375787:L205F;ENSP00000356029:L205F	ENSP00000316333:L205F	L	+	1	0	CD55	205566754	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.306000	0.00256	-6.252000	0.00005	-1.216000	0.01612	CTT		0.398	CD55-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088208.2	NM_000574	
MIR205HG	642587	broad.mit.edu	37	1	209605594	209605594	+	lincRNA	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:209605594A>G	ENST00000384891.1	+	0	220					NR_029622.1				MIR205 host gene (non-protein coding)																		GACAACCATGAGgcctcggca	0.582																																					p.E70G												.	.	0			c.A209G	1						.						56.0	48.0	51.0					1																	209605594		2203	4300	6503	207672217			642587	exon4					1q32.2	2014-02-12	2011-11-07		ENSG00000230937	ENSG00000230937		"""Long non-coding RNAs"""	43562	non-coding RNA	RNA, long non-coding	"""long intergenic non-protein coding RNA 510"""						Standard	NM_001104548		Approved	LINC00510	uc009xcn.3		OTTHUMG00000036267		1.37:g.209605594A>G		Somatic		Capture	Illumina HiSeq	Phase_I	207672217	NM_001104548		Missense_Mutation	SNP	ENST00000384891.1	37																																																																																					0.582	MIR205HG-202	KNOWN	basic	miRNA	lincRNA			
TRAF3IP3	80342	broad.mit.edu	37	1	209933457	209933457	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:209933457C>T	ENST00000367024.1	+	3	589	c.73C>T	c.(73-75)Cgc>Tgc	p.R25C	TRAF3IP3_ENST00000400959.3_Missense_Mutation_p.R25C|TRAF3IP3_ENST00000367026.3_Missense_Mutation_p.R25C|TRAF3IP3_ENST00000010338.4_Missense_Mutation_p.R25C|TRAF3IP3_ENST00000367025.3_Missense_Mutation_p.R25C			Q9Y228	T3JAM_HUMAN	TRAF3 interacting protein 3	25						integral component of membrane (GO:0016021)		p.R25C(1)		breast(2)|endometrium(1)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32				OV - Ovarian serous cystadenocarcinoma(81;0.045)		CAAGTGTGAGCGCAGGCAAGA	0.627																																					p.R25C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C73T	1						.						31.0	32.0	32.0					1																	209933457		2203	4300	6503	208000080	SO:0001583	missense	80342	exon3				CCDS1490.1, CCDS1490.2, CCDS73023.1	1q32.3-q41	2008-02-05			ENSG00000009790	ENSG00000009790			30766	protein-coding gene	gene with protein product	"""TRAF3 interacting Jun N terminal kinase (JNK) activating modulator"""	608255				14572659	Standard	XR_247044		Approved	T3JAM	uc001hho.3	Q9Y228	OTTHUMG00000036480	ENST00000367024.1:c.73C>T	1.37:g.209933457C>T	ENSP00000355991:p.Arg25Cys	Somatic		Capture	Illumina HiSeq	Phase_I	208000080	NM_025228	A1L464|A6NIU9|Q2YDB5|Q4VY06|Q7Z706	Missense_Mutation	SNP	ENST00000367024.1	37	CCDS1490.2	.	.	.	.	.	.	.	.	.	.	C	26.4	4.731257	0.89390	.	.	ENSG00000009790	ENST00000400959;ENST00000367025;ENST00000479796;ENST00000458110;ENST00000367026;ENST00000367024;ENST00000010338	T;T;T;T;T	0.70869	-0.52;0.44;-0.37;0.44;-0.37	5.66	5.66	0.87406	.	0.149239	0.38548	N	0.001642	D	0.82628	0.5078	M	0.67953	2.075	0.54753	D	0.999989	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.997;0.998;0.998;0.997	D	0.83973	0.0328	10	0.87932	D	0	-11.3909	15.2561	0.73585	0.0:1.0:0.0:0.0	.	25;25;25;25	Q9Y228;Q9Y228-2;Q9Y228-3;E2QRE5	T3JAM_HUMAN;.;.;.	C	25	ENSP00000383743:R25C;ENSP00000355992:R25C;ENSP00000355993:R25C;ENSP00000355991:R25C;ENSP00000010338:R25C	ENSP00000010338:R25C	R	+	1	0	TRAF3IP3	208000080	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.058000	0.30504	2.665000	0.90641	0.655000	0.94253	CGC		0.627	TRAF3IP3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088734.2		
DTL	51514	broad.mit.edu	37	1	212273745	212273745	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:212273745C>A	ENST00000366991.4	+	14	1727	c.1413C>A	c.(1411-1413)acC>acA	p.T471T	RN7SKP98_ENST00000517070.1_RNA|DTL_ENST00000542077.1_Silent_p.T429T|DTL_ENST00000475419.1_3'UTR	NM_016448.2	NP_057532.2	Q9NZJ0	DTL_HUMAN	denticleless E3 ubiquitin protein ligase homolog (Drosophila)	471					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|chromosome (GO:0005694)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.T471T(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(81;0.00796)|all cancers(67;0.0385)|Epithelial(68;0.102)		CTATTAAAACCTCTCCTGCCA	0.522																																					p.T471T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1413A	1						.						95.0	99.0	98.0					1																	212273745		2203	4300	6503	210340368	SO:0001819	synonymous_variant	51514	exon14			AF195765	CCDS1502.1, CCDS65778.1	1q32	2013-01-10	2012-02-23		ENSG00000143476	ENSG00000143476		"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"""	30288	protein-coding gene	gene with protein product	"""RA regulated nuclear matrix associated protein"", ""DDB1 and CUL4 associated factor 2"""	610617	"""denticleless homolog (Drosophila)"""			11278750	Standard	NM_001286229		Approved	RAMP, L2DTL, DCAF2	uc009xdc.3	Q9NZJ0	OTTHUMG00000037133	ENST00000366991.4:c.1413C>A	1.37:g.212273745C>A		Somatic		Capture	Illumina HiSeq	Phase_I	210340368	NM_016448	A8K8H8|D3DT98|Q5VT77|Q96SN0|Q9NW03|Q9NW34|Q9NWM5	Silent	SNP	ENST00000366991.4	37	CCDS1502.1																																																																																				0.522	DTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090182.1	NM_016448	
FAM71A	149647	broad.mit.edu	37	1	212799468	212799468	+	Missense_Mutation	SNP	G	G	A	rs535062338		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:212799468G>A	ENST00000294829.3	+	1	1680	c.1249G>A	c.(1249-1251)Gct>Act	p.A417T	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	417						nucleus (GO:0005634)		p.A417T(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		CCAGGCCAGCGCTGAAGGCTG	0.612													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19740	0.0		0.0	False		,,,				2504	0.0				p.A417T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1249A	1						.						52.0	59.0	57.0					1																	212799468		2203	4300	6503	210866091	SO:0001583	missense	149647	exon1				CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.1249G>A	1.37:g.212799468G>A	ENSP00000294829:p.Ala417Thr	Somatic		Capture	Illumina HiSeq	Phase_I	210866091	NM_153606	Q5VTZ1	Missense_Mutation	SNP	ENST00000294829.3	37	CCDS1507.1	.	.	.	.	.	.	.	.	.	.	G	7.485	0.649406	0.14516	.	.	ENSG00000162771	ENST00000294829;ENST00000545975	T	0.03801	3.8	4.06	-0.714	0.11219	.	.	.	.	.	T	0.02418	0.0074	N	0.20685	0.6	0.09310	N	1	B	0.25850	0.136	B	0.12156	0.007	T	0.47724	-0.9095	9	0.08179	T	0.78	0.0	5.5052	0.16850	0.3033:0.1466:0.5501:0.0	.	417	Q8IYT1	FA71A_HUMAN	T	417;192	ENSP00000294829:A417T	ENSP00000294829:A417T	A	+	1	0	FAM71A	210866091	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.530000	0.02221	0.079000	0.16929	0.655000	0.94253	GCT		0.612	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606	
CENPF	1063	broad.mit.edu	37	1	214794051	214794051	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:214794051G>A	ENST00000366955.3	+	6	795	c.627G>A	c.(625-627)cgG>cgA	p.R209R		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0	Interaction with SNAP25 and required for localization to the cytoplasm. {ECO:0000250}.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.R209R(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		ACATTGCCCGGCATCAGGCTT	0.433																																					p.R209R	Colon(80;575 1284 11000 14801 43496)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G627A	1						.						116.0	129.0	125.0					1																	214794051		2203	4300	6503	212860674	SO:0001819	synonymous_variant	1063	exon6			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.627G>A	1.37:g.214794051G>A		Somatic		Capture	Illumina HiSeq	Phase_I	212860674	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																				0.433	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
USH2A	7399	broad.mit.edu	37	1	215848822	215848822	+	Missense_Mutation	SNP	G	G	C	rs574981142		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:215848822G>C	ENST00000307340.3	-	63	12817	c.12431C>G	c.(12430-12432)gCg>gGg	p.A4144G	USH2A_ENST00000366943.2_Missense_Mutation_p.A4144G	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4144	Fibronectin type-III 26. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.A4144V(1)|p.A4144G(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AGGCTGAGGCGCCGAGTGTGC	0.572										HNSCC(13;0.011)																											p.A4144G												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C12431G	1						.						45.0	46.0	46.0					1																	215848822		2203	4300	6503	213915445	SO:0001583	missense	7399	exon63			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.12431C>G	1.37:g.215848822G>C	ENSP00000305941:p.Ala4144Gly	Somatic		Capture	Illumina HiSeq	Phase_I	213915445	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	1.350	-0.591684	0.03799	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.53640	0.61;0.61	5.25	-1.52	0.08637	Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.201570	0.06293	N	0.699559	T	0.28632	0.0709	N	0.25647	0.755	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.13124	-1.0521	10	0.23891	T	0.37	.	2.3063	0.04174	0.4514:0.1227:0.3003:0.1256	.	4144	O75445	USH2A_HUMAN	G	4144	ENSP00000305941:A4144G;ENSP00000355910:A4144G	ENSP00000305941:A4144G	A	-	2	0	USH2A	213915445	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-0.362000	0.07602	-0.641000	0.05487	-0.142000	0.14014	GCG		0.572	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
NBPF3	84224	broad.mit.edu	37	1	21809744	21809744	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:21809744G>A	ENST00000318249.5	+	15	2117	c.1767G>A	c.(1765-1767)caG>caA	p.Q589Q	NBPF3_ENST00000454000.2_Silent_p.Q519Q|NBPF3_ENST00000342104.5_Silent_p.Q577Q|NBPF3_ENST00000318220.6_Silent_p.Q533Q	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	589	NBPF 5. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.Q589Q(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CCTCATTCCAGCAGTATAGAA	0.448																																					p.Q589Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1767A	1						.						110.0	65.0	81.0					1																	21809744		2153	4199	6352	21682331	SO:0001819	synonymous_variant	84224	exon15			BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.1767G>A	1.37:g.21809744G>A		Somatic		Capture	Illumina HiSeq	Phase_I	21682331	NM_032264	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Silent	SNP	ENST00000318249.5	37	CCDS216.1																																																																																				0.448	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	
RRP15	51018	broad.mit.edu	37	1	218504325	218504325	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:218504325G>A	ENST00000366932.3	+	5	771	c.741G>A	c.(739-741)acG>acA	p.T247T		NM_016052.3	NP_057136.2	Q9Y3B9	RRP15_HUMAN	ribosomal RNA processing 15 homolog (S. cerevisiae)	247						mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.T247T(1)	ACBD6/RRP15(2)	NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	14				all cancers(67;0.0315)|OV - Ovarian serous cystadenocarcinoma(81;0.0411)|GBM - Glioblastoma multiforme(131;0.06)|Epithelial(68;0.248)		CAGGTTGGACGATCCTACGTG	0.408																																					p.T247T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G741A	1						.						84.0	76.0	79.0					1																	218504325		2203	4300	6503	216570948	SO:0001819	synonymous_variant	51018	exon5				CCDS1520.2	1q41	2008-02-05			ENSG00000067533	ENSG00000067533			24255	protein-coding gene	gene with protein product		611193	"""KIAA0507"""	KIAA0507		15769876	Standard	NM_016052		Approved	CGI-115	uc001hlj.3	Q9Y3B9	OTTHUMG00000039494	ENST00000366932.3:c.741G>A	1.37:g.218504325G>A		Somatic		Capture	Illumina HiSeq	Phase_I	216570948	NM_016052		Silent	SNP	ENST00000366932.3	37	CCDS1520.2																																																																																				0.408	RRP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095284.1	NM_016052	
HLX	3142	broad.mit.edu	37	1	221053499	221053499	+	Silent	SNP	G	G	A	rs182881175	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:221053499G>A	ENST00000366903.6	+	1	1801	c.300G>A	c.(298-300)gcG>gcA	p.A100A	HLA-AS1_ENST00000552026.1_RNA|HLX_ENST00000549319.1_5'Flank	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	100	Pro-rich.				cell differentiation (GO:0030154)|embryonic digestive tract morphogenesis (GO:0048557)|enteric nervous system development (GO:0048484)|liver development (GO:0001889)|multicellular organismal development (GO:0007275)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.A100A(1)		breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		CAGTGGTGGCGCCCTCCGAAG	0.701													G|||	2	0.000399361	0.0	0.0029	5008	,	,		11532	0.0		0.0	False		,,,				2504	0.0				p.A100A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G300A	1						.	G		0,4196		0,0,2098	10.0	14.0	13.0		300	3.9	1.0	1		13	1,8309		0,1,4154	no	coding-synonymous	HLX	NM_021958.3		0,1,6252	AA,AG,GG		0.012,0.0,0.0080		100/489	221053499	1,12505	2098	4155	6253	219120122	SO:0001819	synonymous_variant	3142	exon1			BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630		"""Homeoboxes / ANTP class : NKL subclass"""	4978	protein-coding gene	gene with protein product		142995	"""H2.0 (Drosophila)-like homeo box 1"", ""H2.0-like homeobox 1 (Drosophila)"", ""H2.0-like homeobox 1"""	HLX1		1676597, 7806220	Standard	NM_021958		Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	ENST00000366903.6:c.300G>A	1.37:g.221053499G>A		Somatic		Capture	Illumina HiSeq	Phase_I	219120122	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Silent	SNP	ENST00000366903.6	37	CCDS1527.1																																																																																				0.701	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
TP53BP2	7159	broad.mit.edu	37	1	223984042	223984042	+	De_novo_Start_OutOfFrame	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:223984042G>A	ENST00000391879.2	-	0	426				TP53BP2_ENST00000343537.7_Silent_p.N733N|TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391878.2_Silent_p.N604N			Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2						cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)	p.N604N(1)		NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		GCCTTGGTGCGTTAGACAGTT	0.453																																					p.N733N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2199T	1						.						139.0	135.0	137.0					1																	223984042		2203	4300	6503	222050665			7159	exon13			U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	12000	protein-coding gene	gene with protein product		602143	"""tumor protein p53-binding protein, 2"""			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000391879.2:c.-103C>T	1.37:g.223984042G>A		Somatic		Capture	Illumina HiSeq	Phase_I	222050665	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Silent	SNP	ENST00000391879.2	37																																																																																					0.453	TP53BP2-201	KNOWN	basic	protein_coding	protein_coding		NM_001031685, NM_005426	
PARP1	142	broad.mit.edu	37	1	226576429	226576429	+	Silent	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:226576429T>G	ENST00000366794.5	-	5	788	c.645A>C	c.(643-645)ggA>ggC	p.G215G		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	215					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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 regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.G215G(1)		breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CTTCATCCACTCCATCCACCT	0.443								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.G215G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A645C	1						.						175.0	177.0	176.0					1																	226576429		2203	4300	6503	224643052	SO:0001819	synonymous_variant	142	exon5			BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.645A>C	1.37:g.226576429T>G		Somatic		Capture	Illumina HiSeq	Phase_I	224643052	NM_001618	B1ANJ4|Q8IUZ9	Silent	SNP	ENST00000366794.5	37	CCDS1554.1																																																																																				0.443	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
C1orf95	375057	broad.mit.edu	37	1	226784583	226784583	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:226784583C>T	ENST00000366788.3	+	2	388	c.283C>T	c.(283-285)Ctg>Ttg	p.L95L	C1orf95_ENST00000366789.4_Silent_p.L95L	NM_001003665.3	NP_001003665.1	Q69YW2	STUM_HUMAN	chromosome 1 open reading frame 95	95						integral component of membrane (GO:0016021)		p.L95L(1)		large_intestine(1)|lung(4)|ovary(3)	8	Breast(184;0.133)	Prostate(94;0.0885)		GBM - Glioblastoma multiforme(131;0.113)		CGTCTTCTGGCTGAACATTGC	0.602																																					p.L95L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C283T	1						.						166.0	145.0	152.0					1																	226784583		2203	4300	6503	224851206	SO:0001819	synonymous_variant	375057	exon2			AF035308	CCDS31044.1	1q42.12	2012-06-26			ENSG00000203685	ENSG00000203685			30491	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001003665		Approved	DKFZp761P211	uc021pjw.1	Q69YW2	OTTHUMG00000037583	ENST00000366788.3:c.283C>T	1.37:g.226784583C>T		Somatic		Capture	Illumina HiSeq	Phase_I	224851206	NM_001003665	A6NGL2	Silent	SNP	ENST00000366788.3	37	CCDS31044.1																																																																																				0.602	C1orf95-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091634.1	NM_001003665	
ITPKB	3707	broad.mit.edu	37	1	226924779	226924779	+	Silent	SNP	G	G	A	rs140396711		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:226924779G>A	ENST00000272117.3	-	1	380	c.381C>T	c.(379-381)gcC>gcT	p.A127A	ITPKB_ENST00000366784.1_Silent_p.A127A|ITPKB_ENST00000429204.1_Silent_p.A127A			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	127					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)	p.A127A(1)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				GCTTCCTCTTGGCCTCCTCCG	0.657																																					p.A127A	Colon(84;110 1851 5306 33547)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C381T	1						.	G		2,4358		0,2,2178	51.0	53.0	53.0		381	3.0	1.0	1	dbSNP_134	53	0,8542		0,0,4271	no	coding-synonymous	ITPKB	NM_002221.3		0,2,6449	AA,AG,GG		0.0,0.0459,0.0155		127/947	226924779	2,12900	2180	4271	6451	224991402	SO:0001819	synonymous_variant	3707	exon2			AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.381C>T	1.37:g.226924779G>A		Somatic		Capture	Illumina HiSeq	Phase_I	224991402	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	37	CCDS1555.1																																																																																				0.657	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
EPHA8	2046	broad.mit.edu	37	1	22895825	22895825	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:22895825G>A	ENST00000166244.3	+	2	210	c.138G>A	c.(136-138)tgG>tgA	p.W46*	EPHA8_ENST00000538803.1_Nonsense_Mutation_p.W46*|EPHA8_ENST00000374644.4_Nonsense_Mutation_p.W46*	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	46	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.W46*(2)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		ACTGGGGCTGGCTCACGTATC	0.577																																					p.W46X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.G138A	1						.						133.0	130.0	131.0					1																	22895825		2203	4300	6503	22768412	SO:0001587	stop_gained	2046	exon2			BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.138G>A	1.37:g.22895825G>A	ENSP00000166244:p.Trp46*	Somatic		Capture	Illumina HiSeq	Phase_I	22768412	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Nonsense_Mutation	SNP	ENST00000166244.3	37	CCDS225.1	.	.	.	.	.	.	.	.	.	.	G	34	5.350597	0.95830	.	.	ENSG00000070886	ENST00000166244;ENST00000374644;ENST00000538803	.	.	.	3.58	3.58	0.41010	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.043	0.58910	0.0:0.0:1.0:0.0	.	.	.	.	X	46	.	ENSP00000166244:W46X	W	+	3	0	EPHA8	22768412	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	8.849000	0.92178	1.999000	0.58509	0.297000	0.19635	TGG		0.577	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
OBSCN	84033	broad.mit.edu	37	1	228467935	228467935	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:228467935C>T	ENST00000422127.1	+	29	7763	c.7719C>T	c.(7717-7719)ggC>ggT	p.G2573G	OBSCN_ENST00000359599.6_Silent_p.G1420G|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.G2573G|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Silent_p.G3002G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2573	Ig-like 25.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.G2627G(1)|p.G2856G(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CGGAGGAGGGCTGGGCCAGCT	0.622																																					p.G2573G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C7719T	1						.						44.0	52.0	49.0					1																	228467935		2146	4250	6396	226534558	SO:0001819	synonymous_variant	84033	exon29			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.7719C>T	1.37:g.228467935C>T		Somatic		Capture	Illumina HiSeq	Phase_I	226534558	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																				0.622	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
AGT	183	broad.mit.edu	37	1	230846504	230846504	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:230846504A>G	ENST00000366667.4	-	2	307	c.93T>C	c.(91-93)gcT>gcC	p.A31A	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	31					activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)	p.A31A(1)		endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GGTCACCTGCAGCCAGGCCAG	0.622																																					p.A31A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T93C	1						.						54.0	52.0	53.0					1																	230846504		2203	4300	6503	228913127	SO:0001819	synonymous_variant	183	exon2			K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"""Serine (or cysteine) peptidase inhibitors"", ""Endogenous ligands"""	333	protein-coding gene	gene with protein product	"""alpha-1 antiproteinase, antitrypsin"""	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.93T>C	1.37:g.230846504A>G		Somatic		Capture	Illumina HiSeq	Phase_I	228913127	NM_000029	Q16358|Q16359|Q96F91	Silent	SNP	ENST00000366667.4	37	CCDS1585.1																																																																																				0.622	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029	
DISC1	27185	broad.mit.edu	37	1	232162278	232162278	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:232162278G>T	ENST00000439617.2	+	12	2458	c.2405G>T	c.(2404-2406)aGt>aTt	p.S802I	DISC1_ENST00000366637.3_Missense_Mutation_p.S112I	NM_001164537.1|NM_001164540.1|NM_018662.2	NP_001158009.1|NP_001158012.1|NP_061132.2	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	802	Interaction with ATF4 and ATF5.|Interaction with NDEL1.|Interaction with PAFAH1B1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)		p.S834I(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				GCAATCCACAGTCATGATGAA	0.373																																					p.S680I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2039T	1						.						57.0	55.0	56.0					1																	232162278		1915	4135	6050	230228901	SO:0001583	missense	27185	exon10			AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000439617.2:c.2405G>T	1.37:g.232162278G>T	ENSP00000403888:p.Ser802Ile	Somatic		Capture	Illumina HiSeq	Phase_I	230228901	NM_001164540	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000439617.2	37		.	.	.	.	.	.	.	.	.	.	G	12.69	2.013325	0.35511	.	.	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366638;ENST00000532576	T	0.10288	2.89	5.31	2.29	0.28610	.	0.293099	0.35677	N	0.003053	T	0.12220	0.0297	N	0.19112	0.55	0.09310	N	1	D;D;D;D;D	0.59767	0.96;0.986;0.96;0.986;0.986	P;P;P;P;P	0.58454	0.684;0.839;0.684;0.839;0.839	T	0.07712	-1.0758	10	0.54805	T	0.06	-1.6923	6.4401	0.21845	0.1678:0.1469:0.6853:0.0	.	834;680;834;780;802	C4P096;C4P094;E2QRA4;Q9NRI5-2;Q9NRI5	.;.;.;.;DISC1_HUMAN	I	802;780;834;680	ENSP00000403888:S802I	ENSP00000355597:S780I	S	+	2	0	DISC1	230228901	0.021000	0.18746	0.000000	0.03702	0.471000	0.32888	1.642000	0.37207	0.325000	0.23359	-0.251000	0.11542	AGT		0.373	DISC1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000092351.2	NM_018662	
MAP10	54627	broad.mit.edu	37	1	232941228	232941228	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:232941228G>A	ENST00000418460.1	+	1	586	c.459G>A	c.(457-459)tcG>tcA	p.S153S		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	11					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)	p.S153S(2)									GGCTCTTCTCGCTGGAGCTGC	0.677																																					p.S153S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G459A	1						.						8.0	10.0	9.0					1																	232941228		1972	4142	6114	231007851	SO:0001819	synonymous_variant	54627	exon1			AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.459G>A	1.37:g.232941228G>A		Somatic		Capture	Illumina HiSeq	Phase_I	231007851	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Silent	SNP	ENST00000418460.1	37	CCDS44334.1																																																																																				0.677	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
KIAA1804	84451	broad.mit.edu	37	1	233497879	233497879	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:233497879G>T	ENST00000366624.3	+	5	1653	c.1392G>T	c.(1390-1392)gaG>gaT	p.E464D	MLK4_ENST00000366623.3_Missense_Mutation_p.E464D	NM_032435.2	NP_115811.2												p.E464D(1)									AGCGGCGTGAGCAGCAGCTGG	0.577																																					p.E464D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1392T	1						.						39.0	41.0	41.0					1																	233497879		2203	4300	6503	231564502	SO:0001583	missense	84451	exon5																														ENST00000366624.3:c.1392G>T	1.37:g.233497879G>T	ENSP00000355583:p.Glu464Asp	Somatic		Capture	Illumina HiSeq	Phase_I	231564502	NM_032435		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055582	0.75960	.	.	ENSG00000143674	ENST00000366623;ENST00000366624	T;T	0.79352	-1.02;-1.26	4.77	1.19	0.21007	.	0.000000	0.85682	D	0.000000	D	0.84593	0.5506	M	0.79614	2.46	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.991	T	0.80953	-0.1152	10	0.44086	T	0.13	.	8.3234	0.32142	0.3167:0.0:0.6833:0.0	.	464;464	Q5TCX8;Q5TCX8-2	M3KL4_HUMAN;.	D	464	ENSP00000355582:E464D;ENSP00000355583:E464D	ENSP00000355582:E464D	E	+	3	2	RP5-862P8.2	231564502	1.000000	0.71417	0.990000	0.47175	0.898000	0.52572	3.007000	0.49536	0.035000	0.15519	-0.150000	0.13652	GAG		0.577	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
HNRNPR	10236	broad.mit.edu	37	1	23637493	23637493	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:23637493A>G	ENST00000374612.1	-	11	1479	c.1356T>C	c.(1354-1356)ggT>ggC	p.G452G	HNRNPR_ENST00000476660.1_5'UTR|HNRNPR_ENST00000374616.3_Silent_p.G455G|HNRNPR_ENST00000427764.2_Silent_p.G414G|HNRNPR_ENST00000302271.6_Silent_p.G452G|HNRNPR_ENST00000426846.2_Silent_p.G292G|HNRNPR_ENST00000478691.1_Silent_p.G354G|HNRNPR_ENST00000606561.1_Silent_p.G313G	NM_001102398.1|NM_005826.3	NP_001095868.1|NP_005817.1	O43390	HNRPR_HUMAN	heterogeneous nuclear ribonucleoprotein R	452	RNA-binding RGG-box.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.G452G(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00394)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;6.83e-27)|Colorectal(126;6.01e-08)|COAD - Colon adenocarcinoma(152;3.32e-06)|GBM - Glioblastoma multiforme(114;6.69e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00357)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0875)|LUSC - Lung squamous cell carcinoma(448;0.19)		CTCTCCCCCCACCACGACCCC	0.458																																					p.G354G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1062C	1						.						95.0	102.0	100.0					1																	23637493		2203	4300	6503	23510080	SO:0001819	synonymous_variant	10236	exon10			AF000364	CCDS232.1, CCDS44085.1, CCDS60020.1, CCDS72726.1, CCDS72727.1	1p36.12	2013-02-12		2007-08-16	ENSG00000125944	ENSG00000125944		"""RNA binding motif (RRM) containing"""	5047	protein-coding gene	gene with protein product		607201		HNRPR		9421497	Standard	XM_005245711		Approved	hnRNP-R	uc001bgp.4	O43390	OTTHUMG00000003224	ENST00000374612.1:c.1356T>C	1.37:g.23637493A>G		Somatic		Capture	Illumina HiSeq	Phase_I	23510080	NM_001102399	Q2L7G6|Q5TEH1|Q9BV64|S4R3J4	Silent	SNP	ENST00000374612.1	37	CCDS232.1																																																																																				0.458	HNRNPR-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008889.1	NM_005826	
LGALS8	3964	broad.mit.edu	37	1	236706917	236706917	+	Missense_Mutation	SNP	G	G	A	rs555456164		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:236706917G>A	ENST00000366584.4	+	8	1173	c.607G>A	c.(607-609)Gtt>Att	p.V203I	LGALS8_ENST00000527974.1_Missense_Mutation_p.V245I|RP11-385F5.4_ENST00000433131.1_RNA|LGALS8_ENST00000352231.2_Missense_Mutation_p.V245I|LGALS8_ENST00000323938.6_Missense_Mutation_p.V176I|LGALS8_ENST00000526634.1_Missense_Mutation_p.V203I|LGALS8_ENST00000341872.6_Missense_Mutation_p.V203I|LGALS8_ENST00000526589.1_Missense_Mutation_p.V245I|LGALS8_ENST00000525042.1_Missense_Mutation_p.V186I|LGALS8_ENST00000450372.2_Missense_Mutation_p.V245I|LGALS8_ENST00000416919.2_Missense_Mutation_p.V186I	NM_201544.2	NP_963838.1	O00214	LEG8_HUMAN	lectin, galactoside-binding, soluble, 8	203	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.				plasma cell differentiation (GO:0002317)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)	p.V245I(1)		kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(5)	20	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			AACTGTCGTCGTTAAAGGAGA	0.537													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20764	0.0		0.0	False		,,,				2504	0.0				p.V203I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G607A	1						.						114.0	98.0	103.0					1																	236706917		2203	4300	6503	234773540	SO:0001583	missense	3964	exon8			X91790	CCDS1611.1, CCDS1612.1	1q43	2011-08-04	2008-07-25		ENSG00000116977	ENSG00000116977		"""Lectins, galactoside-binding"""	6569	protein-coding gene	gene with protein product	"""galectin 8"""	606099				7852431, 8692978	Standard	NM_201545		Approved	PCTA-1	uc001hxy.2	O00214	OTTHUMG00000039953	ENST00000366584.4:c.607G>A	1.37:g.236706917G>A	ENSP00000355543:p.Val203Ile	Somatic		Capture	Illumina HiSeq	Phase_I	234773540	NM_201544	O15215|Q5T3P5|Q5T3Q4|Q8TEV1|Q96B92|Q9BXC8|Q9H584|Q9H585|Q9UEZ6|Q9UP32|Q9UP33|Q9UP34	Missense_Mutation	SNP	ENST00000366584.4	37	CCDS1612.1	.	.	.	.	.	.	.	.	.	.	G	0.328	-0.957705	0.02267	.	.	ENSG00000116977	ENST00000527974;ENST00000352231;ENST00000526589;ENST00000341872;ENST00000450372;ENST00000366584;ENST00000238181;ENST00000356238;ENST00000416919;ENST00000323938;ENST00000526634;ENST00000525042	T;T;T;T;T;T;T;T;T;T;T	0.10005	2.92;2.92;2.92;2.92;2.92;2.92;2.92;2.92;2.92;2.92;2.92	5.31	-9.27	0.00659	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.685502	0.15242	N	0.272843	T	0.02571	0.0078	N	0.01284	-0.91	0.09310	N	1	B;B;B	0.10296	0.0;0.002;0.003	B;B;B	0.12837	0.001;0.008;0.003	T	0.28964	-1.0027	10	0.02654	T	1	-1.5539	17.8148	0.88628	0.5306:0.0:0.4694:0.0	.	186;203;245	F6V2D4;O00214;O00214-2	.;LEG8_HUMAN;.	I	245;245;245;203;245;203;144;244;186;176;203;186	ENSP00000431398:V245I;ENSP00000309576:V245I;ENSP00000435460:V245I;ENSP00000342139:V203I;ENSP00000408657:V245I;ENSP00000355543:V203I;ENSP00000238181:V144I;ENSP00000410843:V186I;ENSP00000434860:V176I;ENSP00000437040:V203I;ENSP00000431884:V186I	ENSP00000238181:V144I	V	+	1	0	LGALS8	234773540	0.017000	0.18338	0.008000	0.14137	0.607000	0.37147	-0.192000	0.09587	-1.936000	0.01048	-2.097000	0.00363	GTT		0.537	LGALS8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000096365.2	NM_006499	
RYR2	6262	broad.mit.edu	37	1	237711781	237711781	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:237711781T>A	ENST00000366574.2	+	26	3274	c.2957T>A	c.(2956-2958)aTc>aAc	p.I986N	RYR2_ENST00000542537.1_Missense_Mutation_p.I970N|RYR2_ENST00000360064.6_Missense_Mutation_p.I984N	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	986	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.I984N(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CTGAGCTTTATCAAACTCACC	0.458																																					p.I986N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2957A	1						.						57.0	54.0	55.0					1																	237711781		1906	4118	6024	235778404	SO:0001583	missense	6262	exon26			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.2957T>A	1.37:g.237711781T>A	ENSP00000355533:p.Ile986Asn	Somatic		Capture	Illumina HiSeq	Phase_I	235778404	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.247818	0.80024	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.92965	-3.14;-3.14;-3.14	5.81	5.81	0.92471	Ryanodine receptor Ryr (1);	0.078757	0.47093	D	0.000251	D	0.92267	0.7547	M	0.78344	2.41	0.80722	D	1	B	0.16802	0.019	B	0.20955	0.032	D	0.89817	0.3986	10	0.87932	D	0	.	16.167	0.81768	0.0:0.0:0.0:1.0	.	986	Q92736	RYR2_HUMAN	N	986;984;970	ENSP00000355533:I986N;ENSP00000353174:I984N;ENSP00000443798:I970N	ENSP00000353174:I984N	I	+	2	0	RYR2	235778404	1.000000	0.71417	0.990000	0.47175	0.969000	0.65631	6.121000	0.71602	2.210000	0.71456	0.533000	0.62120	ATC		0.458	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
FMN2	56776	broad.mit.edu	37	1	240371067	240371067	+	Silent	SNP	C	C	T	rs373490785		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:240371067C>T	ENST00000319653.9	+	5	3185	c.2955C>T	c.(2953-2955)ggC>ggT	p.G985G		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	985	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G1128G(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCGGAGCGGGCATACCCCCTC	0.711																																					p.G985G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2955T	1						.						15.0	17.0	17.0					1																	240371067		2194	4273	6467	238437690	SO:0001819	synonymous_variant	56776	exon5			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2955C>T	1.37:g.240371067C>T		Somatic		Capture	Illumina HiSeq	Phase_I	238437690	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																				0.711	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
EXO1	9156	broad.mit.edu	37	1	242052807	242052807	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:242052807C>A	ENST00000366548.3	+	16	3039	c.2446C>A	c.(2446-2448)Cca>Aca	p.P816T	EXO1_ENST00000348581.5_Missense_Mutation_p.P816T|EXO1_ENST00000518483.1_3'UTR	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	816	Interaction with MLH1.|Interaction with MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)	p.P816T(1)		NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			ACCCCTGTCCCCAGTCAGAGA	0.363								Editing and processing nucleases																													p.P816T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2446A	1						.						87.0	89.0	88.0					1																	242052807		2203	4300	6503	240119430	SO:0001583	missense	9156	exon16			AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"""rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"""	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.2446C>A	1.37:g.242052807C>A	ENSP00000355506:p.Pro816Thr	Somatic		Capture	Illumina HiSeq	Phase_I	240119430	NM_130398	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	37	CCDS1620.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.88|19.88	3.909106|3.909106	0.72868|0.72868	.|.	.|.	ENSG00000174371|ENSG00000174371	ENST00000521202|ENST00000366548;ENST00000348581	.|T;T	.|0.58210	.|0.35;0.35	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.72366|0.72366	0.3451|0.3451	M|M	0.69823|0.69823	2.125|2.125	0.45108|0.45108	D|D	0.998128|0.998128	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.997;0.999	T|T	0.74680|0.74680	-0.3584|-0.3584	6|10	.|0.87932	.|D	.|0	-26.1007|-26.1007	16.7056|16.7056	0.85371|0.85371	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|815;816	.|A8K5H6;Q9UQ84	.|.;EXO1_HUMAN	H|T	180|816	.|ENSP00000355506:P816T;ENSP00000311873:P816T	.|ENSP00000311873:P816T	P|P	+|+	2|1	0|0	EXO1|EXO1	240119430|240119430	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.761000|0.761000	0.43186|0.43186	4.434000|4.434000	0.59935|0.59935	2.662000|2.662000	0.90505|0.90505	0.655000|0.655000	0.94253|0.94253	CCC|CCA		0.363	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027	
OR1C1	26188	broad.mit.edu	37	1	247921328	247921328	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:247921328G>A	ENST00000408896.2	-	1	654	c.381C>T	c.(379-381)tgC>tgT	p.C127C		NM_012353.2	NP_036485.2	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C, member 1	127					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C127C(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(32)|skin(2)|upper_aerodigestive_tract(1)	46	all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)	all_cancers(173;0.0247)	OV - Ovarian serous cystadenocarcinoma(106;0.0168)			GTAAGGGGTGGCAAATCGCCA	0.507																																					p.C127C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C381T	1						.						73.0	69.0	70.0					1																	247921328		2018	4180	6198	245987951	SO:0001819	synonymous_variant	26188	exon1			X89674	CCDS41481.1	1q44	2012-08-09			ENSG00000221888	ENSG00000221888		"""GPCR / Class A : Olfactory receptors"""	8182	protein-coding gene	gene with protein product						9119360	Standard	NM_012353		Approved	TPCR27, HSTPCR27	uc010pza.2	Q15619	OTTHUMG00000040198	ENST00000408896.2:c.381C>T	1.37:g.247921328G>A		Somatic		Capture	Illumina HiSeq	Phase_I	245987951	NM_012353	B9EIR9|Q5VVD2|Q6IF97|Q8NGZ1|Q96R83	Silent	SNP	ENST00000408896.2	37	CCDS41481.1																																																																																				0.507	OR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096855.1		
OR2L13	284521	broad.mit.edu	37	1	248262694	248262694	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:248262694A>G	ENST00000358120.2	+	2	162	c.17A>G	c.(16-18)cAc>cGc	p.H6R	OR2L13_ENST00000366478.2_Missense_Mutation_p.H6R			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H6R(2)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			AAATGGAATCACACTTCAAAT	0.353																																					p.H6R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A17G	1						.						134.0	129.0	131.0					1																	248262694		2203	4300	6503	246329317	SO:0001583	missense	284521	exon3			BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"""GPCR / Class A : Olfactory receptors"""	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.17A>G	1.37:g.248262694A>G	ENSP00000350836:p.His6Arg	Somatic		Capture	Illumina HiSeq	Phase_I	246329317	NM_175911	Q5VUR5	Missense_Mutation	SNP	ENST00000358120.2	37	CCDS1637.1	.	.	.	.	.	.	.	.	.	.	A	6.880	0.531723	0.13127	.	.	ENSG00000196071	ENST00000366478;ENST00000358120	T;T	0.03580	3.88;3.88	4.07	1.7	0.24286	.	0.719520	0.11972	N	0.511717	T	0.03178	0.0093	L	0.28776	0.89	0.09310	N	1	B	0.20887	0.049	B	0.19148	0.024	T	0.43228	-0.9404	10	0.52906	T	0.07	.	5.1843	0.15176	0.7181:0.1818:0.1001:0.0	.	6	Q8N349	OR2LD_HUMAN	R	6	ENSP00000355434:H6R;ENSP00000350836:H6R	ENSP00000350836:H6R	H	+	2	0	OR2L13	246329317	0.000000	0.05858	0.132000	0.22025	0.769000	0.43574	-0.273000	0.08548	0.145000	0.18977	-0.256000	0.11100	CAC		0.353	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911	
OR2M5	127059	broad.mit.edu	37	1	248308963	248308963	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:248308963C>T	ENST00000366476.1	+	1	514	c.514C>T	c.(514-516)Cgg>Tgg	p.R172W		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	172						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R172W(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			CTGTGGGTCTCGGGAAATAGC	0.433																																					p.R172W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C514T	1						.						279.0	264.0	269.0					1																	248308963		2203	4298	6501	246375586	SO:0001583	missense	127059	exon1				CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"""GPCR / Class A : Olfactory receptors"""	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.514C>T	1.37:g.248308963C>T	ENSP00000355432:p.Arg172Trp	Somatic		Capture	Illumina HiSeq	Phase_I	246375586	NM_001004690		Missense_Mutation	SNP	ENST00000366476.1	37	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	c	15.25	2.776674	0.49786	.	.	ENSG00000162727	ENST00000366476	T	0.00137	8.68	3.28	-5.55	0.02536	GPCR, rhodopsin-like superfamily (1);	0.298455	0.18176	N	0.149296	T	0.00144	0.0004	M	0.70595	2.14	0.09310	N	1	B	0.24368	0.102	B	0.24269	0.052	T	0.48151	-0.9060	10	0.62326	D	0.03	.	3.7218	0.08459	0.3336:0.2069:0.0:0.4595	.	172	A3KFT3	OR2M5_HUMAN	W	172	ENSP00000355432:R172W	ENSP00000355432:R172W	R	+	1	2	OR2M5	246375586	0.000000	0.05858	0.000000	0.03702	0.877000	0.50540	0.127000	0.15790	-0.689000	0.05149	-0.326000	0.08463	CGG		0.433	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690	
OR2M4	26245	broad.mit.edu	37	1	248402598	248402598	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:248402598A>G	ENST00000306687.1	+	1	368	c.368A>G	c.(367-369)tAt>tGt	p.Y123C		NM_017504.1	NP_059974.1	Q96R27	OR2M4_HUMAN	olfactory receptor, family 2, subfamily M, member 4	123					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y123C(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(27)|skin(3)|upper_aerodigestive_tract(2)	50	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TATGACCGCTATGTGGCTATA	0.468																																					p.Y123C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A368G	1						.						167.0	133.0	144.0					1																	248402598		2203	4300	6503	246469221	SO:0001583	missense	26245	exon1			X64992	CCDS31108.1	1q44	2012-08-09			ENSG00000171180	ENSG00000171180		"""GPCR / Class A : Olfactory receptors"""	8270	protein-coding gene	gene with protein product						1370859, 9119360	Standard	NM_017504		Approved	HTPCRX18, TPCR100, HSHTPCRX18, OST710	uc010pzh.2	Q96R27	OTTHUMG00000040456	ENST00000306687.1:c.368A>G	1.37:g.248402598A>G	ENSP00000306688:p.Tyr123Cys	Somatic		Capture	Illumina HiSeq	Phase_I	246469221	NM_017504	Q15611|Q8NG82	Missense_Mutation	SNP	ENST00000306687.1	37	CCDS31108.1	.	.	.	.	.	.	.	.	.	.	a	16.34	3.096996	0.56075	.	.	ENSG00000171180	ENST00000306687	T	0.56444	0.46	3.49	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38272	N	0.001752	T	0.68192	0.2974	M	0.76170	2.325	0.35490	D	0.79892	D	0.76494	0.999	D	0.67231	0.95	T	0.78339	-0.2242	10	0.72032	D	0.01	.	11.3709	0.49699	1.0:0.0:0.0:0.0	.	123	Q96R27	OR2M4_HUMAN	C	123	ENSP00000306688:Y123C	ENSP00000306688:Y123C	Y	+	2	0	OR2M4	246469221	1.000000	0.71417	0.994000	0.49952	0.721000	0.41392	3.232000	0.51302	1.566000	0.49654	0.443000	0.29094	TAT		0.468	OR2M4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097352.1	NM_017504	
ACTRT2	140625	broad.mit.edu	37	1	2938479	2938479	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:2938479C>T	ENST00000378404.2	+	1	434	c.229C>T	c.(229-231)Cgt>Tgt	p.R77C		NM_080431.4	NP_536356.3	Q8TDY3	ACTT2_HUMAN	actin-related protein T2	77						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R77C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		CCCTTTCGAGCGTGGCCTGAT	0.602																																					p.R77C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C229T	1						.						76.0	76.0	76.0					1																	2938479		2203	4300	6503	2928339	SO:0001583	missense	140625	exon1			AF440740, AB057364	CCDS45.1	1p36.3	2008-02-05	2005-11-22		ENSG00000169717	ENSG00000169717			24026	protein-coding gene	gene with protein product		608535				11750065, 12243744	Standard	NM_080431		Approved	Arp-T2, ARPM2, FLJ25424	uc001ajz.3	Q8TDY3	OTTHUMG00000000562	ENST00000378404.2:c.229C>T	1.37:g.2938479C>T	ENSP00000367658:p.Arg77Cys	Somatic		Capture	Illumina HiSeq	Phase_I	2928339	NM_080431	B1AN52|Q8NHS6|Q8TDG1	Missense_Mutation	SNP	ENST00000378404.2	37	CCDS45.1	.	.	.	.	.	.	.	.	.	.	C	16.28	3.079424	0.55753	.	.	ENSG00000169717	ENST00000378404;ENST00000543312	D	0.97480	-4.4	5.03	5.03	0.67393	.	0.245701	0.28647	N	0.014617	D	0.98779	0.9589	M	0.92833	3.35	0.58432	D	0.999999	D	0.89917	1.0	D	0.77004	0.989	D	0.99830	1.1053	10	0.87932	D	0	.	16.9328	0.86195	0.0:1.0:0.0:0.0	.	77	Q8TDY3	ACTT2_HUMAN	C	77	ENSP00000367658:R77C	ENSP00000367658:R77C	R	+	1	0	ACTRT2	2928339	1.000000	0.71417	0.981000	0.43875	0.043000	0.13939	3.844000	0.55873	2.331000	0.79229	0.561000	0.74099	CGT		0.602	ACTRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001331.1	NM_080431	
PRDM16	63976	broad.mit.edu	37	1	3328480	3328480	+	Silent	SNP	G	G	T	rs374254884		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:3328480G>T	ENST00000270722.5	+	9	1768	c.1719G>T	c.(1717-1719)gcG>gcT	p.A573A	PRDM16_ENST00000511072.1_Silent_p.A574A|PRDM16_ENST00000378391.2_Silent_p.A573A|PRDM16_ENST00000442529.2_Silent_p.A573A|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000514189.1_Silent_p.A574A|PRDM16_ENST00000441472.2_Silent_p.A573A|PRDM16_ENST00000378398.3_Silent_p.A574A			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	573					brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)	p.A573A(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		CGGCAGCTGCGGGGCCCGAGG	0.667			T	EVI1	"""MDS, AML"""																																p.A573A			Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1719T	1						.						29.0	38.0	35.0					1																	3328480		2063	4197	6260	3318340	SO:0001819	synonymous_variant	63976	exon9			AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.1719G>T	1.37:g.3328480G>T		Somatic		Capture	Illumina HiSeq	Phase_I	3318340	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																				0.667	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
MEGF6	1953	broad.mit.edu	37	1	3511983	3511983	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:3511983C>G	ENST00000356575.4	-	3	521	c.295G>C	c.(295-297)Gtg>Ctg	p.V99L		NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	99	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.V99L(1)		cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GTGGTATACACCTGCCTGTAG	0.627																																					p.V99L	Ovarian(73;978 3658)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G295C	1						.						39.0	47.0	44.0					1																	3511983		2025	4179	6204	3501843	SO:0001583	missense	1953	exon3			AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"""EGF-like-domain, multiple 3"""	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.295G>C	1.37:g.3511983C>G	ENSP00000348982:p.Val99Leu	Somatic		Capture	Illumina HiSeq	Phase_I	3501843	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	c	14.78	2.637323	0.47049	.	.	ENSG00000162591	ENST00000356575	D	0.85955	-2.05	3.92	3.92	0.45320	EMI domain (1);	0.084758	0.46758	U	0.000280	D	0.83427	0.5252	M	0.75264	2.295	0.46113	D	0.998876	B	0.10296	0.003	B	0.09377	0.004	T	0.81602	-0.0858	10	0.44086	T	0.13	-15.075	12.1288	0.53932	0.0:1.0:0.0:0.0	.	99	O75095	MEGF6_HUMAN	L	99	ENSP00000348982:V99L	ENSP00000348982:V99L	V	-	1	0	MEGF6	3501843	1.000000	0.71417	0.998000	0.56505	0.417000	0.31264	3.841000	0.55850	2.126000	0.65437	0.486000	0.48141	GTG		0.627	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
WRAP73	49856	broad.mit.edu	37	1	3555382	3555382	+	Missense_Mutation	SNP	C	C	T	rs548238349		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:3555382C>T	ENST00000270708.7	-	4	417	c.344G>A	c.(343-345)cGg>cAg	p.R115Q	WRAP73_ENST00000378322.3_Missense_Mutation_p.R115Q	NM_017818.3	NP_060288.3	Q9P2S5	WRP73_HUMAN	WD repeat containing, antisense to TP73	115						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.R115Q(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)	12						GACGGTTATCCGCAGCTGTTG	0.522													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18632	0.0		0.0	False		,,,				2504	0.0				p.R115Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G344A	1						.						123.0	122.0	123.0					1																	3555382		2203	4299	6502	3545242	SO:0001583	missense	49856	exon4			AB034912, EF494669	CCDS48.1	1p36.3	2013-05-21	2011-04-13	2011-04-13	ENSG00000116213	ENSG00000116213		"""WD repeat domain containing"""	12759	protein-coding gene	gene with protein product		606040	"""WD repeat domain 8"""	WDR8			Standard	NM_017818		Approved		uc001ako.3	Q9P2S5	OTTHUMG00000000612	ENST00000270708.7:c.344G>A	1.37:g.3555382C>T	ENSP00000270708:p.Arg115Gln	Somatic		Capture	Illumina HiSeq	Phase_I	3545242	NM_017818	Q5T0D6|Q9BUH7|Q9NTK7|Q9NX56	Missense_Mutation	SNP	ENST00000270708.7	37	CCDS48.1	.	.	.	.	.	.	.	.	.	.	C	35	5.458202	0.96240	.	.	ENSG00000116213	ENST00000270708;ENST00000378322;ENST00000424367;ENST00000419924	T;T;T	0.47869	0.83;0.83;0.83	5.18	5.18	0.71444	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.68072	0.2961	M	0.70595	2.14	0.80722	D	1	D;D;D	0.89917	0.99;1.0;1.0	P;D;D	0.97110	0.787;0.999;1.0	T	0.66712	-0.5854	10	0.36615	T	0.2	-61.434	17.6919	0.88270	0.0:1.0:0.0:0.0	.	115;115;115	B4DYE9;Q9P2S5;Q5T0D5	.;WRP73_HUMAN;.	Q	115	ENSP00000270708:R115Q;ENSP00000367573:R115Q;ENSP00000416192:R115Q	ENSP00000270708:R115Q	R	-	2	0	WRAP73	3545242	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.710000	0.84655	2.411000	0.81874	0.650000	0.86243	CGG		0.522	WRAP73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001470.1		
CHD5	26038	broad.mit.edu	37	1	6202223	6202223	+	Missense_Mutation	SNP	C	C	T	rs567329094		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:6202223C>T	ENST00000262450.3	-	15	2500	c.2401G>A	c.(2401-2403)Gcc>Acc	p.A801T	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.A801T(2)		breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		CTCCGAATGGCGTTGTCCTCA	0.577													C|||	1	0.000199681	0.0	0.0	5008	,	,		18654	0.0		0.0	False		,,,				2504	0.001				p.A801T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2401A	1						.						169.0	158.0	162.0					1																	6202223		2203	4300	6503	6124810	SO:0001583	missense	26038	exon15			AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.2401G>A	1.37:g.6202223C>T	ENSP00000262450:p.Ala801Thr	Somatic		Capture	Illumina HiSeq	Phase_I	6124810	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	CCDS57.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.021467	0.93462	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000536802;ENST00000538279	D	0.91407	-2.84	4.07	4.07	0.47477	DEAD-like helicase (2);SNF2-related (1);	0.073472	0.53938	D	0.000051	D	0.91744	0.7389	L	0.28344	0.845	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.92805	0.6259	10	0.54805	T	0.06	-22.6321	16.6218	0.84932	0.0:1.0:0.0:0.0	.	801	Q8TDI0	CHD5_HUMAN	T	801;317;209;209	ENSP00000262450:A801T	ENSP00000262450:A801T	A	-	1	0	CHD5	6124810	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	7.693000	0.84214	1.977000	0.57605	0.561000	0.74099	GCC		0.577	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
DNAJC11	55735	broad.mit.edu	37	1	6704653	6704653	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:6704653G>A	ENST00000377577.5	-	10	1185	c.1062C>T	c.(1060-1062)agC>agT	p.S354S	DNAJC11_ENST00000465508.1_5'UTR|DNAJC11_ENST00000542246.1_Silent_p.S316S|DNAJC11_ENST00000349363.6_Intron|DNAJC11_ENST00000294401.7_Silent_p.S354S|DNAJC11_ENST00000377573.5_Silent_p.S264S	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	354						extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)		p.S354S(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1)	32	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		GAACTCCAACGCTGACAGCTG	0.542																																					p.S354S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1062T	1						.						91.0	84.0	87.0					1																	6704653		2203	4300	6503	6627240	SO:0001819	synonymous_variant	55735	exon10			AF306695	CCDS87.1	1p36.23	2011-09-02			ENSG00000007923	ENSG00000007923		"""Heat shock proteins / DNAJ (HSP40)"""	25570	protein-coding gene	gene with protein product		614827				12964007	Standard	NM_018198		Approved	FLJ10737	uc001aof.2	Q9NVH1	OTTHUMG00000001443	ENST00000377577.5:c.1062C>T	1.37:g.6704653G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6627240	NM_018198	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Silent	SNP	ENST00000377577.5	37	CCDS87.1																																																																																				0.542	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198	
SLC45A1	50651	broad.mit.edu	37	1	8403938	8403938	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:8403938T>C	ENST00000471889.1	+	9	2497	c.2112T>C	c.(2110-2112)agT>agC	p.S704S	SLC45A1_ENST00000289877.8_Silent_p.S704S|SLC45A1_ENST00000377479.2_Silent_p.S738S			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	704					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)	p.S704S(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(2)	33	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		CCGTGGGCAGTGCCAACGGGG	0.607																																					p.S704S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2112C	1						.						110.0	83.0	92.0					1																	8403938		2203	4300	6503	8326525	SO:0001819	synonymous_variant	50651	exon8			AF118274	CCDS30577.1	1p36.23	2014-01-28	2005-10-04	2005-10-04	ENSG00000162426	ENSG00000162426		"""Solute carriers"""	17939	protein-coding gene	gene with protein product	"""H+/sugar symporter"""	605763	"""deleted in neuroblastoma 5"""	DNB5		10729226	Standard	XM_005263467		Approved		uc001apb.3	Q9Y2W3	OTTHUMG00000000503	ENST00000471889.1:c.2112T>C	1.37:g.8403938T>C		Somatic		Capture	Illumina HiSeq	Phase_I	8326525	NM_001080397	Q5VY46|Q5VY49	Silent	SNP	ENST00000471889.1	37	CCDS30577.1																																																																																				0.607	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5		
CA6	765	broad.mit.edu	37	1	9009385	9009385	+	Missense_Mutation	SNP	C	C	T	rs377435950		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:9009385C>T	ENST00000377443.2	+	2	147	c.143C>T	c.(142-144)tCg>tTg	p.S48L	CA6_ENST00000377436.3_Missense_Mutation_p.S48L|CA6_ENST00000377442.2_Intron|CA6_ENST00000480186.3_Missense_Mutation_p.S48L|CA6_ENST00000476083.1_Intron	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	48					bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.S48L(2)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	CAGAGACAGTCGCCTATCAAC	0.597																																					p.S48L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C143T	1						.	C	LEU/SER	0,4406		0,0,2203	48.0	44.0	46.0		143	5.6	1.0	1		46	1,8599	1.2+/-3.3	0,1,4299	no	missense	CA6	NM_001215.2	145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	48/309	9009385	1,13005	2203	4300	6503	8931972	SO:0001583	missense	765	exon2			M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"""Carbonic anhydrases"""	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.143C>T	1.37:g.9009385C>T	ENSP00000366662:p.Ser48Leu	Somatic		Capture	Illumina HiSeq	Phase_I	8931972	NM_001215	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Missense_Mutation	SNP	ENST00000377443.2	37	CCDS30578.1	.	.	.	.	.	.	.	.	.	.	C	19.02	3.746400	0.69418	0.0	1.16E-4	ENSG00000131686	ENST00000319474;ENST00000549778;ENST00000377443;ENST00000377436	T;T;T;T	0.77877	-1.13;-0.99;-0.99;-0.99	5.55	5.55	0.83447	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	D	0.92753	0.7696	H	0.98446	4.235	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.94932	0.8083	10	0.87932	D	0	.	15.3572	0.74437	0.0:1.0:0.0:0.0	.	48	P23280	CAH6_HUMAN	L	48	ENSP00000325786:S48L;ENSP00000447108:S48L;ENSP00000366662:S48L;ENSP00000366654:S48L	ENSP00000325786:S48L	S	+	2	0	CA6	8931972	1.000000	0.71417	0.976000	0.42696	0.026000	0.11368	6.567000	0.73983	2.773000	0.95371	0.655000	0.94253	TCG		0.597	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1		
CLSTN1	22883	broad.mit.edu	37	1	9793559	9793559	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:9793559C>A	ENST00000377298.4	-	16	3119	c.2327G>T	c.(2326-2328)cGc>cTc	p.R776L	CLSTN1_ENST00000361311.4_Missense_Mutation_p.R766L|CLSTN1_ENST00000377288.3_Missense_Mutation_p.R757L|CLSTN1_ENST00000477264.1_5'Flank	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	776					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)	p.R776L(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		GTTCCGATAGCGCAGCAGGTG	0.572																																					p.R766L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2297T	1						.						92.0	77.0	82.0					1																	9793559		2203	4300	6503	9716146	SO:0001583	missense	22883	exon15			AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"""Cadherins / Cadherin-related"""	17447	protein-coding gene	gene with protein product	"""cadherin-related family member 12"""	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.2327G>T	1.37:g.9793559C>A	ENSP00000366513:p.Arg776Leu	Somatic		Capture	Illumina HiSeq	Phase_I	9716146	NM_014944	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Missense_Mutation	SNP	ENST00000377298.4	37	CCDS30580.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.398030	0.83120	.	.	ENSG00000171603	ENST00000377298;ENST00000361311;ENST00000435891;ENST00000377288;ENST00000539822	T;T;T;T	0.27402	1.67;1.67;1.67;1.67	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.57548	0.2061	M	0.76574	2.34	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.85130	0.994;0.997;0.994;0.997	T	0.57033	-0.7880	10	0.41790	T	0.15	-34.0028	18.7323	0.91739	0.0:1.0:0.0:0.0	.	757;766;776;131	B4E3Q1;O94985-2;O94985;B3KMD3	.;.;CSTN1_HUMAN;.	L	776;766;577;757;757	ENSP00000366513:R776L;ENSP00000354997:R766L;ENSP00000401934:R577L;ENSP00000366502:R757L	ENSP00000354997:R766L	R	-	2	0	CLSTN1	9716146	1.000000	0.71417	1.000000	0.80357	0.368000	0.29767	4.887000	0.63156	2.437000	0.82529	0.655000	0.94253	CGC		0.572	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1		
SPEN	23013	broad.mit.edu	37	1	16259480	16259480	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:16259480delC	ENST00000375759.3	+	11	6949	c.6745delC	c.(6745-6747)cccfs	p.P2250fs		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2250	Interaction with MSX2. {ECO:0000250}.|RID.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.A2251fs*102(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		AGATCTGCAACCCCCCGCAGG	0.557																																					p.P2249fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.6745delC	1						.						75.0	83.0	80.0					1																	16259480		2203	4300	6503	16132067	SO:0001589	frameshift_variant	23013	exon11				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.6745delC	1.37:g.16259480delC	ENSP00000364912:p.Pro2250fs	Somatic		Capture	Illumina HiSeq	Phase_I	16132067	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Frame_Shift_Del	DEL	ENST00000375759.3	37	CCDS164.1																																																																																				0.557	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
PQLC2	54896	broad.mit.edu	37	1	19652844	19652844	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:19652844delG	ENST00000375153.3	+	5	1128	c.488delG	c.(487-489)cggfs	p.R163fs	PQLC2_ENST00000400548.2_Frame_Shift_Del_p.R98fs|PQLC2_ENST00000375155.3_Frame_Shift_Del_p.R163fs	NM_001040125.1	NP_001035214.1	Q6ZP29	LAAT1_HUMAN	PQ loop repeat containing 2	163					amino acid homeostasis (GO:0080144)|arginine transport (GO:0015809)|lysine transport (GO:0015819)	integral component of organelle membrane (GO:0031301)|lysosomal membrane (GO:0005765)	arginine transmembrane transporter activity (GO:0015181)|basic amino acid transmembrane transporter activity (GO:0015174)|L-lysine transmembrane transporter activity (GO:0015189)	p.R165fs*59(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(1)	10		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;1.89e-05)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GAAGCCTTCCGGGGGCGGGCG	0.701																																					p.R163fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.488delG	1						.						24.0	24.0	24.0					1																	19652844		2203	4299	6502	19525431	SO:0001589	frameshift_variant	54896	exon6			BC015324	CCDS195.2, CCDS30618.1	1p36.13	2013-10-11			ENSG00000040487	ENSG00000040487			26001	protein-coding gene	gene with protein product		614760				23169667	Standard	XM_005245915		Approved	FLJ20320	uc001bby.3	Q6ZP29	OTTHUMG00000002521	ENST00000375153.3:c.488delG	1.37:g.19652844delG	ENSP00000364295:p.Arg163fs	Somatic		Capture	Illumina HiSeq	Phase_I	19525431	NM_017765	B3KWQ5|Q6ZMJ3|Q6ZP27|Q9NXC7	Frame_Shift_Del	DEL	ENST00000375153.3	37	CCDS195.2																																																																																				0.701	PQLC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007255.1	NM_017765	
HSPG2	3339	broad.mit.edu	37	1	22167772	22167772	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:22167772delG	ENST00000374695.3	-	71	9414	c.9335delC	c.(9334-9336)cctfs	p.P3112fs		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3112	Ig-like C2-type 16.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.P3112fs*13(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GGACACTGTAGGGGGCCCTGT	0.647																																					p.P3112fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.9335delC	1						.						41.0	44.0	43.0					1																	22167772		2203	4300	6503	22040359	SO:0001589	frameshift_variant	3339	exon71			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.9335delC	1.37:g.22167772delG	ENSP00000363827:p.Pro3112fs	Somatic		Capture	Illumina HiSeq	Phase_I	22040359	NM_005529	Q16287|Q5SZI3|Q9H3V5	Frame_Shift_Del	DEL	ENST00000374695.3	37	CCDS30625.1																																																																																				0.647	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
SRRM1	10250	broad.mit.edu	37	1	24995841	24995841	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:24995841T>C	ENST00000323848.9	+	14	2282	c.1967T>C	c.(1966-1968)tTa>tCa	p.L656S	SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000447431.2_Missense_Mutation_p.L668S|SRRM1_ENST00000374389.4_Missense_Mutation_p.L665S|snoU13_ENST00000459464.1_RNA	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	656	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.L656S(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		TCACCTTCATTATCATCCAAG	0.567																																					p.L656S	Ovarian(68;897 1494 3282 17478)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1967C	1						.						67.0	66.0	67.0					1																	24995841		2203	4300	6503	24868428	SO:0001583	missense	10250	exon14			AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"""Ser/Arg-related nuclear matrix protein"", ""plenty of prolines 101-like"""	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.1967T>C	1.37:g.24995841T>C	ENSP00000326261:p.Leu656Ser	Somatic		Capture	Illumina HiSeq	Phase_I	24868428	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	T	11.67	1.708691	0.30322	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.39592	1.07;1.07;1.07	5.85	5.85	0.93711	.	0.149877	0.26971	N	0.021566	T	0.47857	0.1468	N	0.14661	0.345	0.38106	D	0.937401	D;B	0.71674	0.998;0.007	D;B	0.78314	0.991;0.003	T	0.53049	-0.8493	10	0.33940	T	0.23	-1.7662	16.2271	0.82306	0.0:0.0:0.0:1.0	.	668;656	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	S	656;668;665	ENSP00000326261:L656S;ENSP00000391430:L668S;ENSP00000363510:L665S	ENSP00000326261:L656S	L	+	2	0	SRRM1	24868428	0.160000	0.22878	0.126000	0.21872	0.921000	0.55340	3.357000	0.52277	2.234000	0.73211	0.460000	0.39030	TTA		0.567	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	
RHCE	6006	broad.mit.edu	37	1	25712334	25712334	+	Splice_Site	SNP	A	A	C	rs79321360	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:25712334A>C	ENST00000294413.7	-	7	999	c.941T>G	c.(940-942)gTg>gGg	p.V314G	RHCE_ENST00000413854.1_Splice_Site_p.V314G|RHCE_ENST00000425135.1_Intron|RHCE_ENST00000455194.1_Splice_Site_p.V209G|RHCE_ENST00000374352.2_Splice_Site_p.V298G|RHCE_ENST00000340849.4_Splice_Site_p.V209G|RHCE_ENST00000349320.3_Splice_Site_p.V298G|RHCE_ENST00000346452.4_Splice_Site_p.V163G|RHCE_ENST00000349438.4_Intron|RHCE_ENST00000243186.6_Splice_Site_p.V314G	NM_020485.4	NP_065231	P18577	RHCE_HUMAN	Rh blood group, CcEe antigens	314						integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)	p.V314G(1)		endometrium(8)|large_intestine(6)|lung(3)	17		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0426)|OV - Ovarian serous cystadenocarcinoma(117;2.12e-27)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|STAD - Stomach adenocarcinoma(196;0.00035)|KIRC - Kidney renal clear cell carcinoma(1967;0.000769)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|GBM - Glioblastoma multiforme(114;0.00458)|READ - Rectum adenocarcinoma(331;0.0649)		GTTACAACACACCTGTGGACA	0.527																																					p.V209G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T626G	1						.						211.0	173.0	186.0					1																	25712334		2203	4300	6503	25584921	SO:0001630	splice_region_variant	6006	exon5			BC075081	CCDS30634.1, CCDS30635.1, CCDS30636.1, CCDS30637.1	1p36.11	2014-09-17	2006-02-23		ENSG00000188672	ENSG00000188672		"""CD molecules"", ""Blood group antigens"""	10008	protein-coding gene	gene with protein product		111700	"""Rhesus blood group, CcEe antigens"""	RH		8220426	Standard	NM_138618		Approved	CD240CE	uc001bkf.3	P18577	OTTHUMG00000007650	ENST00000294413.7:c.940-1T>G	1.37:g.25712334A>C		Somatic		Capture	Illumina HiSeq	Phase_I	25584921	NM_138617	A7DW68|B7UDF3|B7UDF4|B7UDF5|B7UDF6|B7UDF7|B7UDF8|B7UDF9|B7UDG0|B7UDG1|B7UDG2|B7UDG3|Q02163|Q02164|Q02165|Q16160|Q2MJW0|Q2VC86|Q3LTM6|Q6AZX5|Q6J2U3|Q7RU06|Q8IZT2|Q8IZT3|Q8IZT4|Q8IZT5|Q9UD13|Q9UD14|Q9UD15|Q9UD16|Q9UD73|Q9UD74|Q9UEC2|Q9UEC3|Q9UPN0	Missense_Mutation	SNP	ENST00000294413.7	37	CCDS30635.1	.	.	.	.	.	.	.	.	.	.	N	10.21	1.287340	0.23478	.	.	ENSG00000188672	ENST00000413854;ENST00000539650;ENST00000455194;ENST00000374352;ENST00000243186;ENST00000340849;ENST00000349320;ENST00000346452;ENST00000294413;ENST00000447203	T;T;T;T;T;T;T;T	0.25085	1.82;1.87;2.01;1.82;1.82;2.01;2.25;2.17	4.91	-7.42	0.01388	Ammonium transporter AmtB-like (3);	1.493850	0.03760	N	0.257957	T	0.12987	0.0315	L	0.28694	0.88	0.09310	N	1	B;P;B;B	0.36789	0.001;0.57;0.005;0.0	B;B;B;B	0.29353	0.006;0.101;0.018;0.0	T	0.14090	-1.0485	10	0.15066	T	0.55	0.8095	8.4161	0.32672	0.2921:0.2672:0.4407:0.0	rs1132768;rs3193884;rs17418112	298;163;209;314	Q5VSJ9;E7EQ47;Q5VSJ7;P18577	.;.;.;RHCE_HUMAN	G	314;243;209;298;314;209;298;163;314;314	ENSP00000415417:V314G;ENSP00000416275:V209G;ENSP00000363472:V298G;ENSP00000243186:V314G;ENSP00000345084:V209G;ENSP00000311185:V298G;ENSP00000344485:V163G;ENSP00000294413:V314G	ENSP00000243186:V314G	V	-	2	0	RHCE	25584921	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.974000	0.03794	-1.452000	0.01931	-2.008000	0.00441	GTG		0.527	RHCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020312.2	NM_020485	Missense_Mutation
ARID1A	8289	broad.mit.edu	37	1	27057738	27057738	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:27057738G>A	ENST00000324856.7	+	3	1817	c.1446G>A	c.(1444-1446)caG>caA	p.Q482Q	ARID1A_ENST00000457599.2_Silent_p.Q482Q|ARID1A_ENST00000374152.2_Silent_p.Q99Q	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	482	Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.Q482Q(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AGCAGCAGCAGCCACCCTACT	0.572			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.Q482Q			Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1446A	1						.						326.0	304.0	312.0					1																	27057738		2203	4300	6503	26930325	SO:0001819	synonymous_variant	8289	exon3			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1446G>A	1.37:g.27057738G>A		Somatic		Capture	Illumina HiSeq	Phase_I	26930325	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Silent	SNP	ENST00000324856.7	37	CCDS285.1																																																																																				0.572	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
FAM46B	115572	broad.mit.edu	37	1	27338914	27338914	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:27338914G>A	ENST00000289166.5	-	1	413	c.248C>T	c.(247-249)cCc>cTc	p.P83L		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	83								p.P82L(1)		breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		GATCTGCCGGGGCTGCACGCT	0.622																																					p.P83L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C248T	1						.						27.0	28.0	28.0					1																	27338914		2202	4300	6502	27211501	SO:0001583	missense	115572	exon1			AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.248C>T	1.37:g.27338914G>A	ENSP00000289166:p.Pro83Leu	Somatic		Capture	Illumina HiSeq	Phase_I	27211501	NM_052943		Missense_Mutation	SNP	ENST00000289166.5	37	CCDS294.2	.	.	.	.	.	.	.	.	.	.	G	17.49	3.402108	0.62288	.	.	ENSG00000158246	ENST00000289166	T	0.19938	2.11	5.49	5.49	0.81192	Domain of unknown function DUF1693 (1);	0.052622	0.85682	D	0.000000	T	0.30792	0.0776	L	0.35487	1.065	0.80722	D	1	D	0.57899	0.981	P	0.62649	0.905	T	0.01007	-1.1483	10	0.06099	T	0.92	-15.5361	19.1609	0.93531	0.0:0.0:1.0:0.0	.	83	Q96A09	FA46B_HUMAN	L	83	ENSP00000289166:P83L	ENSP00000289166:P83L	P	-	2	0	FAM46B	27211501	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.043000	0.93799	2.860000	0.98153	0.655000	0.94253	CCC		0.622	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012347.2	NM_052943	
SYTL1	84958	broad.mit.edu	37	1	27676920	27676920	+	Missense_Mutation	SNP	C	C	T	rs376143341		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:27676920C>T	ENST00000543823.1	+	9	1411	c.949C>T	c.(949-951)Cgc>Tgc	p.R317C	SYTL1_ENST00000490170.1_3'UTR|SYTL1_ENST00000318074.5_Missense_Mutation_p.R305C			Q8IYJ3	SYTL1_HUMAN	synaptotagmin-like 1	317	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|melanosome (GO:0042470)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)	p.R305C(1)		NS(1)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	12		Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0908)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.0013)|KIRC - Kidney renal clear cell carcinoma(1967;0.00158)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GCAGAGCAAGCGCAAGACGGC	0.587																																					p.R305C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C913T	1						.	C	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	112.0	99.0	104.0		949,913	3.9	1.0	1		104	0,8600		0,0,4300	no	missense,missense	SYTL1	NM_001193308.1,NM_032872.2	180,180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	317/563,305/551	27676920	1,13005	2203	4300	6503	27549507	SO:0001583	missense	84958	exon10			AK027902	CCDS298.1, CCDS53286.1	1p35.3	2008-02-05			ENSG00000142765	ENSG00000142765			15584	protein-coding gene	gene with protein product		608042				12137562	Standard	NM_032872		Approved	SLP1, JFC1, FLJ14996, exophilin-7	uc001bnw.2	Q8IYJ3	OTTHUMG00000005770	ENST00000543823.1:c.949C>T	1.37:g.27676920C>T	ENSP00000440704:p.Arg317Cys	Somatic		Capture	Illumina HiSeq	Phase_I	27549507	NM_032872	Q5SSC9|Q96BB6|Q96GU6|Q96S89|Q96SI0	Missense_Mutation	SNP	ENST00000543823.1	37	CCDS53286.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.108755	0.77096	2.27E-4	0.0	ENSG00000142765	ENST00000318074;ENST00000543823;ENST00000485269	T;T	0.69926	-0.44;-0.44	3.87	3.87	0.44632	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.113654	0.56097	D	0.000035	T	0.81941	0.4929	M	0.89030	3	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.84157	0.0426	10	0.87932	D	0	-22.5923	9.2091	0.37306	0.3415:0.6585:0.0:0.0	.	317;317;305	A8KAH3;Q8IYJ3;Q8IYJ3-2	.;SYTL1_HUMAN;.	C	305;317;70	ENSP00000316464:R305C;ENSP00000440704:R317C	ENSP00000316464:R305C	R	+	1	0	SYTL1	27549507	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.753000	0.38359	2.155000	0.67459	0.462000	0.41574	CGC		0.587	SYTL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032872	
FGR	2268	broad.mit.edu	37	1	27950395	27950395	+	Silent	SNP	C	C	T	rs148928565		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:27950395C>T	ENST00000374005.3	-	3	321	c.33G>A	c.(31-33)ccG>ccA	p.P11P	FGR_ENST00000399173.1_Silent_p.P11P|FGR_ENST00000374004.1_Silent_p.P11P|FGR_ENST00000545953.1_Silent_p.P11P|FGR_ENST00000468038.1_5'UTR	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN	FGR proto-oncogene, Src family tyrosine kinase	11					blood coagulation (GO:0007596)|defense response to Gram-positive bacterium (GO:0050830)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of innate immune response (GO:0045088)|regulation of phagocytosis (GO:0050764)|regulation of protein kinase activity (GO:0045859)|response to virus (GO:0009615)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|Fc-gamma receptor I complex binding (GO:0034988)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphotyrosine binding (GO:0001784)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)	p.P11P(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		CCGTGGCCACCGGCTCCAATT	0.617													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19952	0.0		0.0	False		,,,				2504	0.0				p.P11P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G33A	1						.	C	,,	4,4402	8.1+/-20.4	0,4,2199	76.0	69.0	71.0		33,33,33	-9.8	0.0	1	dbSNP_134	71	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	FGR	NM_001042729.1,NM_001042747.1,NM_005248.2	,,	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	,,	11/530,11/530,11/530	27950395	4,13002	2203	4300	6503	27822982	SO:0001819	synonymous_variant	2268	exon3			BC064382	CCDS305.1	1p36.2-p36.1	2014-06-25	2014-06-25		ENSG00000000938	ENSG00000000938		"""SH2 domain containing"""	3697	protein-coding gene	gene with protein product		164940	"""Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog"", ""v-fgr feline Gardner-Rasheed sarcoma viral oncogene homolog"", ""feline Gardner-Rasheed sarcoma viral oncogene homolog"""	SRC2		3922831	Standard	NM_001042729		Approved	c-fgr, p55c-fgr	uc001bom.3	P09769	OTTHUMG00000003516	ENST00000374005.3:c.33G>A	1.37:g.27950395C>T		Somatic		Capture	Illumina HiSeq	Phase_I	27822982	NM_001042747	D3DPL7|Q9UIQ3	Silent	SNP	ENST00000374005.3	37	CCDS305.1																																																																																				0.617	FGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009772.1	NM_005248	
SESN2	83667	broad.mit.edu	37	1	28598305	28598305	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:28598305T>C	ENST00000253063.3	+	3	598	c.277T>C	c.(277-279)Ttc>Ctc	p.F93L		NM_031459.4	NP_113647.1	P58004	SESN2_HUMAN	sestrin 2	93					autophagy (GO:0006914)|fatty acid beta-oxidation (GO:0006635)|glucose import (GO:0046323)|mitochondrial DNA metabolic process (GO:0032042)|protein kinase B signaling (GO:0043491)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of response to reactive oxygen species (GO:1901031)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.F93L(1)		cervix(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(2)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	27		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.98e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|READ - Rectum adenocarcinoma(331;0.0649)		CTTTACCAGCTTCTGGCGCCT	0.622																																					p.F93L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T277C	1						.						92.0	79.0	83.0					1																	28598305		2203	4300	6503	28470892	SO:0001583	missense	83667	exon3			AY123223	CCDS321.1	1p35.2	2008-02-05			ENSG00000130766	ENSG00000130766			20746	protein-coding gene	gene with protein product		607767				12607115, 12203114	Standard	NM_031459		Approved	SES2, DKFZp761M0212, HI95, SEST2	uc001bps.3	P58004	OTTHUMG00000003532	ENST00000253063.3:c.277T>C	1.37:g.28598305T>C	ENSP00000253063:p.Phe93Leu	Somatic		Capture	Illumina HiSeq	Phase_I	28470892	NM_031459	Q5T7D0|Q96SI5	Missense_Mutation	SNP	ENST00000253063.3	37	CCDS321.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.858802	0.91433	.	.	ENSG00000130766	ENST00000253063	T	0.46819	0.86	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.51975	0.1706	M	0.78285	2.405	0.80722	D	1	B	0.31256	0.316	B	0.36666	0.23	T	0.56625	-0.7948	10	0.54805	T	0.06	-21.417	10.5687	0.45188	0.0:0.0784:0.0:0.9216	.	93	P58004	SESN2_HUMAN	L	93	ENSP00000253063:F93L	ENSP00000253063:F93L	F	+	1	0	SESN2	28470892	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	4.776000	0.62354	2.094000	0.63399	0.533000	0.62120	TTC		0.622	SESN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009840.1		
CSMD2	114784	broad.mit.edu	37	1	34089011	34089011	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:34089011T>C	ENST00000373380.1	-	15	2520	c.2300A>G	c.(2299-2301)gAt>gGt	p.D767G	CSMD2_ENST00000373377.1_5'UTR|CSMD2_ENST00000373388.2_5'UTR|CSMD2_ENST00000373381.4_Missense_Mutation_p.D1894G			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1854	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D1854G(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				ATCTGCACCATCAAATACTTC	0.488																																					p.D1854G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A5561G	1						.						128.0	114.0	119.0					1																	34089011		2203	4300	6503	33861598	SO:0001583	missense	114784	exon36			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.2300A>G	1.37:g.34089011T>C	ENSP00000362478:p.Asp767Gly	Somatic		Capture	Illumina HiSeq	Phase_I	33861598	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	37		.	.	.	.	.	.	.	.	.	.	T	26.2	4.711862	0.89112	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.67698	-0.28;-0.28	5.69	5.69	0.88448	CUB (5);	0.124766	0.52532	D	0.000067	D	0.85745	0.5768	M	0.93638	3.44	0.80722	D	1	D;D;D	0.89917	0.983;1.0;0.999	D;D;D	0.97110	0.929;0.993;1.0	D	0.87902	0.2691	10	0.42905	T	0.14	.	14.7749	0.69724	0.0:0.0:0.0:1.0	.	767;1854;1894	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	G	1894;767	ENSP00000362479:D1894G;ENSP00000362478:D767G	ENSP00000241312:D1854G	D	-	2	0	CSMD2	33861598	1.000000	0.71417	0.947000	0.38551	0.986000	0.74619	7.669000	0.83911	2.170000	0.68504	0.459000	0.35465	GAT		0.488	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896	
OSCP1	127700	broad.mit.edu	37	1	36904439	36904439	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:36904439T>C	ENST00000356637.5	-	3	278	c.215A>G	c.(214-216)tAc>tGc	p.Y72C	OSCP1_ENST00000315643.9_Missense_Mutation_p.Y72C|OSCP1_ENST00000354267.3_Missense_Mutation_p.Y62C|OSCP1_ENST00000433045.2_Missense_Mutation_p.Y17C|OSCP1_ENST00000235532.5_Missense_Mutation_p.Y62C			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	72					transport (GO:0006810)	plasma membrane (GO:0005886)		p.Y72C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	22						CTTCTTGGAGTAGAGCTCTTG	0.478																																					p.Y62C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A185G	1						.						103.0	100.0	101.0					1																	36904439		2203	4300	6503	36677026	SO:0001583	missense	127700	exon2				CCDS409.1, CCDS410.1, CCDS409.2	1p34.3	2009-07-06	2009-07-06	2009-07-06	ENSG00000116885	ENSG00000116885			29971	protein-coding gene	gene with protein product	"""oxidored nitro domain containing protein"""	608854	"""chromosome 1 open reading frame 102"""	C1orf102		12477932	Standard	NM_145047		Approved	NOR1	uc001caq.3	Q8WVF1	OTTHUMG00000008139	ENST00000356637.5:c.215A>G	1.37:g.36904439T>C	ENSP00000349052:p.Tyr72Cys	Somatic		Capture	Illumina HiSeq	Phase_I	36677026	NM_206837	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Missense_Mutation	SNP	ENST00000356637.5	37		.	.	.	.	.	.	.	.	.	.	T	22.7	4.329134	0.81690	.	.	ENSG00000116885	ENST00000235532;ENST00000356637;ENST00000433045;ENST00000445843;ENST00000315643;ENST00000354267	T;T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45;1.45	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.62208	0.2409	M	0.86740	2.835	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.993;0.996;0.997	T	0.68515	-0.5388	10	0.72032	D	0.01	.	15.825	0.78698	0.0:0.0:0.0:1.0	.	62;62;72	Q8WVF1-4;Q8WVF1-3;Q8WVF1	.;.;OSCP1_HUMAN	C	62;72;17;32;72;62	ENSP00000235532:Y62C;ENSP00000349052:Y72C;ENSP00000390820:Y17C;ENSP00000396417:Y32C;ENSP00000314541:Y72C;ENSP00000346216:Y62C	ENSP00000235532:Y62C	Y	-	2	0	OSCP1	36677026	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.944000	0.70219	2.333000	0.79357	0.533000	0.62120	TAC		0.478	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047	
PPIE	10450	broad.mit.edu	37	1	40209538	40209538	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:40209538C>T	ENST00000324379.5	+	6	345	c.326C>T	c.(325-327)aCg>aTg	p.T109M	PPIE_ENST00000480169.1_3'UTR|PPIE_ENST00000356511.2_Missense_Mutation_p.T109M|PPIE_ENST00000372830.1_Missense_Mutation_p.T109M|PPIE_ENST00000470213.1_Missense_Mutation_p.T109M	NM_006112.3	NP_006103.1	Q9UNP9	PPIE_HUMAN	peptidylprolyl isomerase E (cyclophilin E)	109					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral genome replication (GO:0045070)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|nucleotide binding (GO:0000166)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.T109M(1)		kidney(3)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	9	all_cancers(7;1.63e-13)|all_lung(5;2.27e-16)|all_epithelial(6;1.35e-15)|Lung NSC(20;1.49e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;2.7e-17)|all cancers(16;5.5e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TCTGGGAAGACGCTTGAAGAG	0.468																																					p.T109M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C326T	1						.						100.0	103.0	102.0					1																	40209538		2203	4300	6503	39982125	SO:0001583	missense	10450	exon6			AF042385	CCDS442.1, CCDS443.1, CCDS53299.1	1p32	2013-02-12			ENSG00000084072	ENSG00000084072		"""RNA binding motif (RRM) containing"""	9258	protein-coding gene	gene with protein product	"""peptidyl-prolyl cis-trans isomerase E"", ""cyclophilin 33"", ""cyclophilin E"", ""PPIase E"", ""rotamase E"", ""peptidylprolyl isomerase E, isoform 1"""	602435				9747881	Standard	NM_203456		Approved	CyP-33, MGC3736, MGC111222	uc001cdw.3	Q9UNP9	OTTHUMG00000009248	ENST00000324379.5:c.326C>T	1.37:g.40209538C>T	ENSP00000312769:p.Thr109Met	Somatic		Capture	Illumina HiSeq	Phase_I	39982125	NM_001195007	B2R971|O43634|O43635|Q32Q72|Q3S611|Q5TGA0|Q5TGA2|Q5TGA3|Q9UIZ5	Missense_Mutation	SNP	ENST00000324379.5	37	CCDS443.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.208260	0.79240	.	.	ENSG00000084072	ENST00000470018;ENST00000324379;ENST00000356511;ENST00000497370;ENST00000470213;ENST00000372835;ENST00000372830	T;T;T;T;T;T	0.74526	2.98;2.97;1.43;3.61;-0.85;2.96	4.91	4.91	0.64330	.	0.055178	0.64402	D	0.000001	D	0.86247	0.5887	M	0.83953	2.67	0.80722	D	1	D;D;D;D	0.89917	0.997;1.0;1.0;0.999	P;D;P;P	0.63113	0.72;0.911;0.891;0.77	D	0.88356	0.2984	10	0.72032	D	0.01	-16.6903	17.8829	0.88845	0.0:1.0:0.0:0.0	.	43;109;109;109	B4E3F2;Q5TGA3;Q9UNP9-2;Q9UNP9	.;.;.;PPIE_HUMAN	M	43;109;109;43;109;58;109	ENSP00000312769:T109M;ENSP00000348904:T109M;ENSP00000433475:T43M;ENSP00000431714:T109M;ENSP00000361925:T58M;ENSP00000361918:T109M	ENSP00000312769:T109M	T	+	2	0	PPIE	39982125	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.579000	0.67457	2.571000	0.86741	0.655000	0.94253	ACG		0.468	PPIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025642.2	NM_006112	
CAP1	10487	broad.mit.edu	37	1	40529971	40529971	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:40529971C>A	ENST00000372797.3	+	5	928	c.367C>A	c.(367-369)Cga>Aga	p.R123R	CAP1_ENST00000372792.2_Silent_p.R123R|CAP1_ENST00000372802.1_Silent_p.R122R|CAP1_ENST00000372798.1_Silent_p.R122R|CAP1_ENST00000340450.3_Silent_p.R122R|CAP1_ENST00000372805.3_Silent_p.R123R	NM_001105530.1|NM_006367.3	NP_001099000|NP_006358	Q13114	TRAF3_HUMAN	CAP, adenylate cyclase-associated protein 1 (yeast)	0					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R123R(1)		endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	12	Lung NSC(20;5.03e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;4.63e-18)|Epithelial(16;1.27e-16)|all cancers(16;2.3e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GGAGAAGAACCGAGGCAGCAA	0.498																																					p.R123R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C367A	1						.						97.0	88.0	91.0					1																	40529971		1932	4126	6058	40302558	SO:0001819	synonymous_variant	10487	exon5			L12168	CCDS41309.1	1p34.3	2010-07-13			ENSG00000131236	ENSG00000131236			20040	protein-coding gene	gene with protein product						1406678, 8761950	Standard	NM_006367		Approved	CAP	uc001cey.4	Q01518	OTTHUMG00000004493	ENST00000372797.3:c.367C>A	1.37:g.40529971C>A		Somatic		Capture	Illumina HiSeq	Phase_I	40302558	NM_006367	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Silent	SNP	ENST00000372797.3	37	CCDS41309.1																																																																																				0.498	CAP1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000013109.1	NM_006367	
RLF	6018	broad.mit.edu	37	1	40661382	40661382	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:40661382A>G	ENST00000372771.4	+	4	580	c.553A>G	c.(553-555)Aaa>Gaa	p.K185E		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	185					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.K185E(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			AGGGGTGTGGAAAAACCCAGT	0.393																																					p.K185E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A553G	1						.						83.0	84.0	83.0					1																	40661382		2203	4300	6503	40433969	SO:0001583	missense	6018	exon4				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"""Zinc fingers, C2H2-type"""	10025	protein-coding gene	gene with protein product		180610	"""rearranged L-myc fusion sequence"""			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.553A>G	1.37:g.40661382A>G	ENSP00000361857:p.Lys185Glu	Somatic		Capture	Illumina HiSeq	Phase_I	40433969	NM_012421	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.484553	0.84854	.	.	ENSG00000117000	ENST00000372771	T	0.14266	2.52	5.1	5.1	0.69264	.	0.089312	0.85682	D	0.000000	T	0.18676	0.0448	L	0.38175	1.15	0.42433	D	0.992684	D	0.58268	0.982	P	0.49799	0.622	T	0.01068	-1.1462	10	0.72032	D	0.01	-17.6315	14.8735	0.70478	1.0:0.0:0.0:0.0	.	185	Q13129	RLF_HUMAN	E	185	ENSP00000361857:K185E	ENSP00000361857:K185E	K	+	1	0	RLF	40433969	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.749000	0.74883	1.919000	0.55581	0.377000	0.23210	AAA		0.393	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421	
HIVEP3	59269	broad.mit.edu	37	1	42048460	42048460	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:42048460T>C	ENST00000372583.1	-	4	2894	c.2009A>G	c.(2008-2010)cAg>cGg	p.Q670R	HIVEP3_ENST00000247584.5_Missense_Mutation_p.Q670R|HIVEP3_ENST00000460604.1_5'Flank|HIVEP3_ENST00000429157.2_Missense_Mutation_p.Q670R|HIVEP3_ENST00000372584.1_Missense_Mutation_p.Q670R	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	670	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q670R(1)		NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				CTTTGCGATCTGAAGCTCTGA	0.453																																					p.Q670R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2009G	1						.						123.0	124.0	124.0					1																	42048460		2203	4300	6503	41821047	SO:0001583	missense	59269	exon4			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.2009A>G	1.37:g.42048460T>C	ENSP00000361664:p.Gln670Arg	Somatic		Capture	Illumina HiSeq	Phase_I	41821047	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	.	.	.	.	.	.	.	.	.	.	T	36	5.602384	0.96614	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.12569	2.67;2.67;2.67;2.67	4.48	4.48	0.54585	Zinc finger, C2H2 (1);	0.000000	0.49305	D	0.000146	T	0.27559	0.0677	L	0.50333	1.59	0.37508	D	0.917025	D;D	0.62365	0.991;0.985	P;P	0.61874	0.895;0.789	T	0.07347	-1.0777	10	0.44086	T	0.13	-1.2137	13.5915	0.61964	0.0:0.0:0.0:1.0	.	670;670	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	R	670	ENSP00000361665:Q670R;ENSP00000361664:Q670R;ENSP00000247584:Q670R;ENSP00000410828:Q670R	ENSP00000247584:Q670R	Q	-	2	0	HIVEP3	41821047	1.000000	0.71417	0.949000	0.38748	0.976000	0.68499	5.405000	0.66351	1.889000	0.54706	0.459000	0.35465	CAG		0.453	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
GUCA2B	2981	broad.mit.edu	37	1	42620501	42620501	+	Missense_Mutation	SNP	G	G	A	rs140898399		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:42620501G>A	ENST00000372581.1	+	2	271	c.241G>A	c.(241-243)Gcc>Acc	p.A81T		NM_007102.2	NP_009033.1	Q16661	GUC2B_HUMAN	guanylate cyclase activator 2B (uroguanylin)	81					body fluid secretion (GO:0007589)|cGMP biosynthetic process (GO:0006182)|excretion (GO:0007588)|negative regulation of blood pressure (GO:0045776)|positive regulation of guanylate cyclase activity (GO:0031284)	extracellular vesicular exosome (GO:0070062)	calcium sensitive guanylate cyclase activator activity (GO:0008048)	p.A81T(1)		breast(1)|large_intestine(2)	3	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCCTGTCTGCGCCTCGCAGGA	0.682													G|||	1	0.000199681	0.0	0.0	5008	,	,		19122	0.001		0.0	False		,,,				2504	0.0				p.A81T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G241A	1						.						53.0	52.0	52.0					1																	42620501		2203	4300	6503	42393088	SO:0001583	missense	2981	exon2			BC069301	CCDS464.1	1p34-p33	2014-01-30			ENSG00000044012	ENSG00000044012		"""Endogenous ligands"""	4683	protein-coding gene	gene with protein product	"""prepro-uroguanylin"""	601271				8605041, 9268639	Standard	NM_007102		Approved		uc001chc.1	Q16661	OTTHUMG00000007024	ENST00000372581.1:c.241G>A	1.37:g.42620501G>A	ENSP00000361662:p.Ala81Thr	Somatic		Capture	Illumina HiSeq	Phase_I	42393088	NM_007102	Q52LV0	Missense_Mutation	SNP	ENST00000372581.1	37	CCDS464.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	8.324	0.825005	0.16678	.	.	ENSG00000044012	ENST00000372581	T	0.43688	0.94	4.83	-2.88	0.05682	.	0.954188	0.08731	N	0.902024	T	0.23965	0.0580	N	0.16307	0.4	0.09310	N	1	B	0.20671	0.047	B	0.15484	0.013	T	0.20306	-1.0279	10	0.29301	T	0.29	-3.245	9.9138	0.41421	0.6222:0.0:0.3778:0.0	.	81	Q16661	GUC2B_HUMAN	T	81	ENSP00000361662:A81T	ENSP00000361662:A81T	A	+	1	0	GUCA2B	42393088	0.000000	0.05858	0.003000	0.11579	0.484000	0.33280	-2.476000	0.00986	-0.725000	0.04901	-0.192000	0.12808	GCC		0.682	GUCA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018307.1	NM_007102	
ERMAP	114625	broad.mit.edu	37	1	43308370	43308370	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:43308370G>A	ENST00000372517.2	+	12	1139	c.895G>A	c.(895-897)Gtg>Atg	p.V299M	RP11-342M1.3_ENST00000444563.1_RNA|RP11-342M1.3_ENST00000416809.2_RNA|ERMAP_ENST00000487556.1_3'UTR|RP11-342M1.3_ENST00000425076.1_RNA|RP11-342M1.3_ENST00000414798.1_RNA|ERMAP_ENST00000328249.3_Missense_Mutation_p.V209M|ERMAP_ENST00000372514.3_Missense_Mutation_p.V299M	NM_001017922.1	NP_001017922.1	Q96PL5	ERMAP_HUMAN	erythroblast membrane-associated protein (Scianna blood group)	299	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		Missing (in Sc-3 allele).			cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V299M(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GGAGGTGTATGTGGGAGACAA	0.527																																					p.V299M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G895A	1						.						165.0	143.0	150.0					1																	43308370		2203	4300	6503	43080957	SO:0001583	missense	114625	exon12			AF311284	CCDS475.1	1p34	2014-07-19	2006-02-23		ENSG00000164010	ENSG00000164010		"""Blood group antigens"", ""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	15743	protein-coding gene	gene with protein product		609017	"""Radin blood group"", ""Scianna blood group"", ""erythroblast membrane-associated protein"", ""erythroblast membrane-associated protein (RD and SC blood groups)"""	RD, SC		11549310	Standard	XM_005270415		Approved	BTN5	uc001cie.1	Q96PL5	OTTHUMG00000007619	ENST00000372517.2:c.895G>A	1.37:g.43308370G>A	ENSP00000361595:p.Val299Met	Somatic		Capture	Illumina HiSeq	Phase_I	43080957	NM_001017922	D3DPW8|Q5VV53|Q6DUE0|Q7Z3X0|Q8NCV8|Q8NCW2|Q8NCW3|Q96PL6	Missense_Mutation	SNP	ENST00000372517.2	37	CCDS475.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.107403	0.77096	.	.	ENSG00000164010	ENST00000372517;ENST00000372514;ENST00000328249	T;T;T	0.74526	-0.85;-0.85;-0.85	5.16	5.16	0.70880	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.096682	0.44285	D	0.000476	D	0.88919	0.6568	M	0.91920	3.255	0.44754	D	0.997752	D	0.89917	1.0	D	0.91635	0.999	D	0.91017	0.4854	10	0.87932	D	0	.	16.1986	0.82053	0.0:0.0:1.0:0.0	.	299	Q96PL5	ERMAP_HUMAN	M	299;299;209	ENSP00000361595:V299M;ENSP00000361592:V299M;ENSP00000332439:V209M	ENSP00000332439:V209M	V	+	1	0	ERMAP	43080957	1.000000	0.71417	0.965000	0.40720	0.691000	0.40173	5.500000	0.66943	2.699000	0.92147	0.655000	0.94253	GTG		0.527	ERMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020180.1	NM_018538	
PTPRF	5792	broad.mit.edu	37	1	44069663	44069663	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:44069663G>A	ENST00000359947.4	+	16	3180	c.2840G>A	c.(2839-2841)cGc>cAc	p.R947H	PTPRF_ENST00000422171.2_Missense_Mutation_p.R295H|PTPRF_ENST00000372413.3_Missense_Mutation_p.R938H|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000372414.3_Missense_Mutation_p.R947H|PTPRF_ENST00000438120.1_Missense_Mutation_p.R938H	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	947	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R937H(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AGGAACGGGCGCATCATCAGC	0.597																																					p.R938H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2813A	1						.						100.0	81.0	88.0					1																	44069663		2203	4300	6503	43842250	SO:0001583	missense	5792	exon15			Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.2840G>A	1.37:g.44069663G>A	ENSP00000353030:p.Arg947His	Somatic		Capture	Illumina HiSeq	Phase_I	43842250	NM_130440	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Missense_Mutation	SNP	ENST00000359947.4	37	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.730|2.730	-0.264545|-0.264545	0.05754|0.05754	.|.	.|.	ENSG00000142949|ENSG00000142949	ENST00000429895|ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000422171	.|T;T;T;T;T	.|0.56776	.|0.44;0.44;0.44;0.44;0.44	5.19|5.19	1.17|1.17	0.20885|0.20885	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.752409	.|0.10938	.|N	.|0.617652	T|T	0.39118|0.39118	0.1066|0.1066	L|L	0.39692|0.39692	1.235|1.235	0.33558|0.33558	D|D	0.597036|0.597036	.|B;B;B;B	.|0.10296	.|0.001;0.001;0.0;0.003	.|B;B;B;B	.|0.13407	.|0.009;0.002;0.0;0.006	T|T	0.42344|0.42344	-0.9457|-0.9457	5|10	.|0.12430	.|T	.|0.62	.|.	8.8577|8.8577	0.35238|0.35238	0.5205:0.0:0.4795:0.0|0.5205:0.0:0.4795:0.0	.|.	.|592;295;938;947	.|Q59FI2;F2Z3B8;P10586-2;P10586	.|.;.;.;PTPRF_HUMAN	T|H	593|947;938;947;938;295	.|ENSP00000353030:R947H;ENSP00000398822:R938H;ENSP00000361491:R947H;ENSP00000361490:R938H;ENSP00000387885:R295H	.|ENSP00000353030:R947H	A|R	+|+	1|2	0|0	PTPRF|PTPRF	43842250|43842250	0.998000|0.998000	0.40836|0.40836	0.995000|0.995000	0.50966|0.50966	0.157000|0.157000	0.22087|0.22087	0.790000|0.790000	0.26900|0.26900	0.032000|0.032000	0.15435|0.15435	-0.150000|-0.150000	0.13652|0.13652	GCA|CGC		0.597	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
ST3GAL3	6487	broad.mit.edu	37	1	44363951	44363951	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:44363951C>T	ENST00000361392.4	+	7	619	c.442C>T	c.(442-444)Ctg>Ttg	p.L148L	ST3GAL3_ENST00000545417.1_Intron|ST3GAL3_ENST00000372368.2_Silent_p.L202L|ST3GAL3_ENST00000531816.1_Intron|ST3GAL3_ENST00000361812.4_Intron|ST3GAL3_ENST00000353126.3_Silent_p.L148L|ST3GAL3_ENST00000372377.4_Intron|ST3GAL3_ENST00000372369.1_Silent_p.L148L|ST3GAL3_ENST00000372374.2_Silent_p.L117L|ST3GAL3_ENST00000332628.6_Silent_p.L117L|ST3GAL3_ENST00000372372.2_Silent_p.L186L|ST3GAL3_ENST00000528371.1_Silent_p.L132L|ST3GAL3_ENST00000372375.2_Silent_p.L202L|ST3GAL3_ENST00000372362.2_Intron|ST3GAL3_ENST00000372366.1_Silent_p.L147L|ST3GAL3_ENST00000372365.1_Silent_p.L148L|ST3GAL3_ENST00000533933.1_Silent_p.L148L|ST3GAL3_ENST00000531993.1_Silent_p.L132L|ST3GAL3_ENST00000262915.3_Silent_p.L217L|ST3GAL3_ENST00000461375.1_3'UTR|ST3GAL3_ENST00000347631.2_Silent_p.L163L|ST3GAL3_ENST00000351035.3_Silent_p.L186L|ST3GAL3_ENST00000361746.4_Silent_p.L217L|ST3GAL3_ENST00000335430.6_Silent_p.L132L|ST3GAL3_ENST00000361400.4_Silent_p.L132L|ST3GAL3_ENST00000372367.1_Silent_p.L147L|ST3GAL3_ENST00000531451.1_Intron|ST3GAL3_ENST00000330208.2_Intron	NM_001270459.1|NM_006279.3|NM_174964.2	NP_001257388.1|NP_006270.1|NP_777624.1	Q11203	SIAT6_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	148					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|N-acetyllactosaminide alpha-2,3-sialyltransferase activity (GO:0008118)	p.L217L(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(3)|skin(1)	19	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)				AGAGTACCGCCTGACCCCTGC	0.547																																					p.L163L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C487T	1						.						116.0	99.0	105.0					1																	44363951		2203	4300	6503	44136538	SO:0001819	synonymous_variant	6487	exon7			L23768	CCDS492.1, CCDS493.1, CCDS494.1, CCDS495.1, CCDS496.1, CCDS497.1, CCDS498.1, CCDS499.1, CCDS500.1, CCDS53310.1, CCDS57988.1, CCDS57989.1, CCDS57990.1, CCDS57991.1, CCDS57992.1, CCDS57993.1, CCDS57994.1	1p34.1	2014-01-31	2005-02-07	2005-02-07	ENSG00000126091	ENSG00000126091	2.4.99.6	"""Sialyltransferases"""	10866	protein-coding gene	gene with protein product	"""ST3Gal III"""	606494	"""sialyltransferase 6 (N-acetyllacosaminide alpha 2,3-sialyltransferase)"", ""mental retardation, non-syndromic, autosomal recessive, 12"""	SIAT6, MRT12		8333853, 21907012	Standard	NM_174963		Approved		uc001cjz.4	Q11203	OTTHUMG00000007561	ENST00000361392.4:c.442C>T	1.37:g.44363951C>T		Somatic		Capture	Illumina HiSeq	Phase_I	44136538	NM_174964	A9Z1W2|D3DPX8|Q5T4W9|Q5T4X0|Q5T4X7|Q5T4X8|Q5T4X9|Q5T4Y0|Q5T4Y2|Q5T4Y3|Q5T4Y4|Q86UR6|Q86UR7|Q86UR8|Q86UR9|Q86US0|Q86US1|Q86US2|Q8IX41|Q8IX42|Q8IX43|Q8IX44|Q8IX45|Q8IX46|Q8IX47|Q8IX48|Q8IX49|Q8IX50|Q8IX51|Q8IX52|Q8IX53|Q8IX54|Q8IX55|Q8IX56|Q8IX57|Q8IX58	Silent	SNP	ENST00000361392.4	37	CCDS492.1																																																																																				0.547	ST3GAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019964.1	NM_174963	
LRRC41	10489	broad.mit.edu	37	1	46751172	46751172	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:46751172G>A	ENST00000343304.6	-	4	1642	c.1357C>T	c.(1357-1359)Ctg>Ttg	p.L453L	LRRC41_ENST00000472710.1_5'UTR	NM_006369.4	NP_006360.3	Q15345	LRC41_HUMAN	leucine rich repeat containing 41	453					protein ubiquitination (GO:0016567)	membrane (GO:0016020)		p.L453L(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					GAAGCTTCCAGTGCTGGAAGC	0.562																																					p.L453L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1357T	1						.						100.0	95.0	97.0					1																	46751172		2203	4300	6503	46523759	SO:0001819	synonymous_variant	10489	exon4			AK024051	CCDS533.1	1p34.1	2008-02-05			ENSG00000132128	ENSG00000132128			16917	protein-coding gene	gene with protein product						11384984	Standard	XM_005270376		Approved	MUF1	uc001cpn.3	Q15345	OTTHUMG00000007810	ENST00000343304.6:c.1357C>T	1.37:g.46751172G>A		Somatic		Capture	Illumina HiSeq	Phase_I	46523759	NM_006369	A8K5G8|Q3MJ96|Q5TDF5|Q71RA8|Q9BSM0	Silent	SNP	ENST00000343304.6	37	CCDS533.1																																																																																				0.562	LRRC41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021438.1	NM_006369	
ATPAF1	64756	broad.mit.edu	37	1	47101518	47101518	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:47101518A>G	ENST00000371937.4	-	9	1021	c.917T>C	c.(916-918)gTc>gCc	p.V306A	ATPAF1_ENST00000574428.1_Missense_Mutation_p.V238A|ATPAF1_ENST00000542495.1_Missense_Mutation_p.V155A|ATPAF1_ENST00000576409.1_Missense_Mutation_p.V329A|ATPAF1_ENST00000329231.4_Missense_Mutation_p.V261A|ATPAF1_ENST00000532925.1_Missense_Mutation_p.V218A	NM_022745.4	NP_073582.3	Q5TC12	ATPF1_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 1	306					protein complex assembly (GO:0006461)	mitochondrion (GO:0005739)		p.V306A(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(4)	8	Acute lymphoblastic leukemia(166;0.155)					TTCAGCGATGACAGACATATA	0.458																																					p.V306A	Melanoma(138;107 1777 21672 30337 52312)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T917C	1						.						253.0	242.0	245.0					1																	47101518		2203	4300	6503	46874105	SO:0001583	missense	64756	exon9			AK026004	CCDS541.1, CCDS41327.1, CCDS541.2, CCDS41327.2, CCDS57997.1, CCDS57998.1	1p33-p32.3	2012-10-12			ENSG00000123472	ENSG00000123472		"""Mitochondrial respiratory chain complex assembly factors"""	18803	protein-coding gene	gene with protein product		608917				11410595	Standard	NM_022745		Approved	FLJ22351, Atp11p, ATP11	uc001cqh.4	Q5TC12	OTTHUMG00000007988	ENST00000371937.4:c.917T>C	1.37:g.47101518A>G	ENSP00000361005:p.Val306Ala	Somatic		Capture	Illumina HiSeq	Phase_I	46874105	NM_022745	B1AQW7|B7Z7D6|B7Z7I6|Q9H6E3	Missense_Mutation	SNP	ENST00000371937.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.7|28.7	4.942480|4.942480	0.92526|0.92526	.|.	.|.	ENSG00000123472|ENSG00000123472	ENST00000534216|ENST00000371937;ENST00000526821;ENST00000542495;ENST00000329231;ENST00000532925	.|T	.|0.54479	.|0.57	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.75027|0.75027	0.3794|0.3794	M|M	0.83603|0.83603	2.65|2.65	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|0.999;0.999;1.0	.|D;D;D	.|0.79108	.|0.989;0.982;0.992	T|T	0.79075|0.79075	-0.1952|-0.1952	5|10	.|0.72032	.|D	.|0.01	-15.4542|-15.4542	16.1215|16.1215	0.81361|0.81361	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|218;238;306	.|B7Z7I6;A8MRA7;Q5TC12	.|.;.;ATPF1_HUMAN	P|A	161|306;152;155;238;218	.|ENSP00000361005:V306A	.|ENSP00000330685:V238A	S|V	-|-	1|2	0|0	ATPAF1|ATPAF1	46874105|46874105	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.684000|8.684000	0.91242|0.91242	2.208000|2.208000	0.71279|0.71279	0.528000|0.528000	0.53228|0.53228	TCA|GTC		0.458	ATPAF1-201	KNOWN	basic	protein_coding	protein_coding		NM_022745	
FAF1	11124	broad.mit.edu	37	1	51049377	51049377	+	Silent	SNP	G	G	A	rs140546895	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:51049377G>A	ENST00000396153.2	-	11	1429	c.978C>T	c.(976-978)aaC>aaT	p.N326N	FAF1_ENST00000545823.1_Silent_p.N84N|FAF1_ENST00000472808.1_5'UTR|FAF1_ENST00000371778.4_Silent_p.N326N|RNU6-1026P_ENST00000384465.1_RNA	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	326					apoptotic process (GO:0006915)|cell death (GO:0008219)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein complex assembly (GO:0031334)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of cell adhesion (GO:0030155)|regulation of protein catabolic process (GO:0042176)|regulation of protein kinase activity (GO:0045859)	CD95 death-inducing signaling complex (GO:0031265)|Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	heat shock protein binding (GO:0031072)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.N326N(1)|p.0?(1)		breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		CATTTTCTGCGTTTTCTGGCA	0.294													G|||	4	0.000798722	0.003	0.0	5008	,	,		15467	0.0		0.0	False		,,,				2504	0.0				p.N326N												.	.	2	Whole gene deletion(1)|Substitution - coding silent(1)	thyroid(1)|large_intestine(1)	c.C978T	1						.	G		5,4399	9.9+/-24.2	0,5,2197	106.0	109.0	108.0		978	2.4	1.0	1	dbSNP_134	108	0,8592		0,0,4296	no	coding-synonymous	FAF1	NM_007051.2		0,5,6493	AA,AG,GG		0.0,0.1135,0.0385		326/651	51049377	5,12991	2202	4296	6498	50821965	SO:0001819	synonymous_variant	11124	exon11			AF132938	CCDS554.1	1p32.3	2012-09-20			ENSG00000185104	ENSG00000185104		"""UBX domain containing"""	3578	protein-coding gene	gene with protein product	"""TNFRSF6-associated factor 1"", ""UBX domain protein 3A"""	604460				10462485	Standard	NM_007051		Approved	CGI-03, hFAF1, HFAF1s, UBXD12, UBXN3A	uc001cse.1	Q9UNN5	OTTHUMG00000007930	ENST00000396153.2:c.978C>T	1.37:g.51049377G>A		Somatic		Capture	Illumina HiSeq	Phase_I	50821965	NM_007051	Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Silent	SNP	ENST00000396153.2	37	CCDS554.1																																																																																				0.294	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1	NM_007051	
FAF1	11124	broad.mit.edu	37	1	51253782	51253782	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:51253782delG	ENST00000396153.2	-	4	708	c.257delC	c.(256-258)cctfs	p.P86fs	FAF1_ENST00000371778.4_Frame_Shift_Del_p.P86fs	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	86					apoptotic process (GO:0006915)|cell death (GO:0008219)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein complex assembly (GO:0031334)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of cell adhesion (GO:0030155)|regulation of protein catabolic process (GO:0042176)|regulation of protein kinase activity (GO:0045859)	CD95 death-inducing signaling complex (GO:0031265)|Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	heat shock protein binding (GO:0031072)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.0?(3)|p.P86fs*2(1)		breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		TGGCATTACAGGTCGAAACGC	0.463																																					p.P86fs												.	.	4	Whole gene deletion(3)|Deletion - Frameshift(1)	thyroid(1)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	c.257delC	1						.						113.0	99.0	104.0					1																	51253782		2203	4300	6503	51026370	SO:0001589	frameshift_variant	11124	exon4			AF132938	CCDS554.1	1p32.3	2012-09-20			ENSG00000185104	ENSG00000185104		"""UBX domain containing"""	3578	protein-coding gene	gene with protein product	"""TNFRSF6-associated factor 1"", ""UBX domain protein 3A"""	604460				10462485	Standard	NM_007051		Approved	CGI-03, hFAF1, HFAF1s, UBXD12, UBXN3A	uc001cse.1	Q9UNN5	OTTHUMG00000007930	ENST00000396153.2:c.257delC	1.37:g.51253782delG	ENSP00000379457:p.Pro86fs	Somatic		Capture	Illumina HiSeq	Phase_I	51026370	NM_007051	Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Frame_Shift_Del	DEL	ENST00000396153.2	37	CCDS554.1																																																																																				0.463	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1	NM_007051	
ORC1	4998	broad.mit.edu	37	1	52850308	52850308	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:52850308C>A	ENST00000371568.3	-	11	1887	c.1669G>T	c.(1669-1671)Gcc>Tcc	p.A557S	ORC1_ENST00000371566.1_Missense_Mutation_p.A557S	NM_001190818.1|NM_001190819.1|NM_004153.3	NP_001177747.1|NP_001177748.1|NP_004144.2	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	557	Necessary and sufficient for ORC complex assembly.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear origin of replication recognition complex (GO:0005664)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.A557S(1)		breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						ACATCATTGGCTTGGGCTGCC	0.527																																					p.A557S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1669T	1						.						112.0	90.0	97.0					1																	52850308		2203	4300	6503	52622896	SO:0001583	missense	4998	exon11				CCDS566.1	1p32	2010-10-12	2010-10-12	2010-10-12	ENSG00000085840	ENSG00000085840		"""ATPases / AAA-type"""	8487	protein-coding gene	gene with protein product	"""origin recognition complex, subunit 1, S. cerevisiae, homolog-like"", ""origin recognition complex 1"", ""replication control protein 1"""	601902	"""origin recognition complex, subunit 1 (yeast homolog)-like"", ""origin recognition complex, subunit 1-like (yeast)"", ""origin recognition complex, subunit 1 homolog (S. cerevisiae)"""	ORC1L		8884289	Standard	NM_004153		Approved	HSORC1, PARC1	uc001ctu.3	Q13415	OTTHUMG00000008104	ENST00000371568.3:c.1669G>T	1.37:g.52850308C>A	ENSP00000360623:p.Ala557Ser	Somatic		Capture	Illumina HiSeq	Phase_I	52622896	NM_001190818	D3DQ34|Q13471|Q5T0F5	Missense_Mutation	SNP	ENST00000371568.3	37	CCDS566.1	.	.	.	.	.	.	.	.	.	.	C	5.774	0.327110	0.10900	.	.	ENSG00000085840	ENST00000371568;ENST00000371566	T;T	0.55413	0.52;0.52	5.91	-1.92	0.07618	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.877209	0.10315	N	0.689437	T	0.27629	0.0679	N	0.04373	-0.215	0.09310	N	1	B;B	0.20459	0.045;0.045	B;B	0.26416	0.069;0.069	T	0.28933	-1.0028	10	0.08381	T	0.77	-0.1805	13.4936	0.61411	0.0:0.3978:0.0:0.6022	.	552;557	B7Z8H0;Q13415	.;ORC1_HUMAN	S	557	ENSP00000360623:A557S;ENSP00000360621:A557S	ENSP00000360621:A557S	A	-	1	0	ORC1	52622896	0.000000	0.05858	0.028000	0.17463	0.719000	0.41307	-0.508000	0.06344	-0.371000	0.08004	-0.140000	0.14226	GCC		0.527	ORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022202.1	NM_004153	
ECHDC2	55268	broad.mit.edu	37	1	53377426	53377426	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:53377426C>T	ENST00000371522.4	-	2	251	c.158G>A	c.(157-159)cGc>cAc	p.R53H	ECHDC2_ENST00000480312.2_5'UTR|ECHDC2_ENST00000536120.1_Missense_Mutation_p.R7H|ECHDC2_ENST00000541281.1_Missense_Mutation_p.R7H|ECHDC2_ENST00000358358.5_Missense_Mutation_p.R53H	NM_001198961.1	NP_001185890.1	Q86YB7	ECHD2_HUMAN	enoyl CoA hydratase domain containing 2	53					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	lyase activity (GO:0016829)	p.R53H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	12						CAAGGCATTGCGGGCAGAAGG	0.592																																					p.R53H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G158A	1						.						71.0	67.0	68.0					1																	53377426		2203	4300	6503	53150014	SO:0001583	missense	55268	exon2			AF258590	CCDS571.1, CCDS55600.1, CCDS72794.1	1p32.3	2010-04-30	2010-04-30		ENSG00000121310	ENSG00000121310			23408	protein-coding gene	gene with protein product			"""enoyl Coenzyme A hydratase domain containing 2"""				Standard	NM_018281		Approved	FLJ10948	uc001cup.4	Q86YB7	OTTHUMG00000008927	ENST00000371522.4:c.158G>A	1.37:g.53377426C>T	ENSP00000360577:p.Arg53His	Somatic		Capture	Illumina HiSeq	Phase_I	53150014	NM_001198962	D3DQ36|Q9NV38	Missense_Mutation	SNP	ENST00000371522.4	37	CCDS55600.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.259731	0.80246	.	.	ENSG00000121310	ENST00000371522;ENST00000358358;ENST00000536120;ENST00000467988;ENST00000541281	T;T;T;T;T	0.78126	-0.23;-1.15;-0.23;-1.15;0.82	4.43	4.43	0.53597	Crotonase, core (1);	0.051869	0.64402	D	0.000001	D	0.84238	0.5428	M	0.72353	2.195	0.47994	D	0.999564	D;D;D	0.89917	0.983;1.0;1.0	P;D;D	0.68943	0.765;0.961;0.96	D	0.84286	0.0497	10	0.54805	T	0.06	.	8.5892	0.33677	0.0:0.8968:0.0:0.1032	.	7;53;53	B4DSN9;Q86YB7;Q86YB7-2	.;ECHD2_HUMAN;.	H	53;53;7;53;7	ENSP00000360577:R53H;ENSP00000351125:R53H;ENSP00000439264:R7H;ENSP00000441962:R53H;ENSP00000445358:R7H	ENSP00000351125:R53H	R	-	2	0	ECHDC2	53150014	0.991000	0.36638	1.000000	0.80357	0.980000	0.70556	1.227000	0.32576	2.466000	0.83321	0.556000	0.70494	CGC		0.592	ECHDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024712.3	NM_018281	
LRP8	7804	broad.mit.edu	37	1	53736981	53736981	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:53736981T>C	ENST00000306052.6	-	7	1145	c.1044A>G	c.(1042-1044)tcA>tcG	p.S348S	LRP8_ENST00000371454.2_Silent_p.S348S|LRP8_ENST00000354412.3_Silent_p.S219S|LRP8_ENST00000465675.1_5'UTR|LRP8_ENST00000347547.2_Silent_p.S178S|RP4-784A16.1_ENST00000432653.1_RNA	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	348	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.S348S(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						TGCAGATGTGTGAGCAGCCGC	0.617																																					p.S219S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A657G	1						.						74.0	68.0	70.0					1																	53736981		2203	4300	6503	53509569	SO:0001819	synonymous_variant	7804	exon6			D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"""Low density lipoprotein receptors"""	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.1044A>G	1.37:g.53736981T>C		Somatic		Capture	Illumina HiSeq	Phase_I	53509569	NM_017522	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Silent	SNP	ENST00000306052.6	37	CCDS578.1	.	.	.	.	.	.	.	.	.	.	T	2.591	-0.295245	0.05532	.	.	ENSG00000157193	ENST00000475501	.	.	.	5.14	1.17	0.20885	.	.	.	.	.	T	0.46151	0.1378	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23940	-1.0174	4	.	.	.	.	4.1374	0.10178	0.2938:0.0:0.4253:0.2809	.	.	.	.	R	37	.	.	H	-	2	0	LRP8	53509569	0.998000	0.40836	0.990000	0.47175	0.002000	0.02628	0.404000	0.20999	0.060000	0.16281	-1.275000	0.01399	CAC		0.617	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631	
C8A	731	broad.mit.edu	37	1	57383353	57383353	+	Silent	SNP	G	G	A	rs147108278		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:57383353G>A	ENST00000361249.3	+	11	1815	c.1719G>A	c.(1717-1719)tcG>tcA	p.S573S		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	573	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)		p.S573S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						GAGGGGCCTCGTGTCCAGGGC	0.577													G|||	1	0.000199681	0.0	0.0	5008	,	,		17594	0.0		0.0	False		,,,				2504	0.001				p.S573S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1719A	1						.	G		0,4406		0,0,2203	59.0	58.0	58.0		1719	-9.4	0.0	1	dbSNP_134	58	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	C8A	NM_000562.2		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		573/585	57383353	4,13002	2203	4300	6503	57155941	SO:0001819	synonymous_variant	731	exon11			M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"""Complement system"""	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.1719G>A	1.37:g.57383353G>A		Somatic		Capture	Illumina HiSeq	Phase_I	57155941	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Silent	SNP	ENST00000361249.3	37	CCDS606.1																																																																																				0.577	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562	
DOCK7	85440	broad.mit.edu	37	1	62979248	62979248	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:62979248G>A	ENST00000340370.5	-	32	4073	c.4056C>T	c.(4054-4056)agC>agT	p.S1352S	DOCK7_ENST00000251157.5_Silent_p.S1383S	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1383					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)	p.S1352S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TAAAGGTCAAGCTATTCATTC	0.378																																					p.S1352S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4056T	1						.						102.0	95.0	97.0					1																	62979248		2203	4300	6503	62751836	SO:0001819	synonymous_variant	85440	exon32				CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.4056C>T	1.37:g.62979248G>A		Somatic		Capture	Illumina HiSeq	Phase_I	62751836	NM_033407	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	G	7.951	0.744950	0.15710	.	.	ENSG00000116641	ENST00000454575	.	.	.	5.45	0.721	0.18219	.	.	.	.	.	T	0.56016	0.1957	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50013	-0.8877	4	.	.	.	.	9.1392	0.36892	0.6304:0.0:0.3696:0.0	.	.	.	.	F	555	.	.	L	-	1	0	DOCK7	62751836	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.709000	0.37909	0.375000	0.24679	-0.471000	0.05019	CTT		0.378	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
DOCK7	85440	broad.mit.edu	37	1	63009372	63009372	+	Silent	SNP	C	C	T	rs370940626		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:63009372C>T	ENST00000340370.5	-	23	2828	c.2811G>A	c.(2809-2811)acG>acA	p.T937T	DOCK7_ENST00000251157.5_Silent_p.T968T	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	968					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)	p.T937T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						AGAAACTTGACGTCTCTGTGT	0.373													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17781	0.0		0.0	False		,,,				2504	0.0				p.T937T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2811A	1						.	C		1,4405	2.1+/-5.4	0,1,2202	147.0	135.0	139.0		2811	2.4	1.0	1		139	0,8600		0,0,4300	no	coding-synonymous	DOCK7	NM_033407.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		937/2110	63009372	1,13005	2203	4300	6503	62781960	SO:0001819	synonymous_variant	85440	exon23				CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.2811G>A	1.37:g.63009372C>T		Somatic		Capture	Illumina HiSeq	Phase_I	62781960	NM_033407	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	C	6.389	0.439872	0.12104	2.27E-4	0.0	ENSG00000116641	ENST00000454575	.	.	.	5.3	2.38	0.29361	.	.	.	.	.	T	0.61060	0.2317	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55667	-0.8105	4	.	.	.	.	11.075	0.48025	0.2592:0.616:0.1247:0.0	.	.	.	.	I	140	.	.	V	-	1	0	DOCK7	62781960	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.244000	0.43124	0.362000	0.24319	0.650000	0.86243	GTC		0.373	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
WDR78	79819	broad.mit.edu	37	1	67391874	67391874	+	5'Flank	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:67391874G>A	ENST00000371026.3	-	0	0				WDR78_ENST00000371022.3_5'Flank|WDR78_ENST00000431318.1_5'Flank|MIER1_ENST00000401041.1_Nonsense_Mutation_p.W39*|WDR78_ENST00000371023.3_5'Flank|MIER1_ENST00000371016.1_5'UTR|MIER1_ENST00000371018.3_5'UTR|MIER1_ENST00000355977.6_5'UTR|MIER1_ENST00000357692.2_5'UTR|MIER1_ENST00000371012.2_5'UTR|MIER1_ENST00000371014.1_Nonsense_Mutation_p.W39*	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78						hematopoietic progenitor cell differentiation (GO:0002244)			p.W39*(1)		NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						TTCGGACGTGGTTAAGAACCA	0.502																																					p.W39X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G117A	1						.						170.0	164.0	166.0					1																	67391874		2005	4175	6180	67164462	SO:0001631	upstream_gene_variant	57708	exon2			BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"""WD repeat domain containing"""	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165		1.37:g.67391874G>A	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	67164462	NM_001077700	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Nonsense_Mutation	SNP	ENST00000371026.3	37	CCDS635.1	.	.	.	.	.	.	.	.	.	.	G	37	6.059278	0.97246	.	.	ENSG00000198160	ENST00000401041;ENST00000371014	.	.	.	4.56	4.56	0.56223	.	1.134460	0.06638	N	0.760610	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.5364	13.5444	0.61695	0.0:0.0:1.0:0.0	.	.	.	.	X	39	.	ENSP00000360053:W39X	W	+	3	0	MIER1	67164462	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.316000	0.43761	2.481000	0.83766	0.655000	0.94253	TGG		0.502	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	
WLS	79971	broad.mit.edu	37	1	68564333	68564333	+	Silent	SNP	G	G	A	rs561611966		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:68564333G>A	ENST00000354777.2	-	12	1859	c.1614C>T	c.(1612-1614)aaC>aaT	p.N538N	WLS_ENST00000540432.1_Silent_p.N540N|GNG12-AS1_ENST00000413628.1_RNA|GNG12-AS1_ENST00000420587.1_RNA	NM_001002292.3	NP_001002292.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	0					anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)	p.N538N(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						cagaagctgcgttgtcattga	0.393													G|||	1	0.000199681	0.0	0.0	5008	,	,		17576	0.0		0.0	False		,,,				2504	0.001				p.N538N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1614T	1						.						139.0	127.0	131.0					1																	68564333		2203	4300	6503	68336921	SO:0001819	synonymous_variant	79971	exon12			BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"""wntless homolog"""	611514	"""chromosome 1 open reading frame 139"", ""G protein-coupled receptor 177"", ""wntless homolog (Drosophila)"""	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000354777.2:c.1614C>T	1.37:g.68564333G>A		Somatic		Capture	Illumina HiSeq	Phase_I	68336921	NM_001002292	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Silent	SNP	ENST00000354777.2	37	CCDS30750.1																																																																																				0.393	WLS-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025370.1	NM_024911	
RPE65	6121	broad.mit.edu	37	1	68897190	68897190	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:68897190G>A	ENST00000262340.5	-	11	1260	c.1207C>T	c.(1207-1209)Ctg>Ttg	p.L403L		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	403					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)	p.L403L(1)		central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						TCAGGCTCCAGCCAGATAGTC	0.448																																					p.L403L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1207T	1						.						58.0	62.0	60.0					1																	68897190		2203	4300	6503	68669778	SO:0001819	synonymous_variant	6121	exon11			U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"""retinol isomerase"", ""all-trans-retinyl-palmitate hydrolase"", ""retinoid isomerohydrolase"", ""BCO family, member 3"""	180069	"""retinal pigment epithelium-specific protein (65kD)"""	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.1207C>T	1.37:g.68897190G>A		Somatic		Capture	Illumina HiSeq	Phase_I	68669778	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	37	CCDS643.1																																																																																				0.448	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329	
NEGR1	257194	broad.mit.edu	37	1	72058515	72058515	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:72058515T>G	ENST00000357731.5	-	6	1164	c.925A>C	c.(925-927)Agc>Cgc	p.S309R	NEGR1_ENST00000306821.3_Missense_Mutation_p.S181R|NEGR1_ENST00000434200.1_Missense_Mutation_p.S263R	NM_173808.2	NP_776169.2	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1	309	Ig-like C2-type 3.				feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|positive regulation of neuron projection development (GO:0010976)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.S309R(1)		endometrium(1)|kidney(4)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		AGAGGCAGGCTCGCATTGGTT	0.478																																					p.S309R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A925C	1						.						124.0	124.0	124.0					1																	72058515		2203	4300	6503	71831103	SO:0001583	missense	257194	exon6			AK092307	CCDS661.1	1p31.1	2013-01-11			ENSG00000172260	ENSG00000172260		"""Immunoglobulin superfamily / I-set domain containing"""	17302	protein-coding gene	gene with protein product	"""a kindred of IgLON"", ""neurotractin"", ""IgLON family member 4"""	613173				10075727	Standard	NM_173808		Approved	KILON, MGC46680, Ntra, IGLON4	uc001dfw.3	Q7Z3B1	OTTHUMG00000009698	ENST00000357731.5:c.925A>C	1.37:g.72058515T>G	ENSP00000350364:p.Ser309Arg	Somatic		Capture	Illumina HiSeq	Phase_I	71831103	NM_173808	Q5VT21|Q6UY06|Q8N440|Q8NAQ3	Missense_Mutation	SNP	ENST00000357731.5	37	CCDS661.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.829979	0.91036	.	.	ENSG00000172260	ENST00000357731;ENST00000306821;ENST00000434200	T;T;T	0.68181	-0.31;-0.31;-0.31	6.03	6.03	0.97812	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.78059	0.4224	M	0.75777	2.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.79174	-0.1912	10	0.49607	T	0.09	-13.5224	16.5582	0.84512	0.0:0.0:0.0:1.0	.	263;309	B4DI94;Q7Z3B1	.;NEGR1_HUMAN	R	309;181;263	ENSP00000350364:S309R;ENSP00000305938:S181R;ENSP00000413294:S263R	ENSP00000305938:S181R	S	-	1	0	NEGR1	71831103	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.649000	0.83500	2.308000	0.77769	0.533000	0.62120	AGC		0.478	NEGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026722.4	NM_173808	
LRRIQ3	127255	broad.mit.edu	37	1	74507481	74507481	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:74507481delA	ENST00000395089.1	-	6	1133	c.1134delT	c.(1132-1134)tttfs	p.F378fs	LRRIQ3_ENST00000354431.4_Frame_Shift_Del_p.F378fs			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	378								p.P379fs*26(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						GATATGCAGGAAAAAAATGTT	0.348																																					p.F378fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1134delT	1						.						92.0	86.0	88.0					1																	74507481		1828	4094	5922	74280069	SO:0001589	frameshift_variant	127255	exon7			BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"""leucine rich repeat containing 44"""	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.1134delT	1.37:g.74507481delA	ENSP00000378524:p.Phe378fs	Somatic		Capture	Illumina HiSeq	Phase_I	74280069	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Frame_Shift_Del	DEL	ENST00000395089.1	37	CCDS41350.1																																																																																				0.348	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258	
FPGT-TNNI3K	100526835	broad.mit.edu	37	1	74797162	74797162	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:74797162C>T	ENST00000370899.3	+	8	813	c.776C>T	c.(775-777)gCt>gTt	p.A259V	FPGT-TNNI3K_ENST00000370895.1_Missense_Mutation_p.A259V|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.A272V|TNNI3K_ENST00000326637.3_Missense_Mutation_p.A158V|TNNI3K_ENST00000370891.2_Missense_Mutation_p.A259V	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough									p.A158V(1)									CAACATGGAGCTAATGTCAAT	0.383																																					p.A259V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C776T	1						.						129.0	105.0	113.0					1																	74797162		2203	4300	6503	74569750	SO:0001583	missense	51086	exon8					1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.776C>T	1.37:g.74797162C>T	ENSP00000359936:p.Ala259Val	Somatic		Capture	Illumina HiSeq	Phase_I	74569750	NM_001199327		Missense_Mutation	SNP	ENST00000370899.3	37		.	.	.	.	.	.	.	.	.	.	C	28.4	4.915147	0.92178	.	.	ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000370895;ENST00000557284;ENST00000370891;ENST00000326637	T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55	5.45	4.52	0.55395	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.72550	0.3474	L	0.41236	1.265	0.58432	D	0.999999	D;D;D;D	0.89917	0.983;0.972;1.0;1.0	D;D;D;D	0.87578	0.926;0.91;0.998;0.992	T	0.76143	-0.3067	10	0.52906	T	0.07	.	15.8306	0.78745	0.0:0.8637:0.1363:0.0	.	158;259;259;259	Q59H18;Q59H18-1;Q59H18-4;Q59H18-3	TNI3K_HUMAN;.;.;.	V	259;259;259;259;158	ENSP00000359936:A259V;ENSP00000359932:A259V;ENSP00000450895:A259V;ENSP00000359928:A259V;ENSP00000322251:A158V	ENSP00000322251:A158V	A	+	2	0	RP11-653A5.2;AC093158.1	74569750	1.000000	0.71417	0.997000	0.53966	0.911000	0.54048	4.153000	0.58118	1.497000	0.48584	0.655000	0.94253	GCT		0.383	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3		
FUBP1	8880	broad.mit.edu	37	1	78426049	78426049	+	Silent	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:78426049T>A	ENST00000370768.2	-	15	1557	c.1476A>T	c.(1474-1476)ggA>ggT	p.G492G	FUBP1_ENST00000436586.2_Silent_p.G513G|FUBP1_ENST00000370767.1_Silent_p.G492G	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	492	Pro-rich.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)	p.G492G(1)		central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						GGCCTGGTGGTCCAGGATTAT	0.532			"""F, N"""		oligodendroglioma																																p.G492G			Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1476T	1						.						38.0	43.0	41.0					1																	78426049		2203	4300	6503	78198637	SO:0001819	synonymous_variant	8880	exon15			U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.1476A>T	1.37:g.78426049T>A		Somatic		Capture	Illumina HiSeq	Phase_I	78198637	NM_003902	Q12828	Silent	SNP	ENST00000370768.2	37	CCDS683.1																																																																																				0.532	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902	
TTLL7	79739	broad.mit.edu	37	1	84383310	84383310	+	Frame_Shift_Del	DEL	T	T	-	rs200358438		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:84383310delT	ENST00000260505.8	-	14	1941	c.1564delA	c.(1564-1566)actfs	p.T523fs	TTLL7_ENST00000477524.1_5'UTR	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	523					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)	p.T522fs*19(1)		kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		GTCTTGGTAGTTTTTCCCATC	0.343																																					p.T522fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1564delA	1						.						160.0	147.0	151.0					1																	84383310		2203	4300	6503	84155898	SO:0001589	frameshift_variant	79739	exon14			AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"""Tubulin tyrosine ligase-like family"""	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.1564delA	1.37:g.84383310delT	ENSP00000260505:p.Thr523fs	Somatic		Capture	Illumina HiSeq	Phase_I	84155898	NM_024686	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Frame_Shift_Del	DEL	ENST00000260505.8	37	CCDS690.2																																																																																				0.343	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027498.1	NM_024686	
MCOLN2	255231	broad.mit.edu	37	1	85406567	85406567	+	Missense_Mutation	SNP	G	G	A	rs116001957	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:85406567G>A	ENST00000370608.3	-	8	1022	c.955C>T	c.(955-957)Cgg>Tgg	p.R319W	MCOLN2_ENST00000284027.5_Missense_Mutation_p.R291W|MCOLN2_ENST00000531325.1_5'UTR	NM_153259.2	NP_694991.2	Q8IZK6	MCLN2_HUMAN	mucolipin 2	319					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R319W(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	18				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		CTTACCTTCCGTAACCTTAGA	0.463													G|||	25	0.00499201	0.0159	0.0058	5008	,	,		21438	0.0		0.0	False		,,,				2504	0.0				p.R319W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C955T	1						.	G	TRP/ARG	58,4348	55.5+/-91.7	0,58,2145	148.0	110.0	123.0		955	4.8	1.0	1	dbSNP_132	123	3,8597	3.0+/-9.4	0,3,4297	yes	missense	MCOLN2	NM_153259.2	101	0,61,6442	AA,AG,GG		0.0349,1.3164,0.469	probably-damaging	319/567	85406567	61,12945	2203	4300	6503	85179155	SO:0001583	missense	255231	exon8			AK094010	CCDS30762.1	1p22	2011-12-16			ENSG00000153898	ENSG00000153898		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	13357	protein-coding gene	gene with protein product		607399				16382100	Standard	XM_005270719		Approved	TRPML2, FLJ36691, TRP-ML2	uc001dkm.3	Q8IZK6	OTTHUMG00000009954	ENST00000370608.3:c.955C>T	1.37:g.85406567G>A	ENSP00000359640:p.Arg319Trp	Somatic		Capture	Illumina HiSeq	Phase_I	85179155	NM_153259	A6NI99|Q2M3I6|Q5TAG5|Q8N9R3	Missense_Mutation	SNP	ENST00000370608.3	37	CCDS30762.1	11	0.005036630036630037	8	0.016260162601626018	3	0.008287292817679558	0	0.0	0	0.0	G	18.12	3.552170	0.65311	0.013164	3.49E-4	ENSG00000153898	ENST00000370608;ENST00000284027	T;T	0.78707	-1.2;-1.2	5.69	4.76	0.60689	.	0.208508	0.43919	D	0.000507	T	0.67896	0.2942	L	0.49126	1.545	0.58432	D	0.999993	D	0.65815	0.995	P	0.47528	0.549	T	0.67829	-0.5569	10	0.31617	T	0.26	-26.6444	15.2679	0.73678	0.0:0.0:0.8543:0.1457	.	319	Q8IZK6	MCLN2_HUMAN	W	319;291	ENSP00000359640:R319W;ENSP00000284027:R291W	ENSP00000284027:R291W	R	-	1	2	MCOLN2	85179155	1.000000	0.71417	0.983000	0.44433	0.922000	0.55478	4.972000	0.63756	1.351000	0.45789	0.655000	0.94253	CGG		0.463	MCOLN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027567.2	NM_153259	
C1orf52	148423	broad.mit.edu	37	1	85724229	85724229	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:85724229T>C	ENST00000471115.1	-	2	461	c.453A>G	c.(451-453)gaA>gaG	p.E151E	C1orf52_ENST00000294661.4_5'UTR|C1orf52_ENST00000344356.5_Silent_p.E151E	NM_198077.3	NP_932343.1	Q8N6N3	CA052_HUMAN	chromosome 1 open reading frame 52	151							poly(A) RNA binding (GO:0044822)	p.E151E(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)	10				all cancers(265;0.0105)|Epithelial(280;0.0293)		TCTCCTCCCCTTCTGGTAGAA	0.428																																					p.E151E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A453G	1						.						210.0	196.0	201.0					1																	85724229		2203	4300	6503	85496817	SO:0001819	synonymous_variant	148423	exon2			BC029538	CCDS703.1	1p22.3	2008-02-05			ENSG00000162642	ENSG00000162642			24871	protein-coding gene	gene with protein product						11891061	Standard	NM_198077		Approved	gm117, FLJ44982	uc001dkv.3	Q8N6N3	OTTHUMG00000009966	ENST00000471115.1:c.453A>G	1.37:g.85724229T>C		Somatic		Capture	Illumina HiSeq	Phase_I	85496817	NM_198077	B3KX89|Q8TDK5|Q8TDK6	Silent	SNP	ENST00000471115.1	37	CCDS703.1																																																																																				0.428	C1orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027616.2	NM_198077	
COL24A1	255631	broad.mit.edu	37	1	86249233	86249233	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:86249233T>G	ENST00000370571.2	-	51	4596	c.4230A>C	c.(4228-4230)gaA>gaC	p.E1410D	COL24A1_ENST00000436319.1_Missense_Mutation_p.E1410D	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1410	Collagen-like 16.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)	p.E1410D(1)		NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		CAGCATCCCCTTCAGGACCCT	0.353																																					p.E1410D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4230C	1						.						122.0	115.0	117.0					1																	86249233		1840	4085	5925	86021821	SO:0001583	missense	255631	exon51			AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.4230A>C	1.37:g.86249233T>G	ENSP00000359603:p.Glu1410Asp	Somatic		Capture	Illumina HiSeq	Phase_I	86021821	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	T	12.22	1.872250	0.33069	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.93307	-3.2;-3.1	5.48	-3.93	0.04143	.	0.000000	0.39083	N	0.001464	T	0.65943	0.2740	N	0.11201	0.11	0.26770	N	0.969815	P;P	0.34977	0.478;0.458	B;B	0.38880	0.148;0.284	T	0.73672	-0.3909	10	0.13853	T	0.58	.	3.6705	0.08272	0.5974:0.1259:0.0997:0.177	.	1410;1410	Q17RW2;Q17RW2-2	COOA1_HUMAN;.	D	1410	ENSP00000359603:E1410D;ENSP00000392531:E1410D	ENSP00000359603:E1410D	E	-	3	2	COL24A1	86021821	0.021000	0.18746	0.961000	0.40146	0.883000	0.51084	-1.096000	0.03353	-0.281000	0.09141	-0.242000	0.12053	GAA		0.353	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
ODF2L	57489	broad.mit.edu	37	1	86814494	86814494	+	3'UTR	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:86814494delT	ENST00000359242.3	-	0	5572				ODF2L_ENST00000317336.7_Frame_Shift_Del_p.N654fs|ODF2L_ENST00000370567.1_Frame_Shift_Del_p.N625fs|ODF2L_ENST00000394731.1_Frame_Shift_Del_p.N494fs|ODF2L_ENST00000370566.3_Frame_Shift_Del_p.N572fs	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like							centrosome (GO:0005813)		p.N625fs*16(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		AATACTCTCATTTTGATTTTC	0.254																																					p.N572fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1715delA	1						.						37.0	38.0	37.0					1																	86814494		2196	4256	6452	86587082	SO:0001624	3_prime_UTR_variant	57489	exon16				CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.*3380A>-	1.37:g.86814494delT		Somatic		Capture	Illumina HiSeq	Phase_I	86587082	NM_001184766	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Frame_Shift_Del	DEL	ENST00000359242.3	37	CCDS41354.2																																																																																				0.254	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2		
CLCA2	9635	broad.mit.edu	37	1	86921029	86921029	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:86921029C>T	ENST00000370565.4	+	14	2813	c.2651C>T	c.(2650-2652)gCg>gTg	p.A884V		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	884					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)	p.A884V(1)		NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		ATTGCCCAGGCGCCTCTGTTT	0.418																																					p.A884V	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2651T	1						.						192.0	196.0	195.0					1																	86921029		2203	4300	6503	86693617	SO:0001583	missense	9635	exon14				CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2651C>T	1.37:g.86921029C>T	ENSP00000359596:p.Ala884Val	Somatic		Capture	Illumina HiSeq	Phase_I	86693617	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	.	.	.	.	.	.	.	.	.	.	C	1.243	-0.620812	0.03636	.	.	ENSG00000137975	ENST00000370565	T	0.02812	4.15	5.62	0.179	0.15063	.	0.826255	0.10592	N	0.656597	T	0.00524	0.0017	N	0.25094	0.71	0.09310	N	1	B	0.17268	0.021	B	0.09377	0.004	T	0.45745	-0.9240	10	0.02654	T	1	-0.6236	9.6846	0.40091	0.0:0.4394:0.0:0.5606	.	884	Q9UQC9	CLCA2_HUMAN	V	884	ENSP00000359596:A884V	ENSP00000359596:A884V	A	+	2	0	CLCA2	86693617	0.016000	0.18221	0.003000	0.11579	0.385000	0.30292	0.074000	0.14662	-0.248000	0.09583	0.591000	0.81541	GCG		0.418	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
PKN2	5586	broad.mit.edu	37	1	89299050	89299050	+	Silent	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:89299050T>G	ENST00000370521.3	+	22	3233	c.2874T>G	c.(2872-2874)acT>acG	p.T958T	PKN2_ENST00000544045.1_Silent_p.T632T|PKN2_ENST00000495119.1_3'UTR|PKN2_ENST00000370505.3_Silent_p.T801T|PKN2_ENST00000370513.5_Silent_p.T910T	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	958	AGC-kinase C-terminal.|Necessary for the catalytic activity.				apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.T958T(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		CTATTCTGACTCCACCTCGAG	0.398																																					p.T958T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2874G	1						.						104.0	101.0	102.0					1																	89299050		1942	4121	6063	89071638	SO:0001819	synonymous_variant	5586	exon22			U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"""cardiolipin-activated protein kinase Pak2"""	602549	"""protein kinase C-like 2"""	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.2874T>G	1.37:g.89299050T>G		Somatic		Capture	Illumina HiSeq	Phase_I	89071638	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Silent	SNP	ENST00000370521.3	37	CCDS714.1																																																																																				0.398	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256	
GBP2	2634	broad.mit.edu	37	1	89579786	89579786	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:89579786C>T	ENST00000370466.3	-	7	1330	c.1062G>A	c.(1060-1062)ctG>ctA	p.L354L	GBP2_ENST00000463660.1_5'UTR	NM_004120.3	NP_004111.2	P32456	GBP2_HUMAN	guanylate binding protein 2, interferon-inducible	354					cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.L354L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1)	20		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		TGTCCCTGTGCAGGTCCAGCA	0.512																																					p.L354L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1062A	1						.						114.0	112.0	113.0					1																	89579786		2203	4300	6503	89352374	SO:0001819	synonymous_variant	2634	exon7			BC073163	CCDS719.1	1p22.2	2008-02-05			ENSG00000162645	ENSG00000162645			4183	protein-coding gene	gene with protein product		600412				1715024	Standard	NM_004120		Approved		uc001dmz.1	P32456	OTTHUMG00000010662	ENST00000370466.3:c.1062G>A	1.37:g.89579786C>T		Somatic		Capture	Illumina HiSeq	Phase_I	89352374	NM_004120	Q6GPH0|Q6IAU2|Q86TB0	Silent	SNP	ENST00000370466.3	37	CCDS719.1																																																																																				0.512	GBP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029406.2	NM_004120	
LRRC8C	84230	broad.mit.edu	37	1	90179038	90179038	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:90179038T>C	ENST00000370454.4	+	3	1164	c.909T>C	c.(907-909)taT>taC	p.Y303Y	LRRC8C_ENST00000479252.1_Intron|RP11-302M6.4_ENST00000370453.5_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	303					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.Y303Y(1)		breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		TGACTGGATATAAAAACTTTT	0.368																																					p.Y303Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T909C	1						.						164.0	148.0	153.0					1																	90179038		2203	4300	6503	89951626	SO:0001819	synonymous_variant	84230	exon3				CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"""hypothetical protein AD158"""	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.909T>C	1.37:g.90179038T>C		Somatic		Capture	Illumina HiSeq	Phase_I	89951626	NM_032270	B3KXS9|Q29RV6|Q9H075	Silent	SNP	ENST00000370454.4	37	CCDS725.1																																																																																				0.368	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270	
BARHL2	343472	broad.mit.edu	37	1	91178100	91178100	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:91178100A>G	ENST00000370445.4	-	3	974	c.933T>C	c.(931-933)ttT>ttC	p.F311F		NM_020063.1	NP_064447.1	Q9NY43	BARH2_HUMAN	BarH-like homeobox 2	311					cell fate determination (GO:0001709)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|positive regulation of translation (GO:0045727)|regulation of axon extension (GO:0030516)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	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 (GO:0043565)	p.F311F(1)		cervix(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_lung(203;0.0263)|Lung SC(238;0.128)		all cancers(265;0.000897)|Epithelial(280;0.00516)|OV - Ovarian serous cystadenocarcinoma(397;0.211)		AAGGCGATGGAAACATCCTCT	0.617																																					p.F311F	GBM(199;3561 4100 22440)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T933C	1						.						36.0	36.0	36.0					1																	91178100		2202	4300	6502	90950688	SO:0001819	synonymous_variant	343472	exon3			AJ251753	CCDS730.1	1p22.2	2011-07-08	2007-07-09		ENSG00000143032	ENSG00000143032		"""Homeoboxes / ANTP class : NKL subclass"""	954	protein-coding gene	gene with protein product		605212	"""BarH (Drosophila)-like 2"""				Standard	NM_020063		Approved		uc001dns.3	Q9NY43	OTTHUMG00000010020	ENST00000370445.4:c.933T>C	1.37:g.91178100A>G		Somatic		Capture	Illumina HiSeq	Phase_I	90950688	NM_020063	A0AVP2|Q7Z4N7	Silent	SNP	ENST00000370445.4	37	CCDS730.1																																																																																				0.617	BARHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027728.2		
ZNF644	84146	broad.mit.edu	37	1	91405939	91405939	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:91405939G>A	ENST00000370440.1	-	3	1189	c.972C>T	c.(970-972)gaC>gaT	p.D324D	ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000337393.5_Silent_p.D324D|ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000361321.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	324					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D324D(1)		breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		GTTCTAGAAAGTCTACTTCTT	0.353																																					p.D324D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C972T	1						.						95.0	94.0	94.0					1																	91405939		2203	4298	6501	91178527	SO:0001819	synonymous_variant	84146	exon3			AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.972C>T	1.37:g.91405939G>A		Somatic		Capture	Illumina HiSeq	Phase_I	91178527	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Silent	SNP	ENST00000370440.1	37	CCDS731.1																																																																																				0.353	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186	
RPAP2	79871	broad.mit.edu	37	1	92801969	92801969	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:92801969T>C	ENST00000610020.1	+	10	1713	c.1604T>C	c.(1603-1605)cTt>cCt	p.L535P		NM_024813.2	NP_079089.2	Q8IXW5	RPAP2_HUMAN	RNA polymerase II associated protein 2	535					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|snRNA transcription (GO:0009301)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleolus (GO:0005730)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)	p.L535P(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	22		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)		CTTAAAAATCTTGTTCGAACT	0.303																																					p.L535P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1604C	1						.						73.0	78.0	76.0					1																	92801969		2203	4297	6500	92574557	SO:0001583	missense	79871	exon10			AK023212	CCDS740.1	1p22.1	2014-01-28	2007-07-26	2007-07-26	ENSG00000122484	ENSG00000122484			25791	protein-coding gene	gene with protein product		611476	"""chromosome 1 open reading frame 82"""	C1orf82		17643375	Standard	NM_024813		Approved	FLJ13150	uc001dot.2	Q8IXW5	OTTHUMG00000010288	ENST00000610020.1:c.1604T>C	1.37:g.92801969T>C	ENSP00000476948:p.Leu535Pro	Somatic		Capture	Illumina HiSeq	Phase_I	92574557	NM_024813	C9JKB5|Q49AS7|Q9H8Y2	Missense_Mutation	SNP	ENST00000610020.1	37	CCDS740.1	.	.	.	.	.	.	.	.	.	.	T	19.34	3.807998	0.70797	.	.	ENSG00000122484	ENST00000370343;ENST00000394482	.	.	.	5.74	5.74	0.90152	.	0.059223	0.64402	D	0.000002	T	0.73992	0.3658	M	0.78801	2.425	0.38502	D	0.948246	D	0.89917	1.0	D	0.87578	0.998	T	0.79778	-0.1660	8	0.87932	D	0	-15.2308	13.4234	0.61011	0.0:0.0:0.0:1.0	.	535	Q8IXW5	RPAP2_HUMAN	P	535	.	ENSP00000359368:L535P	L	+	2	0	RPAP2	92574557	1.000000	0.71417	0.929000	0.37066	0.994000	0.84299	4.777000	0.62361	2.197000	0.70478	0.528000	0.53228	CTT		0.303	RPAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028368.2	NM_024813	
ARHGAP29	9411	broad.mit.edu	37	1	94654843	94654843	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:94654843T>A	ENST00000260526.6	-	14	1687	c.1505A>T	c.(1504-1506)gAt>gTt	p.D502V	ARHGAP29_ENST00000482481.1_5'UTR	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	502					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)	p.D502V(1)		NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		GCGTACAACATCCTCTAAAGA	0.363																																					p.D502V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1505T	1						.						89.0	88.0	89.0					1																	94654843		2203	4299	6502	94427431	SO:0001583	missense	9411	exon14				CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"""Rho GTPase activating proteins"""	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.1505A>T	1.37:g.94654843T>A	ENSP00000260526:p.Asp502Val	Somatic		Capture	Illumina HiSeq	Phase_I	94427431	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	37	CCDS748.1	.	.	.	.	.	.	.	.	.	.	T	16.05	3.012291	0.54468	.	.	ENSG00000137962	ENST00000260526	T	0.25414	1.8	5.76	3.3	0.37823	.	0.185189	0.26248	N	0.025470	T	0.14056	0.0340	L	0.58101	1.795	0.80722	D	1	B;P	0.36392	0.379;0.551	B;B	0.40602	0.155;0.334	T	0.03514	-1.1029	10	0.56958	D	0.05	-23.4796	5.9146	0.19048	0.1461:0.0781:0.0:0.7758	.	502;502	F8VWZ8;Q52LW3	.;RHG29_HUMAN	V	502	ENSP00000260526:D502V	ENSP00000260526:D502V	D	-	2	0	ARHGAP29	94427431	0.880000	0.30214	0.942000	0.38095	0.790000	0.44656	2.384000	0.44362	1.108000	0.41662	0.528000	0.53228	GAT		0.363	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815	
PTBP2	58155	broad.mit.edu	37	1	97278459	97278459	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:97278459G>A	ENST00000426398.2	+	12	1406	c.1363G>A	c.(1363-1365)Gcc>Acc	p.A455T	PTBP2_ENST00000541987.1_3'UTR|PTBP2_ENST00000370197.1_Missense_Mutation_p.A460T|PTBP2_ENST00000394184.3_Missense_Mutation_p.A471T|PTBP2_ENST00000482253.1_3'UTR|PTBP2_ENST00000370198.1_Missense_Mutation_p.A460T|PTBP2_ENST00000609116.1_Missense_Mutation_p.A455T	NM_021190.2	NP_067013.1	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2	455	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splice site selection (GO:0006376)|negative regulation of RNA splicing (GO:0033119)|regulation of neural precursor cell proliferation (GO:2000177)	spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A455T(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|skin(1)	26		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)		TCCTCCTTCTGCCACCCTTCA	0.318																																					p.A455T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1363A	1						.						56.0	60.0	58.0					1																	97278459		2188	4294	6482	97051047	SO:0001583	missense	58155	exon12			AB051232	CCDS754.1, CCDS72828.1, CCDS72829.1, CCDS72830.1	1p21.3	2013-07-16			ENSG00000117569	ENSG00000117569		"""RNA binding motif (RRM) containing"""	17662	protein-coding gene	gene with protein product		608449				11003644	Standard	XM_005271084		Approved	brPTB, nPTB, PTB, PTBLP	uc001drq.3	Q9UKA9	OTTHUMG00000010685	ENST00000426398.2:c.1363G>A	1.37:g.97278459G>A	ENSP00000412788:p.Ala455Thr	Somatic		Capture	Illumina HiSeq	Phase_I	97051047	NM_021190	Q8N0Z1|Q8N160|Q8NFB0|Q8NFB1|Q969N9|Q96Q76	Missense_Mutation	SNP	ENST00000426398.2	37	CCDS754.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.216816	0.79352	.	.	ENSG00000117569	ENST00000236228;ENST00000543738;ENST00000370198;ENST00000370197;ENST00000426398;ENST00000394184	T;T;T;T;T	0.46819	0.89;0.88;0.87;0.9;0.86	5.16	5.16	0.70880	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.096491	0.64402	D	0.000001	T	0.56337	0.1978	M	0.66506	2.035	0.80722	D	1	B;D;B;D;B;B;B	0.58268	0.052;0.982;0.001;0.981;0.013;0.02;0.022	B;P;B;P;B;B;B	0.56700	0.045;0.728;0.001;0.804;0.046;0.068;0.068	T	0.59643	-0.7416	10	0.59425	D	0.04	-3.9397	19.0112	0.92874	0.0:0.0:1.0:0.0	.	463;471;127;460;455;455;460	B4DSU5;B4DSS8;B4DSI2;Q9UKA9-4;Q9UKA9;Q9UKA9-2;Q9UKA9-3	.;.;.;.;PTBP2_HUMAN;.;.	T	455;127;460;460;455;471	ENSP00000236228:A455T;ENSP00000359217:A460T;ENSP00000359216:A460T;ENSP00000412788:A455T;ENSP00000377738:A471T	ENSP00000236228:A455T	A	+	1	0	PTBP2	97051047	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.809000	0.99208	2.555000	0.86185	0.557000	0.71058	GCC		0.318	PTBP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029453.1		
LPPR4	9890	broad.mit.edu	37	1	99772168	99772168	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:99772168C>T	ENST00000370185.3	+	7	2391	c.1894C>T	c.(1894-1896)Ccc>Tcc	p.P632S	LPPR4_ENST00000370184.1_Missense_Mutation_p.P474S|LPPR4_ENST00000457765.1_Missense_Mutation_p.P574S	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		632					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)	p.P632S(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		GAACAACAGGCCCATCATACA	0.557																																					p.P632S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1894T	1						.						89.0	85.0	86.0					1																	99772168		2203	4300	6503	99544756	SO:0001583	missense	9890	exon7																														ENST00000370185.3:c.1894C>T	1.37:g.99772168C>T	ENSP00000359204:p.Pro632Ser	Somatic		Capture	Illumina HiSeq	Phase_I	99544756	NM_014839	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Missense_Mutation	SNP	ENST00000370185.3	37	CCDS757.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.261204	0.80246	.	.	ENSG00000117600	ENST00000370185;ENST00000457765;ENST00000370184	T;T;T	0.66460	0.27;-0.21;-0.17	5.9	5.9	0.94986	.	0.202757	0.42172	D	0.000755	T	0.78489	0.4291	M	0.65975	2.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.989	T	0.75133	-0.3425	9	.	.	.	-37.5518	20.2822	0.98520	0.0:1.0:0.0:0.0	.	574;632	E7EPS1;Q7Z2D5	.;LPPR4_HUMAN	S	632;574;474	ENSP00000359204:P632S;ENSP00000394913:P574S;ENSP00000359203:P474S	.	P	+	1	0	RP4-788L13.1	99544756	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.399000	0.79935	2.806000	0.96561	0.655000	0.94253	CCC		0.557	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2		
LPPR4	9890	broad.mit.edu	37	1	99772386	99772386	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:99772386C>T	ENST00000370185.3	+	7	2609	c.2112C>T	c.(2110-2112)cgC>cgT	p.R704R	LPPR4_ENST00000370184.1_Silent_p.R546R|LPPR4_ENST00000457765.1_Silent_p.R646R	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		704					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)	p.R704R(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		CCACCATCCGCGTCACCCCAG	0.507																																					p.R704R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2112T	1						.						66.0	58.0	61.0					1																	99772386		2203	4300	6503	99544974	SO:0001819	synonymous_variant	9890	exon7																														ENST00000370185.3:c.2112C>T	1.37:g.99772386C>T		Somatic		Capture	Illumina HiSeq	Phase_I	99544974	NM_014839	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Silent	SNP	ENST00000370185.3	37	CCDS757.1																																																																																				0.507	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2		
GSTM3	2947	broad.mit.edu	37	1	110280279	110280279	+	Splice_Site	DEL	T	T	-	rs59389091		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:110280279delT	ENST00000540225.1	-	7	777	c.467delA	c.(466-468)aag>ag	p.K156fs	GSTM3_ENST00000488824.1_5'UTR|RP4-735C1.4_ENST00000431955.1_RNA|GSTM3_ENST00000361066.2_Splice_Site_p.K156fs|GSTM3_ENST00000256594.3_Splice_Site_p.K156fs			P21266	GSTM3_HUMAN	glutathione S-transferase mu 3 (brain)	156	GST C-terminal.				cellular detoxification of nitrogen compound (GO:0070458)|establishment of blood-nerve barrier (GO:0008065)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|nitrobenzene metabolic process (GO:0018916)|response to estrogen (GO:0043627)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)	p.K156fs*30(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|skin(1)	9		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Colorectal(144;0.0339)|Lung(183;0.0426)|all cancers(265;0.113)|Epithelial(280;0.125)|COAD - Colon adenocarcinoma(174;0.134)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)|Vitamin E(DB00163)	TCTTCCTACCTTTTCCCCGGC	0.438																																					p.K156fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.467delA	1						.						129.0	148.0	141.0					1																	110280279		2203	4300	6503	110081802	SO:0001630	splice_region_variant	2947	exon7			BC000088	CCDS812.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134202	ENSG00000134202	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4635	protein-coding gene	gene with protein product		138390	"""glutathione S-transferase M3 (brain)"""			2345169	Standard	NM_000849		Approved	GST5	uc001dyo.2	P21266	OTTHUMG00000011640	ENST00000540225.1:c.468+1A>-	1.37:g.110280279delT		Somatic		Capture	Illumina HiSeq	Phase_I	110081802	NM_000849	O60550|Q96HA3	Frame_Shift_Del	DEL	ENST00000540225.1	37	CCDS812.1																																																																																				0.438	GSTM3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032182.1	NM_000849	Frame_Shift_Del
RPRD2	23248	broad.mit.edu	37	1	150418750	150418750	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:150418750delC	ENST00000369068.4	+	7	747	c.743delC	c.(742-744)tccfs	p.S248fs	RPRD2_ENST00000401000.4_Frame_Shift_Del_p.S222fs|RPRD2_ENST00000539519.1_Frame_Shift_Del_p.S222fs|RPRD2_ENST00000492220.1_3'UTR	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	248						DNA-directed RNA polymerase II, holoenzyme (GO:0016591)		p.K249fs*6(2)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						GAGGCAAGCTCCAAGCTGGAA	0.343																																					p.S248fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.743delC	1						.						57.0	55.0	56.0					1																	150418750		1807	4068	5875	148685374	SO:0001589	frameshift_variant	23248	exon7			BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"""KIAA0460"""	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.743delC	1.37:g.150418750delC	ENSP00000358064:p.Ser248fs	Somatic		Capture	Illumina HiSeq	Phase_I	148685374	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Frame_Shift_Del	DEL	ENST00000369068.4	37	CCDS44216.1																																																																																				0.343	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203	
PIP5K1A	8394	broad.mit.edu	37	1	151206914	151206914	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:151206914delT	ENST00000368888.4	+	8	1303	c.881delT	c.(880-882)cttfs	p.L294fs	PIP5K1A_ENST00000464105.1_3'UTR|PIP5K1A_ENST00000441902.2_Frame_Shift_Del_p.L282fs|PIP5K1A_ENST00000368890.4_Frame_Shift_Del_p.L281fs|PIP5K1A_ENST00000414290.2_5'Flank|PIP5K1A_ENST00000409426.1_Frame_Shift_Del_p.L282fs	NM_001135638.1	NP_001129110.1	Q99755	PI51A_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, alpha	294	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				actin cytoskeleton reorganization (GO:0031532)|activation of Rac GTPase activity (GO:0032863)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|fibroblast migration (GO:0010761)|focal adhesion assembly (GO:0048041)|glycerophospholipid metabolic process (GO:0006650)|keratinocyte differentiation (GO:0030216)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|protein targeting to plasma membrane (GO:0072661)|ruffle assembly (GO:0097178)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|kinase binding (GO:0019900)	p.L296fs*25(1)		breast(1)|central_nervous_system(1)|ovary(1)|skin(1)|stomach(1)	5	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181)			CCTGATGGTCTTTTTTTGGAT	0.438																																					p.L282fs	Pancreas(80;36 1443 2325 16095 21302)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.845delT	1						.						79.0	76.0	77.0					1																	151206914		2203	4300	6503	149473538	SO:0001589	frameshift_variant	8394	exon7			U78575	CCDS990.1, CCDS44219.1, CCDS44220.1, CCDS44221.1	1q21.3	2010-04-08			ENSG00000143398	ENSG00000143398			8994	protein-coding gene	gene with protein product		603275				8955136, 10828584	Standard	NM_003557		Approved		uc001exj.3	Q99755	OTTHUMG00000012351	ENST00000368888.4:c.881delT	1.37:g.151206914delT	ENSP00000357883:p.Leu294fs	Somatic		Capture	Illumina HiSeq	Phase_I	149473538	NM_001135636	A8K4Q0|B4DIN0|Q99754|Q99756	Frame_Shift_Del	DEL	ENST00000368888.4	37	CCDS44219.1																																																																																				0.438	PIP5K1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034425.2	NM_003557	
PCP4L1	654790	broad.mit.edu	37	1	161254154	161254156	+	In_Frame_Del	DEL	GGA	GGA	-	rs549268381		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	GGA	GGA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:161254154_161254156delGGA	ENST00000504449.1	+	3	338_340	c.90_92delGGA	c.(88-93)gcggag>gcg	p.E35del		NM_001102566.1	NP_001096036.1	A6NKN8	PC4L1_HUMAN	Purkinje cell protein 4 like 1	35								p.A30A(1)|p.E35delE(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4	all_cancers(52;4.16e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			TCAAGAAGGCGGAGGAGGAGGAG	0.488																																					p.30_31del												.	.	2	Substitution - coding silent(1)|Deletion - In frame(1)	large_intestine(1)|lung(1)	c.90_92del	1						.																																			159520780	SO:0001651	inframe_deletion	654790	exon3			BC028905	CCDS53412.1	1q23.3	2006-02-27	2006-02-27		ENSG00000248485	ENSG00000248485			20448	protein-coding gene	gene with protein product			"""purkinje cell protein 4 like 1"""				Standard	NM_001102566		Approved	IQM1	uc001gad.3	A6NKN8	OTTHUMG00000034340	ENST00000504449.1:c.90_92delGGA	1.37:g.161254163_161254165delGGA	ENSP00000426296:p.Glu35del	Somatic		Capture	Illumina HiSeq	Phase_I	159520778	NM_001102566	B2RV24|B9EJG4	In_Frame_Del	DEL	ENST00000504449.1	37	CCDS53412.1																																																																																				0.488	PCP4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082986.2		
POGK	57645	broad.mit.edu	37	1	166818499	166818499	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:166818499delA	ENST00000367875.1	+	5	1043	c.683delA	c.(682-684)gaafs	p.E228fs	POGK_ENST00000367876.4_Frame_Shift_Del_p.E228fs|POGK_ENST00000537173.1_Frame_Shift_Del_p.E110fs|POGK_ENST00000536514.1_Frame_Shift_Del_p.E143fs			Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	228					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.N230fs*8(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	22						GGAGTATTGGAAAAAAACGTT	0.552																																					p.E228fs	GBM(76;192 1530 30153 48742)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.683delA	1						.						45.0	48.0	47.0					1																	166818499		2203	4300	6503	165085123	SO:0001589	frameshift_variant	57645	exon5			AB040946	CCDS1254.1	1q23.2	2013-01-08			ENSG00000143157	ENSG00000143157		"""-"""	18800	protein-coding gene	gene with protein product	"""KRAB box domain containing 2"""						Standard	NM_017542		Approved	KIAA15131, LST003, BASS2, KRBOX2	uc001gdt.1	Q9P215	OTTHUMG00000034325	ENST00000367875.1:c.683delA	1.37:g.166818499delA	ENSP00000356849:p.Glu228fs	Somatic		Capture	Illumina HiSeq	Phase_I	165085123	NM_017542	Q5TIJ1|Q8TE07	Frame_Shift_Del	DEL	ENST00000367875.1	37	CCDS1254.1																																																																																				0.552	POGK-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082888.1	NM_017542	
CD247	919	broad.mit.edu	37	1	167408614	167408614	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:167408614delG	ENST00000362089.5	-	3	258	c.186delC	c.(184-186)cccfs	p.P62fs	CD247_ENST00000483825.1_5'UTR|CD247_ENST00000392122.3_Frame_Shift_Del_p.P62fs			P20963	CD3Z_HUMAN	CD247 molecule	62	ITAM 1. {ECO:0000255|PROSITE- ProRule:PRU00379}.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	alpha-beta T cell receptor complex (GO:0042105)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)	p.A63fs*15(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)	6			LUSC - Lung squamous cell carcinoma(543;0.236)		Muromonab(DB00075)	GCTGGTACGCGGGGGCGTCTG	0.667																																					p.P62fs	Ovarian(192;1815 2869 36877 43334)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.186delC	1						.						71.0	69.0	69.0					1																	167408614		2203	4300	6503	165675238	SO:0001589	frameshift_variant	919	exon3			BC025703	CCDS1260.1, CCDS1261.1	1q24.2	2014-09-17	2006-03-28	2006-03-09	ENSG00000198821	ENSG00000198821		"""CD molecules"""	1677	protein-coding gene	gene with protein product		186780	"""CD3z antigen, zeta polypeptide (TiT3 complex)"", ""CD247 antigen"""	CD3Z		2974162	Standard	NM_198053		Approved	CD3H, CD3Q	uc001gei.4	P20963	OTTHUMG00000034593	ENST00000362089.5:c.186delC	1.37:g.167408614delG	ENSP00000354782:p.Pro62fs	Somatic		Capture	Illumina HiSeq	Phase_I	165675238	NM_198053	B1AK49|Q5VX13|Q8TAX4	Frame_Shift_Del	DEL	ENST00000362089.5	37	CCDS1261.1																																																																																				0.667	CD247-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083707.1	NM_198053	
UBE2T	29089	broad.mit.edu	37	1	202304824	202304824	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:202304824delG	ENST00000367274.4	-	2	208	c.59delC	c.(58-60)ccafs	p.P20fs		NM_014176.3	NP_054895.1	Q9NPD8	UBE2T_HUMAN	ubiquitin-conjugating enzyme E2T (putative)	20					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|protein autoubiquitination (GO:0051865)|protein K11-linked ubiquitination (GO:0070979)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)	p.P20fs*20(1)		large_intestine(1)|lung(3)|skin(1)	5						TGTGATGCCTGGGGGTGGCTC	0.473																																					p.P20fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.59delC	1						.						159.0	138.0	145.0					1																	202304824		2203	4300	6503	200571447	SO:0001589	frameshift_variant	29089	exon2			AF161499	CCDS1425.1	1q32.1	2008-02-05			ENSG00000077152	ENSG00000077152		"""Ubiquitin-conjugating enzymes E2"""	25009	protein-coding gene	gene with protein product		610538				11042152	Standard	NM_014176		Approved	HSPC150	uc001gxx.4	Q9NPD8	OTTHUMG00000041392	ENST00000367274.4:c.59delC	1.37:g.202304824delG	ENSP00000356243:p.Pro20fs	Somatic		Capture	Illumina HiSeq	Phase_I	200571447	NM_014176	Q2TU36	Frame_Shift_Del	DEL	ENST00000367274.4	37	CCDS1425.1																																																																																				0.473	UBE2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099163.1	NM_014176	
CR1	1378	broad.mit.edu	37	1	207696973	207696973	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:207696973delC	ENST00000367049.4	+	5	505	c.505delC	c.(505-507)cccfs	p.P170fs	CR1_ENST00000400960.2_Frame_Shift_Del_p.P170fs|CR1_ENST00000367050.4_3'UTR|CR1_ENST00000367052.1_Frame_Shift_Del_p.P170fs|CR1_ENST00000367053.1_Frame_Shift_Del_p.P170fs|CR1_ENST00000367051.1_Intron	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	170	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.T176fs*21(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TTGTGGGCTACCCCCCACCAT	0.433																																					p.P169fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.505delC	1						.						82.0	74.0	76.0					1																	207696973		1852	4078	5930	205763596	SO:0001589	frameshift_variant	1378	exon5			Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.505delC	1.37:g.207696973delC	ENSP00000356016:p.Pro170fs	Somatic		Capture	Illumina HiSeq	Phase_I	205763596	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Frame_Shift_Del	DEL	ENST00000367049.4	37	CCDS44308.1																																																																																				0.433	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
DTL	51514	broad.mit.edu	37	1	212253986	212253986	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:212253986delA	ENST00000366991.4	+	13	1469	c.1155delA	c.(1153-1155)ctafs	p.L385fs	DTL_ENST00000542077.1_Frame_Shift_Del_p.L343fs|MIR3122_ENST00000577243.1_RNA|DTL_ENST00000475419.1_3'UTR	NM_016448.2	NP_057532.2	Q9NZJ0	DTL_HUMAN	denticleless E3 ubiquitin protein ligase homolog (Drosophila)	385					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|chromosome (GO:0005694)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.I387fs*4(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(81;0.00796)|all cancers(67;0.0385)|Epithelial(68;0.102)		ACAATACACTAAAAATCTGGC	0.398																																					p.L385fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1155delA	1						.						164.0	181.0	175.0					1																	212253986		2203	4299	6502	210320609	SO:0001589	frameshift_variant	51514	exon13			AF195765	CCDS1502.1, CCDS65778.1	1q32	2013-01-10	2012-02-23		ENSG00000143476	ENSG00000143476		"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"""	30288	protein-coding gene	gene with protein product	"""RA regulated nuclear matrix associated protein"", ""DDB1 and CUL4 associated factor 2"""	610617	"""denticleless homolog (Drosophila)"""			11278750	Standard	NM_001286229		Approved	RAMP, L2DTL, DCAF2	uc009xdc.3	Q9NZJ0	OTTHUMG00000037133	ENST00000366991.4:c.1155delA	1.37:g.212253986delA	ENSP00000355958:p.Leu385fs	Somatic		Capture	Illumina HiSeq	Phase_I	210320609	NM_016448	A8K8H8|D3DT98|Q5VT77|Q96SN0|Q9NW03|Q9NW34|Q9NWM5	Frame_Shift_Del	DEL	ENST00000366991.4	37	CCDS1502.1																																																																																				0.398	DTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090182.1	NM_016448	
FLVCR1	28982	broad.mit.edu	37	1	213046124	213046124	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:213046124delA	ENST00000366971.4	+	3	1186	c.988delA	c.(988-990)aaafs	p.K330fs		NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1	330					blood vessel development (GO:0001568)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|head morphogenesis (GO:0060323)|heme export (GO:0097037)|heme transport (GO:0015886)|in utero embryonic development (GO:0001701)|mitochondrial transport (GO:0006839)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|regulation of organ growth (GO:0046620)|spleen development (GO:0048536)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	heme transporter activity (GO:0015232)|transporter activity (GO:0005215)	p.N331fs*8(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(2)	12				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)		AAACCTGTTTAAAAACATTCC	0.388																																					p.K330fs	Esophageal Squamous(199;2235 2952 19233 26256)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.988delA	1						.						84.0	90.0	88.0					1																	213046124		2203	4300	6503	211112747	SO:0001589	frameshift_variant	28982	exon3			AF118637	CCDS1510.1	1q32.3	2014-05-30			ENSG00000162769	ENSG00000162769		"""Solute carriers"""	24682	protein-coding gene	gene with protein product		609144	"""ataxia, posterior column 1, with retinitis pigmentosa"""	AXPC1		10400745, 10648427, 21070897	Standard	NM_014053		Approved	FLVCR, MFSD7B, PCA	uc001hjt.3	Q9Y5Y0	OTTHUMG00000036924	ENST00000366971.4:c.988delA	1.37:g.213046124delA	ENSP00000355938:p.Lys330fs	Somatic		Capture	Illumina HiSeq	Phase_I	211112747	NM_014053	Q1HE16|Q86XY9|Q9NVR9	Frame_Shift_Del	DEL	ENST00000366971.4	37	CCDS1510.1																																																																																				0.388	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053	
CAPN2	824	broad.mit.edu	37	1	223957610	223957613	+	Splice_Site	DEL	AAGT	AAGT	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	AAGT	AAGT	AAGT	-	AAGT	AAGT	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:223957610_223957613delAAGT	ENST00000295006.5	+	17	2132_2133	c.1823_1824delAAGT	c.(1822-1824)caa>c	p.Q608fs	CAPN2_ENST00000474026.1_3'UTR|CAPN2_ENST00000433674.2_Splice_Site_p.Q530fs	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	608	Domain IV.|EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)	p.?(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		CAAAAATACCAAGTAAGATCCCAG	0.485																																					p.608_608del												.	.	1	Unknown(1)	large_intestine(1)	c.1823_1824del	1						.																																			222024236	SO:0001630	splice_region_variant	824	exon17			J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"""EF-hand domain containing"""	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.1824+1AAGT>-	1.37:g.223957610_223957613delAAGT		Somatic		Capture	Illumina HiSeq	Phase_I	222024233	NM_001748	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Splice_Site	DEL	ENST00000295006.5	37	CCDS31035.1																																																																																				0.485	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748	Frame_Shift_Del
WNT9A	7483	broad.mit.edu	37	1	228111954	228111954	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:228111954delC	ENST00000272164.5	-	3	510	c.500delG	c.(499-501)ggcfs	p.G167fs		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	167					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)	p.G167fs*38(1)|p.C168fs*6(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				GTCTCCGCAGCCCCCCCACTG	0.627																																					p.G167fs												.	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(1)|pancreas(1)	c.500delG	1						.						107.0	103.0	104.0					1																	228111954		2203	4300	6503	226178577	SO:0001589	frameshift_variant	7483	exon3			AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"""Wingless-type MMTV integration sites"""	12778	protein-coding gene	gene with protein product		602863	"""wingless-type MMTV integration site family, member 14"""	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.500delG	1.37:g.228111954delC	ENSP00000272164:p.Gly167fs	Somatic		Capture	Illumina HiSeq	Phase_I	226178577	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Frame_Shift_Del	DEL	ENST00000272164.5	37	CCDS31045.1																																																																																				0.627	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395	
SPRTN	83932	broad.mit.edu	37	1	231488884	231488884	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:231488884delT	ENST00000295050.7	+	5	1583	c.1247delT	c.(1246-1248)gttfs	p.V416fs		NM_001010984.2|NM_032018.5	NP_001010984.1|NP_114407.3	Q9H040	SPRTN_HUMAN	SprT-like N-terminal domain	416					cellular response to DNA damage stimulus (GO:0006974)|positive regulation of protein ubiquitination (GO:0031398)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|ubiquitin binding (GO:0043130)	p.F417fs*11(1)									GATAAGACTGTTTTTGACAAT	0.388																																					p.V416fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1247delT	1						.						60.0	61.0	61.0					1																	231488884		2203	4300	6503	229555507	SO:0001589	frameshift_variant	83932	exon5			AL512744	CCDS1594.1, CCDS31054.1, CCDS58066.1	1q42.12-q43	2013-01-30	2012-06-18	2012-06-18	ENSG00000010072	ENSG00000010072			25356	protein-coding gene	gene with protein product	"""SprT-like domain at the N terminus"", ""DNA damage-targeting VCP (p97) adaptor"""		"""chromosome 1 open reading frame 124"""	C1orf124		22681887	Standard	NM_032018		Approved	DKFZP547N043, Spartan, DVC1	uc001hur.4	Q9H040	OTTHUMG00000038022	ENST00000295050.7:c.1247delT	1.37:g.231488884delT	ENSP00000295050:p.Val416fs	Somatic		Capture	Illumina HiSeq	Phase_I	229555507	NM_032018	B1AKT0|B5MEF7|Q5TE78|Q6UWW6|Q96BC5|Q96KA0	Frame_Shift_Del	DEL	ENST00000295050.7	37	CCDS1594.1																																																																																				0.388	SPRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092858.1	NM_032018	
CHML	1122	broad.mit.edu	37	1	241798079	241798079	+	Frame_Shift_Del	DEL	T	T	-	rs150890234		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:241798079delT	ENST00000366553.1	-	1	1153	c.990delA	c.(988-990)aaafs	p.K330fs	OPN3_ENST00000366554.2_Intron|OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	330					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)	p.K330fs*2(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			TGGGAGTTAGTTTTTTAGTTT	0.333																																					p.K330fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.990delA	1						.						128.0	130.0	129.0					1																	241798079		2203	4299	6502	239864702	SO:0001589	frameshift_variant	1122	exon1			X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.990delA	1.37:g.241798079delT	ENSP00000355511:p.Lys330fs	Somatic		Capture	Illumina HiSeq	Phase_I	239864702	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Frame_Shift_Del	DEL	ENST00000366553.1	37	CCDS31073.1																																																																																				0.333	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821	
OR2T11	127077	broad.mit.edu	37	1	248789662	248789662	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr1:248789662G>A	ENST00000330803.2	-	1	829	c.768C>T	c.(766-768)taC>taT	p.Y256Y		NM_001001964.1	NP_001001964.1	Q8NH01	O2T11_HUMAN	olfactory receptor, family 2, subfamily T, member 11 (gene/pseudogene)	256						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y256Y(1)		breast(1)|large_intestine(5)|lung(20)|skin(2)	28	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGGGCAGCACGTATGTGTAGA	0.527																																					p.Y256Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C768T	1						.						74.0	68.0	70.0					1																	248789662		2048	4232	6280	246856285	SO:0001819	synonymous_variant	127077	exon1			BK004476	CCDS31122.1	1q44	2013-10-10	2013-10-10		ENSG00000183130	ENSG00000183130		"""GPCR / Class A : Olfactory receptors"""	19574	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 11"""				Standard	NM_001001964		Approved	OR2T11Q	uc001ier.1	Q8NH01	OTTHUMG00000040384	ENST00000330803.2:c.768C>T	1.37:g.248789662G>A		Somatic		Capture	Illumina HiSeq	Phase_I	246856285	NM_001001964	Q6IEY6	Silent	SNP	ENST00000330803.2	37	CCDS31122.1																																																																																				0.527	OR2T11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097134.1	NM_001001964	
LZTS3	9762	broad.mit.edu	37	20	3146923	3146924	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:3146923_3146924insG	ENST00000329152.3	-	2	1939_1940	c.542_543insC	c.(541-543)ccgfs	p.P181fs	LZTS3_ENST00000360342.3_Frame_Shift_Ins_p.P181fs|LZTS3_ENST00000337576.5_Frame_Shift_Ins_p.P181fs			O60299	LZTS3_HUMAN		181						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)		p.Q182fs*7(1)									CATTGGTCTGCGGGGGGCACAA	0.609																																					p.P181fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.543_544insC	20						.			3,4261		0,3,2129						-4.2	1.0			40	4,8250		0,4,4123	no	frameshift	ProSAPiP1	NM_014731.2		0,7,6252	A1A1,A1R,RR		0.0485,0.0704,0.0559				7,12511				3094924	SO:0001589	frameshift_variant	9762	exon2																														ENST00000329152.3:c.543dupC	20.37:g.3146929_3146929dupG	ENSP00000332123:p.Pro181fs	Somatic		Capture	Illumina HiSeq	Phase_I	3094923	NM_014731	A2A2Q7|D3DVX6|Q8IXX8	Frame_Shift_Ins	INS	ENST00000329152.3	37	CCDS13049.1																																																																																				0.609	LZTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077715.2		
SPTLC3	55304	broad.mit.edu	37	20	13071817	13071817	+	Missense_Mutation	SNP	G	G	A	rs375500511		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:13071817G>A	ENST00000399002.2	+	5	968	c.694G>A	c.(694-696)Gca>Aca	p.A232T	SPTLC3_ENST00000378194.4_Missense_Mutation_p.A232T	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	232					small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)	p.A232T(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						GATGGGATTCGCAACTAACTC	0.413																																					p.A232T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G694A	20						.	G	THR/ALA	0,3856		0,0,1928	138.0	138.0	138.0		694	5.4	1.0	20		138	1,8253		0,1,4126	no	missense	SPTLC3	NM_018327.2	58	0,1,6054	AA,AG,GG		0.0121,0.0,0.0083	probably-damaging	232/553	13071817	1,12109	1928	4127	6055	13019817	SO:0001583	missense	55304	exon5			AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"""chromosome 20 open reading frame 38"", ""serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"""	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.694G>A	20.37:g.13071817G>A	ENSP00000381968:p.Ala232Thr	Somatic		Capture	Illumina HiSeq	Phase_I	13019817	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Missense_Mutation	SNP	ENST00000399002.2	37	CCDS13115.2	.	.	.	.	.	.	.	.	.	.	G	35	5.436453	0.96168	0.0	1.21E-4	ENSG00000172296	ENST00000399002;ENST00000378194	D;D	0.90261	-2.64;-2.64	5.44	5.44	0.79542	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.222920	0.46442	D	0.000291	D	0.94896	0.8350	M	0.75447	2.3	0.80722	D	1	D	0.69078	0.997	D	0.68621	0.959	D	0.94708	0.7889	10	0.52906	T	0.07	-6.8454	18.101	0.89505	0.0:0.0:1.0:0.0	.	232	Q9NUV7	SPTC3_HUMAN	T	232	ENSP00000381968:A232T;ENSP00000367436:A232T	ENSP00000367436:A232T	A	+	1	0	SPTLC3	13019817	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.558000	0.86282	0.644000	0.83932	GCA		0.413	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327	
NDUFAF5	79133	broad.mit.edu	37	20	13797788	13797788	+	Missense_Mutation	SNP	G	G	A	rs142611230		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:13797788G>A	ENST00000378106.5	+	11	1089	c.970G>A	c.(970-972)Gca>Aca	p.A324T	NDUFAF5_ENST00000463598.1_Missense_Mutation_p.A296T|NDUFAF5_ENST00000475968.1_3'UTR	NM_024120.4	NP_077025.2	Q5TEU4	NDUF5_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 5	324					mitochondrial respiratory chain complex I assembly (GO:0032981)	extrinsic component of mitochondrial inner membrane (GO:0031314)	methyltransferase activity (GO:0008168)	p.A324T(1)									AAGAGGTTCCGCAACTGTGTC	0.353																																					p.A296T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G886A	20						.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	99.0	113.0	108.0		886,970	4.4	0.8	20	dbSNP_134	108	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C20orf7	NM_001039375.2,NM_024120.4	58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	296/318,324/346	13797788	1,13005	2203	4300	6503	13745788	SO:0001583	missense	79133	exon10				CCDS13118.1, CCDS33441.1	20p12.1	2012-10-12	2012-05-08	2012-05-08	ENSG00000101247	ENSG00000101247		"""Mitochondrial respiratory chain complex assembly factors"""	15899	protein-coding gene	gene with protein product		612360	"""chromosome 20 open reading frame 7"""	C20orf7		18940309, 21607760	Standard	NM_024120		Approved	dJ842G6.1	uc002wom.3	Q5TEU4	OTTHUMG00000031909	ENST00000378106.5:c.970G>A	20.37:g.13797788G>A	ENSP00000367346:p.Ala324Thr	Somatic		Capture	Illumina HiSeq	Phase_I	13745788	NM_001039375	A8K166|Q6GPH3|Q9H6F4	Missense_Mutation	SNP	ENST00000378106.5	37	CCDS13118.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.838556	0.51057	0.0	1.16E-4	ENSG00000101247	ENST00000378106;ENST00000463598	D;T	0.83419	-1.72;-1.48	5.33	4.37	0.52481	.	0.000000	0.85682	D	0.000000	D	0.90335	0.6976	M	0.90870	3.155	0.54753	D	0.999987	D;D	0.59767	0.986;0.976	P;P	0.54815	0.761;0.581	D	0.91889	0.5522	10	0.62326	D	0.03	-49.6394	13.6665	0.62398	0.0:0.0:0.8451:0.1549	.	296;324	Q5TEU4-2;Q5TEU4	.;CT007_HUMAN	T	324;296	ENSP00000367346:A324T;ENSP00000420497:A296T	ENSP00000367346:A324T	A	+	1	0	C20orf7	13745788	1.000000	0.71417	0.849000	0.33467	0.069000	0.16628	8.052000	0.89448	1.224000	0.43551	-0.181000	0.13052	GCA		0.353	NDUFAF5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078057.2	NM_001039375	
MACROD2	140733	broad.mit.edu	37	20	15948255	15948255	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:15948255G>A	ENST00000310348.4	+	13	965	c.965G>A	c.(964-966)cGt>cAt	p.R322H	MACROD2_ENST00000402914.1_Missense_Mutation_p.R87H|MACROD2_ENST00000217246.4_Missense_Mutation_p.R322H|MACROD2_ENST00000378058.3_Missense_Mutation_p.R87H			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	322	Glu-rich.				brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)	p.R87H(1)|p.R322H(1)		breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				CATTCTGTGCGTGACCAAGAT	0.348																																					p.R87H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G260A	20						.						133.0	134.0	133.0					20																	15948255		2203	4300	6503	15896255	SO:0001583	missense	140733	exon9			BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"""chromosome 20 open reading frame 133"""	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.965G>A	20.37:g.15948255G>A	ENSP00000309809:p.Arg322His	Somatic		Capture	Illumina HiSeq	Phase_I	15896255	NM_001033087	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	37	CCDS13120.2	.	.	.	.	.	.	.	.	.	.	g	7.535	0.659488	0.14645	.	.	ENSG00000172264	ENST00000217246;ENST00000310348;ENST00000402914;ENST00000378058	T;T;T;T	0.45668	2.48;2.47;0.89;0.89	5.33	1.05	0.20165	.	0.644521	0.14708	N	0.303106	T	0.19005	0.0456	N	0.08118	0	0.09310	N	1	B;B	0.23891	0.056;0.093	B;B	0.20384	0.013;0.029	T	0.17745	-1.0359	10	0.27785	T	0.31	0.0	6.1196	0.20146	0.2414:0.1383:0.6203:0.0	.	322;322	A1Z1Q3;A1Z1Q3-2	MACD2_HUMAN;.	H	322;322;87;87	ENSP00000217246:R322H;ENSP00000309809:R322H;ENSP00000385290:R87H;ENSP00000367297:R87H	ENSP00000217246:R322H	R	+	2	0	MACROD2	15896255	0.379000	0.25123	0.264000	0.24511	0.101000	0.19017	0.506000	0.22658	0.302000	0.22762	-0.119000	0.15052	CGT		0.348	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676	
SEC23B	10483	broad.mit.edu	37	20	18523019	18523019	+	Missense_Mutation	SNP	G	G	A	rs141588462	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:18523019G>A	ENST00000336714.3	+	13	1916	c.1484G>A	c.(1483-1485)cGc>cAc	p.R495H	SEC23B_ENST00000377475.3_Missense_Mutation_p.R495H|SEC23B_ENST00000377465.1_Missense_Mutation_p.R495H|SEC23B_ENST00000262544.2_Missense_Mutation_p.R495H	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	495					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)	p.R495H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						ACCCAGAGACGCATCCGCGTG	0.512													G|||	25	0.00499201	0.0182	0.0014	5008	,	,		19918	0.0		0.0	False		,,,				2504	0.0				p.R495H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1484A	20						.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	95,4311	76.2+/-114.5	0,95,2108	200.0	168.0	179.0		1484,1430,1484,1484,1484	4.8	1.0	20	dbSNP_134	179	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	SEC23B	NM_001172745.1,NM_001172746.1,NM_006363.4,NM_032985.4,NM_032986.3	29,29,29,29,29	0,95,6408	AA,AG,GG		0.0,2.1562,0.7304	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	495/768,477/750,495/768,495/768,495/768	18523019	95,12911	2203	4300	6503	18471019	SO:0001583	missense	10483	exon13			X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"""Sec23 (S. cerevisiae) homolog B"", ""congenital dyserythropoietic anemia, type II"""	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.1484G>A	20.37:g.18523019G>A	ENSP00000338844:p.Arg495His	Somatic		Capture	Illumina HiSeq	Phase_I	18471019	NM_032986	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	37	CCDS13137.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	28.9	4.960080	0.92791	0.021562	0.0	ENSG00000101310	ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465;ENST00000422877	T;T;T;T;D	0.98280	-1.33;-1.33;-1.33;-1.33;-4.84	4.83	4.83	0.62350	Sec23/Sec24 beta-sandwich (1);	0.000000	0.85682	D	0.000000	D	0.96648	0.8906	M	0.83312	2.635	0.80722	D	1	D;D	0.57899	0.981;0.961	P;P	0.50162	0.633;0.613	D	0.93827	0.7124	10	0.45353	T	0.12	-14.8731	17.1113	0.86675	0.0:0.0:1.0:0.0	.	477;495	B4DJW8;Q15437	.;SC23B_HUMAN	H	495;495;495;495;3	ENSP00000338844:R495H;ENSP00000262544:R495H;ENSP00000366695:R495H;ENSP00000366685:R495H;ENSP00000409882:R3H	ENSP00000262544:R495H	R	+	2	0	SEC23B	18471019	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.657000	0.98554	2.520000	0.84964	0.655000	0.94253	CGC		0.512	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5		
SLC24A3	57419	broad.mit.edu	37	20	19664857	19664857	+	Silent	SNP	C	C	T	rs149435919	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:19664857C>T	ENST00000328041.6	+	11	1136	c.939C>T	c.(937-939)gaC>gaT	p.D313D		NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	313					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)	p.D313D(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TCATGGTAGACGAGCTGCTGT	0.507													C|||	4	0.000798722	0.003	0.0	5008	,	,		19650	0.0		0.0	False		,,,				2504	0.0				p.D313D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C939T	20						.			11,4395	17.9+/-39.9	0,11,2192	123.0	115.0	117.0		939	-9.6	0.6	20	dbSNP_134	117	0,8600		0,0,4300	no	coding-synonymous	SLC24A3	NM_020689.3		0,11,6492	TT,TC,CC		0.0,0.2497,0.0846		313/645	19664857	11,12995	2203	4300	6503	19612857	SO:0001819	synonymous_variant	57419	exon11			AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"""Solute carriers"""	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.939C>T	20.37:g.19664857C>T		Somatic		Capture	Illumina HiSeq	Phase_I	19612857	NM_020689	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Silent	SNP	ENST00000328041.6	37	CCDS13140.1																																																																																				0.507	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689	
GGTLC1	92086	broad.mit.edu	37	20	23966824	23966824	+	Missense_Mutation	SNP	G	G	A	rs369309954		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:23966824G>A	ENST00000335694.4	-	3	397	c.193C>T	c.(193-195)Cgc>Tgc	p.R65C	GGTLC1_ENST00000286890.4_Missense_Mutation_p.R65C|GGTLC1_ENST00000278765.4_Missense_Mutation_p.R65C	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	65					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)	p.R65C(2)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						ACTGGGGAGCGCACCTTGGAG	0.572													.|||	1	0.000199681	0.0008	0.0	5008	,	,		14114	0.0		0.0	False		,,,				2504	0.0				p.R65C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C193T	20						.	G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	86.0	91.0	90.0		193,193	0.8	0.0	20		90	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	GGTLC1	NM_178311.2,NM_178312.2	180,180	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	65/226,65/226	23966824	2,13004	2203	4300	6503	23914824	SO:0001583	missense	92086	exon3			AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"""Gamma-glutamyltransferases"""	16437	protein-coding gene	gene with protein product		612338	"""gamma-glutamyltransferase-like activity 4"", ""gamma-glutamyltransferase-like activity 3"""	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.193C>T	20.37:g.23966824G>A	ENSP00000337587:p.Arg65Cys	Somatic		Capture	Illumina HiSeq	Phase_I	23914824	NM_178312	D3DW43|Q08246	Missense_Mutation	SNP	ENST00000335694.4	37	CCDS13163.1	.	.	.	.	.	.	.	.	.	.	g	5.681	0.310245	0.10733	0.0	2.33E-4	ENSG00000149435	ENST00000286890;ENST00000278765;ENST00000335694	T;T;T	0.06449	3.3;3.3;3.3	0.844	0.844	0.18943	.	0.393001	0.26598	N	0.023490	T	0.08447	0.0210	M	0.80746	2.51	0.31237	N	0.695648	B	0.22480	0.07	B	0.20955	0.032	T	0.04930	-1.0917	10	0.46703	T	0.11	-19.0395	4.3059	0.10947	1.0E-4:0.0:0.6173:0.3826	.	65	Q9BX51	GGTL1_HUMAN	C	65	ENSP00000286890:R65C;ENSP00000278765:R65C;ENSP00000337587:R65C	ENSP00000278765:R65C	R	-	1	0	GGTLC1	23914824	0.731000	0.28111	0.024000	0.17045	0.024000	0.10985	1.350000	0.34010	0.088000	0.17205	0.089000	0.15464	CGC		0.572	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2	
TRIB3	57761	broad.mit.edu	37	20	368852	368852	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:368852C>T	ENST00000217233.3	+	2	751	c.198C>T	c.(196-198)tcC>tcT	p.S66S	TRIB3_ENST00000422053.2_Silent_p.S93S	NM_021158.3	NP_066981.2	Q96RU7	TRIB3_HUMAN	tribbles pseudokinase 3	66	Interaction with DDIT3/CHOP.				cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of protein binding (GO:0032092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|regulation of glucose transport (GO:0010827)|regulation of MAP kinase activity (GO:0043405)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|transcription corepressor activity (GO:0003714)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase regulator activity (GO:0055106)	p.S66S(1)		breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|skin(1)	21		all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231)		Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112)		CCACTGCCTCCCGTCTTGGGC	0.662																																					p.S66S	Melanoma(101;421 2374 19538)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C198T	20						.						61.0	59.0	60.0					20																	368852		2203	4300	6503	316852	SO:0001819	synonymous_variant	57761	exon2			AF250311	CCDS12997.1	20p13-p12.2	2013-10-03	2013-10-03	2004-05-04	ENSG00000101255	ENSG00000101255			16228	protein-coding gene	gene with protein product		607898	"""chromosome 20 open reading frame 97"", ""tribbles homolog 3 (Drosophila)"""	C20orf97		12791994, 16715410	Standard	XM_005260773		Approved	dJ1103G7.3, TRB3	uc002wdm.3	Q96RU7	OTTHUMG00000031627	ENST00000217233.3:c.198C>T	20.37:g.368852C>T		Somatic		Capture	Illumina HiSeq	Phase_I	316852	NM_021158	Q53GU4|Q53ZW7|Q6I9Y9|Q8TAI6|Q9H5M8|Q9NUD2	Silent	SNP	ENST00000217233.3	37	CCDS12997.1																																																																																				0.662	TRIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077441.2	NM_021158	
ITPA	3704	broad.mit.edu	37	20	3199166	3199166	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:3199166T>G	ENST00000380113.3	+	6	491	c.299T>G	c.(298-300)cTc>cGc	p.L100R	ITPA_ENST00000455664.2_Missense_Mutation_p.L83R|ITPA_ENST00000483354.1_3'UTR|ITPA_ENST00000399838.3_Missense_Mutation_p.L59R	NM_033453.3|NM_181493.2	NP_258412.1|NP_852470.1			inosine triphosphatase (nucleoside triphosphate pyrophosphatase)									p.L100R(1)		autonomic_ganglia(1)|large_intestine(3)|ovary(1)|stomach(1)	6						CCCGCAGGTCTCCACCAGCTC	0.647											OREG0025730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L100R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T299G	20						.						44.0	36.0	39.0					20																	3199166		2203	4300	6503	3147166	SO:0001583	missense	3704	exon6			AF026816	CCDS13051.1, CCDS46576.1, CCDS58762.1	20p	2002-02-01			ENSG00000125877	ENSG00000125877	3.6.1.19		6176	protein-coding gene	gene with protein product		147520		C20orf37		11278832	Standard	NM_033453		Approved	HLC14-06-P, dJ794I6.3	uc002wid.4	Q9BY32	OTTHUMG00000031738	ENST00000380113.3:c.299T>G	20.37:g.3199166T>G	ENSP00000369456:p.Leu100Arg	Somatic	609	Capture	Illumina HiSeq	Phase_I	3147166	NM_033453		Missense_Mutation	SNP	ENST00000380113.3	37	CCDS13051.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.906034	0.92107	.	.	ENSG00000125877	ENST00000380113;ENST00000455664;ENST00000399838	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.88735	0.6517	H	0.98996	4.395	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.92418	0.5943	9	0.87932	D	0	.	12.5301	0.56109	0.0:0.0:0.0:1.0	.	83;100	B2BCH7;Q9BY32	.;ITPA_HUMAN	R	100;83;59	.	ENSP00000369456:L100R	L	+	2	0	ITPA	3147166	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.325000	0.72901	2.219000	0.72066	0.533000	0.62120	CTC		0.647	ITPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077719.2		
KIF3B	9371	broad.mit.edu	37	20	30918119	30918119	+	Missense_Mutation	SNP	C	C	T	rs370914318		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:30918119C>T	ENST00000375712.3	+	8	2311	c.2144C>T	c.(2143-2145)gCc>gTc	p.A715V	KIF3B_ENST00000418717.2_Missense_Mutation_p.A341V	NM_004798.3	NP_004789.1	O15066	KIF3B_HUMAN	kinesin family member 3B	715	Globular.				anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|determination of left/right symmetry (GO:0007368)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic spindle organization (GO:0007052)|plus-end-directed vesicle transport along microtubule (GO:0072383)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|plus-end kinesin complex (GO:0005873)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|Rho GTPase binding (GO:0017048)	p.A715V(1)		NS(2)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			AAATCCAAGGCCAGGTGAGTG	0.438																																					p.A715V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2144T	20						.	C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	89.0	90.0	90.0		2144	4.6	1.0	20		90	0,8600		0,0,4300	no	missense	KIF3B	NM_004798.3	64	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	715/748	30918119	1,13005	2203	4300	6503	30381780	SO:0001583	missense	9371	exon8			AB002357	CCDS13200.1	20q11.21	2012-08-01			ENSG00000101350	ENSG00000101350		"""Kinesins"""	6320	protein-coding gene	gene with protein product		603754				9205841	Standard	NM_004798		Approved	KIAA0359, FLA8, KLP-11	uc002wxq.3	O15066	OTTHUMG00000032214	ENST00000375712.3:c.2144C>T	20.37:g.30918119C>T	ENSP00000364864:p.Ala715Val	Somatic		Capture	Illumina HiSeq	Phase_I	30381780	NM_004798	B2RMP4|B4DSR5|E1P5M5	Missense_Mutation	SNP	ENST00000375712.3	37	CCDS13200.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.232901	0.58777	2.27E-4	0.0	ENSG00000101350	ENST00000375712;ENST00000418717	T;T	0.74315	-0.83;0.52	4.62	4.62	0.57501	.	0.517277	0.22309	N	0.061750	T	0.57858	0.2082	N	0.08118	0	0.45607	D	0.998542	B;B	0.23058	0.039;0.079	B;B	0.16289	0.015;0.007	T	0.56836	-0.7913	10	0.46703	T	0.11	.	18.0393	0.89314	0.0:1.0:0.0:0.0	.	341;715	B4DSR5;O15066	.;KIF3B_HUMAN	V	715;341	ENSP00000364864:A715V;ENSP00000406287:A341V	ENSP00000364864:A715V	A	+	2	0	KIF3B	30381780	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	4.188000	0.58351	2.559000	0.86315	0.655000	0.94253	GCC		0.438	KIF3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078619.1	NM_004798	
TRPC4AP	26133	broad.mit.edu	37	20	33589874	33589874	+	IGR	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:33589874G>A	ENST00000252015.2	-	0	3226				MYH7B_ENST00000262873.7_Missense_Mutation_p.A1976T			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein						calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)	p.A1976T(1)		breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			GACCCGGGACGCCCTGGGCCC	0.647											OREG0025884	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A1976T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5926A	20						.						37.0	50.0	46.0					20																	33589874		2169	4260	6429	33053535	SO:0001628	intergenic_variant	57644	exon44			AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 158"""	608430	"""chromosome 20 open reading frame 188"""	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319		20.37:g.33589874G>A		Somatic	841	Capture	Illumina HiSeq	Phase_I	33053535	NM_020884	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	37	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.118027	0.56505	.	.	ENSG00000078814	ENST00000262873;ENST00000446156;ENST00000453028;ENST00000435272;ENST00000433934;ENST00000456649	D;D;T;T;T;T	0.85861	-2.04;-1.72;-1.07;-1.08;-1.05;-1.11	4.45	4.45	0.53987	.	0.000000	0.34555	N	0.003865	T	0.65450	0.2692	N	0.05414	-0.055	0.31953	N	0.609398	P	0.47545	0.897	B	0.29524	0.103	T	0.70051	-0.4978	10	0.17369	T	0.5	.	17.274	0.87110	0.0:0.0:1.0:0.0	.	1934	A7E2Y1	MYH7B_HUMAN	T	1976;131;109;136;136;109	ENSP00000262873:A1976T;ENSP00000395858:A131T;ENSP00000409103:A109T;ENSP00000391939:A136T;ENSP00000412594:A136T;ENSP00000396368:A109T	ENSP00000262873:A1976T	A	+	1	0	MYH7B	33053535	0.010000	0.17322	1.000000	0.80357	0.887000	0.51463	0.923000	0.28757	2.319000	0.78375	0.561000	0.74099	GCC		0.647	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
DLGAP4	22839	broad.mit.edu	37	20	35125297	35125297	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:35125297A>C	ENST00000373907.2	+	7	2037	c.1838A>C	c.(1837-1839)gAc>gCc	p.D613A	DLGAP4_ENST00000401952.2_Missense_Mutation_p.D613A|DLGAP4_ENST00000373913.3_Missense_Mutation_p.D613A|DLGAP4_ENST00000339266.5_Missense_Mutation_p.D613A|DLGAP4_ENST00000340491.4_Missense_Mutation_p.D74A|DLGAP4_ENST00000475894.1_3'UTR			Q9Y2H0	DLGP4_HUMAN	discs, large (Drosophila) homolog-associated protein 4	613					cell-cell signaling (GO:0007267)	membrane (GO:0016020)|synapse (GO:0045202)		p.D613A(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(20)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				GACAGCCTGGACAGCAGTACC	0.627																																					p.D74A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A221C	20						.						91.0	80.0	83.0					20																	35125297		2203	4300	6503	34558711	SO:0001583	missense	22839	exon2			AF088030	CCDS13274.1, CCDS13275.1	20q11.23	2010-02-05			ENSG00000080845	ENSG00000080845			24476	protein-coding gene	gene with protein product						9115257	Standard	XM_005260329		Approved	DAP4, KIAA0964, SAPAP4	uc010zvp.2	Q9Y2H0	OTTHUMG00000032390	ENST00000373907.2:c.1838A>C	20.37:g.35125297A>C	ENSP00000363014:p.Asp613Ala	Somatic		Capture	Illumina HiSeq	Phase_I	34558711	NM_183006	E1P5T5|Q5QPG4|Q5T2Y4|Q5T2Y5|Q9H137|Q9H138|Q9H1L7	Missense_Mutation	SNP	ENST00000373907.2	37		.	.	.	.	.	.	.	.	.	.	A	25.7	4.665834	0.88251	.	.	ENSG00000080845	ENST00000373913;ENST00000401952;ENST00000373907;ENST00000339266;ENST00000340491	T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43	5.77	5.77	0.91146	.	0.126839	0.64402	D	0.000001	T	0.54240	0.1846	M	0.65498	2.005	0.80722	D	1	P;D	0.89917	0.904;1.0	P;D	0.74348	0.823;0.983	T	0.56553	-0.7960	10	0.72032	D	0.01	.	15.5635	0.76269	1.0:0.0:0.0:0.0	.	74;613	Q9Y2H0-3;Q9Y2H0-1	.;.	A	613;613;613;613;74	ENSP00000363023:D613A;ENSP00000384954:D613A;ENSP00000363014:D613A;ENSP00000341633:D613A;ENSP00000345700:D74A	ENSP00000341633:D613A	D	+	2	0	DLGAP4	34558711	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.272000	0.72575	2.326000	0.78906	0.533000	0.62120	GAC		0.627	DLGAP4-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000079025.2	NM_014902	
TGIF2	60436	broad.mit.edu	37	20	35219344	35219344	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:35219344G>A	ENST00000373874.2	+	3	423	c.224G>A	c.(223-225)cGg>cAg	p.R75Q	TGIF2_ENST00000373872.4_Missense_Mutation_p.R75Q|RP5-977B1.11_ENST00000561134.1_RNA|TGIF2-C20orf24_ENST00000558530.1_Intron	NM_001199514.1|NM_001199515.1	NP_001186443.1|NP_001186444.1	Q9GZN2	TGIF2_HUMAN	TGFB-induced factor homeobox 2	75					gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway (GO:0038092)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R75Q(1)		cervix(3)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				GCCCGGCGGCGGCTTCTCCCA	0.532																																					p.R75Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G224A	20						.						132.0	150.0	144.0					20																	35219344		2203	4300	6503	34652758	SO:0001583	missense	60436	exon3			AB042646	CCDS13278.1	20q11.23	2012-12-12	2007-02-07		ENSG00000118707	ENSG00000118707		"""Homeoboxes / TALE class"""	15764	protein-coding gene	gene with protein product		607294	"""TGFB-induced factor 2 (TALE family homeobox)"""			11006116	Standard	NM_021809		Approved		uc021wcv.1	Q9GZN2	OTTHUMG00000172332	ENST00000373874.2:c.224G>A	20.37:g.35219344G>A	ENSP00000362981:p.Arg75Gln	Somatic		Capture	Illumina HiSeq	Phase_I	34652758	NM_001199513	B2R9U3|E1P5T9|H0YNI0	Missense_Mutation	SNP	ENST00000373874.2	37	CCDS13278.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.873233	0.91664	.	.	ENSG00000118707	ENST00000373874;ENST00000373872	D;D	0.98602	-5.02;-5.02	5.61	4.66	0.58398	Homeodomain-related (1);Homeobox (2);Homeobox KN domain (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99411	0.9792	H	0.99261	4.49	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.98087	1.0407	10	0.87932	D	0	-24.2156	13.3415	0.60547	0.0756:0.0:0.9244:0.0	.	75	Q9GZN2	TGIF2_HUMAN	Q	75	ENSP00000362981:R75Q;ENSP00000362979:R75Q	ENSP00000362979:R75Q	R	+	2	0	TGIF2	34652758	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.414000	0.97362	1.366000	0.46076	0.561000	0.74099	CGG		0.532	TGIF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079004.2	NM_021809	
SRC	6714	broad.mit.edu	37	20	36026211	36026211	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:36026211G>A	ENST00000373578.2	+	9	1162	c.813G>A	c.(811-813)cgG>cgA	p.R271R	SRC_ENST00000373567.2_Silent_p.R271R|SRC_ENST00000358208.4_Silent_p.R271R|SRC_ENST00000373558.2_Silent_p.R277R|SRC_ENST00000477066.1_3'UTR|SRC_ENST00000360723.4_Silent_p.R277R|SRC_ENST00000445403.1_Silent_p.R271R	NM_198291.1	NP_938033.1	P12931	SRC_HUMAN	SRC proto-oncogene, non-receptor tyrosine kinase	271	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cellular response to progesterone stimulus (GO:0071393)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|membrane organization (GO:0061024)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of protein homooligomerization (GO:0032463)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oogenesis (GO:0048477)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of integrin activation (GO:0033625)|positive regulation of podosome assembly (GO:0071803)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone receptor signaling pathway (GO:0050847)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of bone resorption (GO:0045124)|regulation of caveolin-mediated endocytosis (GO:2001286)|regulation of cell-cell adhesion (GO:0022407)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of epithelial cell migration (GO:0010632)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of protein binding (GO:0043393)|regulation of vascular permeability (GO:0043114)|response to interleukin-1 (GO:0070555)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|T cell costimulation (GO:0031295)|transforming growth factor beta receptor signaling pathway (GO:0007179)|uterus development (GO:0060065)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|growth factor receptor binding (GO:0070851)|heme binding (GO:0020037)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)	p.R271R(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(16)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)			Bosutinib(DB06616)|Dasatinib(DB01254)|Ponatinib(DB08901)	AGTCGCTGCGGCTGGAGGTCA	0.697																																					p.R271R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G813A	20						.						35.0	39.0	38.0					20																	36026211		2203	4300	6503	35459625	SO:0001819	synonymous_variant	6714	exon9			AF077754	CCDS13294.1	20q12-q13	2014-06-25	2014-06-25		ENSG00000197122	ENSG00000197122		"""SH2 domain containing"""	11283	protein-coding gene	gene with protein product		190090	"""v-src avian sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog"""	SRC1		2582238	Standard	NM_005417		Approved	ASV, c-src	uc002xgy.3	P12931	OTTHUMG00000032417	ENST00000373578.2:c.813G>A	20.37:g.36026211G>A		Somatic		Capture	Illumina HiSeq	Phase_I	35459625	NM_005417	E1P5V4|Q76P87|Q86VB9|Q9H5A8	Silent	SNP	ENST00000373578.2	37	CCDS13294.1																																																																																				0.697	SRC-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268142.1	NM_005417	
TGM2	7052	broad.mit.edu	37	20	36760872	36760872	+	Missense_Mutation	SNP	T	T	C	rs148045565		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:36760872T>C	ENST00000361475.2	-	11	1819	c.1646A>G	c.(1645-1647)gAg>gGg	p.E549G	TGM2_ENST00000536701.1_Missense_Mutation_p.E468G|TGM2_ENST00000536724.1_Missense_Mutation_p.E489G	NM_004613.2|NM_198951.1	NP_004604.2|NP_945189.1	P21980	TGM2_HUMAN	transglutaminase 2	549					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|branching involved in salivary gland morphogenesis (GO:0060445)|isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein homooligomerization (GO:0051260)|salivary gland cavitation (GO:0060662)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.E549G(1)		endometrium(2)|large_intestine(11)|liver(1)|lung(7)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)	ACGGTATTTCTCATAGAGGAT	0.547													T|||	1	0.000199681	0.0008	0.0	5008	,	,		20024	0.0		0.0	False		,,,				2504	0.0				p.E549G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1646G	20						.						177.0	178.0	177.0					20																	36760872		2203	4300	6503	36194286	SO:0001583	missense	7052	exon11			M98478	CCDS13302.1	20q12	2013-05-02	2013-05-02		ENSG00000198959	ENSG00000198959	2.3.2.13	"""Transglutaminases"""	11778	protein-coding gene	gene with protein product	"""C polypeptide, protein-glutamine-gamma-glutamyltransferase"""	190196	"""transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)"""			7912692, 11390390	Standard	NM_004613		Approved	TGC	uc002xhr.3	P21980	OTTHUMG00000032437	ENST00000361475.2:c.1646A>G	20.37:g.36760872T>C	ENSP00000355330:p.Glu549Gly	Somatic		Capture	Illumina HiSeq	Phase_I	36194286	NM_004613	E1P5V9|Q16436|Q6B838|Q9BTN7|Q9UH35	Missense_Mutation	SNP	ENST00000361475.2	37	CCDS13302.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	9.289	1.050021	0.19827	.	.	ENSG00000198959	ENST00000361475;ENST00000536701;ENST00000536724	T;T;T	0.30981	1.51;1.51;1.51	4.67	3.48	0.39840	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.693293	0.14694	N	0.303994	T	0.33702	0.0872	M	0.64997	1.995	0.19300	N	0.999973	B;P;B;B	0.37233	0.316;0.588;0.366;0.24	B;B;B;B	0.41174	0.179;0.349;0.273;0.332	T	0.12142	-1.0559	10	0.27785	T	0.31	-11.674	11.1188	0.48277	0.0:0.0:0.1534:0.8466	.	489;468;489;549	F5H6P0;B4DIT7;B4DTN7;P21980	.;.;.;TGM2_HUMAN	G	549;468;489	ENSP00000355330:E549G;ENSP00000444701:E468G;ENSP00000437479:E489G	ENSP00000355330:E549G	E	-	2	0	TGM2	36194286	0.975000	0.34042	0.570000	0.28473	0.060000	0.15804	3.363000	0.52321	1.862000	0.54008	0.459000	0.35465	GAG		0.547	TGM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079151.2	NM_198951	
CHD6	84181	broad.mit.edu	37	20	40117211	40117211	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:40117211C>T	ENST00000373233.3	-	13	1891	c.1714G>A	c.(1714-1716)Gtc>Atc	p.V572I	CHD6_ENST00000309279.7_Missense_Mutation_p.V572I	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	572	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Required for DNA-dependent ATPase activity.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)	p.V572I(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GTGATGACGACGTGGAACTTG	0.443																																					p.V572I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1714A	20						.						88.0	86.0	87.0					20																	40117211		2203	4300	6503	39550625	SO:0001583	missense	84181	exon13			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.1714G>A	20.37:g.40117211C>T	ENSP00000362330:p.Val572Ile	Somatic		Capture	Illumina HiSeq	Phase_I	39550625	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676427	0.67928	.	.	ENSG00000124177	ENST00000373233;ENST00000309279	D;D	0.94184	-3.37;-3.37	5.34	5.34	0.76211	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.48286	D	0.000196	D	0.87593	0.6216	L	0.27975	0.815	0.44149	D	0.996945	P	0.42973	0.796	B	0.37508	0.252	D	0.88400	0.3014	10	0.54805	T	0.06	-16.1185	12.736	0.57225	0.0:0.9247:0.0:0.0753	.	572	Q8TD26	CHD6_HUMAN	I	572	ENSP00000362330:V572I;ENSP00000308684:V572I	ENSP00000308684:V572I	V	-	1	0	CHD6	39550625	1.000000	0.71417	0.938000	0.37757	0.962000	0.63368	5.717000	0.68446	2.659000	0.90383	0.655000	0.94253	GTC		0.443	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
ADRA1D	146	broad.mit.edu	37	20	4202289	4202289	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:4202289C>T	ENST00000379453.4	-	2	1716	c.1600G>A	c.(1600-1602)Gcc>Acc	p.A534T		NM_000678.3	NP_000669.1	P25100	ADA1D_HUMAN	adrenoceptor alpha 1D	534				KPPSAFREWRLLGPFRRPTTQLRAKVSSLSHKIRAGGAQRA EAACAQRSEVEAVSLGVPHEVAEGATCQAYELADYSNLRET DI -> SHPAPSASGGCWGRSGDPRPSCAPKSPACRTRSPP GARSAQRQRAPSAQRWRLCP (in Ref. 1). {ECO:0000305}.	adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)	p.A534T(1)		endometrium(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	14					Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	GAGCGCTGGGCGCACGCTGCC	0.706																																					p.A534T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1600A	20						.						19.0	22.0	21.0					20																	4202289		2197	4283	6480	4150289	SO:0001583	missense	146	exon2			U03864	CCDS13079.1	20p13	2012-08-08	2012-05-09		ENSG00000171873	ENSG00000171873		"""GPCR / Class A : Adrenoceptors : alpha"""	280	protein-coding gene	gene with protein product		104219	"""adrenergic, alpha-1D-, receptor"""			8039425	Standard	NM_000678		Approved	ADRA1R, ADRA1A, ADRA1	uc002wkr.2	P25100	OTTHUMG00000031779	ENST00000379453.4:c.1600G>A	20.37:g.4202289C>T	ENSP00000368766:p.Ala534Thr	Somatic		Capture	Illumina HiSeq	Phase_I	4150289	NM_000678	Q9NPY0	Missense_Mutation	SNP	ENST00000379453.4	37	CCDS13079.1	.	.	.	.	.	.	.	.	.	.	C	9.756	1.168907	0.21621	.	.	ENSG00000171873	ENST00000379453	T	0.61158	0.13	3.23	-2.08	0.07254	.	1.510520	0.05497	U	0.557646	T	0.40670	0.1126	L	0.44542	1.39	0.09310	N	1	P	0.39404	0.672	B	0.25614	0.062	T	0.28038	-1.0056	10	0.36615	T	0.2	.	7.0676	0.25161	0.3869:0.3627:0.2504:0.0	.	534	P25100	ADA1D_HUMAN	T	534	ENSP00000368766:A534T	ENSP00000368766:A534T	A	-	1	0	ADRA1D	4150289	0.001000	0.12720	0.003000	0.11579	0.384000	0.30261	-0.494000	0.06451	-0.473000	0.06871	-2.386000	0.00229	GCC		0.706	ADRA1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077812.2	NM_000678	
CHD6	84181	broad.mit.edu	37	20	40126826	40126826	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:40126826T>C	ENST00000373233.3	-	7	1133	c.956A>G	c.(955-957)tAc>tGc	p.Y319C	CHD6_ENST00000373222.3_Missense_Mutation_p.Y354C|CHD6_ENST00000309279.7_Missense_Mutation_p.Y319C	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	319	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.|Required for DNA-dependent ATPase activity.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)	p.Y319C(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				ATACTTAACGTAGAACAGCTC	0.388																																					p.Y319C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A956G	20						.						60.0	58.0	59.0					20																	40126826		2203	4300	6503	39560240	SO:0001583	missense	84181	exon7			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.956A>G	20.37:g.40126826T>C	ENSP00000362330:p.Tyr319Cys	Somatic		Capture	Illumina HiSeq	Phase_I	39560240	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.1|22.1	4.240708|4.240708	0.79912|0.79912	.|.	.|.	ENSG00000124177|ENSG00000124177	ENST00000440697|ENST00000373233;ENST00000309279;ENST00000373222	.|T;T;D	.|0.86230	.|-0.67;-0.67;-2.09	5.36|5.36	5.36|5.36	0.76844|0.76844	.|Chromo domain (1);Chromo domain-like (1);Chromo domain/shadow (1);	.|0.000000	.|0.51477	.|D	.|0.000093	D|D	0.93187|0.93187	0.7830|0.7830	M|M	0.79123|0.79123	2.44|2.44	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.78314	.|0.991;0.984	D|D	0.94050|0.94050	0.7317|0.7317	5|10	.|0.87932	.|D	.|0	-14.4083|-14.4083	15.6553|15.6553	0.77129|0.77129	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|354;319	.|Q8TD26-2;Q8TD26	.|.;CHD6_HUMAN	A|C	22|319;319;354	.|ENSP00000362330:Y319C;ENSP00000308684:Y319C;ENSP00000362319:Y354C	.|ENSP00000308684:Y319C	T|Y	-|-	1|2	0|0	CHD6|CHD6	39560240|39560240	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.292000|7.292000	0.78731|0.78731	2.167000|2.167000	0.68274|0.68274	0.528000|0.528000	0.53228|0.53228	ACG|TAC		0.388	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
MYBL2	4605	broad.mit.edu	37	20	42331534	42331534	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:42331534G>A	ENST00000217026.4	+	8	1483	c.1356G>A	c.(1354-1356)tcG>tcA	p.S452S	MYBL2_ENST00000396863.4_Silent_p.S428S	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	452					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S452S(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TGCCCTTCTCGCCCTCCCAGG	0.577																																					p.S452S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1356A	20						.						103.0	88.0	93.0					20																	42331534		2203	4300	6503	41764948	SO:0001819	synonymous_variant	4605	exon8				CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.1356G>A	20.37:g.42331534G>A		Somatic		Capture	Illumina HiSeq	Phase_I	41764948	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Silent	SNP	ENST00000217026.4	37	CCDS13322.1																																																																																				0.577	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466	
TOX2	84969	broad.mit.edu	37	20	42683113	42683113	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:42683113G>A	ENST00000358131.5	+	5	1061	c.853G>A	c.(853-855)Gtg>Atg	p.V285M	TOX2_ENST00000341197.4_Missense_Mutation_p.V276M|TOX2_ENST00000435864.2_3'UTR|TOX2_ENST00000372999.1_Missense_Mutation_p.V234M|TOX2_ENST00000423191.2_Missense_Mutation_p.V234M	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	285					female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.V285M(1)|p.V234M(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			TTTCGGTGACGTGTCCAAAAT	0.597																																					p.V234M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G700A	20						.						70.0	62.0	65.0					20																	42683113		2203	4300	6503	42116527	SO:0001583	missense	84969	exon6			BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"""granulosa cell HMG box 1"""	611163	"""chromosome 20 open reading frame 100"""	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.853G>A	20.37:g.42683113G>A	ENSP00000350849:p.Val285Met	Somatic		Capture	Illumina HiSeq	Phase_I	42116527	NM_032883	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	Missense_Mutation	SNP	ENST00000358131.5	37	CCDS42875.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.748623	0.89753	.	.	ENSG00000124191	ENST00000341197;ENST00000423191;ENST00000372999;ENST00000358131;ENST00000435864	D;D;D;D;D	0.98531	-4.98;-4.98;-4.98;-4.98;-4.98	5.44	5.44	0.79542	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	D	0.000000	D	0.98890	0.9624	M	0.79475	2.455	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.998;0.998;0.999;0.999	D	0.99877	1.1105	10	0.87932	D	0	.	18.2447	0.89981	0.0:0.0:1.0:0.0	.	154;276;234;285;234	B4DQV8;G3XAC7;A8K1J1;Q96NM4;E1P5X0	.;.;.;TOX2_HUMAN;.	M	276;234;234;285;154	ENSP00000344724:V276M;ENSP00000390278:V234M;ENSP00000362090:V234M;ENSP00000350849:V285M;ENSP00000396777:V154M	ENSP00000344724:V276M	V	+	1	0	TOX2	42116527	1.000000	0.71417	0.979000	0.43373	0.707000	0.40811	9.869000	0.99810	2.556000	0.86216	0.650000	0.86243	GTG		0.597	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2		
YWHAB	7529	broad.mit.edu	37	20	43530343	43530343	+	Missense_Mutation	SNP	C	C	T	rs11544163		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:43530343C>T	ENST00000372839.3	+	3	443	c.169C>T	c.(169-171)Cgc>Tgc	p.R57C	YWHAB_ENST00000353703.4_Missense_Mutation_p.R57C|YWHAB_ENST00000479421.1_3'UTR	NM_003404.3	NP_003395.1	P31946	1433B_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta	57					activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cytoplasmic sequestering of protein (GO:0051220)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway (GO:0097193)|MAPK cascade (GO:0000165)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of protein dephosphorylation (GO:0035308)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of catalytic activity (GO:0043085)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein heterooligomerization (GO:0051291)|protein targeting (GO:0006605)|Ras protein signal transduction (GO:0007265)|RNA metabolic process (GO:0016070)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|phosphoprotein binding (GO:0051219)|phosphoserine binding (GO:0050815)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)	p.R57C(1)		breast(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(1)	12		Myeloproliferative disorder(115;0.0122)				GGTAGGCGCCCGCCGCTCTTC	0.522																																					p.R57C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C169T	20						.						66.0	65.0	65.0					20																	43530343		2203	4300	6503	42963757	SO:0001583	missense	7529	exon2			X57346	CCDS13339.1	20q13.1	2013-12-03	2013-12-03		ENSG00000166913	ENSG00000166913			12849	protein-coding gene	gene with protein product	"""14-3-3 beta"", ""14-3-3 alpha"""	601289	"""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, alpha polypeptide"", ""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide"""	YWHAA		8617504, 7890696	Standard	NM_003404		Approved		uc002xmu.3	P31946	OTTHUMG00000032549	ENST00000372839.3:c.169C>T	20.37:g.43530343C>T	ENSP00000361930:p.Arg57Cys	Somatic		Capture	Illumina HiSeq	Phase_I	42963757	NM_139323	A8K9K2|E1P616	Missense_Mutation	SNP	ENST00000372839.3	37	CCDS13339.1	.	.	.	.	.	.	.	.	.	.	C	31	5.104961	0.94245	.	.	ENSG00000166913	ENST00000353703;ENST00000372839;ENST00000428262;ENST00000445830	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	5.65	5.65	0.86999	14-3-3 domain (4);	0.048169	0.85682	D	0.000000	T	0.72755	0.3500	M	0.92923	3.36	0.80722	D	1	D	0.58970	0.984	P	0.54706	0.759	T	0.79766	-0.1665	10	0.87932	D	0	-7.0726	20.1057	0.97893	0.0:1.0:0.0:0.0	.	57	P31946	1433B_HUMAN	C	57	ENSP00000300161:R57C;ENSP00000361930:R57C;ENSP00000394729:R57C;ENSP00000394558:R57C	ENSP00000300161:R57C	R	+	1	0	YWHAB	42963757	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.827000	0.97445	0.650000	0.86243	CGC		0.522	YWHAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079386.3	NM_003404	
WFDC8	90199	broad.mit.edu	37	20	44184457	44184457	+	Missense_Mutation	SNP	G	G	A	rs545695082	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:44184457G>A	ENST00000357199.4	-	4	406	c.328C>T	c.(328-330)Cgc>Tgc	p.R110C	WFDC8_ENST00000289953.2_Missense_Mutation_p.R110C	NM_181510.2	NP_852611.2	Q8IUA0	WFDC8_HUMAN	WAP four-disulfide core domain 8	110	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R110C(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|stomach(1)|upper_aerodigestive_tract(1)	15		Myeloproliferative disorder(115;0.0122)				AAATGCCAGCGCTGTGCCTCA	0.458													G|||	2	0.000399361	0.0015	0.0	5008	,	,		20764	0.0		0.0	False		,,,				2504	0.0				p.R110C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C328T	20						.						112.0	100.0	104.0					20																	44184457		2203	4300	6503	43617871	SO:0001583	missense	90199	exon4			AL031663	CCDS13361.1	20q13.11	2013-01-21	2003-02-21	2003-02-21	ENSG00000158901	ENSG00000158901		"""WAP four-disulfide core domain containing"""	16163	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 170"""	C20orf170		12206714	Standard	NM_130896		Approved	dJ461P17.1, WAP8	uc002xow.3	Q8IUA0	OTTHUMG00000046342	ENST00000357199.4:c.328C>T	20.37:g.44184457G>A	ENSP00000361735:p.Arg110Cys	Somatic		Capture	Illumina HiSeq	Phase_I	43617871	NM_130896	E1P623|Q5TDV2|Q96A34	Missense_Mutation	SNP	ENST00000357199.4	37	CCDS13361.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.927543	0.52759	.	.	ENSG00000158901	ENST00000357199;ENST00000289953	T;T	0.63096	-0.02;-0.02	4.26	3.29	0.37713	Proteinase inhibitor I2, Kunitz metazoa (5);	0.463132	0.20651	N	0.088214	T	0.81597	0.4856	H	0.94264	3.515	0.09310	N	0.999994	D	0.89917	1.0	D	0.67103	0.949	T	0.73033	-0.4110	10	0.87932	D	0	.	9.5521	0.39317	0.0:0.0:0.7905:0.2095	.	110	Q8IUA0	WFDC8_HUMAN	C	110	ENSP00000361735:R110C;ENSP00000289953:R110C	ENSP00000289953:R110C	R	-	1	0	WFDC8	43617871	0.065000	0.20965	0.011000	0.14972	0.059000	0.15707	2.441000	0.44864	1.358000	0.45922	0.655000	0.94253	CGC		0.458	WFDC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106958.1		
PLTP	5360	broad.mit.edu	37	20	44531138	44531138	+	Missense_Mutation	SNP	C	C	T	rs373242157		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:44531138C>T	ENST00000477313.1	-	10	1642	c.1048G>A	c.(1048-1050)Gtc>Atc	p.V350I	PLTP_ENST00000354050.4_Missense_Mutation_p.V298I|PLTP_ENST00000372431.3_Missense_Mutation_p.V350I|PLTP_ENST00000542937.1_Missense_Mutation_p.V370I|PLTP_ENST00000420868.2_Missense_Mutation_p.V255I|PLTP_ENST00000372420.1_Missense_Mutation_p.V262I			P55058	PLTP_HUMAN	phospholipid transfer protein	350					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)	p.V350I(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				GCAATGGTGACGCTAGCAGTG	0.637																																					p.V350I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1048A	20						.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	73.0	69.0	70.0		763,784,1048,892	2.0	0.7	20		70	0,8600		0,0,4300	no	missense,missense,missense,missense	PLTP	NM_001242920.1,NM_001242921.1,NM_006227.3,NM_182676.2	29,29,29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign,benign	255/399,262/406,350/494,298/442	44531138	1,13005	2203	4300	6503	43964545	SO:0001583	missense	5360	exon11			L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"""BPI fold containing"""	9093	protein-coding gene	gene with protein product	"""BPI fold containing family E"""	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.1048G>A	20.37:g.44531138C>T	ENSP00000417138:p.Val350Ile	Somatic		Capture	Illumina HiSeq	Phase_I	43964545	NM_006227	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Missense_Mutation	SNP	ENST00000477313.1	37	CCDS13386.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.482187	0.44147	2.27E-4	0.0	ENSG00000100979	ENST00000372420;ENST00000372431;ENST00000354050;ENST00000477313;ENST00000542937;ENST00000420868	T;T;T;T;T;T	0.07800	3.16;3.16;3.16;3.16;3.16;3.16	5.28	2.05	0.26809	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.255468	0.39341	N	0.001395	T	0.06096	0.0158	L	0.44542	1.39	0.35093	D	0.764543	P;P;P;P;P;P;P	0.46142	0.794;0.794;0.794;0.794;0.846;0.794;0.873	B;B;B;B;B;B;B	0.37943	0.229;0.229;0.165;0.229;0.261;0.229;0.229	T	0.31194	-0.9952	10	0.07644	T	0.81	-35.7331	11.5913	0.50947	0.1141:0.3065:0.5794:0.0	.	255;255;262;350;298;350;370	E7EV16;B4DRB4;B4DDD5;Q53H91;P55058-2;P55058;B3KUE5	.;.;.;.;.;PLTP_HUMAN;.	I	262;350;298;350;370;255	ENSP00000361497:V262I;ENSP00000361508:V350I;ENSP00000335290:V298I;ENSP00000417138:V350I;ENSP00000440296:V370I;ENSP00000411671:V255I	ENSP00000335290:V298I	V	-	1	0	PLTP	43964545	0.571000	0.26659	0.721000	0.30653	0.843000	0.47879	0.962000	0.29280	0.768000	0.33290	0.655000	0.94253	GTC		0.637	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227	
PLTP	5360	broad.mit.edu	37	20	44533495	44533495	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:44533495G>T	ENST00000477313.1	-	9	1480	c.886C>A	c.(886-888)Ccc>Acc	p.P296T	PLTP_ENST00000354050.4_Missense_Mutation_p.P244T|PLTP_ENST00000372431.3_Missense_Mutation_p.P296T|PLTP_ENST00000542937.1_Missense_Mutation_p.P316T|PLTP_ENST00000420868.2_Missense_Mutation_p.P201T|PLTP_ENST00000372420.1_Missense_Mutation_p.P208T			P55058	PLTP_HUMAN	phospholipid transfer protein	296					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)	p.P296T(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				AGGTCGTGGGGCACCTGAACA	0.602																																					p.P296T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C886A	20						.						112.0	105.0	108.0					20																	44533495		2203	4300	6503	43966902	SO:0001583	missense	5360	exon10			L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"""BPI fold containing"""	9093	protein-coding gene	gene with protein product	"""BPI fold containing family E"""	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.886C>A	20.37:g.44533495G>T	ENSP00000417138:p.Pro296Thr	Somatic		Capture	Illumina HiSeq	Phase_I	43966902	NM_006227	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Missense_Mutation	SNP	ENST00000477313.1	37	CCDS13386.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.007558	0.75046	.	.	ENSG00000100979	ENST00000372420;ENST00000372431;ENST00000354050;ENST00000477313;ENST00000542937;ENST00000420868	T;T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63;2.63	5.0	5.0	0.66597	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.106568	0.64402	D	0.000003	T	0.36635	0.0974	M	0.67953	2.075	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;1.0;0.999;0.999	D;D;D;D;D;D;D	0.81914	0.995;0.995;0.987;0.986;0.987;0.986;0.986	T	0.07065	-1.0792	10	0.72032	D	0.01	-36.5572	16.6413	0.85127	0.0:0.0:1.0:0.0	.	201;201;208;296;244;296;316	E7EV16;B4DRB4;B4DDD5;Q53H91;P55058-2;P55058;B3KUE5	.;.;.;.;.;PLTP_HUMAN;.	T	208;296;244;296;316;201	ENSP00000361497:P208T;ENSP00000361508:P296T;ENSP00000335290:P244T;ENSP00000417138:P296T;ENSP00000440296:P316T;ENSP00000411671:P201T	ENSP00000335290:P244T	P	-	1	0	PLTP	43966902	1.000000	0.71417	0.999000	0.59377	0.668000	0.39293	7.013000	0.76373	2.610000	0.88304	0.563000	0.77884	CCC		0.602	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227	
PRND	23627	broad.mit.edu	37	20	4705653	4705653	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:4705653C>T	ENST00000305817.2	+	2	527	c.456C>T	c.(454-456)ggC>ggT	p.G152G		NM_012409.2	NP_036541.2	Q9UKY0	PRND_HUMAN	prion protein 2 (dublet)	152	Globular.				protein homooligomerization (GO:0051260)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.G152G(1)		breast(3)|endometrium(2)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	13						TGGAGAGGGGCGCAGGACTTC	0.587																																					p.G152G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C456T	20						.						38.0	36.0	37.0					20																	4705653		2203	4300	6503	4653653	SO:0001819	synonymous_variant	23627	exon2			AF106918	CCDS13081.1	20p13	2013-09-19			ENSG00000171864	ENSG00000171864			15748	protein-coding gene	gene with protein product	"""prion-like protein doppel"""	604263				10525406, 10577243	Standard	NM_012409		Approved	DPL, dJ1068H6.4, DOPPEL, PrPLP	uc002wkz.3	Q9UKY0	OTTHUMG00000031789	ENST00000305817.2:c.456C>T	20.37:g.4705653C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4653653	NM_012409	A7U7M5|Q9H311|Q9H312|Q9NTM4	Silent	SNP	ENST00000305817.2	37	CCDS13081.1																																																																																				0.587	PRND-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077827.2	NM_012409	
MMP9	4318	broad.mit.edu	37	20	44640877	44640877	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:44640877G>A	ENST00000372330.3	+	7	1118	c.1099G>A	c.(1099-1101)Gga>Aga	p.G367R	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	367	Fibronectin type-II 3. {ECO:0000255|PROSITE-ProRule:PRU00479}.				collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G367R(1)		breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	CGAGGGCCGCGGAGATGGGCG	0.652																																					p.G367R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1099A	20						.						69.0	82.0	78.0					20																	44640877		2203	4300	6503	44074284	SO:0001583	missense	4318	exon7				CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"""matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)"", ""matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"""	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.1099G>A	20.37:g.44640877G>A	ENSP00000361405:p.Gly367Arg	Somatic		Capture	Illumina HiSeq	Phase_I	44074284	NM_004994	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	37	CCDS13390.1	.	.	.	.	.	.	.	.	.	.	G	6.090	0.384948	0.11524	.	.	ENSG00000100985	ENST00000372330	T	0.46819	0.86	4.89	-5.58	0.02512	Peptidase M10, metallopeptidase (1);Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);Peptidase, metallopeptidase (1);	2.506030	0.00887	N	0.002183	T	0.29093	0.0723	N	0.13299	0.325	0.20196	N	0.999926	B	0.11235	0.004	B	0.08055	0.003	T	0.15407	-1.0438	10	0.30078	T	0.28	.	8.8512	0.35201	0.4748:0.3832:0.142:0.0	.	367	P14780	MMP9_HUMAN	R	367	ENSP00000361405:G367R	ENSP00000361405:G367R	G	+	1	0	MMP9	44074284	0.000000	0.05858	0.002000	0.10522	0.077000	0.17291	-0.038000	0.12144	-1.424000	0.01999	-2.320000	0.00252	GGA		0.652	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1		
PREX1	57580	broad.mit.edu	37	20	47271846	47271846	+	Missense_Mutation	SNP	C	C	T	rs139250516		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:47271846C>T	ENST00000371941.3	-	19	2213	c.2191G>A	c.(2191-2193)Gtc>Atc	p.V731I	PREX1_ENST00000396220.1_Missense_Mutation_p.V731I	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	731					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V731I(4)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			ACAGCATAGACGTACGGTGGG	0.572																																					p.V731I												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G2191A	20						.	C	ILE/VAL	0,4406		0,0,2203	145.0	97.0	114.0		2191	3.9	0.4	20	dbSNP_134	114	3,8597	3.0+/-9.4	0,3,4297	no	missense	PREX1	NM_020820.3	29	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign	731/1660	47271846	3,13003	2203	4300	6503	46705253	SO:0001583	missense	57580	exon19			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2191G>A	20.37:g.47271846C>T	ENSP00000361009:p.Val731Ile	Somatic		Capture	Illumina HiSeq	Phase_I	46705253	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.652121	0.47362	0.0	3.49E-4	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.19394	2.15;2.15	4.85	3.9	0.45041	PDZ/DHR/GLGF (2);	0.000000	0.48767	U	0.000165	T	0.16599	0.0399	L	0.31120	0.905	0.45930	D	0.998761	P;D	0.54047	0.846;0.964	B;B	0.42462	0.185;0.388	T	0.02087	-1.1216	10	0.33940	T	0.23	.	12.9814	0.58567	0.0:0.9215:0.0:0.0785	.	731;28	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	I	731	ENSP00000361009:V731I;ENSP00000379522:V731I	ENSP00000361009:V731I	V	-	1	0	PREX1	46705253	0.441000	0.25626	0.445000	0.26908	0.401000	0.30781	1.075000	0.30716	1.021000	0.39600	0.655000	0.94253	GTC		0.572	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
ARFGEF2	10564	broad.mit.edu	37	20	47592683	47592683	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:47592683G>A	ENST00000371917.4	+	14	1905	c.1905G>A	c.(1903-1905)gaG>gaA	p.E635E		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	635					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)	p.E635E(1)		breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			ATGACCCTGAGCAATTTGAGG	0.512																																					p.E635E	Esophageal Squamous(176;1738 1974 26285 33069 35354)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1905A	20						.						108.0	80.0	90.0					20																	47592683		2203	4300	6503	47026090	SO:0001819	synonymous_variant	10564	exon14			AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.1905G>A	20.37:g.47592683G>A		Somatic		Capture	Illumina HiSeq	Phase_I	47026090	NM_006420	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	37	CCDS13411.1																																																																																				0.512	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420	
GPCPD1	56261	broad.mit.edu	37	20	5556563	5556563	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:5556563C>T	ENST00000379019.4	-	9	979	c.767G>A	c.(766-768)tGt>tAt	p.C256Y	GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	256					glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)	glycerophosphocholine phosphodiesterase activity (GO:0047389)|starch binding (GO:2001070)	p.C256Y(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						TGATAAGAGACAAGCTGTACC	0.408																																					p.C256Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G767A	20						.						90.0	80.0	84.0					20																	5556563		2203	4300	6503	5504563	SO:0001583	missense	56261	exon9				CCDS13090.1	20p12.3	2011-01-25			ENSG00000125772	ENSG00000125772			26957	protein-coding gene	gene with protein product		614124				10718198, 20576599	Standard	NM_019593		Approved	KIAA1434, GDE5, GDPD6	uc002wme.4	Q9NPB8	OTTHUMG00000031806	ENST00000379019.4:c.767G>A	20.37:g.5556563C>T	ENSP00000368305:p.Cys256Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	5504563	NM_019593	D3DW06|Q9BQL8|Q9NUX0	Missense_Mutation	SNP	ENST00000379019.4	37	CCDS13090.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.445235	0.43429	.	.	ENSG00000125772	ENST00000379019	T	0.38560	1.13	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.38665	0.1049	N	0.14661	0.345	0.80722	D	1	D	0.67145	0.996	P	0.56700	0.804	T	0.08848	-1.0702	10	0.02654	T	1	-5.9177	19.3281	0.94270	0.0:1.0:0.0:0.0	.	256	Q9NPB8	GPCP1_HUMAN	Y	256	ENSP00000368305:C256Y	ENSP00000368305:C256Y	C	-	2	0	GPCPD1	5504563	1.000000	0.71417	0.865000	0.33974	0.637000	0.38172	7.776000	0.85560	2.629000	0.89072	0.650000	0.86243	TGT		0.408	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593	
ZNF217	7764	broad.mit.edu	37	20	52198622	52198622	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:52198622G>A	ENST00000371471.2	-	2	1169	c.744C>T	c.(742-744)agC>agT	p.S248S	ZNF217_ENST00000540425.1_5'Flank|ZNF217_ENST00000302342.3_Silent_p.S248S			O75362	ZN217_HUMAN	zinc finger protein 217	248					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.S248S(2)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			CTGTCTGCGCGCTGCTGGTAC	0.483																																					p.S248S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C744T	20						.						102.0	99.0	100.0					20																	52198622		2203	4300	6503	51632029	SO:0001819	synonymous_variant	7764	exon1			AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.744C>T	20.37:g.52198622G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51632029	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																				0.483	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
CTCFL	140690	broad.mit.edu	37	20	56099043	56099043	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:56099043C>A	ENST00000608263.1	-	1	880	c.219G>T	c.(217-219)gaG>gaT	p.E73D	CTCFL_ENST00000423479.3_Missense_Mutation_p.E73D|CTCFL_ENST00000539382.1_Intron|CTCFL_ENST00000608425.1_Missense_Mutation_p.E73D|CTCFL_ENST00000433949.3_Intron|CTCFL_ENST00000609232.1_Missense_Mutation_p.E73D|CTCFL_ENST00000608440.1_Missense_Mutation_p.E73D|CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000481655.2_Missense_Mutation_p.E73D|CTCFL_ENST00000432255.2_Missense_Mutation_p.E73D|CTCFL_ENST00000429804.3_Missense_Mutation_p.E73D|CTCFL_ENST00000371196.2_Missense_Mutation_p.E73D|CTCFL_ENST00000422869.2_Missense_Mutation_p.E73D|CTCFL_ENST00000608158.1_Missense_Mutation_p.E73D|CTCFL_ENST00000243914.3_Missense_Mutation_p.E73D	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	73					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|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 (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)	p.E73D(1)		NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			TCTCGCTCTCCTCCGAGGGGG	0.587																																					p.E73D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G219T	20						.						95.0	93.0	94.0					20																	56099043		2203	4299	6502	55532449	SO:0001583	missense	140690	exon2				CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"""Zinc fingers, C2H2-type"""	16234	protein-coding gene	gene with protein product	"""cancer/testis antigen 27"""	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.219G>T	20.37:g.56099043C>A	ENSP00000476783:p.Glu73Asp	Somatic		Capture	Illumina HiSeq	Phase_I	55532449	NM_080618	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	37	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.060848	0.36373	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000422109;ENST00000426658;ENST00000432255;ENST00000422869	T;T;T;T;T;T;T;T;T	0.11277	2.79;2.82;2.82;2.98;2.86;3.15;2.85;3.44;2.86	4.76	3.82	0.43975	.	0.862029	0.09665	N	0.771975	T	0.25865	0.0630	M	0.63428	1.95	0.09310	N	1	P;P;P;D;P;P;P;B	0.64830	0.808;0.808;0.675;0.994;0.652;0.675;0.666;0.396	B;B;B;D;B;B;B;B	0.70716	0.161;0.161;0.121;0.97;0.099;0.242;0.099;0.099	T	0.12993	-1.0526	10	0.23891	T	0.37	-9.712	7.4341	0.27145	0.0:0.8008:0.0:0.1992	.	73;73;73;73;73;73;73;73	A6XGM3;A6XGM0;A6XGM9;A6XGM8;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;.;.;.;CTCFL_HUMAN	D	73	ENSP00000415579:E73D;ENSP00000243914:E73D;ENSP00000360239:E73D;ENSP00000415329:E73D;ENSP00000392034:E73D;ENSP00000413713:E73D;ENSP00000403369:E73D;ENSP00000409344:E73D;ENSP00000399061:E73D	ENSP00000243914:E73D	E	-	3	2	CTCFL	55532449	0.001000	0.12720	0.039000	0.18376	0.002000	0.02628	-0.056000	0.11787	0.984000	0.38629	-0.142000	0.14014	GAG		0.587	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618	
CHGB	1114	broad.mit.edu	37	20	5903379	5903379	+	Missense_Mutation	SNP	G	G	A	rs140646779	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:5903379G>A	ENST00000378961.4	+	4	793	c.589G>A	c.(589-591)Gct>Act	p.A197T		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	197						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)	p.A197T(1)		breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GACACAAAACGCTTTTCTCAA	0.483													G|||	8	0.00159744	0.0053	0.0	5008	,	,		20700	0.0		0.0	False		,,,				2504	0.001				p.A197T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G589A	20						.	G	THR/ALA	12,4394	20.2+/-43.8	0,12,2191	84.0	89.0	87.0		589	-1.3	0.0	20	dbSNP_134	87	0,8600		0,0,4300	yes	missense	CHGB	NM_001819.2	58	0,12,6491	AA,AG,GG		0.0,0.2724,0.0923	benign	197/678	5903379	12,12994	2203	4300	6503	5851379	SO:0001583	missense	1114	exon4				CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.589G>A	20.37:g.5903379G>A	ENSP00000368244:p.Ala197Thr	Somatic		Capture	Illumina HiSeq	Phase_I	5851379	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	12.87	2.068984	0.36470	0.002724	0.0	ENSG00000089199	ENST00000378961;ENST00000455042	T;T	0.01613	4.73;4.73	5.57	-1.31	0.09230	.	0.729028	0.13189	N	0.406844	T	0.01905	0.0060	L	0.46741	1.465	0.09310	N	1	B	0.28178	0.202	B	0.19946	0.027	T	0.42241	-0.9463	10	0.27082	T	0.32	-0.4833	10.9692	0.47431	0.3793:0.0:0.6207:0.0	.	197	P05060	SCG1_HUMAN	T	197;177	ENSP00000368244:A197T;ENSP00000416643:A177T	ENSP00000368244:A197T	A	+	1	0	CHGB	5851379	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	0.254000	0.18314	-0.188000	0.10499	0.563000	0.77884	GCT		0.483	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
CDH26	60437	broad.mit.edu	37	20	58569464	58569464	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:58569464C>T	ENST00000244047.5	+	11	1897	c.1586C>T	c.(1585-1587)cCg>cTg	p.P529L	CDH26_ENST00000244049.3_5'Flank|CDH26_ENST00000497614.1_3'UTR|CDH26_ENST00000350849.6_5'Flank|CDH26_ENST00000348616.4_Missense_Mutation_p.P529L			Q8IXH8	CAD26_HUMAN	cadherin 26	529					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P529L(2)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			GACCTGGAGCCGTTCTCTGAC	0.532																																					p.P529L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1586T	20						.						64.0	60.0	61.0					20																	58569464		2203	4300	6503	58002859	SO:0001583	missense	60437	exon11			AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"""Cadherins / Major cadherins"""	15902	protein-coding gene	gene with protein product			"""cadherin-like 26"""				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.1586C>T	20.37:g.58569464C>T	ENSP00000244047:p.Pro529Leu	Somatic		Capture	Illumina HiSeq	Phase_I	58002859	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Missense_Mutation	SNP	ENST00000244047.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.70|15.70	2.909974|2.909974	0.52439|0.52439	.|.	.|.	ENSG00000124215|ENSG00000124215	ENST00000244047;ENST00000348616|ENST00000370991	T;T|.	0.61392|.	0.11;0.11|.	4.58|4.58	3.63|3.63	0.41609|0.41609	Cadherin-like (1);|.	0.069672|.	0.56097|.	N|.	0.000021|.	T|T	0.72326|0.72326	0.3446|0.3446	M|M	0.79258|0.79258	2.445|2.445	0.58432|0.58432	D|D	0.999998|0.999998	D;D|.	0.89917|.	1.0;0.976|.	D;P|.	0.91635|.	0.999;0.868|.	T|T	0.72347|0.72347	-0.4321|-0.4321	10|5	0.20046|.	T|.	0.44|.	.|.	11.3195|11.3195	0.49412|0.49412	0.0:0.9088:0.0:0.0912|0.0:0.9088:0.0:0.0912	.|.	529;529|.	Q8IXH8;Q8IXH8-4|.	CAD26_HUMAN;.|.	L|C	529|121	ENSP00000244047:P529L;ENSP00000339390:P529L|.	ENSP00000244047:P529L|.	P|R	+|+	2|1	0|0	CDH26|CDH26	58002859|58002859	0.992000|0.992000	0.36948|0.36948	0.645000|0.645000	0.29479|0.29479	0.357000|0.357000	0.29423|0.29423	3.171000|3.171000	0.50824|0.50824	0.903000|0.903000	0.36546|0.36546	0.655000|0.655000	0.94253|0.94253	CCG|CGT		0.532	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980	
ARFGAP1	55738	broad.mit.edu	37	20	61909497	61909497	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:61909497G>A	ENST00000370283.4	+	6	612	c.472G>A	c.(472-474)Gcc>Acc	p.A158T	ARFGAP1_ENST00000353546.3_Missense_Mutation_p.A158T|ARFGAP1_ENST00000547204.1_Missense_Mutation_p.A84T|ARFGAP1_ENST00000519273.2_Missense_Mutation_p.A45T|ARFGAP1_ENST00000519604.1_Missense_Mutation_p.A105T|ARFGAP1_ENST00000370275.4_Missense_Mutation_p.A158T	NM_018209.2	NP_060679.1	Q8N6T3	ARFG1_HUMAN	ADP-ribosylation factor GTPase activating protein 1	158					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPI coating of Golgi vesicle (GO:0048205)|endoplasmic reticulum unfolded protein response (GO:0030968)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cytosol (GO:0005829)|Golgi-associated vesicle membrane (GO:0030660)|synapse (GO:0045202)	ARF GTPase activator activity (GO:0008060)|GTPase activator activity (GO:0005096)|zinc ion binding (GO:0008270)	p.A158T(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)	13	all_cancers(38;1.59e-09)					GAGTGTGACCGCCTCCTCGGA	0.587																																					p.A158T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G472A	20						.						95.0	94.0	94.0					20																	61909497		2203	4300	6503	61379942	SO:0001583	missense	55738	exon6			AK001629	CCDS13515.1, CCDS13516.1, CCDS63326.1, CCDS63327.1, CCDS63328.1	20q13.33	2009-11-30	2002-08-20	2002-08-23	ENSG00000101199	ENSG00000101199		"""ADP-ribosylation factor GTPase activating proteins"""	15852	protein-coding gene	gene with protein product		608377	"""ADP-ribosylation factor 1 GTPase activating protein"""	ARF1GAP		11210549	Standard	NM_018209		Approved	FLJ10767, bA261N11.3	uc002yel.3	Q8N6T3	OTTHUMG00000032965	ENST00000370283.4:c.472G>A	20.37:g.61909497G>A	ENSP00000359306:p.Ala158Thr	Somatic		Capture	Illumina HiSeq	Phase_I	61379942	NM_175609	B7Z3U0|B7Z8H8|B7ZBI3|E1P5I9|E7EV62|Q6PK71|Q96KC4|Q96T02|Q9NSU3|Q9NVF6|Q9UIL0	Missense_Mutation	SNP	ENST00000370283.4	37	CCDS13515.1	.	.	.	.	.	.	.	.	.	.	G	6.892	0.534101	0.13188	.	.	ENSG00000101199	ENST00000370283;ENST00000547204;ENST00000549047;ENST00000519604;ENST00000519273;ENST00000370275;ENST00000518601;ENST00000353546;ENST00000522403	T;T;T;T;T;T;T;T;T	0.48836	1.47;0.84;0.89;0.9;0.8;1.46;0.84;1.49;1.51	5.11	-0.574	0.11738	.	0.605446	0.16972	N	0.192076	T	0.18383	0.0441	N	0.16903	0.455	0.22710	N	0.998825	P;B;B;B;B	0.37352	0.591;0.008;0.022;0.001;0.001	B;B;B;B;B	0.25506	0.061;0.005;0.007;0.001;0.002	T	0.12889	-1.0530	10	0.23891	T	0.37	-21.4535	1.7773	0.03024	0.2002:0.1151:0.448:0.2368	.	45;105;158;158;158	B7Z8H8;E7EV62;B7ZBI2;Q8N6T3;Q8N6T3-2	.;.;.;ARFG1_HUMAN;.	T	158;84;84;105;45;158;84;158;158	ENSP00000359306:A158T;ENSP00000449800:A84T;ENSP00000447037:A84T;ENSP00000430500:A105T;ENSP00000443716:A45T;ENSP00000359298:A158T;ENSP00000429674:A84T;ENSP00000314615:A158T;ENSP00000430929:A158T	ENSP00000314615:A158T	A	+	1	0	ARFGAP1	61379942	0.000000	0.05858	0.003000	0.11579	0.137000	0.21094	0.176000	0.16782	-0.348000	0.08286	0.563000	0.77884	GCC		0.587	ARFGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080134.3	NM_018209	
SIGLEC1	6614	broad.mit.edu	37	20	3674302	3674302	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:3674302delC	ENST00000344754.4	-	13	3299	c.3300delG	c.(3298-3300)gggfs	p.G1100fs	SIGLEC1_ENST00000202578.4_Frame_Shift_Del_p.G1100fs	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1100	Ig-like C2-type 11.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.Q1101fs*3(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						TCACCAGCTGCCCCTCCCGCA	0.647																																					p.G1100fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3300delG	20						.						58.0	41.0	47.0					20																	3674302		2203	4300	6503	3622302	SO:0001589	frameshift_variant	6614	exon13			AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.3300delG	20.37:g.3674302delC	ENSP00000341141:p.Gly1100fs	Somatic		Capture	Illumina HiSeq	Phase_I	3622302	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Frame_Shift_Del	DEL	ENST00000344754.4	37	CCDS13060.1																																																																																				0.647	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
ASXL1	171023	broad.mit.edu	37	20	31022625	31022625	+	Frame_Shift_Del	DEL	G	G	-	rs151317625	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:31022625delG	ENST00000375687.4	+	13	2534	c.2110delG	c.(2110-2112)gggfs	p.G704fs	ASXL1_ENST00000306058.5_Frame_Shift_Del_p.G699fs	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	704					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.G704R(1)|p.E705fs*20(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						TCCTCTAAATGGGGAGCATAC	0.582			"""F, N, Mis"""		"""MDS, CMML"""																																p.G704fs			Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.2110delG	20						.						53.0	47.0	49.0					20																	31022625		2203	4300	6503	30486286	SO:0001589	frameshift_variant	171023	exon12			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"""additional sex combs like 1 (Drosophila)"""			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.2110delG	20.37:g.31022625delG	ENSP00000364839:p.Gly704fs	Somatic		Capture	Illumina HiSeq	Phase_I	30486286	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Frame_Shift_Del	DEL	ENST00000375687.4	37	CCDS13201.1																																																																																				0.582	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338	
BPIFA1	51297	broad.mit.edu	37	20	31825965	31825965	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:31825965delG	ENST00000354297.4	+	3	336	c.265delG	c.(265-267)gggfs	p.G90fs	BPIFA1_ENST00000375422.2_Frame_Shift_Del_p.G90fs|BPIFA1_ENST00000375413.4_Frame_Shift_Del_p.G90fs	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	90					antibacterial humoral response (GO:0019731)|innate immune response (GO:0045087)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|regulation of liquid surface tension (GO:0050828)|regulation of sodium ion transmembrane transport (GO:1902305)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)	p.G90fs*6(1)									TGGCCTCCTTGGGGGACTGCT	0.542																																					p.G89fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.265delG	20						.						81.0	76.0	78.0					20																	31825965		2203	4300	6503	31289626	SO:0001589	frameshift_variant	51297	exon3			AB024937	CCDS13217.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000198183	ENSG00000198183		"""BPI fold containing"""	15749	protein-coding gene	gene with protein product		607412	"""palate, lung and nasal epithelium carcinoma associated"", ""palate, lung and nasal epithelium associated"""	PLUNC		11018263, 11251963, 21787333	Standard	NM_130852		Approved	LUNX, bA49G10.5, SPLUNC1	uc002wyv.3	Q9NP55	OTTHUMG00000032243	ENST00000354297.4:c.265delG	20.37:g.31825965delG	ENSP00000346251:p.Gly90fs	Somatic		Capture	Illumina HiSeq	Phase_I	31289626	NM_016583	A8K9R3|E1P5M9|Q9NZT0	Frame_Shift_Del	DEL	ENST00000354297.4	37	CCDS13217.1																																																																																				0.542	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852	
RALGAPB	57148	broad.mit.edu	37	20	37177336	37177336	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:37177336delT	ENST00000262879.6	+	20	3191	c.2907delT	c.(2905-2907)gatfs	p.D969fs	RALGAPB_ENST00000397042.3_Frame_Shift_Del_p.D965fs|RALGAPB_ENST00000397040.1_Frame_Shift_Del_p.D969fs|RALGAPB_ENST00000397038.1_Frame_Shift_Del_p.D747fs			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	969					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.F971fs*53(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						TTCTAGATGATTTTTTCCCCT	0.378																																					p.D969fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2907delT	20						.						69.0	70.0	69.0					20																	37177336		2203	4300	6503	36610750	SO:0001589	frameshift_variant	57148	exon20			AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.2907delT	20.37:g.37177336delT	ENSP00000262879:p.Asp969fs	Somatic		Capture	Illumina HiSeq	Phase_I	36610750	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Frame_Shift_Del	DEL	ENST00000262879.6	37	CCDS13305.1																																																																																				0.378	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	
SEMG2	6407	broad.mit.edu	37	20	43850761	43850761	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:43850761delA	ENST00000372769.3	+	2	578	c.488delA	c.(487-489)gaafs	p.E163fs		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	163	Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)	p.R165fs*7(1)		autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				TCAAACACAGAAAAAAGGCTA	0.438																																					p.E163fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.488delA	20						.						99.0	89.0	92.0					20																	43850761		2203	4300	6503	43284175	SO:0001589	frameshift_variant	6407	exon2				CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"""Semenogelin 2"""	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.488delA	20.37:g.43850761delA	ENSP00000361855:p.Glu163fs	Somatic		Capture	Illumina HiSeq	Phase_I	43284175	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Frame_Shift_Del	DEL	ENST00000372769.3	37	CCDS13346.1																																																																																				0.438	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008	
C20orf195	79025	broad.mit.edu	37	20	62187781	62187781	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr20:62187781C>T	ENST00000370098.3	+	2	857	c.765C>T	c.(763-765)tgC>tgT	p.C255C	C20orf195_ENST00000370097.1_Silent_p.C255C	NM_024059.2	NP_076964.1	Q9BVV2	CT195_HUMAN	chromosome 20 open reading frame 195	255	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular vesicular exosome (GO:0070062)		p.C255C(1)		large_intestine(3)|lung(4)	7	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			AGCAGGAGTGCGCCCAGTGTG	0.632																																					p.C255C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C765T	20						.						99.0	96.0	97.0					20																	62187781		2203	4300	6503	61658225	SO:0001819	synonymous_variant	79025	exon2				CCDS13526.1	20q13.33	2014-02-12			ENSG00000125531	ENSG00000125531			28764	protein-coding gene	gene with protein product						12477932	Standard	NM_024059		Approved	MGC5356	uc002yfj.3	Q9BVV2	OTTHUMG00000032980	ENST00000370098.3:c.765C>T	20.37:g.62187781C>T		Somatic		Capture	Illumina HiSeq	Phase_I	61658225	NM_024059		Silent	SNP	ENST00000370098.3	37	CCDS13526.1																																																																																				0.632	C20orf195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080155.1	NM_024059	
CXADR	1525	broad.mit.edu	37	21	18919506	18919506	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:18919506C>T	ENST00000284878.7	+	2	953	c.205C>T	c.(205-207)Caa>Taa	p.Q69*	CXADR_ENST00000400169.1_Nonsense_Mutation_p.Q69*|CXADR_ENST00000400166.1_Nonsense_Mutation_p.Q69*|CXADR_ENST00000356275.6_Nonsense_Mutation_p.Q69*|CXADR_ENST00000306618.10_Nonsense_Mutation_p.Q69*|CXADR_ENST00000400165.1_Nonsense_Mutation_p.Q69*	NM_001338.4	NP_001329.1	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor	69	Ig-like C2-type 1.				actin cytoskeleton reorganization (GO:0031532)|AV node cell to bundle of His cell communication (GO:0086067)|blood coagulation (GO:0007596)|cardiac muscle fiber development (GO:0048739)|cell-cell junction organization (GO:0045216)|defense response to virus (GO:0051607)|epithelial structure maintenance (GO:0010669)|gamma-delta T cell activation (GO:0046629)|germ cell migration (GO:0008354)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|homotypic cell-cell adhesion (GO:0034109)|leukocyte migration (GO:0050900)|mitochondrion organization (GO:0007005)|neutrophil chemotaxis (GO:0030593)|regulation of immune response (GO:0050776)|transepithelial transport (GO:0070633)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|adherens junction (GO:0005912)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|filopodium (GO:0030175)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|cell adhesion molecule binding (GO:0050839)|connexin binding (GO:0071253)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|virus receptor activity (GO:0001618)	p.Q69*(1)		endometrium(2)|large_intestine(5)|lung(1)|ovary(1)|prostate(2)	11				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		GAAGGTGGATCAAGTGGTAAG	0.502																																					p.Q69X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C205T	21						.						84.0	68.0	73.0					21																	18919506		2203	4300	6503	17841377	SO:0001587	stop_gained	1525	exon2			Y07593	CCDS33519.1, CCDS56204.1, CCDS56205.1, CCDS56206.1, CCDS56207.1	21q21.1	2013-01-29			ENSG00000154639	ENSG00000154639		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2559	protein-coding gene	gene with protein product		602621				9036860, 9096397	Standard	NM_001338		Approved	CAR	uc002yki.3	P78310	OTTHUMG00000074508	ENST00000284878.7:c.205C>T	21.37:g.18919506C>T	ENSP00000284878:p.Gln69*	Somatic		Capture	Illumina HiSeq	Phase_I	17841377	NM_001338	B2R8V8|B7WPI3|D3YHP0|O00694|Q8WWT6|Q8WWT7|Q8WWT8|Q9UKV4	Nonsense_Mutation	SNP	ENST00000284878.7	37	CCDS33519.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.728896	0.89390	.	.	ENSG00000154639	ENST00000284878;ENST00000400166;ENST00000356275;ENST00000400169;ENST00000400165;ENST00000306618	.	.	.	5.11	5.11	0.69529	.	0.196004	0.53938	D	0.000041	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	14.8285	0.70130	0.0:0.8449:0.155:0.0	.	.	.	.	X	69	.	ENSP00000284878:Q69X	Q	+	1	0	CXADR	17841377	0.979000	0.34478	1.000000	0.80357	0.974000	0.67602	0.611000	0.24268	2.764000	0.94973	0.655000	0.94253	CAA		0.502	CXADR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000158209.1		
GABPA	2551	broad.mit.edu	37	21	27136590	27136590	+	Missense_Mutation	SNP	C	C	T	rs2829897		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:27136590C>T	ENST00000354828.3	+	8	1399	c.872C>T	c.(871-873)gCg>gTg	p.A291V	GABPA_ENST00000400075.3_Missense_Mutation_p.A291V	NM_001197297.1	NP_001184226.1	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha subunit 60kDa	291			A -> V (in dbSNP:rs2829897).		cell differentiation (GO:0030154)|in utero embryonic development (GO:0001701)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)	p.A291V(2)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	24						AATAGTAGTGCGAAAGCAGCC	0.373																																					p.A291V												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C872T	21						.	C	VAL/ALA,VAL/ALA	0,4406		0,0,2203	59.0	63.0	61.0		872,872	4.7	1.0	21	dbSNP_100	61	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	GABPA	NM_001197297.1,NM_002040.3	64,64	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	291/455,291/455	27136590	1,13003	2203	4299	6502	26058461	SO:0001583	missense	2551	exon8				CCDS13575.1	21q21-q22.1	2008-07-31	2002-08-29		ENSG00000154727	ENSG00000154727			4071	protein-coding gene	gene with protein product	"""human nuclear respiratory factor-2 subunit alpha"", ""nuclear respiratory factor 2 alpha subunit"""	600609	"""GA-binding protein transcription factor, alpha subunit (60kD)"""			8441384	Standard	NM_002040		Approved	E4TF1A, NFT2, NRF2, E4TF1-60, NRF2A	uc002yly.4	Q06546	OTTHUMG00000078443	ENST00000354828.3:c.872C>T	21.37:g.27136590C>T	ENSP00000346886:p.Ala291Val	Somatic		Capture	Illumina HiSeq	Phase_I	26058461	NM_001197297	Q12939	Missense_Mutation	SNP	ENST00000354828.3	37	CCDS13575.1	.	.	.	.	.	.	.	.	.	.	C	11.43	1.636635	0.29068	0.0	1.16E-4	ENSG00000154727	ENST00000354828;ENST00000400075	T;T	0.12255	2.7;2.7	4.67	4.67	0.58626	.	0.187599	0.47093	D	0.000258	T	0.09642	0.0237	N	0.14661	0.345	0.35814	D	0.824061	B	0.21147	0.052	B	0.09377	0.004	T	0.19418	-1.0306	10	0.29301	T	0.29	.	17.7202	0.88349	0.0:1.0:0.0:0.0	rs2829897;rs2829897	291	Q06546	GABPA_HUMAN	V	291	ENSP00000346886:A291V;ENSP00000382948:A291V	ENSP00000346886:A291V	A	+	2	0	GABPA	26058461	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.317000	0.65822	2.586000	0.87340	0.591000	0.81541	GCG		0.373	GABPA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171365.1	NM_002040	
ADAMTS1	9510	broad.mit.edu	37	21	28212321	28212321	+	Silent	SNP	G	G	A	rs138109740		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:28212321G>A	ENST00000284984.3	-	6	2179	c.1725C>T	c.(1723-1725)tgC>tgT	p.C575C		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	575	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.C575C(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		CTCCTCCACCGCACGTTCTCG	0.488																																					p.C575C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1725T	21						.	G		1,4405		0,1,2202	117.0	97.0	103.0		1725	-0.9	1.0	21	dbSNP_134	103	0,8600		0,0,4300	no	coding-synonymous	ADAMTS1	NM_006988.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		575/968	28212321	1,13005	2203	4300	6503	27134192	SO:0001819	synonymous_variant	9510	exon6			AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	217	protein-coding gene	gene with protein product		605174	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"""			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.1725C>T	21.37:g.28212321G>A		Somatic		Capture	Illumina HiSeq	Phase_I	27134192	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Silent	SNP	ENST00000284984.3	37	CCDS33524.1																																																																																				0.488	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2		
ADAMTS5	11096	broad.mit.edu	37	21	28304463	28304463	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:28304463T>C	ENST00000284987.5	-	6	2030	c.1909A>G	c.(1909-1911)Aat>Gat	p.N637D	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	637	Cys-rich.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.N637D(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						TGATAGCCATTTTTGGCCTCA	0.413																																					p.N637D	Esophageal Squamous(53;683 1080 10100 14424 45938)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1909G	21						.						126.0	109.0	114.0					21																	28304463		2203	4300	6503	27226334	SO:0001583	missense	11096	exon6			AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.1909A>G	21.37:g.28304463T>C	ENSP00000284987:p.Asn637Asp	Somatic		Capture	Illumina HiSeq	Phase_I	27226334	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.727090	0.89390	.	.	ENSG00000154736	ENST00000284987	T	0.01933	4.55	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.06234	0.0161	L	0.31752	0.955	0.54753	D	0.999984	D	0.69078	0.997	D	0.75020	0.985	T	0.60712	-0.7209	10	0.13853	T	0.58	.	15.9053	0.79423	0.0:0.0:0.0:1.0	.	637	Q9UNA0	ATS5_HUMAN	D	637	ENSP00000284987:N637D	ENSP00000284987:N637D	N	-	1	0	ADAMTS5	27226334	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.655000	0.83696	2.156000	0.67533	0.533000	0.62120	AAT		0.413	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
MRAP	56246	broad.mit.edu	37	21	33679034	33679034	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:33679034G>A	ENST00000399784.2	+	4	377	c.190G>A	c.(190-192)Gcc>Acc	p.A64T	AP000266.7_ENST00000450936.1_RNA|MRAP_ENST00000339944.4_Missense_Mutation_p.A64T|MRAP_ENST00000399786.3_Missense_Mutation_p.A64T|MRAP_ENST00000497833.1_3'UTR|MRAP_ENST00000303645.5_Missense_Mutation_p.A64T	NM_178817.3	NP_848932.1	Q8TCY5	MRAP_HUMAN	melanocortin 2 receptor accessory protein	64					brown fat cell differentiation (GO:0050873)|positive regulation of cAMP biosynthetic process (GO:0030819)|protein localization to cell surface (GO:0034394)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	corticotropin hormone receptor binding (GO:0031780)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)|type 5 melanocortin receptor binding (GO:0031783)	p.A64T(1)		endometrium(1)|large_intestine(2)|lung(3)	6						GTCCTGGTCCGCCTCCCCGCA	0.562																																					p.A64T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G190A	21						.						139.0	98.0	112.0					21																	33679034		2203	4300	6503	32600905	SO:0001583	missense	56246	exon4			AF454915	CCDS13612.1, CCDS13613.1	21q22.1	2005-10-30	2005-02-01	2005-02-07	ENSG00000170262	ENSG00000170262			1304	protein-coding gene	gene with protein product		609196	"""chromosome 21 open reading frame 61"""	C21orf61		12036298, 15654338	Standard	NM_178817		Approved	B27, FALP	uc002ypj.3	Q8TCY5	OTTHUMG00000085309	ENST00000399784.2:c.190G>A	21.37:g.33679034G>A	ENSP00000382684:p.Ala64Thr	Somatic		Capture	Illumina HiSeq	Phase_I	32600905	NM_178817	Q5EBR3|Q8TDB7|Q8WXC1|Q8WXC2	Missense_Mutation	SNP	ENST00000399784.2	37	CCDS13613.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.473065	0.43942	.	.	ENSG00000170262	ENST00000399784;ENST00000399786;ENST00000303645;ENST00000339944	D;D;D;D	0.85773	-2.03;-2.03;-2.03;-2.03	5.66	4.78	0.61160	.	0.000000	0.64402	D	0.000010	T	0.70272	0.3205	N	0.08118	0	0.09310	N	1	B;B	0.30193	0.272;0.209	B;B	0.26202	0.067;0.044	T	0.65344	-0.6191	10	0.72032	D	0.01	-9.6618	10.8239	0.46620	0.0866:0.0:0.9134:0.0	.	64;64	Q8TCY5-2;Q8TCY5	.;MRAP_HUMAN	T	64	ENSP00000382684:A64T;ENSP00000382686:A64T;ENSP00000306697:A64T;ENSP00000343661:A64T	ENSP00000306697:A64T	A	+	1	0	MRAP	32600905	0.988000	0.35896	0.011000	0.14972	0.054000	0.15201	4.338000	0.59316	1.394000	0.46624	-0.119000	0.15052	GCC		0.562	MRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000193092.1	NM_178817	
SYNJ1	8867	broad.mit.edu	37	21	34029207	34029207	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:34029207A>G	ENST00000322229.7	-	20	2584	c.2585T>C	c.(2584-2586)gTc>gCc	p.V862A	SYNJ1_ENST00000382491.3_Missense_Mutation_p.V857A|SYNJ1_ENST00000357345.3_Missense_Mutation_p.V862A|SYNJ1_ENST00000433931.2_Missense_Mutation_p.V901A|SYNJ1_ENST00000382499.2_Missense_Mutation_p.V901A|SYNJ1_ENST00000464778.1_5'UTR			O43426	SYNJ1_HUMAN	synaptojanin 1	862	Catalytic. {ECO:0000255}.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)	p.V862A(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						CAGGGCAACGACAGGCCTTAA	0.343																																					p.V901A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2702C	21						.						84.0	86.0	85.0					21																	34029207		2203	4300	6503	32951078	SO:0001583	missense	8867	exon21			AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.2585T>C	21.37:g.34029207A>G	ENSP00000322234:p.Val862Ala	Somatic		Capture	Illumina HiSeq	Phase_I	32951078	NM_003895	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	ENST00000322229.7	37	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.929377	0.92389	.	.	ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229	D;D;D;D;D	0.97710	-4.5;-4.5;-4.5;-4.5;-4.5	5.64	5.64	0.86602	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.057488	0.64402	D	0.000001	D	0.98760	0.9583	M	0.87381	2.88	0.80722	D	1	D;D;D;D;D	0.69078	0.997;0.996;0.996;0.996;0.977	P;D;D;D;P	0.70227	0.906;0.968;0.93;0.927;0.725	D	0.99785	1.1029	10	0.87932	D	0	.	15.8441	0.78874	1.0:0.0:0.0:0.0	.	857;901;862;862;862	B9EGN3;C9JFZ1;O43426-2;O43426;O43426-4	.;.;.;SYNJ1_HUMAN;.	A	857;862;901;901;862	ENSP00000371931:V857A;ENSP00000349903:V862A;ENSP00000371939:V901A;ENSP00000409667:V901A;ENSP00000322234:V862A	ENSP00000322234:V862A	V	-	2	0	SYNJ1	32951078	1.000000	0.71417	0.894000	0.35097	0.996000	0.88848	9.108000	0.94275	2.142000	0.66516	0.482000	0.46254	GTC		0.343	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
SON	6651	broad.mit.edu	37	21	34923563	34923563	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:34923563C>T	ENST00000356577.4	+	3	2501	c.2026C>T	c.(2026-2028)Ccc>Tcc	p.P676S	SON_ENST00000290239.6_Missense_Mutation_p.P676S|SON_ENST00000300278.4_Missense_Mutation_p.P676S|SON_ENST00000381679.4_Missense_Mutation_p.P676S|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	676					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.P676S(2)		breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						CCTGGAGGTGCCCTCGACGAC	0.552																																					p.P676S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2026T	21						.						78.0	78.0	78.0					21																	34923563		2203	4300	6503	33845433	SO:0001583	missense	6651	exon3			AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.2026C>T	21.37:g.34923563C>T	ENSP00000348984:p.Pro676Ser	Somatic		Capture	Illumina HiSeq	Phase_I	33845433	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735368	0.48939	.	.	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.29397	2.52;1.57;2.49;1.57	5.83	5.83	0.93111	.	0.000000	0.56097	D	0.000028	T	0.51702	0.1690	L	0.54323	1.7	0.30326	N	0.787139	D;D;D	0.89917	1.0;1.0;0.988	D;D;P	0.91635	0.998;0.999;0.908	T	0.53136	-0.8481	10	0.72032	D	0.01	.	15.6239	0.76833	0.0:1.0:0.0:0.0	.	676;676;676	P18583;P18583-3;P18583-6	SON_HUMAN;.;.	S	676	ENSP00000348984:P676S;ENSP00000290239:P676S;ENSP00000300278:P676S;ENSP00000371095:P676S	ENSP00000290239:P676S	P	+	1	0	SON	33845433	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.646000	0.54396	2.764000	0.94973	0.557000	0.71058	CCC		0.552	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
SLC5A3	6526	broad.mit.edu	37	21	35468056	35468056	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:35468056C>A	ENST00000381151.3	+	2	1071	c.559C>A	c.(559-561)Ctg>Atg	p.L187M	AP000320.7_ENST00000362077.4_RNA|MRPS6_ENST00000399312.2_Intron|SLC5A3_ENST00000608209.1_Missense_Mutation_p.L187M			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3	187					inositol metabolic process (GO:0006020)|peripheral nervous system development (GO:0007422)|regulation of respiratory gaseous exchange (GO:0043576)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	myo-inositol:sodium symporter activity (GO:0005367)	p.L187M(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	20						CACAGACACTCTGCAGGCTCT	0.463																																					p.L187M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C559A	21						.						101.0	94.0	96.0					21																	35468056		2203	4300	6503	34389926	SO:0001583	missense	6526	exon2				CCDS33549.1	21q22.11	2013-05-22	2008-09-02		ENSG00000198743	ENSG00000198743		"""Solute carriers"""	11038	protein-coding gene	gene with protein product		600444	"""solute carrier family 5 (inositol transporter), member 3"""			7789985	Standard	NM_006933		Approved	SMIT, SMIT1	uc002yto.3	P53794	OTTHUMG00000065821	ENST00000381151.3:c.559C>A	21.37:g.35468056C>A	ENSP00000370543:p.Leu187Met	Somatic		Capture	Illumina HiSeq	Phase_I	34389926	NM_006933	O43489	Missense_Mutation	SNP	ENST00000381151.3	37	CCDS33549.1	.	.	.	.	.	.	.	.	.	.	C	13.88	2.370230	0.42003	.	.	ENSG00000198743	ENST00000381151	D	0.89875	-2.58	5.72	3.92	0.45320	.	0.000000	0.85682	D	0.000000	D	0.92564	0.7638	M	0.70903	2.155	0.43724	D	0.996207	D	0.89917	1.0	D	0.78314	0.991	D	0.91653	0.5336	10	0.87932	D	0	.	8.4507	0.32869	0.0:0.7311:0.1277:0.1413	.	187	P53794	SC5A3_HUMAN	M	187	ENSP00000370543:L187M	ENSP00000370543:L187M	L	+	1	2	SLC5A3	34389926	0.818000	0.29161	0.468000	0.27192	0.992000	0.81027	1.639000	0.37176	0.774000	0.33427	0.609000	0.83330	CTG		0.463	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1		
RUNX1	861	broad.mit.edu	37	21	36253009	36253009	+	Splice_Site	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:36253009A>G	ENST00000344691.4	-	2	1849	c.272T>C	c.(271-273)gTg>gCg	p.V91A	RUNX1_ENST00000300305.3_Splice_Site_p.V118A|RUNX1_ENST00000437180.1_Splice_Site_p.V118A|RUNX1_ENST00000399240.1_Splice_Site_p.V91A|RUNX1_ENST00000358356.5_Splice_Site_p.V91A|RUNX1_ENST00000325074.5_Splice_Site_p.V106A|RUNX1_ENST00000486278.2_Splice_Site_p.V94A	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	91	Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.V118A(1)		breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						TAGGGCCACCACCTAAACACC	0.438			T	"""RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"""	"""AML, preB- ALL, T-ALL"""																																p.V118A			Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T353C	21						.						83.0	71.0	75.0					21																	36253009		2203	4300	6503	35174879	SO:0001630	splice_region_variant	861	exon5			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"""aml1 oncogene"""	151385	"""acute myeloid leukemia 1"""	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.271-1T>C	21.37:g.36253009A>G		Somatic		Capture	Illumina HiSeq	Phase_I	35174879	NM_001754	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Missense_Mutation	SNP	ENST00000344691.4	37	CCDS42922.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.831880	0.91036	.	.	ENSG00000159216	ENST00000344691;ENST00000300305;ENST00000437180;ENST00000325074;ENST00000399240;ENST00000399245;ENST00000358356;ENST00000399237;ENST00000486278;ENST00000455571	D;D;D;D;D;D;D;D;D	0.99724	-6.54;-6.54;-6.54;-6.54;-6.54;-6.54;-6.54;-6.54;-6.54	5.31	5.31	0.75309	Acute myeloid leukemia 1 (AML 1)/Runt (2);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99750	0.9900	M	0.90977	3.165	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.973;0.997;0.999;0.999	D;D;D;D;D	0.91635	0.999;0.992;0.997;0.997;0.997	D	0.97162	0.9838	10	0.87932	D	0	-27.5489	15.5565	0.76200	1.0:0.0:0.0:0.0	.	118;91;118;106;91	Q2TAM6;Q01196-3;Q01196-8;Q01196-10;Q01196	.;.;.;.;RUNX1_HUMAN	A	91;118;118;106;91;94;91;106;94;105	ENSP00000340690:V91A;ENSP00000300305:V118A;ENSP00000409227:V118A;ENSP00000319459:V106A;ENSP00000382184:V91A;ENSP00000351123:V91A;ENSP00000382182:V106A;ENSP00000438019:V94A;ENSP00000388189:V105A	ENSP00000300305:V118A	V	-	2	0	RUNX1	35174879	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.910000	0.92685	2.143000	0.66587	0.533000	0.62120	GTG		0.438	RUNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194230.1		Missense_Mutation
B3GALT5	10317	broad.mit.edu	37	21	41032741	41032741	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:41032741G>A	ENST00000380620.4	+	5	847	c.255G>A	c.(253-255)atG>atA	p.M85I	B3GALT5_ENST00000343118.4_Missense_Mutation_p.M85I|B3GALT5_ENST00000398714.2_Missense_Mutation_p.M85I|AF064860.5_ENST00000416555.1_RNA|B3GALT5_ENST00000380618.1_Missense_Mutation_p.M85I			Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	85			M -> T (in dbSNP:rs3746887). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.7, ECO:0000269|Ref.9}.		protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)	p.M85I(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	16		Prostate(19;2.55e-06)				AAGAGAGGATGGTGAAGGGAA	0.602																																					p.M85I												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.G255A	21						.						60.0	55.0	57.0					21																	41032741		2203	4300	6503	39954611	SO:0001583	missense	10317	exon4			AB020337	CCDS13667.1, CCDS74795.1	21q22.3	2013-02-19			ENSG00000183778	ENSG00000183778		"""Beta 3-glycosyltransferases"""	920	protein-coding gene	gene with protein product	"""homolog of C. elegans Bt toxin resistance gene bre-5"", ""GlcNAc-beta-1,3-galactosyltransferase 5"""	604066				10212226	Standard	NM_006057		Approved	beta3Gal-T5, B3GalT-V, GLCT5, B3T5	uc002yyj.1	Q9Y2C3	OTTHUMG00000086725	ENST00000380620.4:c.255G>A	21.37:g.41032741G>A	ENSP00000369994:p.Met85Ile	Somatic		Capture	Illumina HiSeq	Phase_I	39954611	NM_033171	A8KA86|D3DSI3|Q2M3L5|Q53Z19|Q9NY96|Q9P1X6|Q9P1X7	Missense_Mutation	SNP	ENST00000380620.4	37	CCDS13667.1	.	.	.	.	.	.	.	.	.	.	G	10.70	1.423319	0.25639	.	.	ENSG00000183778	ENST00000380620;ENST00000380618;ENST00000343118;ENST00000398714	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.89	-11.8	0.00035	.	3.016860	0.01379	N	0.012860	T	0.12732	0.0309	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.30149	-0.9988	10	0.37606	T	0.19	.	0.4807	0.00547	0.2459:0.1616:0.2666:0.3259	.	85	Q9Y2C3	B3GT5_HUMAN	I	85	ENSP00000369994:M85I;ENSP00000369992:M85I;ENSP00000343318:M85I;ENSP00000381699:M85I	ENSP00000343318:M85I	M	+	3	0	B3GALT5	39954611	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.471000	0.00460	-2.712000	0.00393	-0.809000	0.03173	ATG		0.602	B3GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195008.2	NM_033170	
SLC37A1	54020	broad.mit.edu	37	21	43994940	43994940	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:43994940G>C	ENST00000352133.2	+	18	2418	c.1436G>C	c.(1435-1437)gGc>gCc	p.G479A	SLC37A1_ENST00000398341.3_Missense_Mutation_p.G479A			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	479					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)	p.G479A(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						GCAGCCCTGGGCCCCCTGCTG	0.542											OREG0026239	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G479A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1436C	21						.						88.0	77.0	81.0					21																	43994940		2203	4300	6503	42868009	SO:0001583	missense	54020	exon19			AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"""Solute carriers"""	11024	protein-coding gene	gene with protein product		608094	"""solute carrier family 37 (glycerol-3-phosphate transporter), member 1"""			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.1436G>C	21.37:g.43994940G>C	ENSP00000344648:p.Gly479Ala	Somatic	920	Capture	Illumina HiSeq	Phase_I	42868009	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	37	CCDS13689.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.596372	0.86953	.	.	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.61980	0.06;0.06	5.28	5.28	0.74379	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.82033	0.4949	M	0.86651	2.83	0.80722	D	1	D	0.71674	0.998	D	0.75020	0.985	D	0.85442	0.1155	10	0.87932	D	0	-10.3874	17.707	0.88311	0.0:0.0:1.0:0.0	.	479	P57057	GLPT_HUMAN	A	479	ENSP00000381383:G479A;ENSP00000344648:G479A	ENSP00000344648:G479A	G	+	2	0	SLC37A1	42868009	1.000000	0.71417	0.996000	0.52242	0.929000	0.56500	7.119000	0.77145	2.467000	0.83353	0.655000	0.94253	GGC		0.542	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		
MCM3AP	8888	broad.mit.edu	37	21	47685378	47685378	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:47685378G>A	ENST00000397708.1	-	13	3345	c.3091C>T	c.(3091-3093)Cag>Tag	p.Q1031*	MCM3AP_ENST00000291688.1_Nonsense_Mutation_p.Q1031*			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1031					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)	p.Q1031*(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					GGTAGAGACTGTGGGAGACTG	0.617																																					p.Q1031X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C3091T	21						.						86.0	88.0	87.0					21																	47685378		2203	4300	6503	46509806	SO:0001587	stop_gained	8888	exon12			AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.3091C>T	21.37:g.47685378G>A	ENSP00000380820:p.Gln1031*	Somatic		Capture	Illumina HiSeq	Phase_I	46509806	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Nonsense_Mutation	SNP	ENST00000397708.1	37	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	G	39	7.473908	0.98306	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	.	.	.	4.9	3.99	0.46301	.	0.095217	0.47455	D	0.000227	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	-1.7959	11.1607	0.48514	0.0:0.1862:0.8138:0.0	.	.	.	.	X	1031	.	ENSP00000291688:Q1031X	Q	-	1	0	MCM3AP	46509806	1.000000	0.71417	0.035000	0.18076	0.003000	0.03518	5.913000	0.69957	1.392000	0.46585	0.591000	0.81541	CAG		0.617	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
PCNT	5116	broad.mit.edu	37	21	47851715	47851715	+	Silent	SNP	C	C	T	rs572339918		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:47851715C>T	ENST00000359568.5	+	38	8444	c.8337C>T	c.(8335-8337)tgC>tgT	p.C2779C	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2779					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)		p.C2779C(1)		NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					AGGAGGCTTGCGTGCACCAGG	0.627													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19408	0.0		0.0	False		,,,				2504	0.0				p.C2779C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C8337T	21						.						35.0	36.0	35.0					21																	47851715		2203	4300	6503	46676143	SO:0001819	synonymous_variant	5116	exon38			AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.8337C>T	21.37:g.47851715C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46676143	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																				0.627	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
DIP2A	23181	broad.mit.edu	37	21	47974166	47974166	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:47974166C>T	ENST00000417564.2	+	26	3136	c.3115C>T	c.(3115-3117)Ctg>Ttg	p.L1039L	DIP2A_ENST00000318711.7_Silent_p.L1040L|DIP2A_ENST00000400274.1_Silent_p.L1035L|DIP2A_ENST00000427143.2_Silent_p.L975L			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1039					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.L1040L(1)|p.L1039L(1)		cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GAAGGGAAGACTGAGTGTTGG	0.577																																					p.L975L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2923T	21						.						109.0	124.0	119.0					21																	47974166		2122	4245	6367	46798594	SO:0001819	synonymous_variant	23181	exon24			AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.3115C>T	21.37:g.47974166C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46798594	NM_001146114	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																				0.577	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
MRAP	56246	broad.mit.edu	37	21	33684272	33684272	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:33684272delC	ENST00000399784.2	+	5	671	c.484delC	c.(484-486)cccfs	p.P163fs	MRAP_ENST00000339944.4_Intron|URB1_ENST00000382751.3_3'UTR|MRAP_ENST00000399786.3_Intron|MRAP_ENST00000497833.1_3'UTR|MRAP_ENST00000303645.5_Frame_Shift_Del_p.P163fs	NM_178817.3	NP_848932.1	Q8TCY5	MRAP_HUMAN	melanocortin 2 receptor accessory protein	163					brown fat cell differentiation (GO:0050873)|positive regulation of cAMP biosynthetic process (GO:0030819)|protein localization to cell surface (GO:0034394)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	corticotropin hormone receptor binding (GO:0031780)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)|type 5 melanocortin receptor binding (GO:0031783)	p.P163fs*>10(1)		endometrium(1)|large_intestine(2)|lung(3)	6						CAGCGAGCCTCCCCCTGGAGA	0.582																																					p.P162fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.484delC	21						.						50.0	48.0	48.0					21																	33684272		2203	4296	6499	32606143	SO:0001589	frameshift_variant	56246	exon5			AF454915	CCDS13612.1, CCDS13613.1	21q22.1	2005-10-30	2005-02-01	2005-02-07	ENSG00000170262	ENSG00000170262			1304	protein-coding gene	gene with protein product		609196	"""chromosome 21 open reading frame 61"""	C21orf61		12036298, 15654338	Standard	NM_178817		Approved	B27, FALP	uc002ypj.3	Q8TCY5	OTTHUMG00000085309	ENST00000399784.2:c.484delC	21.37:g.33684272delC	ENSP00000382684:p.Pro163fs	Somatic		Capture	Illumina HiSeq	Phase_I	32606143	NM_178817	Q5EBR3|Q8TDB7|Q8WXC1|Q8WXC2	Frame_Shift_Del	DEL	ENST00000399784.2	37	CCDS13613.1																																																																																				0.582	MRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000193092.1	NM_178817	
IFNAR1	3454	broad.mit.edu	37	21	34707854	34707854	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:34707854delA	ENST00000270139.3	+	2	253	c.101delA	c.(100-102)caafs	p.Q34fs	IFNAR1_ENST00000442357.2_Frame_Shift_Del_p.Q34fs|IFNAR1_ENST00000493503.1_3'UTR|IFNAR1_ENST00000416947.2_5'UTR	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	34	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)	p.V36fs*1(1)		breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""""""Interferon Alfa-2a(DB00034)|""""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	AAATCTCCTCAAAAAGTAGAG	0.343																																					p.Q34fs	Esophageal Squamous(73;817 1211 32990 35667 42746)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.101delA	21						.						88.0	82.0	84.0					21																	34707854		2203	4300	6503	33629724	SO:0001589	frameshift_variant	3454	exon2				CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"""Interferons"""	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.101delA	21.37:g.34707854delA	ENSP00000270139:p.Gln34fs	Somatic		Capture	Illumina HiSeq	Phase_I	33629724	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Frame_Shift_Del	DEL	ENST00000270139.3	37	CCDS13624.1																																																																																				0.343	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4		
PRMT2	3275	broad.mit.edu	37	21	48064360	48064360	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr21:48064360C>T	ENST00000397637.1	+	4	1241	c.287C>T	c.(286-288)aCg>aTg	p.T96M	PRMT2_ENST00000397638.2_Missense_Mutation_p.T96M|PRMT2_ENST00000458387.2_Missense_Mutation_p.T96M|PRMT2_ENST00000334494.4_Missense_Mutation_p.T96M|PRMT2_ENST00000355680.3_Missense_Mutation_p.T96M|PRMT2_ENST00000291705.6_Missense_Mutation_p.T96M|PRMT2_ENST00000451211.2_Missense_Mutation_p.T96M|PRMT2_ENST00000397628.1_Missense_Mutation_p.T96M|PRMT2_ENST00000440086.1_Missense_Mutation_p.T96M			P55345	ANM2_HUMAN	protein arginine methyltransferase 2	96	Interaction with ESR1.|Interaction with RB1. {ECO:0000250}.				developmental cell growth (GO:0048588)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|protein methylation (GO:0006479)|regulation of androgen receptor signaling pathway (GO:0060765)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (GO:0042054)|histone-arginine N-methyltransferase activity (GO:0008469)|peroxisome proliferator activated receptor binding (GO:0042975)|progesterone receptor binding (GO:0033142)|protein homodimerization activity (GO:0042803)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|retinoic acid receptor binding (GO:0042974)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.T96M(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	Breast(49;0.247)	Lung NSC(3;0.245)		Epithelial(3;1.03e-07)|OV - Ovarian serous cystadenocarcinoma(3;4.68e-07)|all cancers(3;7.48e-07)|Colorectal(79;0.167)|Lung(125;0.203)|LUSC - Lung squamous cell carcinoma(216;0.23)|READ - Rectum adenocarcinoma(84;0.248)		CCCGAGGACACGTGGCAGGAT	0.557																																					p.T96M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C287T	21						.						171.0	155.0	161.0					21																	48064360		2203	4300	6503	46888788	SO:0001583	missense	3275	exon4			U80213	CCDS13737.1, CCDS56219.1, CCDS56220.1, CCDS68230.1, CCDS68231.1, CCDS74806.1	21q22.3	2014-06-12	2006-02-16	2006-02-16	ENSG00000160310	ENSG00000160310	2.1.1.125	"""Protein arginine methyltransferases"""	5186	protein-coding gene	gene with protein product		601961	"""HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 1"", ""HMT1 hnRNP methyltransferase-like 1 (S. cerevisiae)"""	HRMT1L1		9545638	Standard	XM_005261111		Approved	MGC111373	uc002zjy.3	P55345	OTTHUMG00000048806	ENST00000397637.1:c.287C>T	21.37:g.48064360C>T	ENSP00000380759:p.Thr96Met	Somatic		Capture	Illumina HiSeq	Phase_I	46888788	NM_001535	B7U630|B7U631|B7U632|P78350|Q498Y5|Q5U7D4|Q6FHF0|Q99781|Q9BW15|Q9UMC2	Missense_Mutation	SNP	ENST00000397637.1	37	CCDS13737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.43|17.43	3.386682|3.386682	0.61956|0.61956	.|.	.|.	ENSG00000160310|ENSG00000160310	ENST00000455177|ENST00000355680;ENST00000397638;ENST00000458387;ENST00000451211;ENST00000291705;ENST00000397637;ENST00000334494;ENST00000397628;ENST00000440086	.|T;T;T;T;T;T;T;T;T	.|0.64260	.|1.23;1.23;-0.08;0.11;-0.07;1.23;-0.09;-0.07;0.31	5.4|5.4	4.49|4.49	0.54785|0.54785	.|Src homology-3 domain (1);	.|0.267337	.|0.37178	.|N	.|0.002214	T|T	0.65312|0.65312	0.2679|0.2679	L|L	0.36672|0.36672	1.1|1.1	0.37816|0.37816	D|D	0.928204|0.928204	.|P;P;D;D;D	.|0.76494	.|0.882;0.927;0.998;0.999;0.965	.|B;B;P;P;P	.|0.60117	.|0.276;0.382;0.828;0.869;0.466	T|T	0.64491|0.64491	-0.6395|-0.6395	5|10	.|0.21014	.|T	.|0.42	-7.7793|-7.7793	13.9997|13.9997	0.64427|0.64427	0.0:0.8471:0.1529:0.0|0.0:0.8471:0.1529:0.0	.|.	.|96;96;96;96;96	.|B7U632;B7U630;B7U631;Q498Y5;P55345	.|.;.;.;.;ANM2_HUMAN	C|M	36|96	.|ENSP00000347906:T96M;ENSP00000380760:T96M;ENSP00000407463:T96M;ENSP00000411984:T96M;ENSP00000291705:T96M;ENSP00000380759:T96M;ENSP00000335490:T96M;ENSP00000380752:T96M;ENSP00000397266:T96M	.|ENSP00000291705:T96M	R|T	+|+	1|2	0|0	PRMT2|PRMT2	46888788|46888788	0.826000|0.826000	0.29277|0.29277	0.711000|0.711000	0.30485|0.30485	0.328000|0.328000	0.28507|0.28507	3.951000|3.951000	0.56684|0.56684	1.363000|1.363000	0.46019|0.46019	0.591000|0.591000	0.81541|0.81541	CGT|ACG		0.557	PRMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207401.1	NM_001535	
MKL1	57591	broad.mit.edu	37	22	40816541	40816542	+	Frame_Shift_Ins	INS	-	-	G	rs34028511		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:40816541_40816542insG	ENST00000355630.3	-	11	1510_1511	c.920_921insC	c.(919-921)ccafs	p.P307fs	MKL1_ENST00000402042.1_Frame_Shift_Ins_p.P257fs|MKL1_ENST00000396617.3_Frame_Shift_Ins_p.P307fs|MKL1_ENST00000407029.1_Frame_Shift_Ins_p.P307fs	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	307					negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.V308fs*9(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						GGCTGCGTACTGGGGGGGTCCC	0.658			T	RBM15	acute megakaryocytic leukemia																																p.P307fs			Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.921_922insC	22						.																																			39146488	SO:0001589	frameshift_variant	57591	exon11			AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"""megakaryocytic acute leukemia"", ""myocardin-related transcription factor A"", ""basic, SAP and coiled-coil domain"""	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.921dupC	22.37:g.40816548_40816548dupG	ENSP00000347847:p.Pro307fs	Somatic		Capture	Illumina HiSeq	Phase_I	39146487	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Frame_Shift_Ins	INS	ENST00000355630.3	37	CCDS14003.1																																																																																				0.658	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831	
CECR2	27443	broad.mit.edu	37	22	18029035	18029035	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:18029035G>A	ENST00000400585.2	+	17	4004	c.3566G>A	c.(3565-3567)cGg>cAg	p.R1189Q	CECR2_ENST00000400573.5_Missense_Mutation_p.R1331Q|CECR2_ENST00000262608.8_Missense_Mutation_p.R1332Q			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	1373					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)		p.R1331Q(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		ACCCCTCAGCGGCCGGCCAGT	0.627																																					p.G1332S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3994A	22						.						46.0	51.0	50.0					22																	18029035		1928	4131	6059	16409035	SO:0001583	missense	27443	exon16			AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400585.2:c.3566G>A	22.37:g.18029035G>A	ENSP00000383428:p.Arg1189Gln	Somatic		Capture	Illumina HiSeq	Phase_I	16409035	NM_031413	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Missense_Mutation	SNP	ENST00000400585.2	37		.	.	.	.	.	.	.	.	.	.	G	10.79	1.450398	0.26074	.	.	ENSG00000099954	ENST00000400585;ENST00000400573;ENST00000262608	T;T;T	0.25749	1.9;1.9;1.78	4.95	1.21	0.21127	.	0.196570	0.25944	N	0.027281	T	0.19685	0.0473	L	0.56769	1.78	0.27189	N	0.960477	B;B;B	0.22480	0.07;0.07;0.07	B;B;B	0.08055	0.003;0.003;0.003	T	0.15925	-1.0420	10	0.22706	T	0.39	-11.3603	6.8718	0.24125	0.5061:0.0:0.4939:0.0	.	1373;1189;1331	Q9BXF3;B7WPH3;E2QRE6	CECR2_HUMAN;.;.	Q	1189;1331;1332	ENSP00000383428:R1189Q;ENSP00000383417:R1331Q;ENSP00000262608:R1332Q	ENSP00000262608:R1332Q	R	+	2	0	CECR2	16409035	0.998000	0.40836	0.908000	0.35775	0.439000	0.31926	2.196000	0.42686	0.511000	0.28236	0.305000	0.20034	CGG		0.627	CECR2-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000316226.2	NM_031413	
DGCR2	9993	broad.mit.edu	37	22	19055633	19055633	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:19055633G>A	ENST00000263196.7	-	3	555	c.308C>T	c.(307-309)gCg>gTg	p.A103V	DGCR2_ENST00000473832.1_5'Flank|DGCR2_ENST00000545799.1_Missense_Mutation_p.A103V|DGCR2_ENST00000537045.1_Missense_Mutation_p.A62V	NM_001184781.1|NM_005137.2	NP_001171710.1|NP_005128.1	P98153	IDD_HUMAN	DiGeorge syndrome critical region gene 2	103					cell adhesion (GO:0007155)|cognition (GO:0050890)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.A103V(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)	18	Colorectal(54;0.0993)					AACGGGCTGCGCCACGTTCAC	0.647																																					p.A62V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C185T	22						.						48.0	45.0	46.0					22																	19055633		2203	4300	6503	17435633	SO:0001583	missense	9993	exon2			D79985	CCDS33598.1, CCDS54496.1	22q11.21	2008-06-12			ENSG00000070413	ENSG00000070413			2845	protein-coding gene	gene with protein product	"""integral membrane protein DGCR2"""	600594				7655455, 8630060	Standard	NM_005137		Approved	KIAA0163, LAN, IDD, DGS-C, SEZ-12	uc002zoq.1	P98153	OTTHUMG00000150141	ENST00000263196.7:c.308C>T	22.37:g.19055633G>A	ENSP00000263196:p.Ala103Val	Somatic		Capture	Illumina HiSeq	Phase_I	17435633	NM_001173534	A6NIB5|A8K6K5|B5TY34|B7Z935	Missense_Mutation	SNP	ENST00000263196.7	37	CCDS33598.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.771785	0.90108	.	.	ENSG00000070413	ENST00000537045;ENST00000263196;ENST00000545799;ENST00000447928	T;D;D	0.97553	0.69;-4.43;-4.1	5.38	5.38	0.77491	.	0.047572	0.85682	D	0.000000	D	0.98245	0.9419	M	0.70595	2.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.99072	1.0834	10	0.62326	D	0.03	.	18.7522	0.91820	0.0:0.0:1.0:0.0	.	62;103	B7Z3T5;P98153	.;IDD_HUMAN	V	62;103;103;103	ENSP00000440062:A62V;ENSP00000263196:A103V;ENSP00000445069:A103V	ENSP00000263196:A103V	A	-	2	0	DGCR2	17435633	1.000000	0.71417	0.964000	0.40570	0.408000	0.30992	8.966000	0.93397	2.525000	0.85131	0.650000	0.86243	GCG		0.647	DGCR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316504.1	NM_005137	
UFD1L	7353	broad.mit.edu	37	22	19452787	19452787	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:19452787C>T	ENST00000263202.10	-	6	562	c.433G>A	c.(433-435)Gca>Aca	p.A145T	UFD1L_ENST00000360834.4_Missense_Mutation_p.A134T|UFD1L_ENST00000484101.1_5'UTR|UFD1L_ENST00000399523.1_Missense_Mutation_p.A145T	NM_001035247.2|NM_005659.6	NP_001030324.2|NP_005650.2	Q92890	UFD1_HUMAN	ubiquitin fusion degradation 1 like (yeast)	145					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|skeletal system development (GO:0001501)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.A145T(1)		large_intestine(3)|upper_aerodigestive_tract(1)	4	Colorectal(54;0.0993)					TTCCTAAGTGCGTTTTCTAAT	0.443																																					p.A145T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G433A	22						.						160.0	133.0	142.0					22																	19452787		2203	4300	6503	17832787	SO:0001583	missense	7353	exon6			AJ239058	CCDS13761.1, CCDS33600.1, CCDS33600.2	22q11.2	2014-05-02	2005-10-10		ENSG00000070010	ENSG00000070010			12520	protein-coding gene	gene with protein product		601754	"""ubiquitin fusion degradation 1-like"""			9063746	Standard	NM_005659		Approved	UFD1	uc002zpm.2	Q92890	OTTHUMG00000150130	ENST00000263202.10:c.433G>A	22.37:g.19452787C>T	ENSP00000263202:p.Ala145Thr	Somatic		Capture	Illumina HiSeq	Phase_I	17832787	NM_005659	A8MW31|Q9Y5N0	Missense_Mutation	SNP	ENST00000263202.10	37	CCDS13761.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.297379	0.81025	.	.	ENSG00000070010	ENST00000263202;ENST00000360834;ENST00000399523;ENST00000399525;ENST00000447868;ENST00000421968	T;T;T;D;D	0.95885	0.95;0.95;0.95;-3.84;-3.84	5.18	5.18	0.71444	.	0.047076	0.85682	D	0.000000	D	0.93354	0.7881	L	0.46614	1.455	0.80722	D	1	B;B;B	0.19817	0.039;0.004;0.009	B;B;B	0.24394	0.053;0.012;0.02	D	0.89831	0.3996	10	0.23302	T	0.38	-8.2045	18.8898	0.92395	0.0:1.0:0.0:0.0	.	145;145;145	B4E3I3;A8MW31;Q92890	.;.;UFD1_HUMAN	T	145;134;145;181;49;134	ENSP00000263202:A145T;ENSP00000354079:A134T;ENSP00000382439:A145T;ENSP00000402136:A49T;ENSP00000406680:A134T	ENSP00000263202:A145T	A	-	1	0	UFD1L	17832787	1.000000	0.71417	0.699000	0.30290	0.874000	0.50279	7.302000	0.78861	2.691000	0.91804	0.561000	0.74099	GCA		0.443	UFD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316460.6		
CDC45	8318	broad.mit.edu	37	22	19471394	19471394	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:19471394C>T	ENST00000407835.1	+	6	608	c.352C>T	c.(352-354)Ctc>Ttc	p.L118F	CDC45_ENST00000437685.2_Missense_Mutation_p.L118F|CDC45_ENST00000483431.1_3'UTR|CDC45_ENST00000404724.3_Missense_Mutation_p.L72F|CDC45_ENST00000263201.1_Missense_Mutation_p.L118F			O75419	CDC45_HUMAN	cell division cycle 45	118					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.L118F(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	19						GATCAAATTACTCATTAAACA	0.373																																					p.L118F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C352T	22						.						89.0	88.0	88.0					22																	19471394		2203	4300	6503	17851394	SO:0001583	missense	8318	exon5			AF053074	CCDS13762.1, CCDS54499.1, CCDS54500.1	22q11.21	2013-01-17	2013-01-17	2010-03-24	ENSG00000093009	ENSG00000093009			1739	protein-coding gene	gene with protein product	"""human CDC45"""	603465	"""CDC45 (cell division cycle 45, S.cerevisiae, homolog)-like"", ""CDC45 cell division cycle 45-like (S. cerevisiae)"", ""cell division cycle 45 homolog (S. cerevisiae)"""	CDC45L2, CDC45L		9660782, 9724329, 17608804	Standard	NM_001178010		Approved		uc011aha.2	O75419	OTTHUMG00000150386	ENST00000407835.1:c.352C>T	22.37:g.19471394C>T	ENSP00000385240:p.Leu118Phe	Somatic		Capture	Illumina HiSeq	Phase_I	17851394	NM_001178010	B4DDB4|B4DDU3|E9PDH7|O60856|Q20WK8|Q6UW54|Q9UP68	Missense_Mutation	SNP	ENST00000407835.1	37	CCDS13762.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.802008	0.90538	.	.	ENSG00000093009	ENST00000407835;ENST00000438587;ENST00000437685;ENST00000263201;ENST00000404724	T;T;T;T;T	0.22743	2.0;2.0;2.0;2.0;1.94	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.42517	0.1206	L	0.58428	1.81	0.80722	D	1	D;D;D;D;D	0.76494	0.996;0.999;0.998;0.979;0.996	D;D;D;D;D	0.76071	0.961;0.987;0.961;0.938;0.961	T	0.18366	-1.0339	10	0.87932	D	0	-20.1574	13.6636	0.62382	0.0:0.9207:0.0:0.0793	.	118;113;72;118;118	E9PDH7;B4E092;B4DDB4;B4DDU3;O75419	.;.;.;.;CDC45_HUMAN	F	118;106;118;118;72	ENSP00000385240:L118F;ENSP00000397434:L106F;ENSP00000405726:L118F;ENSP00000263201:L118F;ENSP00000384978:L72F	ENSP00000263201:L118F	L	+	1	0	CDC45	17851394	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	5.638000	0.67861	2.730000	0.93505	0.650000	0.86243	CTC		0.373	CDC45-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317903.1	NM_003504	
TANGO2	128989	broad.mit.edu	37	22	20052091	20052091	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:20052091C>T	ENST00000327374.4	+	9	915	c.737C>T	c.(736-738)gCg>gTg	p.A246V	TANGO2_ENST00000447208.2_Missense_Mutation_p.A246V|TANGO2_ENST00000401886.1_Missense_Mutation_p.A184V|AC006547.13_ENST00000596334.1_RNA|AC006547.13_ENST00000609644.1_RNA|AC006547.15_ENST00000600090.1_RNA|AC006547.13_ENST00000601746.1_RNA|AC006547.13_ENST00000608610.1_RNA|AC006547.13_ENST00000600937.1_RNA|AC006547.13_ENST00000595864.1_RNA|TANGO2_ENST00000432883.1_Missense_Mutation_p.A184V|AC006547.13_ENST00000598339.1_RNA|AC006547.13_ENST00000609191.1_RNA|AC006547.13_ENST00000415503.1_RNA|AC006547.13_ENST00000600617.1_RNA|TANGO2_ENST00000398042.2_Missense_Mutation_p.A184V|TANGO2_ENST00000434570.2_3'UTR|TANGO2_ENST00000456048.1_Missense_Mutation_p.A251V|TANGO2_ENST00000401833.1_Missense_Mutation_p.A287V|TANGO2_ENST00000420290.2_Missense_Mutation_p.A148V	NM_001283106.1|NM_001283116.1|NM_001283148.1|NM_001283154.1|NM_152906.4	NP_001270035.1|NP_001270045.1|NP_001270077.1|NP_001270083.1|NP_690870.3	Q6ICL3	TNG2_HUMAN	transport and golgi organization 2 homolog (Drosophila)	246								p.A246V(1)									CTGGTAGATGCGGACGGCCAC	0.572																																					p.A246V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C737T	22						.						144.0	110.0	121.0					22																	20052091		2203	4300	6503	18432091	SO:0001583	missense	128989	exon9				CCDS13772.1, CCDS63404.1, CCDS63405.1, CCDS63406.1, CCDS63407.1, CCDS74821.1, CCDS74822.1	22q11.21	2012-12-13	2012-12-13	2012-12-13	ENSG00000183597	ENSG00000183597			25439	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 25"""	C22orf25		12477932	Standard	XM_005261222		Approved	DKFZp761P1121	uc002zrc.1	Q6ICL3	OTTHUMG00000150510	ENST00000327374.4:c.737C>T	22.37:g.20052091C>T	ENSP00000332721:p.Ala246Val	Somatic		Capture	Illumina HiSeq	Phase_I	18432091	NM_152906	A8MUE9|B7WNV6|B7Z583|B7Z730|D3DX23|Q8IW05|Q8NAL0|Q8TCS0|Q96M16	Missense_Mutation	SNP	ENST00000327374.4	37	CCDS13772.1	.	.	.	.	.	.	.	.	.	.	C	6.811	0.518628	0.13005	.	.	ENSG00000183597	ENST00000401886;ENST00000447208;ENST00000398042;ENST00000327374;ENST00000432883;ENST00000401833;ENST00000420290;ENST00000456048	T;T;T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9	4.64	2.55	0.30701	.	0.611542	0.17643	N	0.166970	T	0.22282	0.0537	M	0.66378	2.025	0.19300	N	0.999977	B;B;B;B;B	0.26081	0.141;0.081;0.026;0.01;0.008	B;B;B;B;B	0.20184	0.028;0.027;0.018;0.007;0.004	T	0.22695	-1.0209	10	0.16896	T	0.51	-2.0936	7.2888	0.26354	0.0:0.8003:0.0:0.1997	.	148;287;251;246;184	B7Z583;B7WNV6;C9JC99;Q6ICL3;Q6ICL3-2	.;.;.;CV025_HUMAN;.	V	184;246;184;246;184;287;148;251	ENSP00000385662:A184V;ENSP00000389797:A246V;ENSP00000381122:A184V;ENSP00000332721:A246V;ENSP00000402926:A184V;ENSP00000384827:A287V;ENSP00000396182:A148V;ENSP00000403645:A251V	ENSP00000332721:A246V	A	+	2	0	C22orf25	18432091	0.001000	0.12720	0.028000	0.17463	0.066000	0.16364	0.633000	0.24598	0.587000	0.29643	0.549000	0.68633	GCG		0.572	TANGO2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318689.2	NM_152906	
UBE2L3	7332	broad.mit.edu	37	22	21965226	21965226	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:21965226C>T	ENST00000342192.4	+	3	402	c.204C>T	c.(202-204)atC>atT	p.I68I	UBE2L3_ENST00000458578.2_Silent_p.I126I|UBE2L3_ENST00000545681.1_Silent_p.I36I	NM_003347.3	NP_003338.1	P68036	UB2L3_HUMAN	ubiquitin-conjugating enzyme E2L 3	68					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein K11-linked ubiquitination (GO:0070979)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)|ubiquitin-protein transferase activity (GO:0004842)	p.I68I(1)	UBE2L3/KRAS(2)	large_intestine(4)	4	Colorectal(54;0.105)					CACCGAAGATCACATTTAAAA	0.453																																					p.I68I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C204T	22						.						50.0	45.0	47.0					22																	21965226		2203	4298	6501	20295226	SO:0001819	synonymous_variant	7332	exon3			AJ000519	CCDS13790.1, CCDS58795.1, CCDS58796.1	22q11.2	2007-02-05			ENSG00000185651	ENSG00000185651		"""Ubiquitin-conjugating enzymes E2"""	12488	protein-coding gene	gene with protein product		603721				8672131, 9693040	Standard	NM_001256356		Approved	UBCH7	uc031rxe.1	P68036	OTTHUMG00000150823	ENST00000342192.4:c.204C>T	22.37:g.21965226C>T		Somatic		Capture	Illumina HiSeq	Phase_I	20295226	NM_003347	B2R4A7|B4DDG1|B4DSZ4|E7EWS7|P51966|P70653|Q9HAV1	Silent	SNP	ENST00000342192.4	37	CCDS13790.1																																																																																				0.453	UBE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320219.1	NM_198157	
TOP3B	8940	broad.mit.edu	37	22	22314767	22314767	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:22314767A>G	ENST00000398793.2	-	14	2014	c.1580T>C	c.(1579-1581)gTc>gCc	p.V527A	TOP3B_ENST00000413067.2_3'UTR|TOP3B_ENST00000357179.5_Missense_Mutation_p.V527A	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	527					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)	p.V527A(2)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		CTCCACCGTGACATAGTTGCG	0.602																																					p.V527A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1580C	22						.						100.0	79.0	86.0					22																	22314767		2203	4300	6503	20644767	SO:0001583	missense	8940	exon14			AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.1580T>C	22.37:g.22314767A>G	ENSP00000381773:p.Val527Ala	Somatic		Capture	Illumina HiSeq	Phase_I	20644767	NM_003935	A0M8Q3|Q9BUP5	Missense_Mutation	SNP	ENST00000398793.2	37	CCDS13797.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.4|23.4	4.410333|4.410333	0.83340|0.83340	.|.	.|.	ENSG00000100038|ENSG00000100038	ENST00000457270|ENST00000357179;ENST00000398793	.|T;T	.|0.30448	.|1.53;1.53	5.69|5.69	5.69|5.69	0.88448|0.88448	.|DNA topoisomerase, type IA, core domain (1);DNA topoisomerase, type IA, central (1);DNA topoisomerase, type IA, DNA-binding (1);DNA topoisomerase, type IA, central region, subdomain 1 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.53110|0.53110	0.1776|0.1776	L|L	0.61218|0.61218	1.895|1.895	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.69078	.|0.997;0.997;0.992	.|D;D;D	.|0.71870	.|0.914;0.975;0.924	T|T	0.55055|0.55055	-0.8200|-0.8200	5|10	.|0.66056	.|D	.|0.02	.|.	15.9526|15.9526	0.79855|0.79855	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|72;527;527	.|B3KU89;O95985;O95985-2	.|.;TOP3B_HUMAN;.	P|A	322|527	.|ENSP00000349705:V527A;ENSP00000381773:V527A	.|ENSP00000349705:V527A	S|V	-|-	1|2	0|0	TOP3B|TOP3B	20644767|20644767	1.000000|1.000000	0.71417|0.71417	0.827000|0.827000	0.32855|0.32855	0.355000|0.355000	0.29361|0.29361	8.903000|8.903000	0.92573|0.92573	2.171000|2.171000	0.68590|0.68590	0.460000|0.460000	0.39030|0.39030	TCA|GTC		0.602	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935	
ZNF280B	140883	broad.mit.edu	37	22	22843277	22843277	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:22843277T>C	ENST00000406426.1	-	4	1189	c.447A>G	c.(445-447)acA>acG	p.T149T	ZNF280B_ENST00000360412.2_Silent_p.T149T			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	149					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T149T(1)		autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		GCAATGAATCTGTGAATGTAA	0.358																																					p.T149T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A447G	22						.						159.0	157.0	158.0					22																	22843277		2203	4300	6503	21173277	SO:0001819	synonymous_variant	140883	exon4			AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"""zinc finger protein 279"", ""suppressor of hairy wing homolog 2 (Drosophila)"""	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.447A>G	22.37:g.22843277T>C		Somatic		Capture	Illumina HiSeq	Phase_I	21173277	NM_080764		Silent	SNP	ENST00000406426.1	37	CCDS13799.1																																																																																				0.358	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764	
BCR	613	broad.mit.edu	37	22	23596095	23596095	+	Silent	SNP	G	G	A	rs547409270		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:23596095G>A	ENST00000305877.8	+	2	2140	c.1389G>A	c.(1387-1389)tcG>tcA	p.S463S	BCR_ENST00000359540.3_Silent_p.S463S	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	463					actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of phagocytosis (GO:0050766)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S463S(1)	BCR/JAK2(6)	central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	35					Bosutinib(DB06616)|Ponatinib(DB08901)	CCTCCTCATCGCCCCACCTCA	0.657			T	"""ABL1,  FGFR1, JAK2 """	"""CML, ALL, AML"""								G|||	1	0.000199681	0.0	0.0	5008	,	,		19130	0.0		0.001	False		,,,				2504	0.0				p.S463S			Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1389A	22						.						40.0	33.0	35.0					22																	23596095		2203	4299	6502	21926095	SO:0001819	synonymous_variant	613	exon2				CCDS13806.1, CCDS13807.1	22q11	2013-01-10			ENSG00000186716	ENSG00000186716		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	1014	protein-coding gene	gene with protein product		151410		D22S11, BCR1		1657398, 18070886	Standard	NM_004327		Approved	D22S662, CML, PHL, ALL	uc002zww.3	P11274	OTTHUMG00000150655	ENST00000305877.8:c.1389G>A	22.37:g.23596095G>A		Somatic		Capture	Illumina HiSeq	Phase_I	21926095	NM_021574	P78501|Q12842|Q4LE80|Q6NZI3	Silent	SNP	ENST00000305877.8	37	CCDS13806.1	.	.	.	.	.	.	.	.	.	.	G	10.82	1.457957	0.26161	.	.	ENSG00000186716	ENST00000334149	.	.	.	5.37	-10.7	0.00240	.	.	.	.	.	T	0.41190	0.1148	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57894	-0.7732	5	0.56958	D	0.05	.	1.2739	0.02027	0.3313:0.1662:0.3166:0.1859	.	.	.	.	H	128	.	ENSP00000335450:R128H	R	+	2	0	BCR	21926095	0.000000	0.05858	0.280000	0.24747	0.951000	0.60555	-2.956000	0.00675	-1.877000	0.01129	-0.229000	0.12294	CGC		0.657	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327	
MMP11	4320	broad.mit.edu	37	22	24123268	24123268	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:24123268A>G	ENST00000215743.3	+	5	891	c.839A>G	c.(838-840)aAt>aGt	p.N280S		NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	280					basement membrane organization (GO:0071711)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|negative regulation of fat cell differentiation (GO:0045599)|proteolysis (GO:0006508)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.N280S(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	27		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)			Marimastat(DB00786)	ATAGACACCAATGAGATTGCA	0.632																																					p.N280S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A839G	22						.						46.0	48.0	47.0					22																	24123268		2203	4300	6503	22453268	SO:0001583	missense	4320	exon5				CCDS13816.1	22q11.23	2008-06-11	2005-08-08		ENSG00000099953	ENSG00000099953			7157	protein-coding gene	gene with protein product		185261	"""matrix metalloproteinase 11 (stromelysin 3)"""	STMY3		1639418, 7657606, 12006591	Standard	NM_005940		Approved		uc002zxx.3	P24347	OTTHUMG00000150742	ENST00000215743.3:c.839A>G	22.37:g.24123268A>G	ENSP00000215743:p.Asn280Ser	Somatic		Capture	Illumina HiSeq	Phase_I	22453268	NM_005940	Q5FX24|Q6PEZ6|Q9UC26	Missense_Mutation	SNP	ENST00000215743.3	37	CCDS13816.1	.	.	.	.	.	.	.	.	.	.	A	13.61	2.289105	0.40494	.	.	ENSG00000099953	ENST00000215743	T	0.12984	2.63	4.9	4.9	0.64082	.	0.405775	0.24947	N	0.034336	T	0.09247	0.0228	L	0.29908	0.895	0.53005	D	0.999969	P	0.35328	0.495	B	0.31245	0.126	T	0.10042	-1.0647	10	0.07482	T	0.82	.	14.2137	0.65779	1.0:0.0:0.0:0.0	.	280	P24347	MMP11_HUMAN	S	280	ENSP00000215743:N280S	ENSP00000215743:N280S	N	+	2	0	MMP11	22453268	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	5.948000	0.70249	2.205000	0.71048	0.529000	0.55759	AAT		0.632	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940	
CABIN1	23523	broad.mit.edu	37	22	24432558	24432558	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:24432558G>A	ENST00000398319.2	+	3	410	c.25G>A	c.(25-27)Gcc>Acc	p.A9T	CABIN1_ENST00000263119.5_Missense_Mutation_p.A9T|CABIN1_ENST00000405822.2_Missense_Mutation_p.A9T	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	9					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)	p.A9T(1)		breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						AGCCTTAAATGCCAGCTCCAC	0.438																																					p.A9T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G25A	22						.						254.0	247.0	249.0					22																	24432558		2203	4300	6503	22762558	SO:0001583	missense	23523	exon3			AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.25G>A	22.37:g.24432558G>A	ENSP00000381364:p.Ala9Thr	Somatic		Capture	Illumina HiSeq	Phase_I	22762558	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.523201	0.85600	.	.	ENSG00000099991	ENST00000454754;ENST00000263119;ENST00000405822;ENST00000445422;ENST00000398319;ENST00000536026	T;T;T;T;T	0.64803	0.42;-0.02;-0.12;0.42;-0.02	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.67021	0.2849	N	0.24115	0.695	0.80722	D	1	D;D;D;D	0.69078	0.997;0.988;0.983;0.971	P;P;D;P	0.66351	0.897;0.794;0.943;0.878	T	0.69888	-0.5023	10	0.49607	T	0.09	.	17.3055	0.87194	0.0:0.0:1.0:0.0	.	9;9;9;9	C9J068;F5H5W5;G5E9F3;Q9Y6J0	.;.;.;CABIN_HUMAN	T	9	ENSP00000394209:A9T;ENSP00000263119:A9T;ENSP00000384694:A9T;ENSP00000412389:A9T;ENSP00000381364:A9T	ENSP00000263119:A9T	A	+	1	0	CABIN1	22762558	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.223000	0.95203	2.416000	0.81992	0.558000	0.71614	GCC		0.438	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295	
ADORA2A	135	broad.mit.edu	37	22	24837097	24837097	+	Silent	SNP	C	C	T	rs145970572		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:24837097C>T	ENST00000337539.7	+	3	1338	c.879C>T	c.(877-879)cgC>cgT	p.R293R	ADORA2A_ENST00000496497.1_3'UTR|ADORA2A-AS1_ENST00000326341.4_RNA|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A-AS1_ENST00000427813.2_RNA	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	293					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)	p.R293R(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	ACCGTATCCGCGAGTTCCGCC	0.602																																					p.R293R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C879T	22						.	C		1,4405	2.1+/-5.4	0,1,2202	76.0	69.0	71.0		879	-10.5	0.3	22	dbSNP_134	71	0,8600		0,0,4300	no	coding-synonymous	ADORA2A	NM_000675.4		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		293/413	24837097	1,13005	2203	4300	6503	23167097	SO:0001819	synonymous_variant	135	exon3			X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"""GPCR / Class A : Adenosine receptors"""	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.879C>T	22.37:g.24837097C>T		Somatic		Capture	Illumina HiSeq	Phase_I	23167097	NM_000675	B2R7E0	Silent	SNP	ENST00000337539.7	37	CCDS13826.1																																																																																				0.602	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675	
SGSM1	129049	broad.mit.edu	37	22	25294233	25294233	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:25294233C>T	ENST00000400359.4	+	20	2489	c.2482C>T	c.(2482-2484)Cgg>Tgg	p.R828W	SGSM1_ENST00000400358.4_Missense_Mutation_p.R773W|SNORD56_ENST00000362913.1_RNA	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	828	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)	p.R773W(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						TGAGGCTCCCCGGGAGGAGCT	0.657																																					p.R773W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2317T	22						.						28.0	35.0	33.0					22																	25294233		2175	4283	6458	23624233	SO:0001583	missense	129049	exon19			AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.2482C>T	22.37:g.25294233C>T	ENSP00000383212:p.Arg828Trp	Somatic		Capture	Illumina HiSeq	Phase_I	23624233	NM_001098497	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Missense_Mutation	SNP	ENST00000400359.4	37	CCDS46674.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.375784	0.61735	.	.	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.07688	3.18;3.17	5.24	4.17	0.49024	Rab-GAP/TBC domain (2);	0.580967	0.15159	U	0.277254	T	0.12944	0.0314	N	0.14661	0.345	0.09310	N	0.999998	D;D;D;D	0.76494	0.995;0.999;0.999;0.996	P;P;P;P	0.62885	0.736;0.859;0.908;0.711	T	0.17561	-1.0365	10	0.51188	T	0.08	-11.5534	13.3505	0.60599	0.1562:0.8438:0.0:0.0	.	773;828;845;828	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1	.;.;.;SGSM1_HUMAN	W	828;773;828	ENSP00000383211:R773W;ENSP00000383212:R828W	ENSP00000383211:R773W	R	+	1	2	SGSM1	23624233	0.000000	0.05858	0.910000	0.35882	0.916000	0.54674	0.017000	0.13399	2.618000	0.88619	0.591000	0.81541	CGG		0.657	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
ASPHD2	57168	broad.mit.edu	37	22	26839163	26839163	+	Silent	SNP	G	G	A	rs377666159		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:26839163G>A	ENST00000215906.5	+	4	1539	c.1101G>A	c.(1099-1101)ccG>ccA	p.P367P	HPS4_ENST00000493455.2_5'Flank	NM_020437.4	NP_065170.2	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2	367					peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.P341P(1)		endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	16						TCTTTGCTCCGGGACGATGAG	0.597													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17480	0.0		0.0	False		,,,				2504	0.0				p.P367P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1101A	22						.	G		1,4405	2.1+/-5.4	0,1,2202	97.0	101.0	100.0		1101	-9.3	0.0	22		100	0,8600		0,0,4300	no	coding-synonymous	ASPHD2	NM_020437.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		367/370	26839163	1,13005	2203	4300	6503	25169163	SO:0001819	synonymous_variant	57168	exon4			AK097157	CCDS13834.2	22q12.1	2006-02-02			ENSG00000128203	ENSG00000128203			30437	protein-coding gene	gene with protein product							Standard	NM_020437		Approved	FLJ39838	uc003acg.2	Q6ICH7	OTTHUMG00000150884	ENST00000215906.5:c.1101G>A	22.37:g.26839163G>A		Somatic		Capture	Illumina HiSeq	Phase_I	25169163	NM_020437	B2RCH3|Q7L0W3|Q9NSN3	Silent	SNP	ENST00000215906.5	37	CCDS13834.2																																																																																				0.597	ASPHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320422.1	NM_020437	
INPP5J	27124	broad.mit.edu	37	22	31522959	31522959	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:31522959A>G	ENST00000331075.5	+	5	1596	c.1547A>G	c.(1546-1548)tAc>tGc	p.Y516C	INPP5J_ENST00000402238.1_5'Flank|INPP5J_ENST00000404390.3_Missense_Mutation_p.Y148C|INPP5J_ENST00000405300.1_Missense_Mutation_p.Y149C|INPP5J_ENST00000401755.1_5'Flank|INPP5J_ENST00000412277.2_Missense_Mutation_p.Y449C|INPP5J_ENST00000400294.2_Missense_Mutation_p.Y149C|INPP5J_ENST00000404453.1_5'Flank	NM_001284285.1	NP_001271214.1	Q15735	PI5PA_HUMAN	inositol polyphosphate-5-phosphatase J	516	Catalytic. {ECO:0000255}.				inositol phosphate metabolic process (GO:0043647)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)	p.Y149C(1)|p.Y516C(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	12						GCCAAGTACTACCACCTGCCC	0.647																																					p.Y148C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A443G	22						.						54.0	55.0	55.0					22																	31522959		2175	4253	6428	29852959	SO:0001583	missense	27124	exon5			U45975	CCDS46687.1, CCDS63453.1, CCDS63454.1, CCDS63455.1, CCDS74847.1	22q12.2	2008-09-09	2008-09-09	2008-09-09	ENSG00000185133	ENSG00000185133			8956	protein-coding gene	gene with protein product		606481	"""phosphatidylinositol (4,5) bisphosphate 5-phosphatase, A"""	PIB5PA		10591208	Standard	NM_001284287		Approved	INPP5	uc003aju.4	Q15735	OTTHUMG00000151206	ENST00000331075.5:c.1547A>G	22.37:g.31522959A>G	ENSP00000333262:p.Tyr516Cys	Somatic		Capture	Illumina HiSeq	Phase_I	29852959	NM_001002837	B3KS54|Q32M61|Q6ZTH6|Q8N902|Q9UDT9	Missense_Mutation	SNP	ENST00000331075.5	37		.	.	.	.	.	.	.	.	.	.	A	13.07	2.128026	0.37533	.	.	ENSG00000185133	ENST00000331075;ENST00000412277;ENST00000420017;ENST00000400294;ENST00000405300;ENST00000404390	T;T;D;T;T;T	0.95103	-1.36;-1.36;-3.61;-1.36;-1.36;-1.36	4.46	3.41	0.39046	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.069152	0.64402	D	0.000020	D	0.86764	0.6011	N	0.12961	0.28	0.42774	D	0.99384	P;B	0.36086	0.536;0.005	B;B	0.34652	0.187;0.004	D	0.83460	0.0053	10	0.40728	T	0.16	.	9.0197	0.36193	0.6872:0.0:0.0:0.3128	.	516;148	Q15735;Q15735-3	PI5PA_HUMAN;.	C	516;449;81;149;149;148	ENSP00000333262:Y516C;ENSP00000392924:Y449C;ENSP00000406570:Y81C;ENSP00000383150:Y149C;ENSP00000384596:Y149C;ENSP00000384534:Y148C	ENSP00000333262:Y516C	Y	+	2	0	INPP5J	29852959	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.817000	0.48034	0.790000	0.33803	0.459000	0.35465	TAC		0.647	INPP5J-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000321784.1	NM_001002837	
PLA2G3	50487	broad.mit.edu	37	22	31536149	31536149	+	Silent	SNP	C	C	T	rs377694018		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:31536149C>T	ENST00000215885.3	-	1	444	c.192G>A	c.(190-192)gcG>gcA	p.A64A		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	64					acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)	p.A64A(1)		large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						GCCTCCTATGCGCATCCCAGC	0.632																																					p.A64A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G192A	22						.	C		1,4405	2.1+/-5.4	0,1,2202	71.0	74.0	73.0		192	-3.9	0.0	22		73	0,8600		0,0,4300	no	coding-synonymous	PLA2G3	NM_015715.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		64/510	31536149	1,13005	2203	4300	6503	29866149	SO:0001819	synonymous_variant	50487	exon1			AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.192G>A	22.37:g.31536149C>T		Somatic		Capture	Illumina HiSeq	Phase_I	29866149	NM_015715	O95768	Silent	SNP	ENST00000215885.3	37	CCDS13889.1																																																																																				0.632	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715	
PATZ1	23598	broad.mit.edu	37	22	31741325	31741325	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:31741325C>T	ENST00000266269.5	-	1	893	c.264G>A	c.(262-264)ggG>ggA	p.G88G	PATZ1_ENST00000351933.4_Silent_p.G88G|PATZ1_ENST00000215919.3_Silent_p.G88G|AC005003.1_ENST00000504184.2_5'Flank|PATZ1_ENST00000405309.3_Silent_p.G88G	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	88	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				male gonad development (GO:0008584)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G88G(2)	EWSR1/PATZ1(2)	NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	12						CCGTCGCGCCCCCTACATCAG	0.687																																					p.G88G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G264A	22						.						16.0	19.0	18.0					22																	31741325		2198	4286	6484	30071325	SO:0001819	synonymous_variant	23598	exon1			AL096880	CCDS13894.1, CCDS13895.1, CCDS13896.1, CCDS46691.1	22q12.2	2013-01-09	2006-09-19	2006-09-19	ENSG00000100105	ENSG00000100105		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	13071	protein-coding gene	gene with protein product		605165	"""zinc finger protein 278"""	ZNF278		10591208, 18241078, 18401526	Standard	NM_014323		Approved	MAZR, dJ400N23, ZBTB19, ZSG, RIAZ, PATZ	uc003akq.3	Q9HBE1	OTTHUMG00000151254	ENST00000266269.5:c.264G>A	22.37:g.31741325C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30071325	NM_032051	Q9HBE2|Q9HBE3|Q9P1A9|Q9UDU0|Q9Y529	Silent	SNP	ENST00000266269.5	37	CCDS13894.1																																																																																				0.687	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	NM_032052	
BPIFC	254240	broad.mit.edu	37	22	32808069	32808069	+	IGR	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:32808069G>A	ENST00000397452.1	-	0	2091				RTCB_ENST00000216038.5_Silent_p.G25G|RTCB_ENST00000451746.2_Silent_p.G25G			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C							extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)	p.G25G(2)									TGGGCACGAAGCCCTTCTTGA	0.572																																					p.G25G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C75T	22						.						106.0	105.0	105.0					22																	32808069		2203	4300	6503	31138069	SO:0001628	intergenic_variant	51493	exon1			AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"""BPI fold containing"""	16503	protein-coding gene	gene with protein product		614109	"""bactericidal/permeability-increasing protein-like 2"""	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273		22.37:g.32808069G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31138069	NM_014306	A2RRF1	Silent	SNP	ENST00000397452.1	37	CCDS13906.1																																																																																				0.572	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932	
TIMP3	7078	broad.mit.edu	37	22	33254108	33254108	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:33254108C>A	ENST00000266085.6	+	4	722	c.421C>A	c.(421-423)Ctg>Atg	p.L141M	SYN3_ENST00000358763.2_Intron|SYN3_ENST00000332840.5_Intron	NM_000362.4	NP_000353.1	P35625	TIMP3_HUMAN	TIMP metallopeptidase inhibitor 3	141	Mediates interaction with EFEMP1.|NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				cellular response to organic substance (GO:0071310)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)	p.L141M(1)		endometrium(2)|large_intestine(3)|lung(1)|urinary_tract(1)	7						TCGGTATCACCTGGGTTGTAA	0.582																																					p.L141M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C421A	22						.						93.0	79.0	84.0					22																	33254108		2203	4300	6503	31584108	SO:0001583	missense	7078	exon4				CCDS13911.1	22q12.3	2013-01-08	2008-07-31		ENSG00000100234	ENSG00000100234			11822	protein-coding gene	gene with protein product		188826	"""tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinflammatory)"""	SFD		8188246, 12652295	Standard	NM_000362		Approved		uc003anb.3	P35625	OTTHUMG00000030784	ENST00000266085.6:c.421C>A	22.37:g.33254108C>A	ENSP00000266085:p.Leu141Met	Somatic		Capture	Illumina HiSeq	Phase_I	31584108	NM_000362	B2RBY9|Q5THV4|Q9UC74|Q9UGS2	Missense_Mutation	SNP	ENST00000266085.6	37	CCDS13911.1	.	.	.	.	.	.	.	.	.	.	C	8.533	0.871421	0.17322	.	.	ENSG00000100234	ENST00000266085;ENST00000538671	D	0.93133	-3.17	5.04	2.91	0.33838	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);	0.000000	0.64402	D	0.000001	D	0.90501	0.7024	N	0.13168	0.305	0.80722	D	1	D	0.59357	0.985	D	0.74348	0.983	D	0.85919	0.1445	10	0.02654	T	1	-20.1463	11.9916	0.53178	0.0:0.8507:0.0:0.1493	.	141	P35625	TIMP3_HUMAN	M	141;75	ENSP00000266085:L141M	ENSP00000266085:L141M	L	+	1	2	TIMP3	31584108	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	2.639000	0.46570	1.256000	0.44068	0.561000	0.74099	CTG		0.582	TIMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075672.2	NM_000362	
CSF2RB	1439	broad.mit.edu	37	22	37333898	37333898	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:37333898T>C	ENST00000403662.3	+	14	2270	c.2048T>C	c.(2047-2049)gTg>gCg	p.V683A	CSF2RB_ENST00000406230.1_Missense_Mutation_p.V689A|CSF2RB_ENST00000262825.5_Missense_Mutation_p.V689A|CSF2RB_ENST00000536485.1_Missense_Mutation_p.V630A			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	683					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.V683A(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	GGGCCAAGGGTGGGAGGACAG	0.652																																					p.V683A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2048C	22						.						32.0	36.0	35.0					22																	37333898		2203	4300	6503	35663844	SO:0001583	missense	1439	exon14			M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"""CD molecules"", ""Fibronectin type III domain containing"""	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.2048T>C	22.37:g.37333898T>C	ENSP00000384053:p.Val683Ala	Somatic		Capture	Illumina HiSeq	Phase_I	35663844	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	37	CCDS13936.1	.	.	.	.	.	.	.	.	.	.	T	0.027	-1.363402	0.01235	.	.	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000536485	D;D;D;D	0.91407	-2.33;-2.84;-2.84;-2.84	5.12	-10.2	0.00374	.	3.111730	0.01004	N	0.003738	T	0.73536	0.3599	N	0.13043	0.29	0.09310	N	1	B;B	0.20887	0.049;0.007	B;B	0.14578	0.011;0.005	T	0.69091	-0.5237	10	0.06625	T	0.88	1.7492	1.8187	0.03105	0.3941:0.2546:0.2341:0.1171	.	689;683	P32927-2;P32927	.;IL3RB_HUMAN	A	683;683;689;689;630	ENSP00000384053:V683A;ENSP00000262825:V689A;ENSP00000385271:V689A;ENSP00000440003:V630A	ENSP00000262825:V689A	V	+	2	0	CSF2RB	35663844	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-3.358000	0.00499	-3.193000	0.00219	-0.472000	0.04984	GTG		0.652	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395	
DMC1	11144	broad.mit.edu	37	22	38945947	38945947	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:38945947A>G	ENST00000216024.2	-	8	753	c.477T>C	c.(475-477)atT>atC	p.I159I	DMC1_ENST00000428462.2_Intron	NM_007068.2	NP_008999.2	Q14565	DMC1_HUMAN	DNA meiotic recombinase 1	159					female gamete generation (GO:0007292)|male meiosis I (GO:0007141)|meiotic nuclear division (GO:0007126)|oocyte maturation (GO:0001556)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	chromosome (GO:0005694)|chromosome, telomeric region (GO:0000781)|condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)	p.I159I(1)		large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11	Melanoma(58;0.0286)					TTTCTGTATCAATGAAGATAA	0.328								Homologous recombination																													p.I159I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T477C	22						.						44.0	45.0	45.0					22																	38945947		2203	4298	6501	37275893	SO:0001819	synonymous_variant	11144	exon8			D63882	CCDS13973.1, CCDS63477.1	22q13.1	2013-05-02	2013-05-02		ENSG00000100206	ENSG00000100206			2927	protein-coding gene	gene with protein product		602721	"""DMC1 (dosage suppressor of mck1, yeast homolog) meiosis-specific homologous recombination"", ""DMC1 dosage suppressor of mck1 homolog, meiosis-specific homologous recombination (yeast)"""			8602360, 8590282, 17541404	Standard	NM_007068		Approved	LIM15	uc003avz.2	Q14565	OTTHUMG00000151088	ENST00000216024.2:c.477T>C	22.37:g.38945947A>G		Somatic		Capture	Illumina HiSeq	Phase_I	37275893	NM_007068	A8K9A2|B4DMW6|Q08AI1|Q99498|Q9UH11	Silent	SNP	ENST00000216024.2	37	CCDS13973.1																																																																																				0.328	DMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321246.2	NM_007068	
MCHR1	2847	broad.mit.edu	37	22	41077061	41077061	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:41077061C>T	ENST00000249016.4	+	2	1094	c.398C>T	c.(397-399)gCg>gTg	p.A133V	MCHR1_ENST00000498400.1_3'UTR|MCHR1_ENST00000381433.2_Missense_Mutation_p.A133V	NM_005297.3	NP_005288.3	Q99705	MCHR1_HUMAN	melanin-concentrating hormone receptor 1	133					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|melanin-concentrating hormone receptor activity (GO:0030273)|neuropeptide receptor activity (GO:0008188)	p.A133V(1)		endometrium(5)|large_intestine(7)|lung(6)|pancreas(1)|urinary_tract(1)	20						GTCATCTTCGCGGTCGTGAAG	0.562																																					p.A133V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C398T	22						.						170.0	137.0	148.0					22																	41077061		2203	4300	6503	39407007	SO:0001583	missense	2847	exon2				CCDS14004.1	22q13.3	2014-06-05	2006-02-15	2006-02-15	ENSG00000128285	ENSG00000128285		"""GPCR / Class A : MCH receptors"""	4479	protein-coding gene	gene with protein product		601751	"""G protein-coupled receptor 24"""	GPR24			Standard	XM_005261581		Approved	SLC1, MCH1R	uc003ayz.3	Q99705	OTTHUMG00000150256	ENST00000249016.4:c.398C>T	22.37:g.41077061C>T	ENSP00000249016:p.Ala133Val	Somatic		Capture	Illumina HiSeq	Phase_I	39407007	NM_005297	B2RBX6|Q5R3J1|Q96S47|Q9BV08	Missense_Mutation	SNP	ENST00000249016.4	37	CCDS14004.1	.	.	.	.	.	.	.	.	.	.	C	17.95	3.514311	0.64522	.	.	ENSG00000128285	ENST00000249016;ENST00000381433	T;T	0.33216	2.22;1.42	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.045709	0.85682	D	0.000000	T	0.10551	0.0258	N	0.00823	-1.155	0.44373	D	0.997274	P	0.45396	0.857	B	0.41174	0.349	T	0.32107	-0.9919	10	0.02654	T	1	.	17.4213	0.87516	0.0:1.0:0.0:0.0	.	133	Q99705	MCHR1_HUMAN	V	133	ENSP00000249016:A133V;ENSP00000370841:A133V	ENSP00000249016:A133V	A	+	2	0	MCHR1	39407007	0.999000	0.42202	0.970000	0.41538	0.908000	0.53690	6.048000	0.71046	2.529000	0.85273	0.655000	0.94253	GCG		0.562	MCHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317142.1	NM_005297	
ST13	6767	broad.mit.edu	37	22	41246838	41246838	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:41246838C>T	ENST00000216218.3	-	2	638	c.157G>A	c.(157-159)Gaa>Aaa	p.E53K		NM_003932.3	NP_003923.2	P50502	F10A1_HUMAN	suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein)	53					chaperone cofactor-dependent protein refolding (GO:0070389)|negative regulation of protein refolding (GO:0061084)|protein folding (GO:0006457)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	dATP binding (GO:0032564)|protein binding, bridging (GO:0030674)	p.E53K(2)		cervix(1)|large_intestine(1)|lung(3)|skin(1)	6						TTGGTATTTTCTTCTGATTTA	0.313																																					p.E53K												.	.	2	Substitution - Missense(2)	large_intestine(1)|skin(1)	c.G157A	22						.						40.0	43.0	42.0					22																	41246838		2202	4295	6497	39576784	SO:0001583	missense	6767	exon2				CCDS14006.1	22q13.2	2013-01-10	2001-11-29		ENSG00000100380	ENSG00000100380		"""Tetratricopeptide (TTC) repeat domain containing"""	11343	protein-coding gene	gene with protein product	"""progesterone receptor-associated p48 protein"""	606796	"""suppression of tumorigenicity 13 (colon carcinoma) (Hsp70-interacting protein)"""			9925927, 8721986	Standard	NM_003932		Approved	SNC6, HSPABP1, HIP, P48, FAM10A1	uc003aze.3	P50502	OTTHUMG00000151201	ENST00000216218.3:c.157G>A	22.37:g.41246838C>T	ENSP00000216218:p.Glu53Lys	Somatic		Capture	Illumina HiSeq	Phase_I	39576784	NM_003932	O14999|Q2TU77	Missense_Mutation	SNP	ENST00000216218.3	37	CCDS14006.1	.	.	.	.	.	.	.	.	.	.	C	16.17	3.048155	0.55110	.	.	ENSG00000100380	ENST00000216218;ENST00000542699;ENST00000401032;ENST00000411695	T;T	0.44482	2.25;0.92	6.07	6.07	0.98685	.	0.323573	0.40222	N	0.001159	T	0.34745	0.0908	L	0.55213	1.73	0.45046	D	0.998069	P;B	0.35433	0.501;0.011	B;B	0.22386	0.039;0.01	T	0.21314	-1.0249	10	0.09084	T	0.74	.	18.4256	0.90608	0.0:1.0:0.0:0.0	.	53;53	B4E0U6;P50502	.;F10A1_HUMAN	K	53;53;53;16	ENSP00000216218:E53K;ENSP00000392067:E16K	ENSP00000216218:E53K	E	-	1	0	ST13	39576784	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.001000	0.57046	2.890000	0.99128	0.585000	0.79938	GAA		0.313	ST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321759.1	NM_003932	
WBP2NL	164684	broad.mit.edu	37	22	42422856	42422856	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:42422856G>A	ENST00000328823.9	+	6	632	c.601G>A	c.(601-603)Gta>Ata	p.V201I	WBP2NL_ENST00000543212.1_Missense_Mutation_p.V127I	NM_152613.2	NP_689826.2	Q6ICG8	WBP2L_HUMAN	WBP2 N-terminal like	201	10 X 7 AA tandem repeat of Y-G-X-P-P-X-G.|Gly-rich.				egg activation (GO:0007343)|male pronucleus assembly (GO:0035039)|meiotic nuclear division (GO:0007126)	perinuclear theca (GO:0033011)	WW domain binding (GO:0050699)	p.V201I(1)		breast(2)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)	14						AGCCCAACCCGTAGGAAATGA	0.582																																					p.V201I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G601A	22						.						97.0	112.0	107.0					22																	42422856		2203	4300	6503	40752802	SO:0001583	missense	164684	exon6			BC022546	CCDS14029.1	22q13.2	2007-07-18			ENSG00000183066	ENSG00000183066			28389	protein-coding gene	gene with protein product	"""postacrosomal sheath WW domain-binding protein"""	610981				17289678	Standard	NM_152613		Approved	FLJ26145, MGC26816, PAWP	uc003bbt.3	Q6ICG8	OTTHUMG00000151270	ENST00000328823.9:c.601G>A	22.37:g.42422856G>A	ENSP00000332983:p.Val201Ile	Somatic		Capture	Illumina HiSeq	Phase_I	40752802	NM_152613	A3KFF7|A8MSG5|B3KXX4|Q8TBF0|Q8TBF3	Missense_Mutation	SNP	ENST00000328823.9	37	CCDS14029.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.814437	0.32053	.	.	ENSG00000183066	ENST00000328823;ENST00000543212	T;T	0.30448	1.53;1.53	4.03	-8.06	0.01102	WW-domain-binding protein (1);	.	.	.	.	T	0.14227	0.0344	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.28073	-1.0055	9	0.17369	T	0.5	.	2.4243	0.04455	0.401:0.327:0.1613:0.1108	.	201	Q6ICG8	WBP2L_HUMAN	I	201;127	ENSP00000332983:V201I;ENSP00000442447:V127I	ENSP00000332983:V201I	V	+	1	0	WBP2NL	40752802	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.304000	0.01134	-1.247000	0.02507	-2.220000	0.00296	GTA		0.582	WBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322037.1	NM_152613	
FAM109B	150368	broad.mit.edu	37	22	42473443	42473443	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:42473443G>A	ENST00000321753.3	+	3	333	c.146G>A	c.(145-147)gGc>gAc	p.G49D	SMDT1_ENST00000331479.3_5'Flank|snoU13_ENST00000458891.1_RNA	NM_001002034.2	NP_001002034.2	Q6ICB4	SESQ2_HUMAN	family with sequence similarity 109, member B	49	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				endosome organization (GO:0007032)|receptor recycling (GO:0001881)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	protein homodimerization activity (GO:0042803)	p.G49D(1)		endometrium(2)|large_intestine(2)|liver(2)|lung(1)|prostate(1)	8						GTCCTCAAGGGCAACCTGCTA	0.677																																					p.G49D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G146A	22						.						64.0	72.0	69.0					22																	42473443		2203	4300	6503	40803389	SO:0001583	missense	150368	exon3			BX648402	CCDS33655.1	22q13.2	2013-01-10			ENSG00000177096	ENSG00000177096		"""Pleckstrin homology (PH) domain containing"""	27161	protein-coding gene	gene with protein product		614240				12477932	Standard	NM_001002034		Approved	DKFZp686J07229	uc003bbz.3	Q6ICB4	OTTHUMG00000151285	ENST00000321753.3:c.146G>A	22.37:g.42473443G>A	ENSP00000312753:p.Gly49Asp	Somatic		Capture	Illumina HiSeq	Phase_I	40803389	NM_001002034	Q3SXQ3|Q8N6L9	Missense_Mutation	SNP	ENST00000321753.3	37	CCDS33655.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.084426	0.76642	.	.	ENSG00000177096	ENST00000321753;ENST00000419475	T;T	0.74632	-0.86;-0.86	5.16	5.16	0.70880	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.053029	0.85682	D	0.000000	D	0.85013	0.5600	M	0.68317	2.08	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.83604	0.0130	10	0.34782	T	0.22	-21.5636	18.6456	0.91409	0.0:0.0:1.0:0.0	.	49	Q6ICB4	SESQ2_HUMAN	D	49	ENSP00000312753:G49D;ENSP00000396170:G49D	ENSP00000312753:G49D	G	+	2	0	FAM109B	40803389	1.000000	0.71417	1.000000	0.80357	0.660000	0.38997	7.857000	0.86963	2.381000	0.81170	0.655000	0.94253	GGC		0.677	FAM109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322084.1	NM_001002034	
PACSIN2	11252	broad.mit.edu	37	22	43284795	43284795	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:43284795C>T	ENST00000263246.3	-	5	664	c.463G>A	c.(463-465)Gca>Aca	p.A155T	PACSIN2_ENST00000402229.1_Missense_Mutation_p.A155T|PACSIN2_ENST00000403744.3_Missense_Mutation_p.A155T|PACSIN2_ENST00000337959.4_Missense_Mutation_p.A155T|PACSIN2_ENST00000407585.1_Missense_Mutation_p.A155T	NM_001184970.1	NP_001171899.1	Q9UNF0	PACN2_HUMAN	protein kinase C and casein kinase substrate in neurons 2	155	F-BAR domain.				actin cytoskeleton organization (GO:0030036)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cell projection morphogenesis (GO:0048858)|membrane tubulation (GO:0097320)|negative regulation of endocytosis (GO:0045806)|protein localization to endosome (GO:0036010)	caveola (GO:0005901)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|transporter activity (GO:0005215)	p.A155T(1)		NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	19		Glioma(61;0.222)				GCTTTCTTTGCTGCTTCTACC	0.517																																					p.A155T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G463A	22						.						208.0	195.0	199.0					22																	43284795		2065	4220	6285	41614739	SO:0001583	missense	11252	exon5			AF128536	CCDS43023.1, CCDS54536.1	22q13.2-q13.33	2009-05-08			ENSG00000100266	ENSG00000100266			8571	protein-coding gene	gene with protein product	"""syndapin II"""	604960				10431838, 11082044	Standard	NM_007229		Approved	SDPII	uc003bdg.4	Q9UNF0	OTTHUMG00000150701	ENST00000263246.3:c.463G>A	22.37:g.43284795C>T	ENSP00000263246:p.Ala155Thr	Somatic		Capture	Illumina HiSeq	Phase_I	41614739	NM_001184971	O95921|Q96HV9|Q9H0D3|Q9NPN1|Q9Y4V2	Missense_Mutation	SNP	ENST00000263246.3	37	CCDS43023.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.017577	0.54576	.	.	ENSG00000100266	ENST00000263246;ENST00000337959;ENST00000407585;ENST00000403744;ENST00000402229	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	5.23	1.64	0.23874	.	0.093855	0.64402	D	0.000001	T	0.20577	0.0495	L	0.60957	1.885	0.52501	D	0.999953	B;B	0.28636	0.048;0.218	B;B	0.34779	0.038;0.189	T	0.09314	-1.0680	10	0.33940	T	0.23	3.7589	14.535	0.67953	0.3747:0.6253:0.0:0.0	.	155;155	Q6FIA3;Q9UNF0	.;PACN2_HUMAN	T	155	ENSP00000263246:A155T;ENSP00000338379:A155T;ENSP00000385952:A155T;ENSP00000385372:A155T;ENSP00000385040:A155T	ENSP00000263246:A155T	A	-	1	0	PACSIN2	41614739	0.790000	0.28787	0.935000	0.37517	0.940000	0.58332	1.502000	0.35704	0.670000	0.31165	0.650000	0.86243	GCA		0.517	PACSIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319665.1	NM_007229	
PARVG	64098	broad.mit.edu	37	22	44583707	44583707	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:44583707C>T	ENST00000444313.3	+	5	680	c.196C>T	c.(196-198)Cgc>Tgc	p.R66C	PARVG_ENST00000415224.1_Missense_Mutation_p.R66C|PARVG_ENST00000422871.1_Missense_Mutation_p.R66C	NM_022141.5	NP_071424.1	Q9HBI0	PARVG_HUMAN	parvin, gamma	66	CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|cell-matrix adhesion (GO:0007160)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	actin binding (GO:0003779)	p.R66C(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(10)	17		Ovarian(80;0.024)|all_neural(38;0.0299)				CATTGTGGTCCGCAGCCTGGA	0.592																																					p.R66C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C196T	22						.						182.0	135.0	151.0					22																	44583707		2203	4300	6503	42915040	SO:0001583	missense	64098	exon5			AF237772	CCDS14057.1	22q13.31	2013-01-24			ENSG00000138964	ENSG00000138964		"""Parvins"""	14654	protein-coding gene	gene with protein product		608122				11171322	Standard	NM_022141		Approved		uc003bep.4	Q9HBI0	OTTHUMG00000150473	ENST00000444313.3:c.196C>T	22.37:g.44583707C>T	ENSP00000391583:p.Arg66Cys	Somatic		Capture	Illumina HiSeq	Phase_I	42915040	NM_001137606	B4DDW5|E7EVM6|Q9BQX5|Q9NSG1	Missense_Mutation	SNP	ENST00000444313.3	37	CCDS14057.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.498091	0.64186	.	.	ENSG00000138964	ENST00000422871;ENST00000444313;ENST00000415224	T;T;T	0.59906	0.23;0.23;0.23	3.83	3.83	0.44106	Calponin homology domain (4);	0.269256	0.31821	N	0.007015	T	0.71576	0.3356	M	0.74258	2.255	0.58432	D	0.999997	D	0.89917	1.0	D	0.80764	0.994	T	0.74259	-0.3723	10	0.87932	D	0	-0.1218	8.6839	0.34225	0.2271:0.7729:0.0:0.0	.	66	Q9HBI0	PARVG_HUMAN	C	66	ENSP00000391453:R66C;ENSP00000391583:R66C;ENSP00000416761:R66C	ENSP00000349378:R66C	R	+	1	0	PARVG	42915040	0.993000	0.37304	1.000000	0.80357	0.917000	0.54804	2.847000	0.48270	1.970000	0.57323	0.555000	0.69702	CGC		0.592	PARVG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318238.4	NM_022141	
IL17REL	400935	broad.mit.edu	37	22	50437746	50437746	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:50437746C>T	ENST00000389983.2	-	9	839	c.575G>A	c.(574-576)cGg>cAg	p.R192Q	IL17REL_ENST00000341280.5_Missense_Mutation_p.R192Q	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	192								p.R192Q(1)		endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GATCTGGATCCGCACCGCGTC	0.667																																					p.R192Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G575A	22						.						66.0	67.0	67.0					22																	50437746		2203	4300	6503	48779873	SO:0001583	missense	400935	exon9			AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.575G>A	22.37:g.50437746C>T	ENSP00000374633:p.Arg192Gln	Somatic		Capture	Illumina HiSeq	Phase_I	48779873	NM_001001694	A6NCN4|A6PVC1	Missense_Mutation	SNP	ENST00000389983.2	37	CCDS33679.1	.	.	.	.	.	.	.	.	.	.	C	14.73	2.622720	0.46840	.	.	ENSG00000188263	ENST00000389983;ENST00000341280	T;T	0.36520	1.25;1.25	3.03	3.03	0.35002	.	0.000000	0.64402	U	0.000019	T	0.54175	0.1842	M	0.72894	2.215	0.09310	N	1	D	0.89917	1.0	D	0.77004	0.989	T	0.38824	-0.9643	10	0.66056	D	0.02	.	9.3491	0.38126	0.0:1.0:0.0:0.0	.	192	Q6ZVW7	I17EL_HUMAN	Q	192	ENSP00000374633:R192Q;ENSP00000342520:R192Q	ENSP00000342520:R192Q	R	-	2	0	IL17REL	48779873	0.047000	0.20315	0.014000	0.15608	0.002000	0.02628	2.515000	0.45512	1.517000	0.48917	0.655000	0.94253	CGG		0.667	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694	
MOV10L1	54456	broad.mit.edu	37	22	50599447	50599447	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:50599447G>A	ENST00000262794.5	+	26	3600	c.3517G>A	c.(3517-3519)Gga>Aga	p.G1173R	MOV10L1_ENST00000395858.3_Missense_Mutation_p.G1127R|MOV10L1_ENST00000545383.1_Missense_Mutation_p.G1173R|MOV10L1_ENST00000540615.1_Intron|MOV10L1_ENST00000395852.1_Missense_Mutation_p.G300R	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	1173					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.G1173R(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TGTTTACATGGGATGCGATTT	0.502																																					p.G1127R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3379A	22						.						263.0	242.0	249.0					22																	50599447		2203	4300	6503	48941574	SO:0001583	missense	54456	exon25			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.3517G>A	22.37:g.50599447G>A	ENSP00000262794:p.Gly1173Arg	Somatic		Capture	Illumina HiSeq	Phase_I	48941574	NM_001164104	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	.	.	.	.	.	.	.	.	.	.	.	14.40	2.523366	0.44866	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000395852	D;D;D;D	0.92911	-2.05;-2.05;-1.8;-3.13	5.14	4.13	0.48395	.	0.046129	0.85682	N	0.000000	D	0.94159	0.8126	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.94045	0.7313	10	0.87932	D	0	-30.1637	11.2059	0.48769	0.0901:0.0:0.9099:0.0	.	300;1127;1173	Q9BXT6-2;A8MXC6;Q9BXT6	.;.;M10L1_HUMAN	R	1173;1173;1127;300	ENSP00000438978:G1173R;ENSP00000262794:G1173R;ENSP00000379199:G1127R;ENSP00000379193:G300R	ENSP00000262794:G1173R	G	+	1	0	MOV10L1	48941574	1.000000	0.71417	0.059000	0.19551	0.007000	0.05969	7.757000	0.85209	1.163000	0.42636	0.498000	0.49722	GGA		0.502	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
TUBGCP6	85378	broad.mit.edu	37	22	50659053	50659053	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:50659053C>T	ENST00000248846.5	-	16	3839	c.3735G>A	c.(3733-3735)gtG>gtA	p.V1245V	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_Silent_p.V1245V			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1245	9 X 27 AA tandem repeats.				G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)	p.V1245V(1)		breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		TGGCGTCGGACACGTGTCCAT	0.627																																					p.V1245V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3735A	22						.						78.0	60.0	66.0					22																	50659053		2203	4300	6503	49001180	SO:0001819	synonymous_variant	85378	exon16			AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.3735G>A	22.37:g.50659053C>T		Somatic		Capture	Illumina HiSeq	Phase_I	49001180	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																				0.627	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
TAB1	10454	broad.mit.edu	37	22	39824173	39824173	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:39824173delC	ENST00000216160.6	+	10	1354	c.1292delC	c.(1291-1293)accfs	p.T431fs	TAB1_ENST00000331454.3_Frame_Shift_Del_p.T431fs	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	431					activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart morphogenesis (GO:0003007)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lung development (GO:0030324)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|protein complex (GO:0043234)	catalytic activity (GO:0003824)|enzyme activator activity (GO:0008047)|kinase activator activity (GO:0019209)	p.T433fs*9(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						GACGAAGCCACCCCCACCCTC	0.642																																					p.T431fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1292delC	22						.						129.0	97.0	108.0					22																	39824173		2203	4300	6503	38154119	SO:0001589	frameshift_variant	10454	exon10			U49928	CCDS13992.1, CCDS13993.1	22q13.1	2010-02-05	2010-02-05	2010-02-05	ENSG00000100324	ENSG00000100324			18157	protein-coding gene	gene with protein product	"""TAK1-binding protein 1"", ""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	602615	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	MAP3K7IP1		8638164, 10187861	Standard	NM_153497		Approved		uc003axt.3	Q15750	OTTHUMG00000151102	ENST00000216160.6:c.1292delC	22.37:g.39824173delC	ENSP00000216160:p.Thr431fs	Somatic		Capture	Illumina HiSeq	Phase_I	38154119	NM_153497	Q2PP09|Q8IZW2	Frame_Shift_Del	DEL	ENST00000216160.6	37	CCDS13993.1																																																																																				0.642	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497	
ARSA	410	broad.mit.edu	37	22	51065321	51065321	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr22:51065321C>T	ENST00000547307.1	-	3	1024	c.619G>A	c.(619-621)Gac>Aac	p.D207N	ARSA_ENST00000216124.5_Missense_Mutation_p.D209N|ARSA_ENST00000395621.3_Missense_Mutation_p.D209N|ARSA_ENST00000453344.2_Missense_Mutation_p.D123N|ARSA_ENST00000356098.5_Missense_Mutation_p.D209N|ARSA_ENST00000395619.3_Missense_Mutation_p.D209N|ARSA_ENST00000547805.1_Missense_Mutation_p.D207N			P15289	ARSA_HUMAN	arylsulfatase A	207					autophagy (GO:0006914)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum lumen (GO:0005788)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|cerebroside-sulfatase activity (GO:0004098)|sulfuric ester hydrolase activity (GO:0008484)	p.D207N(1)		endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|skin(1)	9		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Micafungin(DB01141)|Suramin(DB04786)	GCCATGAGGTCATGGGCGAAA	0.667																																					p.D123N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G367A	22						.						85.0	99.0	95.0					22																	51065321		2203	4300	6503	49412187	SO:0001583	missense	410	exon3			X52150	CCDS14100.1, CCDS46736.1, CCDS14100.2	22q13.33	2013-09-19			ENSG00000100299	ENSG00000100299	3.1.6.8	"""Arylsulfatase family"""	713	protein-coding gene	gene with protein product	"""metachromatic leucodystrophy"""	607574				15772092	Standard	NM_000487		Approved		uc003bmz.5	P15289	OTTHUMG00000150180	ENST00000547307.1:c.619G>A	22.37:g.51065321C>T	ENSP00000448440:p.Asp207Asn	Somatic		Capture	Illumina HiSeq	Phase_I	49412187	NM_001085428	B2RCA6|B7XD04|F8WCC8|Q6ICI5|Q96CJ0	Missense_Mutation	SNP	ENST00000547307.1	37		.	.	.	.	.	.	.	.	.	.	C	7.379	0.628323	0.14257	.	.	ENSG00000100299	ENST00000356098;ENST00000216124;ENST00000547307;ENST00000547805;ENST00000395621;ENST00000453344;ENST00000395619	D;D;D;D;D;D;D	0.95622	-3.76;-3.76;-3.76;-3.76;-3.76;-3.76;-3.76	5.37	0.452	0.16634	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.750936	0.14088	N	0.342226	D	0.89476	0.6726	L	0.43598	1.365	0.20926	N	0.999826	B	0.10296	0.003	B	0.09377	0.004	T	0.77600	-0.2527	10	0.33940	T	0.23	.	0.7792	0.01038	0.167:0.3783:0.1617:0.293	.	207	P15289	ARSA_HUMAN	N	209;209;207;207;209;123;209	ENSP00000348406:D209N;ENSP00000216124:D209N;ENSP00000448440:D207N;ENSP00000448932:D207N;ENSP00000378983:D209N;ENSP00000412542:D123N;ENSP00000378981:D209N	ENSP00000216124:D209N	D	-	1	0	ARSA	49412187	0.122000	0.22280	0.493000	0.27502	0.149000	0.21700	0.585000	0.23879	0.654000	0.30846	0.505000	0.49811	GAC		0.667	ARSA-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000487	
SERPINE2	5270	broad.mit.edu	37	2	224845069	224845070	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:224845069_224845070insT	ENST00000258405.4	-	7	1275_1276	c.1033_1034insA	c.(1033-1035)attfs	p.I345fs	SERPINE2_ENST00000409840.3_Frame_Shift_Ins_p.I344fs|SERPINE2_ENST00000447280.2_Frame_Shift_Ins_p.I356fs|SERPINE2_ENST00000409304.1_Frame_Shift_Ins_p.I344fs	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	345					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.I345fs*2(1)		breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		ACTGACTTCAATTTTTGCTTTT	0.441																																					p.I356fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1067_1068insA	2						.																																			224553314	SO:0001589	frameshift_variant	5270	exon7			M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"""Serine (or cysteine) peptidase inhibitors"""	8951	protein-coding gene	gene with protein product	"""glial-derived nexin 1"""	177010	"""serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"""	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.1034dupA	2.37:g.224845074_224845074dupT	ENSP00000258405:p.Ile345fs	Somatic		Capture	Illumina HiSeq	Phase_I	224553313	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Frame_Shift_Ins	INS	ENST00000258405.4	37	CCDS2460.1																																																																																				0.441	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216	
UGT1A10	54575	broad.mit.edu	37	2	234545676	234545677	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:234545676_234545677insG	ENST00000344644.5	+	1	577_578	c.508_509insG	c.(508-510)aggfs	p.R170fs	UGT1A10_ENST00000373445.1_Frame_Shift_Ins_p.R170fs|UGT1A1_ENST00000373450.4_Intron	NM_019075.2	NP_061948.1	Q9HAW8	UD110_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A10	170					cellular glucuronidation (GO:0052695)|flavone metabolic process (GO:0051552)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)	p.I172fs*7(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(2)|skin(3)	32		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;1.96e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000468)|Lung(119;0.00381)|LUSC - Lung squamous cell carcinoma(224;0.008)	Acetaminophen(DB00316)|Etodolac(DB00749)|Losartan(DB00678)|Mycophenolate mofetil(DB00688)|Valproic Acid(DB00313)	GGTCTTCACCAGGGGAATATTT	0.45																																					p.R170fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.508_509insG	2						.																																			234210416	SO:0001589	frameshift_variant	54575	exon1			U39550	CCDS33403.1	2q37	2010-03-05	2005-07-20		ENSG00000242515	ENSG00000242515		"""UDP glucuronosyltransferases"""	12531	other	complex locus constituent		606435	"""UDP glycosyltransferase 1 family, polypeptide A10"""			9295054, 9325166	Standard	NM_019075		Approved	UGT1J		Q9HAW8	OTTHUMG00000059121	ENST00000344644.5:c.512dupG	2.37:g.234545680_234545680dupG	ENSP00000343838:p.Arg170fs	Somatic		Capture	Illumina HiSeq	Phase_I	234210415	NM_019075	O00474|Q6NT91|Q7Z6H8	Frame_Shift_Ins	INS	ENST00000344644.5	37	CCDS33403.1																																																																																				0.450	UGT1A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130986.1	NM_019075	
UBXN2A	165324	broad.mit.edu	37	2	24222699	24222700	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:24222699_24222700insA	ENST00000309033.4	+	7	986_987	c.742_743insA	c.(742-744)caafs	p.Q248fs	RN7SL610P_ENST00000463845.2_RNA|UBXN2A_ENST00000404924.1_Frame_Shift_Ins_p.Q248fs|UBXN2A_ENST00000446425.2_3'UTR|UBXN2A_ENST00000535786.1_Frame_Shift_Ins_p.Q195fs	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	248					regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)		p.T250fs*5(1)		endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						TCAGAGACTCCAAAAAACTGCA	0.411																																					p.Q248fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.742_743insA	2						.																																			24076204	SO:0001589	frameshift_variant	165324	exon7			BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960		"""UBX domain containing"""	27265	protein-coding gene	gene with protein product			"""UBX domain containing 4"""	UBXD4		12477932	Standard	NM_181713		Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.748dupA	2.37:g.24222705_24222705dupA	ENSP00000312107:p.Gln248fs	Somatic		Capture	Illumina HiSeq	Phase_I	24076203	NM_181713	A8K577|B7ZKP8|Q569G8	Frame_Shift_Ins	INS	ENST00000309033.4	37	CCDS1704.1																																																																																				0.411	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246824.2	NM_181713	
SEPT10	151011	broad.mit.edu	37	2	110301827	110301828	+	3'UTR	INS	-	-	T	rs562796959|rs545969753	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:110301827_110301828insT	ENST00000397712.2	-	0	1801_1802				SEPT10_ENST00000397714.2_3'UTR|SEPT10_ENST00000334001.6_3'UTR|SEPT10_ENST00000468616.1_5'Flank|SEPT10_ENST00000437928.1_3'UTR|SEPT10_ENST00000356688.4_Frame_Shift_Ins_p.L503fs	NM_144710.3	NP_653311.1	Q9P0V9	SEP10_HUMAN	septin 10						cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)			breast(2)|endometrium(3)|large_intestine(4)|lung(8)|prostate(1)	18						CACACTTCTAGTTTTTTTTTAA	0.317													TTTTTTTTT|TTTTTTTTT|TTTTTTTTTT|insertion	16	0.00319489	0.0	0.0086	5008	,	,		16525	0.001		0.008	False		,,,				2504	0.001				.												.	.	0			.	2						.		,	5,3487		0,5,1741					,	-0.1	0.0			63	31,7779		0,31,3874	no	utr-3,utr-3	SEPT10	NM_178584.1,NM_144710.2	,	0,36,5615	A1A1,A1R,RR		0.3969,0.1432,0.3185	,	,		36,11266				109659117	SO:0001624	3_prime_UTR_variant	151011	.			AF146760	CCDS42726.1, CCDS46383.1	2q13	2013-01-21			ENSG00000186522	ENSG00000186522		"""Septins"""	14349	protein-coding gene	gene with protein product	"""sept1-like"""	611737				12711328	Standard	NM_144710		Approved	FLJ11619	uc002tew.4	Q9P0V9	OTTHUMG00000154957	ENST00000397712.2:c.*59->A	2.37:g.110301836_110301836dupT		Somatic		Capture	Illumina HiSeq	Phase_I	109659116	.	B3KRQ9|Q86VP5|Q9HAH6	Frame_Shift_Ins	INS	ENST00000397712.2	37	CCDS46383.1																																																																																				0.317	SEPT10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337804.1	NM_144710	
IL18R1	8809	broad.mit.edu	37	2	102988513	102988513	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:102988513T>A	ENST00000409599.1	+	5	759	c.403T>A	c.(403-405)Ttt>Att	p.F135I	IL18R1_ENST00000233957.1_Missense_Mutation_p.F135I|IL18R1_ENST00000334376.3_Missense_Mutation_p.F135I			Q13478	IL18R_HUMAN	interleukin 18 receptor 1	135	Ig-like C2-type 2.				immune response (GO:0006955)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|signal transduction (GO:0007165)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-18 receptor activity (GO:0042008)|receptor activity (GO:0004872)	p.F135I(1)		breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						AGTTAAAAAATTTTTTCAGAT	0.279																																					p.F135I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T403A	2						.						38.0	41.0	40.0					2																	102988513		2201	4293	6494	102354945	SO:0001583	missense	8809	exon3			U43672	CCDS2060.1	2q12	2013-01-29			ENSG00000115604	ENSG00000115604		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5988	protein-coding gene	gene with protein product		604494				8626725, 10191101	Standard	NM_003855		Approved	IL1RRP, IL-1Rrp, CD218a	uc010fiy.3	Q13478	OTTHUMG00000130780	ENST00000409599.1:c.403T>A	2.37:g.102988513T>A	ENSP00000387211:p.Phe135Ile	Somatic		Capture	Illumina HiSeq	Phase_I	102354945	NM_003855	B2R9Y5|Q52LC9	Missense_Mutation	SNP	ENST00000409599.1	37	CCDS2060.1	.	.	.	.	.	.	.	.	.	.	T	9.598	1.127837	0.20959	.	.	ENSG00000115604	ENST00000410040;ENST00000409599;ENST00000233957;ENST00000334376	T;T;T	0.11063	2.81;2.81;2.81	5.15	-10.3	0.00346	.	2.722080	0.00780	N	0.001266	T	0.07279	0.0184	L	0.29908	0.895	0.09310	N	1	B;B;B	0.20164	0.042;0.038;0.042	B;B;B	0.18871	0.023;0.016;0.023	T	0.08911	-1.0699	10	0.26408	T	0.33	.	8.8123	0.34974	0.2463:0.0678:0.5784:0.1074	.	135;135;135	B7ZKV7;Q86YL8;Q13478	.;.;IL18R_HUMAN	I	135	ENSP00000386663:F135I;ENSP00000387211:F135I;ENSP00000233957:F135I	ENSP00000233957:F135I	F	+	1	0	IL18R1	102354945	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.607000	0.00416	-3.487000	0.00154	-0.466000	0.05196	TTT		0.279	IL18R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253294.2	NM_003855	
C2orf49	79074	broad.mit.edu	37	2	105956154	105956154	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:105956154A>G	ENST00000258457.2	+	2	443	c.214A>G	c.(214-216)Aaa>Gaa	p.K72E	RP11-332H14.2_ENST00000610036.1_lincRNA|C2orf49_ENST00000437250.2_Missense_Mutation_p.K110E|C2orf49_ENST00000410049.1_Missense_Mutation_p.K72E			Q9BVC5	ASHWN_HUMAN	chromosome 2 open reading frame 49	72					embryonic morphogenesis (GO:0048598)	tRNA-splicing ligase complex (GO:0072669)		p.K72E(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6						TAGATGGGGGAAAATGATGGA	0.343																																					p.K72E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A214G	2						.						82.0	83.0	83.0					2																	105956154		2203	4300	6503	105322586	SO:0001583	missense	79074	exon2			BC001310	CCDS2068.1, CCDS74550.1	2q12.2	2009-04-22			ENSG00000135974	ENSG00000135974			28772	protein-coding gene	gene with protein product	"""ashwin"""					12477932	Standard	NM_001286537		Approved	MGC5509, asw	uc002tcs.1	Q9BVC5	OTTHUMG00000130808	ENST00000258457.2:c.214A>G	2.37:g.105956154A>G	ENSP00000258457:p.Lys72Glu	Somatic		Capture	Illumina HiSeq	Phase_I	105322586	NM_024093	B3KXN3|B4E2G9	Missense_Mutation	SNP	ENST00000258457.2	37	CCDS2068.1	.	.	.	.	.	.	.	.	.	.	A	18.67	3.673060	0.67928	.	.	ENSG00000135974	ENST00000258457;ENST00000437250;ENST00000410049	T;T;T	0.58652	0.32;0.32;0.32	5.57	5.57	0.84162	.	0.096213	0.64402	D	0.000001	T	0.72145	0.3424	M	0.77103	2.36	0.48395	D	0.999645	P;D	0.54207	0.932;0.965	P;P	0.55615	0.655;0.78	T	0.76656	-0.2879	10	0.72032	D	0.01	-20.072	15.7375	0.77856	1.0:0.0:0.0:0.0	.	110;72	B4E2G9;Q9BVC5	.;ASHWN_HUMAN	E	72;110;72	ENSP00000258457:K72E;ENSP00000400208:K110E;ENSP00000386361:K72E	ENSP00000258457:K72E	K	+	1	0	C2orf49	105322586	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.105000	0.77031	2.124000	0.65301	0.477000	0.44152	AAA		0.343	C2orf49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253353.2	NM_024093	
UXS1	80146	broad.mit.edu	37	2	106729215	106729215	+	Missense_Mutation	SNP	C	C	T	rs546343589		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:106729215C>T	ENST00000409501.3	-	10	808	c.751G>A	c.(751-753)Gtg>Atg	p.V251M	UXS1_ENST00000428048.2_Missense_Mutation_p.V95M|UXS1_ENST00000409032.1_Missense_Mutation_p.V83M|UXS1_ENST00000540130.1_Missense_Mutation_p.V194M|UXS1_ENST00000283148.7_Missense_Mutation_p.V256M			Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1	251					protein tetramerization (GO:0051262)|UDP-D-xylose biosynthetic process (GO:0033320)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|UDP-glucuronate decarboxylase activity (GO:0048040)	p.V256M(1)|p.V251M(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)	17						CGCACTTCCACGCCTTCCTGG	0.567													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19609	0.0		0.0	False		,,,				2504	0.0				p.V251M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G751A	2						.						50.0	54.0	53.0					2																	106729215		2128	4238	6366	106095647	SO:0001583	missense	80146	exon10			AK027244	CCDS46378.1, CCDS58720.1, CCDS58721.1	2q12.2	2012-02-22			ENSG00000115652	ENSG00000115652	4.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	17729	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 6E, member 12"""	609749				19027726	Standard	NM_001253875		Approved	FLJ23591, UGD, SDR6E1	uc002tdn.3	Q8NBZ7	OTTHUMG00000153150	ENST00000409501.3:c.751G>A	2.37:g.106729215C>T	ENSP00000387019:p.Val251Met	Somatic		Capture	Illumina HiSeq	Phase_I	106095647	NM_025076	Q8NBX3|Q9H5C2	Missense_Mutation	SNP	ENST00000409501.3	37	CCDS46378.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.886404	0.91814	.	.	ENSG00000115652	ENST00000283148;ENST00000540130;ENST00000409501;ENST00000409032;ENST00000428048;ENST00000441952;ENST00000416298;ENST00000444193	D;D;D;D;D;D;D;D	0.93547	-3.24;-3.24;-3.24;-3.24;-3.24;-3.24;-3.24;-3.24	5.25	5.25	0.73442	NAD-dependent epimerase/dehydratase (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.95639	0.8582	M	0.66378	2.025	0.80722	D	1	D;D;D	0.67145	0.965;0.995;0.996	P;P;P	0.59424	0.548;0.776;0.857	D	0.95813	0.8843	10	0.62326	D	0.03	.	18.4398	0.90662	0.0:1.0:0.0:0.0	.	95;256;251	B4E3U7;Q8NBZ7-2;Q8NBZ7	.;.;UXS1_HUMAN	M	256;194;251;83;95;95;83;83	ENSP00000283148:V256M;ENSP00000438265:V194M;ENSP00000387019:V251M;ENSP00000387096:V83M;ENSP00000394334:V95M;ENSP00000416656:V95M;ENSP00000403612:V83M;ENSP00000404468:V83M	ENSP00000283148:V256M	V	-	1	0	UXS1	106095647	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.730000	0.74780	2.452000	0.82932	0.561000	0.74099	GTG		0.567	UXS1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329778.1	NM_025076.3	
ST6GAL2	84620	broad.mit.edu	37	2	107423177	107423177	+	Missense_Mutation	SNP	G	G	A	rs200325346		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:107423177G>A	ENST00000409382.3	-	6	2157	c.1547C>T	c.(1546-1548)gCg>gTg	p.A516V	ST6GAL2_ENST00000361686.4_Missense_Mutation_p.A516V	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	516					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)	p.A516V(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						GCAGTGCACCGCCTGGAAGCC	0.527																																					p.A516V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1547T	2						.						109.0	101.0	103.0					2																	107423177		2203	4300	6503	106789609	SO:0001583	missense	84620	exon6			AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"""sialyltransferase 2 (monosialoganglioside sialyltransferase)"""	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.1547C>T	2.37:g.107423177G>A	ENSP00000386942:p.Ala516Val	Somatic		Capture	Illumina HiSeq	Phase_I	106789609	NM_001142351	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Missense_Mutation	SNP	ENST00000409382.3	37	CCDS2073.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.419666	0.25552	.	.	ENSG00000144057	ENST00000361686;ENST00000409382	T;T	0.15139	2.45;2.45	5.8	4.92	0.64577	.	0.487263	0.24472	N	0.038240	T	0.19005	0.0456	M	0.72118	2.19	0.48696	D	0.999698	P	0.42757	0.789	B	0.32928	0.155	T	0.03993	-1.0986	10	0.52906	T	0.07	-13.47	13.6225	0.62144	0.0734:0.0:0.9266:0.0	.	516	Q96JF0	SIAT2_HUMAN	V	516	ENSP00000355273:A516V;ENSP00000386942:A516V	ENSP00000355273:A516V	A	-	2	0	ST6GAL2	106789609	0.994000	0.37717	0.005000	0.12908	0.029000	0.11900	5.974000	0.70465	1.453000	0.47775	0.655000	0.94253	GCG		0.527	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528	
ST6GAL2	84620	broad.mit.edu	37	2	107450522	107450522	+	Missense_Mutation	SNP	G	G	A	rs533150647		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:107450522G>A	ENST00000409382.3	-	3	1634	c.1024C>T	c.(1024-1026)Cgc>Tgc	p.R342C	ST6GAL2_ENST00000361686.4_Missense_Mutation_p.R342C|AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000409087.3_Missense_Mutation_p.R342C	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	342					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)	p.R342C(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						TTAATGATGCGTATGGTGGTT	0.393													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16791	0.0		0.0	False		,,,				2504	0.0				p.R342C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1024T	2						.						224.0	213.0	217.0					2																	107450522		2203	4300	6503	106816954	SO:0001583	missense	84620	exon3			AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"""sialyltransferase 2 (monosialoganglioside sialyltransferase)"""	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.1024C>T	2.37:g.107450522G>A	ENSP00000386942:p.Arg342Cys	Somatic		Capture	Illumina HiSeq	Phase_I	106816954	NM_001142351	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Missense_Mutation	SNP	ENST00000409382.3	37	CCDS2073.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.606524	0.87157	.	.	ENSG00000144057	ENST00000361686;ENST00000409382;ENST00000409087	T;T;T	0.78924	-1.22;-1.22;-1.22	6.03	6.03	0.97812	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);	0.000000	0.85682	D	0.000000	D	0.92740	0.7692	H	0.96604	3.85	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94296	0.7533	10	0.87932	D	0	-37.1524	19.545	0.95291	0.0:0.0:1.0:0.0	.	342;342	Q96JF0-2;Q96JF0	.;SIAT2_HUMAN	C	342	ENSP00000355273:R342C;ENSP00000386942:R342C;ENSP00000387332:R342C	ENSP00000355273:R342C	R	-	1	0	ST6GAL2	106816954	1.000000	0.71417	0.990000	0.47175	0.813000	0.45954	9.869000	0.99810	2.861000	0.98227	0.655000	0.94253	CGC		0.393	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528	
GREB1	9687	broad.mit.edu	37	2	11720858	11720858	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:11720858C>T	ENST00000381486.2	+	7	1101	c.801C>T	c.(799-801)aaC>aaT	p.N267N	GREB1_ENST00000263834.5_Silent_p.N267N|GREB1_ENST00000389825.3_Silent_p.N157N|GREB1_ENST00000234142.5_Silent_p.N267N|GREB1_ENST00000381483.2_Silent_p.N267N	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	267						integral component of membrane (GO:0016021)		p.N267N(3)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CCTCACTAAACGCAGCAATGG	0.527																																					p.N267N	Ovarian(39;850 945 2785 23371 33093)											.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C801T	2						.						111.0	108.0	109.0					2																	11720858		2203	4300	6503	11638309	SO:0001819	synonymous_variant	9687	exon7				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.801C>T	2.37:g.11720858C>T		Somatic		Capture	Illumina HiSeq	Phase_I	11638309	NM_148903	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	37	CCDS42655.1																																																																																				0.527	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
GREB1	9687	broad.mit.edu	37	2	11758477	11758477	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:11758477G>T	ENST00000381486.2	+	22	3776	c.3476G>T	c.(3475-3477)aGg>aTg	p.R1159M	GREB1_ENST00000396123.1_Missense_Mutation_p.R157M|GREB1_ENST00000234142.5_Missense_Mutation_p.R1159M	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1159	Ser-rich.					integral component of membrane (GO:0016021)		p.R1159M(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GAGCATGCCAGGTCGCCCCAG	0.682																																					p.R1159M	Ovarian(39;850 945 2785 23371 33093)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3476T	2						.						21.0	24.0	23.0					2																	11758477		1985	4078	6063	11675928	SO:0001583	missense	9687	exon22				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.3476G>T	2.37:g.11758477G>T	ENSP00000370896:p.Arg1159Met	Somatic		Capture	Illumina HiSeq	Phase_I	11675928	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	G	8.475	0.858536	0.17178	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.24151	3.21;3.21;1.87	4.85	1.97	0.26223	.	1.876410	0.02527	N	0.093157	T	0.25938	0.0632	L	0.40543	1.245	0.09310	N	1	P	0.47253	0.892	P	0.45610	0.487	T	0.09952	-1.0651	10	0.33141	T	0.24	-1.8024	3.7969	0.08743	0.2886:0.186:0.5254:0.0	.	1159	Q4ZG55	GREB1_HUMAN	M	1159;1159;157	ENSP00000370896:R1159M;ENSP00000234142:R1159M;ENSP00000379429:R157M	ENSP00000234142:R1159M	R	+	2	0	GREB1	11675928	0.018000	0.18449	0.013000	0.15412	0.468000	0.32798	1.068000	0.30629	0.443000	0.26582	-0.140000	0.14226	AGG		0.682	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
LPIN1	23175	broad.mit.edu	37	2	11911638	11911638	+	Silent	SNP	C	C	T	rs145629147	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:11911638C>T	ENST00000256720.2	+	4	522	c.429C>T	c.(427-429)agC>agT	p.S143S	LPIN1_ENST00000396098.1_Silent_p.S149S|LPIN1_ENST00000396099.1_Silent_p.S149S|LPIN1_ENST00000425416.2_Silent_p.S149S|LPIN1_ENST00000449576.2_Silent_p.S192S	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	143					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.S143R(1)|p.S143S(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TCGCTCCCAGCGAGACGCCGT	0.537													c|||	2	0.000399361	0.0015	0.0	5008	,	,		18938	0.0		0.0	False		,,,				2504	0.0				p.S143S												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|kidney(1)	c.C429T	2						.	T		3,4403	6.2+/-15.9	0,3,2200	54.0	52.0	53.0		429	-11.6	0.0	2	dbSNP_134	53	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LPIN1	NM_145693.1		0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308		143/891	11911638	4,13002	2203	4300	6503	11829089	SO:0001819	synonymous_variant	23175	exon4			D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.429C>T	2.37:g.11911638C>T		Somatic		Capture	Illumina HiSeq	Phase_I	11829089	NM_145693	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	37	CCDS1682.1																																																																																				0.537	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
SLC20A1	6574	broad.mit.edu	37	2	113416959	113416959	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:113416959C>T	ENST00000272542.3	+	8	1766	c.1227C>T	c.(1225-1227)gaC>gaT	p.D409D		NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	409					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	high-affinity inorganic phosphate:sodium symporter activity (GO:0005316)|inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|sodium:phosphate symporter activity (GO:0005436)	p.D409D(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						ACTCCGGTGACAAACCCTTAA	0.478																																					p.D409D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1227T	2						.						121.0	114.0	117.0					2																	113416959		2203	4300	6503	113133430	SO:0001819	synonymous_variant	6574	exon8				CCDS2099.1	2q13	2013-05-22			ENSG00000144136	ENSG00000144136		"""Solute carriers"""	10946	protein-coding gene	gene with protein product	"""gibbon ape leukemia virus receptor 1"""	137570		GLVR1		8041748	Standard	NM_005415		Approved	PiT-1, Glvr-1	uc002tib.3	Q8WUM9	OTTHUMG00000131317	ENST00000272542.3:c.1227C>T	2.37:g.113416959C>T		Somatic		Capture	Illumina HiSeq	Phase_I	113133430	NM_005415	Q08344|Q6DHX8|Q9UQ82	Silent	SNP	ENST00000272542.3	37	CCDS2099.1	.	.	.	.	.	.	.	.	.	.	C	7.186	0.590515	0.13812	.	.	ENSG00000144136	ENST00000433924	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.0011	16.5206	0.84315	0.0:1.0:0.0:0.0	.	.	.	.	X	193	.	.	Q	+	1	0	SLC20A1	113133430	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.646000	0.46630	2.517000	0.84864	0.655000	0.94253	CAA		0.478	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415	
CNTNAP5	129684	broad.mit.edu	37	2	125281923	125281923	+	Silent	SNP	C	C	T	rs370061005		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:125281923C>T	ENST00000431078.1	+	9	1732	c.1368C>T	c.(1366-1368)aaC>aaT	p.N456N		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	456	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.N456N(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		TTAGCATCAACGCCAGGAGGA	0.502																																					p.N456N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1368T	2						.	C		0,4160		0,0,2080	78.0	83.0	81.0		1368	-9.6	0.0	2		81	1,8443		0,1,4221	no	coding-synonymous	CNTNAP5	NM_130773.2		0,1,6301	TT,TC,CC		0.0118,0.0,0.0079		456/1307	125281923	1,12603	2080	4222	6302	124998393	SO:0001819	synonymous_variant	129684	exon9			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.1368C>T	2.37:g.125281923C>T		Somatic		Capture	Illumina HiSeq	Phase_I	124998393	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	37	CCDS46401.1																																																																																				0.502	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
UGGT1	56886	broad.mit.edu	37	2	128870789	128870789	+	Missense_Mutation	SNP	G	G	C	rs540119468	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:128870789G>C	ENST00000259253.6	+	6	700	c.653G>C	c.(652-654)aGc>aCc	p.S218T	UGGT1_ENST00000375990.3_Missense_Mutation_p.S194T	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	218					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)	p.S218T(1)		NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						ATATCAAAAAGCAATGCAGGC	0.348																																					p.S218T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G653C	2						.						69.0	72.0	71.0					2																	128870789		2203	4299	6502	128587259	SO:0001583	missense	56886	exon6			AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"""UDP-glucose ceramide glucosyltransferase-like 1"""	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.653G>C	2.37:g.128870789G>C	ENSP00000259253:p.Ser218Thr	Somatic		Capture	Illumina HiSeq	Phase_I	128587259	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	37	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	G	12.23	1.877099	0.33162	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.09073	3.02;3.02	5.58	3.75	0.43078	.	0.144833	0.64402	D	0.000014	T	0.09423	0.0232	L	0.48877	1.53	0.32514	N	0.537107	B;B	0.21688	0.059;0.01	B;B	0.25405	0.06;0.006	T	0.03514	-1.1029	10	0.54805	T	0.06	.	10.1791	0.42957	0.0774:0.4141:0.5085:0.0	.	194;218	Q9NYU2-2;Q9NYU2	.;UGGG1_HUMAN	T	194;218	ENSP00000365158:S194T;ENSP00000259253:S218T	ENSP00000259253:S218T	S	+	2	0	UGGT1	128587259	1.000000	0.71417	0.526000	0.27913	0.765000	0.43378	2.383000	0.44354	0.684000	0.31448	0.585000	0.79938	AGC		0.348	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
POTEF	728378	broad.mit.edu	37	2	130878062	130878062	+	Silent	SNP	C	C	T	rs540331197	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:130878062C>T	ENST00000409914.2	-	3	426	c.27G>A	c.(25-27)ccG>ccA	p.P9P	POTEF_ENST00000360967.5_Silent_p.P9P|POTEF_ENST00000361163.4_Silent_p.P9P|POTEF_ENST00000357462.5_Silent_p.P9P	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	9					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.P9P(2)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						AAGAGGCAGCCGGCATGGAAT	0.547													.|||	2	0.000399361	0.0	0.0014	5008	,	,		15086	0.001		0.0	False		,,,				2504	0.0				p.P9P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G27A	2						.						37.0	37.0	37.0					2																	130878062		2185	4253	6438	130594532	SO:0001819	synonymous_variant	728378	exon3			EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.27G>A	2.37:g.130878062C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130594532	NM_001099771	A6NC34	Silent	SNP	ENST00000409914.2	37	CCDS46409.1																																																																																				0.547	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
TUBA3E	112714	broad.mit.edu	37	2	130952659	130952659	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:130952659C>T	ENST00000312988.7	-	3	468	c.368G>A	c.(367-369)cGc>cAc	p.R123H		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	123					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.R123H(1)		endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					TACCAGTTTGCGGATCCGGTC	0.498																																					p.R123H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G368A	2						.						148.0	142.0	144.0					2																	130952659		2203	4300	6503	130669129	SO:0001583	missense	112714	exon3			BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.368G>A	2.37:g.130952659C>T	ENSP00000318197:p.Arg123His	Somatic		Capture	Illumina HiSeq	Phase_I	130669129	NM_207312		Missense_Mutation	SNP	ENST00000312988.7	37	CCDS2158.1	.	.	.	.	.	.	.	.	.	.	c	12.44	1.938632	0.34189	.	.	ENSG00000152086	ENST00000312988	T	0.72615	-0.67	2.95	2.95	0.34219	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.51477	U	0.000088	D	0.86648	0.5983	H	0.97103	3.94	0.47994	D	0.999563	B	0.32968	0.392	P	0.51135	0.66	D	0.89058	0.3460	10	0.72032	D	0.01	.	11.6556	0.51315	0.0:1.0:0.0:0.0	.	123	Q6PEY2	TBA3E_HUMAN	H	123	ENSP00000318197:R123H	ENSP00000318197:R123H	R	-	2	0	TUBA3E	130669129	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.473000	0.73572	1.656000	0.50722	0.455000	0.32223	CGC		0.498	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
CCDC74A	90557	broad.mit.edu	37	2	132290340	132290340	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:132290340C>A	ENST00000295171.6	+	5	1000	c.862C>A	c.(862-864)Ctg>Atg	p.L288M	CCDC74A_ENST00000467992.2_3'UTR|CCDC74A_ENST00000409856.3_Missense_Mutation_p.L222M	NM_001258304.1|NM_001258305.1|NM_138770.2	NP_001245233.1|NP_001245234.1|NP_620125.1	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	288								p.L288M(1)		endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						TACCAACCTCCTGCAGACCCA	0.667																																					p.L288M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C862A	2						.						39.0	39.0	39.0					2																	132290340		2202	4288	6490	132006810	SO:0001583	missense	90557	exon5				CCDS2167.1, CCDS58732.1, CCDS74578.1	2q21.1	2008-02-05		2006-02-16	ENSG00000163040	ENSG00000163040			25197	protein-coding gene	gene with protein product						12477932	Standard	NM_138770		Approved	FLJ40345	uc002ttb.4	Q96AQ1	OTTHUMG00000131667	ENST00000295171.6:c.862C>A	2.37:g.132290340C>A	ENSP00000295171:p.Leu288Met	Somatic		Capture	Illumina HiSeq	Phase_I	132006810	NM_138770	Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	37	CCDS2167.1	.	.	.	.	.	.	.	.	.	.	.	11.57	1.679010	0.29783	.	.	ENSG00000163040	ENST00000295171;ENST00000409856	T;T	0.37584	1.19;1.19	2.66	2.66	0.31614	.	0.000000	0.29466	U	0.012079	T	0.54191	0.1843	M	0.71581	2.175	0.80722	D	1	D;D	0.76494	0.999;0.991	D;D	0.87578	0.998;0.986	T	0.55477	-0.8135	10	0.59425	D	0.04	.	9.0698	0.36486	0.0:1.0:0.0:0.0	.	222;288	Q96AQ1-2;Q96AQ1	.;CC74A_HUMAN	M	288;222	ENSP00000295171:L288M;ENSP00000387009:L222M	ENSP00000295171:L288M	L	+	1	2	CCDC74A	132006810	1.000000	0.71417	1.000000	0.80357	0.358000	0.29455	1.016000	0.29976	1.192000	0.43071	0.194000	0.17425	CTG		0.667	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770	
GPR39	2863	broad.mit.edu	37	2	133175104	133175104	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:133175104C>T	ENST00000329321.3	+	1	958	c.489C>T	c.(487-489)tcC>tcT	p.S163S		NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	163					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)|metal ion binding (GO:0046872)	p.S163S(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGGTCACCTCCGCCCTGGTGG	0.617																																					p.S163S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C489T	2						.						87.0	71.0	77.0					2																	133175104		2203	4300	6503	132891574	SO:0001819	synonymous_variant	2863	exon1			AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"""GPCR / Class A : Orphans"""	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.489C>T	2.37:g.133175104C>T		Somatic		Capture	Illumina HiSeq	Phase_I	132891574	NM_001508	B2RC12|B6V9G4|Q08AS2|Q53R01	Silent	SNP	ENST00000329321.3	37	CCDS2170.1																																																																																				0.617	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1		
GPR39	2863	broad.mit.edu	37	2	133175407	133175407	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:133175407G>A	ENST00000329321.3	+	1	1261	c.792G>A	c.(790-792)ccG>ccA	p.P264P		NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	264					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)|metal ion binding (GO:0046872)	p.P264P(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CGCGGCCTCCGCAGCTGAGGA	0.612																																					p.P264P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G792A	2						.						50.0	53.0	52.0					2																	133175407		2203	4300	6503	132891877	SO:0001819	synonymous_variant	2863	exon1			AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"""GPCR / Class A : Orphans"""	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.792G>A	2.37:g.133175407G>A		Somatic		Capture	Illumina HiSeq	Phase_I	132891877	NM_001508	B2RC12|B6V9G4|Q08AS2|Q53R01	Silent	SNP	ENST00000329321.3	37	CCDS2170.1																																																																																				0.612	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1		
TMEM163	81615	broad.mit.edu	37	2	135215630	135215630	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:135215630C>T	ENST00000281924.6	-	7	846	c.782G>A	c.(781-783)gGc>gAc	p.G261D		NM_030923.4	NP_112185.1	Q8TC26	TM163_HUMAN	transmembrane protein 163	261						cell junction (GO:0030054)|early endosome membrane (GO:0031901)|integral component of synaptic vesicle membrane (GO:0030285)	zinc ion binding (GO:0008270)	p.G261D(1)		endometrium(1)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(221;0.154)		TATGGTGAGGCCGATCAGAAC	0.557																																					p.G261D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G782A	2						.						167.0	145.0	152.0					2																	135215630		2203	4300	6503	134932100	SO:0001583	missense	81615	exon7				CCDS2172.1	2q21.3	2008-02-05			ENSG00000152128	ENSG00000152128			25380	protein-coding gene	gene with protein product						17623043	Standard	NM_030923		Approved	DKFZP566N034, SV31	uc002ttx.3	Q8TC26	OTTHUMG00000131713	ENST00000281924.6:c.782G>A	2.37:g.135215630C>T	ENSP00000281924:p.Gly261Asp	Somatic		Capture	Illumina HiSeq	Phase_I	134932100	NM_030923	Q53QM3|Q53SV7|Q69YH3|Q9UFG3	Missense_Mutation	SNP	ENST00000281924.6	37	CCDS2172.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.956053	0.92726	.	.	ENSG00000152128	ENST00000281924	T	0.66815	-0.23	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.79690	0.4489	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82297	-0.0527	10	0.87932	D	0	.	17.4448	0.87575	0.0:1.0:0.0:0.0	.	261	Q8TC26	TM163_HUMAN	D	261	ENSP00000281924:G261D	ENSP00000281924:G261D	G	-	2	0	TMEM163	134932100	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.553000	0.82203	2.210000	0.71456	0.484000	0.47621	GGC		0.557	TMEM163-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254631.2	NM_030923	
SPOPL	339745	broad.mit.edu	37	2	139308072	139308072	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:139308072C>T	ENST00000280098.4	+	3	477	c.98C>T	c.(97-99)tCc>tTc	p.S33F		NM_001001664.2	NP_001001664.1	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like	33	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				negative regulation of protein ubiquitination (GO:0031397)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)		p.S33F(1)		breast(2)|cervix(2)|endometrium(2)|large_intestine(2)|lung(11)|skin(2)	21				BRCA - Breast invasive adenocarcinoma(221;0.0296)		GTAAAATTTTCCTATATGTGG	0.328																																					p.S33F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C98T	2						.						69.0	75.0	73.0					2																	139308072		2203	4293	6496	139024542	SO:0001583	missense	339745	exon3				CCDS33298.1	2q22.1	2013-01-09			ENSG00000144228	ENSG00000144228		"""BTB/POZ domain containing"""	27934	protein-coding gene	gene with protein product	"""HIB homolog 2"", ""roadkill homolog 2"""						Standard	NM_001001664		Approved	BTBD33	uc002tvh.3	Q6IQ16	OTTHUMG00000153635	ENST00000280098.4:c.98C>T	2.37:g.139308072C>T	ENSP00000280098:p.Ser33Phe	Somatic		Capture	Illumina HiSeq	Phase_I	139024542	NM_001001664		Missense_Mutation	SNP	ENST00000280098.4	37	CCDS33298.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.273797	0.80580	.	.	ENSG00000144228	ENST00000280098	T	0.44083	0.93	4.72	4.72	0.59763	TRAF-type (1);TRAF-like (1);MATH (1);	0.000000	0.85682	D	0.000000	T	0.59473	0.2196	M	0.71581	2.175	0.80722	D	1	D	0.76494	0.999	P	0.62649	0.905	T	0.56890	-0.7904	10	0.15066	T	0.55	-9.5309	17.7077	0.88313	0.0:1.0:0.0:0.0	.	33	Q6IQ16	SPOPL_HUMAN	F	33	ENSP00000280098:S33F	ENSP00000280098:S33F	S	+	2	0	SPOPL	139024542	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.818000	0.86416	2.142000	0.66516	0.557000	0.71058	TCC		0.328	SPOPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331897.1		
LRP1B	53353	broad.mit.edu	37	2	141245223	141245223	+	Missense_Mutation	SNP	C	C	T	rs142254534	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:141245223C>T	ENST00000389484.3	-	58	10177	c.9206G>A	c.(9205-9207)cGc>cAc	p.R3069H		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3069					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.R3069H(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TCTATTTATGCGACTGCCATT	0.308										TSP Lung(27;0.18)			C|||	2	0.000399361	0.0	0.0	5008	,	,		14996	0.002		0.0	False		,,,				2504	0.0				p.R3069H	Colon(99;50 2074 2507 20106)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G9206A	2						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	95.0	95.0	95.0		9206	4.9	1.0	2	dbSNP_134	95	0,8588		0,0,4294	yes	missense	LRP1B	NM_018557.2	29	0,1,6496	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	3069/4600	141245223	1,12993	2203	4294	6497	140961693	SO:0001583	missense	53353	exon58			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.9206G>A	2.37:g.141245223C>T	ENSP00000374135:p.Arg3069His	Somatic		Capture	Illumina HiSeq	Phase_I	140961693	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	23.8	4.464677	0.84425	2.27E-4	0.0	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.96104	-3.91	5.77	4.89	0.63831	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.068650	0.56097	U	0.000033	D	0.92609	0.7652	L	0.45581	1.43	0.35826	D	0.824936	B	0.26081	0.141	B	0.15484	0.013	D	0.92572	0.6067	10	0.45353	T	0.12	.	14.7642	0.69626	0.0:0.9308:0.0:0.0692	.	3069	Q9NZR2	LRP1B_HUMAN	H	3069;3007	ENSP00000374135:R3069H	ENSP00000374135:R3069H	R	-	2	0	LRP1B	140961693	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.699000	0.54778	1.445000	0.47624	0.650000	0.86243	CGC		0.308	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
LRP1B	53353	broad.mit.edu	37	2	142888235	142888235	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:142888235T>C	ENST00000389484.3	-	1	1035	c.64A>G	c.(64-66)Acc>Gcc	p.T22A	AC078882.1_ENST00000436132.1_RNA	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	22					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.T22A(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GCTCCCACGGTCAGCACCCTG	0.592										TSP Lung(27;0.18)																											p.T22A	Colon(99;50 2074 2507 20106)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A64G	2						.						67.0	56.0	60.0					2																	142888235		2203	4300	6503	142604705	SO:0001583	missense	53353	exon1			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.64A>G	2.37:g.142888235T>C	ENSP00000374135:p.Thr22Ala	Somatic		Capture	Illumina HiSeq	Phase_I	142604705	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.147649	0.37923	.	.	ENSG00000168702	ENST00000389484;ENST00000434794	D;D	0.92647	-2.57;-3.08	5.06	-0.216	0.13153	.	0.454767	0.17513	U	0.171535	T	0.75803	0.3899	N	0.12182	0.205	0.21064	N	0.999791	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.61113	-0.7128	10	0.06891	T	0.86	.	1.2977	0.02073	0.155:0.3403:0.16:0.3447	.	60;22	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	A	22	ENSP00000374135:T22A;ENSP00000413239:T22A	ENSP00000374135:T22A	T	-	1	0	LRP1B	142604705	0.998000	0.40836	0.959000	0.39883	0.952000	0.60782	0.816000	0.27267	-0.103000	0.12175	-0.290000	0.09829	ACC		0.592	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
ARHGAP15	55843	broad.mit.edu	37	2	144193224	144193224	+	Missense_Mutation	SNP	A	A	G	rs375193013		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:144193224A>G	ENST00000295095.6	+	7	696	c.529A>G	c.(529-531)Ata>Gta	p.I177V	AC096558.1_ENST00000549032.1_RNA|AC096558.1_ENST00000442794.1_RNA|RP11-570L15.2_ENST00000546678.1_RNA|AC096558.1_ENST00000550516.1_RNA	NM_018460.3	NP_060930.3	Q53QZ3	RHG15_HUMAN	Rho GTPase activating protein 15	177	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)	p.I177V(1)		endometrium(1)|kidney(5)|large_intestine(8)|liver(2)|lung(15)|ovary(1)|skin(2)	34				BRCA - Breast invasive adenocarcinoma(221;0.151)		TGACTTCATCATATTGGATTG	0.299																																					p.I177V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A529G	2						.	A	VAL/ILE	0,4406		0,0,2203	125.0	115.0	119.0		529	5.5	1.0	2		119	1,8593	1.2+/-3.3	0,1,4296	no	missense	ARHGAP15	NM_018460.3	29	0,1,6499	GG,GA,AA		0.0116,0.0,0.0077	benign	177/476	144193224	1,12999	2203	4297	6500	143909694	SO:0001583	missense	55843	exon7			AY219338	CCDS2184.1	2q22.2-q22.3	2013-01-10			ENSG00000075884	ENSG00000075884		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	21030	protein-coding gene	gene with protein product		610578				12650940, 11042152	Standard	NM_018460		Approved	BM046	uc002tvm.4	Q53QZ3	OTTHUMG00000131845	ENST00000295095.6:c.529A>G	2.37:g.144193224A>G	ENSP00000295095:p.Ile177Val	Somatic		Capture	Illumina HiSeq	Phase_I	143909694	NM_018460	Q53R36|Q53RD7|Q53RT6|Q53SX9|Q584N9|Q6PJE6|Q86WP1|Q8IXX1|Q9NRL8|Q9NZ77|Q9NZ91	Missense_Mutation	SNP	ENST00000295095.6	37	CCDS2184.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.260293	0.39995	0.0	1.16E-4	ENSG00000075884	ENST00000295095	T	0.78924	-1.22	5.52	5.52	0.82312	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.104321	0.64402	D	0.000003	T	0.73071	0.3540	L	0.58101	1.795	0.41751	D	0.989662	B;P	0.37207	0.241;0.587	B;B	0.37508	0.252;0.241	T	0.73864	-0.3848	10	0.41790	T	0.15	.	10.3143	0.43727	0.9262:0.0:0.0738:0.0	.	177;177	B4E0R3;Q53QZ3	.;RHG15_HUMAN	V	177	ENSP00000295095:I177V	ENSP00000295095:I177V	I	+	1	0	ARHGAP15	143909694	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.111000	0.57838	2.215000	0.71742	0.528000	0.53228	ATA		0.299	ARHGAP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254793.2	NM_018460	
MBD5	55777	broad.mit.edu	37	2	149226968	149226968	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:149226968A>G	ENST00000407073.1	+	9	2453	c.1456A>G	c.(1456-1458)Att>Gtt	p.I486V	MBD5_ENST00000404807.1_Missense_Mutation_p.I486V	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	486					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.I486V(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		TTCTAGTGGTATTAAGGTTCC	0.498																																					p.I486V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1456G	2						.						70.0	71.0	70.0					2																	149226968		2203	4300	6503	148943438	SO:0001583	missense	55777	exon9			AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.1456A>G	2.37:g.149226968A>G	ENSP00000386049:p.Ile486Val	Somatic		Capture	Illumina HiSeq	Phase_I	148943438	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	37	CCDS33302.1	.	.	.	.	.	.	.	.	.	.	A	10.20	1.283805	0.23392	.	.	ENSG00000204406	ENST00000407073;ENST00000404807	T;T	0.45276	0.9;0.91	4.39	4.39	0.52855	.	0.343180	0.24698	N	0.036326	T	0.27278	0.0669	N	0.14661	0.345	0.35262	D	0.7797	B	0.18166	0.026	B	0.17098	0.017	T	0.26677	-1.0096	10	0.30854	T	0.27	-0.3604	14.0813	0.64925	1.0:0.0:0.0:0.0	.	486	Q9P267	MBD5_HUMAN	V	486	ENSP00000386049:I486V;ENSP00000384672:I486V	ENSP00000384672:I486V	I	+	1	0	MBD5	148943438	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.599000	0.67592	1.980000	0.57719	0.533000	0.62120	ATT		0.498	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2		
NEB	4703	broad.mit.edu	37	2	152411488	152411488	+	Missense_Mutation	SNP	G	G	A	rs369054525		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:152411488G>A	ENST00000172853.10	-	97	14429	c.14282C>T	c.(14281-14283)cCg>cTg	p.P4761L	NEB_ENST00000604864.1_Missense_Mutation_p.P6462L|NEB_ENST00000397345.3_Missense_Mutation_p.P6462L|NEB_ENST00000427231.2_Missense_Mutation_p.P6462L|NEB_ENST00000603639.1_Missense_Mutation_p.P6462L|NEB_ENST00000409198.1_Missense_Mutation_p.P4761L			P20929	NEBU_HUMAN	nebulin	4761					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.P6462L(1)|p.P4761L(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGCTGTGTTCGGATCATCGTC	0.418													G|||	1	0.000199681	0.0008	0.0	5008	,	,		22107	0.0		0.0	False		,,,				2504	0.0				p.P6462L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C19385T	2						.	G	LEU/PRO,LEU/PRO,LEU/PRO	0,4136		0,0,2068	182.0	183.0	182.0		19385,19385,14282	5.3	1.0	2		182	1,8445		0,1,4222	no	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	98,98,98	0,1,6290	AA,AG,GG		0.0118,0.0,0.0079	probably-damaging,probably-damaging,probably-damaging	6462/8526,6462/8526,4761/6670	152411488	1,12581	2068	4223	6291	152119734	SO:0001583	missense	4703	exon125			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.14282C>T	2.37:g.152411488G>A	ENSP00000172853:p.Pro4761Leu	Somatic		Capture	Illumina HiSeq	Phase_I	152119734	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	G	28.6	4.937846	0.92526	0.0	1.18E-4	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T;T	0.22539	2.19;1.95;1.95;2.26;2.19	6.17	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.47801	0.1465	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.91635	0.999;0.801	T	0.46898	-0.9158	10	0.22109	T	0.4	.	15.8705	0.79117	0.0646:0.0:0.9354:0.0	.	4761;1192	P20929;Q14215	NEBU_HUMAN;.	L	4761;6462;6462;810;1192;4761	ENSP00000386259:P4761L;ENSP00000380505:P6462L;ENSP00000416578:P6462L;ENSP00000410961:P1192L;ENSP00000172853:P4761L	ENSP00000172853:P4761L	P	-	2	0	NEB	152119734	1.000000	0.71417	0.972000	0.41901	0.934000	0.57294	6.849000	0.75414	1.631000	0.50456	0.655000	0.94253	CCG		0.418	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
CACNB4	785	broad.mit.edu	37	2	152727063	152727063	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:152727063C>T	ENST00000539935.1	-	8	748	c.681G>A	c.(679-681)ccG>ccA	p.P227P	CACNB4_ENST00000360283.6_Silent_p.P194P|CACNB4_ENST00000201943.5_Silent_p.P227P|CACNB4_ENST00000534999.1_Silent_p.P193P|CACNB4_ENST00000427385.1_Silent_p.P209P|CACNB4_ENST00000397327.2_Silent_p.P180P	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	227					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.P227P(3)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CTTTCAGTGACGGCCCCACTA	0.498																																					p.P227P												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.G681A	2						.						87.0	87.0	87.0					2																	152727063		2082	4208	6290	152435309	SO:0001819	synonymous_variant	785	exon8			AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"""Calcium channel subunits"""	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.681G>A	2.37:g.152727063C>T		Somatic		Capture	Illumina HiSeq	Phase_I	152435309	NM_001145798	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Silent	SNP	ENST00000539935.1	37	CCDS46426.1																																																																																				0.498	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3	
ERMN	57471	broad.mit.edu	37	2	158182162	158182162	+	5'UTR	SNP	G	G	A	rs374919878		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:158182162G>A	ENST00000410096.1	-	0	284				ERMN_ENST00000535935.1_5'Flank|ERMN_ENST00000409216.1_5'UTR|ERMN_ENST00000420719.2_5'UTR|ERMN_ENST00000397283.2_Missense_Mutation_p.P11L|ERMN_ENST00000409925.1_5'UTR	NM_020711.1	NP_065762.1	Q8TAM6	ERMIN_HUMAN	ermin, ERM-like protein						actin filament organization (GO:0007015)|morphogenesis of a branching structure (GO:0001763)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|internode region of axon (GO:0033269)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|paranode region of axon (GO:0033270)		p.P11L(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12						CATGATGTGCGGTTGAATCCG	0.443																																					p.P11L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C32T	2						.	G	,LEU/PRO	0,3802		0,0,1901	156.0	143.0	147.0		,32	3.0	0.0	2		147	1,8229		0,1,4114	no	utr-5,missense	ERMN	NM_020711.1,NM_001009959.1	,98	0,1,6015	AA,AG,GG		0.0122,0.0,0.0083	,benign	,11/298	158182162	1,12031	1901	4115	6016	157890408	SO:0001623	5_prime_UTR_variant	57471	exon2			AB033015	CCDS42764.1, CCDS46431.1	2q24	2008-02-05	2008-01-15	2008-01-15	ENSG00000136541	ENSG00000136541			29208	protein-coding gene	gene with protein product	"""juxtanodin"", ""ermin"""	610072	"""KIAA1189"""	KIAA1189		16051705, 16421295	Standard	NM_020711		Approved	JN, ERMIN	uc002tzi.3	Q8TAM6	OTTHUMG00000153843	ENST00000410096.1:c.-8C>T	2.37:g.158182162G>A		Somatic		Capture	Illumina HiSeq	Phase_I	157890408	NM_001009959	B4DKA6|Q9ULN1	Missense_Mutation	SNP	ENST00000410096.1	37	CCDS46431.1	.	.	.	.	.	.	.	.	.	.	G	0.375	-0.931686	0.02359	0.0	1.22E-4	ENSG00000136541	ENST00000397283	.	.	.	5.4	2.96	0.34315	.	0.527798	0.14171	N	0.336747	T	0.30759	0.0775	.	.	.	0.18873	N	0.999989	B	0.02656	0.0	B	0.01281	0.0	T	0.28235	-1.0050	8	0.87932	D	0	.	5.7077	0.17917	0.7417:0.1696:0.0887:0.0	.	11	Q8TAM6-2	.	L	11	.	ENSP00000380453:P11L	P	-	2	0	ERMN	157890408	0.000000	0.05858	0.004000	0.12327	0.068000	0.16541	-0.241000	0.08940	0.337000	0.23665	-0.350000	0.07774	CCG		0.443	ERMN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332659.1	NM_001009959	
SCN9A	6335	broad.mit.edu	37	2	167056175	167056175	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:167056175G>A	ENST00000409435.1	-	26	4973	c.4974C>T	c.(4972-4974)taC>taT	p.Y1658Y	SCN9A_ENST00000409672.1_Silent_p.Y1647Y|SCN9A_ENST00000375387.4_Silent_p.Y1659Y|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.Y1659Y			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1658					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.Y1647Y(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CAAAGATGGCGTAGATGAACA	0.443																																					p.Y1647Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4941T	2						.						167.0	165.0	166.0					2																	167056175		2203	4300	6503	166764421	SO:0001819	synonymous_variant	6335	exon27			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.4974C>T	2.37:g.167056175G>A		Somatic		Capture	Illumina HiSeq	Phase_I	166764421	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																				0.443	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
XIRP2	129446	broad.mit.edu	37	2	168100213	168100213	+	Missense_Mutation	SNP	C	C	T	rs548985321		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:168100213C>T	ENST00000409195.1	+	9	2400	c.2311C>T	c.(2311-2313)Cgg>Tgg	p.R771W	XIRP2_ENST00000295237.9_Missense_Mutation_p.R771W|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.R549W|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	596					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.R771W(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAGAACAGCACGGTGGATGTT	0.388													C|||	1	0.000199681	0.0	0.0	5008	,	,		19204	0.0		0.0	False		,,,				2504	0.001				p.R549W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1645T	2						.						72.0	67.0	69.0					2																	168100213		1863	4091	5954	167808459	SO:0001583	missense	129446	exon7			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.2311C>T	2.37:g.168100213C>T	ENSP00000386840:p.Arg771Trp	Somatic		Capture	Illumina HiSeq	Phase_I	167808459	NM_001199144	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.296005	0.60086	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.39229	1.09;1.09;1.09	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.63355	0.2504	M	0.77486	2.375	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.66492	-0.5910	10	0.87932	D	0	-10.5946	10.2698	0.43477	0.135:0.7957:0.0:0.0693	.	596;596;549	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	W	771;771;549	ENSP00000386840:R771W;ENSP00000295237:R771W;ENSP00000387255:R549W	ENSP00000295237:R771W	R	+	1	2	XIRP2	167808459	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	1.731000	0.38135	2.810000	0.96702	0.650000	0.86243	CGG		0.388	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
ABCB11	8647	broad.mit.edu	37	2	169789017	169789017	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:169789017G>A	ENST00000263817.6	-	24	3207	c.3083C>T	c.(3082-3084)gCa>gTa	p.A1028V		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	1028	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)	p.A1028V(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	AAGAGCTGTTGCACTCAGTAC	0.498																																					p.A1028V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3083T	2						.						83.0	80.0	81.0					2																	169789017		2012	4181	6193	169497263	SO:0001583	missense	8647	exon24			AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"""ATP binding cassette transporters / subfamily B"""	42	protein-coding gene	gene with protein product	"""ABC member 16, MDR/TAP subfamily"""	603201	"""progressive familial intrahepatic cholestasis 2"", ""bile salt export pump"""	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.3083C>T	2.37:g.169789017G>A	ENSP00000263817:p.Ala1028Val	Somatic		Capture	Illumina HiSeq	Phase_I	169497263	NM_003742	Q53TL2|Q9UNB2	Missense_Mutation	SNP	ENST00000263817.6	37	CCDS46444.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.180660	0.78677	.	.	ENSG00000073734	ENST00000263817	D	0.90069	-2.61	5.42	3.61	0.41365	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.146153	0.64402	D	0.000009	D	0.94305	0.8170	M	0.85197	2.74	0.39324	D	0.96529	P;P	0.48911	0.917;0.639	D;P	0.63192	0.912;0.717	D	0.95042	0.8179	10	0.87932	D	0	.	15.4244	0.75041	0.0:0.7243:0.2757:0.0	.	470;1028	B4DZQ8;O95342	.;ABCBB_HUMAN	V	1028	ENSP00000263817:A1028V	ENSP00000263817:A1028V	A	-	2	0	ABCB11	169497263	1.000000	0.71417	0.490000	0.27465	0.842000	0.47809	4.511000	0.60462	0.634000	0.30469	0.655000	0.94253	GCA		0.498	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
LRP2	4036	broad.mit.edu	37	2	170131728	170131728	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:170131728C>T	ENST00000263816.3	-	14	2078	c.1793G>A	c.(1792-1794)gGc>gAc	p.G598D	LRP2_ENST00000443831.1_Missense_Mutation_p.G529D	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	598					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.G598D(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	AATGAGGGAGCCTCCATGAAC	0.358																																					p.G598D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1793A	2						.						112.0	95.0	101.0					2																	170131728		2203	4300	6503	169839974	SO:0001583	missense	4036	exon14				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.1793G>A	2.37:g.170131728C>T	ENSP00000263816:p.Gly598Asp	Somatic		Capture	Illumina HiSeq	Phase_I	169839974	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.530013	0.85706	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.91792	-2.91;-2.77	5.97	5.97	0.96955	Six-bladed beta-propeller, TolB-like (1);	0.094954	0.64402	D	0.000001	D	0.94391	0.8196	L	0.45051	1.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.91610	0.5302	10	0.22109	T	0.4	.	20.4239	0.99064	0.0:1.0:0.0:0.0	.	529;598	E9PC35;P98164	.;LRP2_HUMAN	D	598;529	ENSP00000263816:G598D;ENSP00000409813:G529D	ENSP00000263816:G598D	G	-	2	0	LRP2	169839974	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	7.440000	0.80464	2.828000	0.97474	0.655000	0.94253	GGC		0.358	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
PPIG	9360	broad.mit.edu	37	2	170493052	170493052	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:170493052C>T	ENST00000260970.3	+	14	1504	c.1284C>T	c.(1282-1284)gaC>gaT	p.D428D	PPIG_ENST00000409714.3_Silent_p.D413D|PPIG_ENST00000448752.2_Silent_p.D428D|PPIG_ENST00000482772.1_3'UTR	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	428					protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)	p.D428D(1)		NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	AAGTTAAAGACCATAAATCTA	0.328																																					p.D428D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1284T	2						.						49.0	51.0	50.0					2																	170493052		2189	4288	6477	170201298	SO:0001819	synonymous_variant	9360	exon14			X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"""SR-related CTD-associated factor 10"""	606093	"""peptidyl-prolyl isomerase G (cyclophilin G)"""			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.1284C>T	2.37:g.170493052C>T		Somatic		Capture	Illumina HiSeq	Phase_I	170201298	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Silent	SNP	ENST00000260970.3	37	CCDS2235.1																																																																																				0.328	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2		
DCAF17	80067	broad.mit.edu	37	2	172300067	172300067	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:172300067C>T	ENST00000375255.3	+	3	592	c.265C>T	c.(265-267)Cca>Tca	p.P89S	DCAF17_ENST00000539783.1_Missense_Mutation_p.P89S|DCAF17_ENST00000468592.1_3'UTR	NM_025000.3	NP_079276.2	Q5H9S7	DCA17_HUMAN	DDB1 and CUL4 associated factor 17	89					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.P89S(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|prostate(1)	17						TTATGAAATGCCAAAATGTTC	0.318																																					p.P89S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C265T	2						.						115.0	106.0	109.0					2																	172300067		1799	4067	5866	172008313	SO:0001583	missense	80067	exon3			AK023158	CCDS2243.2, CCDS54419.1	2q31.1	2014-01-28	2009-07-17	2009-07-17	ENSG00000115827	ENSG00000115827		"""DDB1 and CUL4 associated factors"""	25784	protein-coding gene	gene with protein product	"""Woodhouse-Sakati syndrome"""	612515	"""chromosome 2 open reading frame 37"""	C2orf37			Standard	NM_001164821		Approved	FLJ13096	uc002ugx.3	Q5H9S7	OTTHUMG00000132259	ENST00000375255.3:c.265C>T	2.37:g.172300067C>T	ENSP00000364404:p.Pro89Ser	Somatic		Capture	Illumina HiSeq	Phase_I	172008313	NM_025000	B2RTW5|Q53TN3|Q9H908	Missense_Mutation	SNP	ENST00000375255.3	37	CCDS2243.2	.	.	.	.	.	.	.	.	.	.	C	17.03	3.283388	0.59867	.	.	ENSG00000115827	ENST00000375255;ENST00000539783	T;T	0.52057	0.68;0.71	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.67692	0.2920	M	0.62723	1.935	0.49389	D	0.99978	B;D	0.89917	0.076;1.0	B;D	0.87578	0.021;0.998	T	0.66881	-0.5811	10	0.48119	T	0.1	-8.8825	18.9359	0.92584	0.0:1.0:0.0:0.0	.	89;89	F5H7W1;Q5H9S7	.;DCA17_HUMAN	S	89	ENSP00000364404:P89S;ENSP00000442238:P89S	ENSP00000364404:P89S	P	+	1	0	DCAF17	172008313	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.971000	0.56831	2.565000	0.86533	0.579000	0.79373	CCA		0.318	DCAF17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255342.2	NM_025000	
SLC25A12	8604	broad.mit.edu	37	2	172691357	172691357	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:172691357A>C	ENST00000422440.2	-	7	668	c.631T>G	c.(631-633)Tca>Gca	p.S211A	SLC25A12_ENST00000392592.4_Missense_Mutation_p.S104A	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	211					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)	p.S211A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	ACCTGGTGTGAGATACTTCCT	0.373																																					p.S211A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T631G	2						.						86.0	78.0	81.0					2																	172691357		2203	4300	6503	172399603	SO:0001583	missense	8604	exon7			Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"""Solute carriers"", ""EF-hand domain containing"""	10982	protein-coding gene	gene with protein product		603667	"""solute carrier family 25 (mitochondrial carrier, Aralar), member 12"""			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.631T>G	2.37:g.172691357A>C	ENSP00000388658:p.Ser211Ala	Somatic		Capture	Illumina HiSeq	Phase_I	172399603	NM_003705	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	37	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	A	11.42	1.633013	0.29068	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	T;T	0.79554	-1.28;-1.2	5.51	4.32	0.51571	EF-hand-like domain (1);	0.256297	0.39985	N	0.001205	T	0.75613	0.3873	L	0.53671	1.685	0.42701	D	0.993616	B;B	0.11235	0.004;0.003	B;B	0.12837	0.008;0.003	T	0.72401	-0.4305	10	0.34782	T	0.22	-9.4724	13.119	0.59314	0.8228:0.1772:0.0:0.0	.	104;211	B3KR64;O75746	.;CMC1_HUMAN	A	211;104	ENSP00000388658:S211A;ENSP00000376371:S104A	ENSP00000376371:S104A	S	-	1	0	SLC25A12	172399603	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.007000	0.40883	2.212000	0.71576	0.460000	0.39030	TCA		0.373	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705	
HAT1	8520	broad.mit.edu	37	2	172848178	172848178	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:172848178T>C	ENST00000264108.4	+	11	1208	c.1172T>C	c.(1171-1173)aTa>aCa	p.I391T	HAT1_ENST00000392584.1_Missense_Mutation_p.I306T|SLC25A12_ENST00000472748.1_Intron	NM_003642.3	NP_003633.1	O14929	HAT1_HUMAN	histone acetyltransferase 1	391					chromatin organization (GO:0006325)|chromatin silencing at telomere (GO:0006348)|DNA packaging (GO:0006323)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4 acetylation (GO:0043967)|internal protein amino acid acetylation (GO:0006475)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	H4 histone acetyltransferase activity (GO:0010485)|histone acetyltransferase activity (GO:0004402)	p.I391T(1)		breast(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|prostate(1)	19			OV - Ovarian serous cystadenocarcinoma(117;0.216)			CAAATAGAAATAAGCATGCAA	0.378																																					p.I391T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1172C	2						.						110.0	109.0	110.0					2																	172848178		2203	4300	6503	172556424	SO:0001583	missense	8520	exon11			AF030424	CCDS2245.1	2q31.2-q33.1	2011-07-01			ENSG00000128708	ENSG00000128708	2.3.1.48	"""Chromatin-modifying enzymes / K-acetyltransferases"""	4821	protein-coding gene	gene with protein product		603053				9427644	Standard	NM_003642		Approved	KAT1	uc002uhi.3	O14929	OTTHUMG00000132282	ENST00000264108.4:c.1172T>C	2.37:g.172848178T>C	ENSP00000264108:p.Ile391Thr	Somatic		Capture	Illumina HiSeq	Phase_I	172556424	NM_003642	Q49A44|Q53QF0|Q53SU4|Q6P594|Q8WWB9	Missense_Mutation	SNP	ENST00000264108.4	37	CCDS2245.1	.	.	.	.	.	.	.	.	.	.	T	10.55	1.380570	0.24944	.	.	ENSG00000128708	ENST00000392584;ENST00000264108	.	.	.	5.94	5.94	0.96194	.	0.171561	0.64402	D	0.000006	T	0.44286	0.1286	N	0.14661	0.345	0.41551	D	0.988577	B	0.02656	0.0	B	0.04013	0.001	T	0.37820	-0.9689	9	0.87932	D	0	-21.2306	16.3945	0.83586	0.0:0.0:0.0:1.0	.	391	O14929	HAT1_HUMAN	T	306;391	.	ENSP00000264108:I391T	I	+	2	0	HAT1	172556424	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.445000	0.66594	2.265000	0.75225	0.482000	0.46254	ATA		0.378	HAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255377.1	NM_003642	
WIPF1	7456	broad.mit.edu	37	2	175431882	175431882	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:175431882G>C	ENST00000392547.2	-	7	1471	c.1372C>G	c.(1372-1374)Ccg>Gcg	p.P458A	WIPF1_ENST00000467149.1_5'UTR|AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000409891.1_Missense_Mutation_p.P458A|AC018890.6_ENST00000412835.1_RNA|WIPF1_ENST00000392546.2_Missense_Mutation_p.P458A|WIPF1_ENST00000359761.3_Missense_Mutation_p.P458A|WIPF1_ENST00000272746.5_Missense_Mutation_p.P458A	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	458					actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)	p.P458A(1)		NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						TCGGAAATCGGATGGAAGTAG	0.453																																					p.P458A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1372G	2						.						125.0	124.0	125.0					2																	175431882		2203	4300	6503	175140128	SO:0001583	missense	7456	exon7			AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935			12736	protein-coding gene	gene with protein product		602357	"""Wiskott-Aldrich syndrome protein interacting protein"""	WASPIP		9405671	Standard	NM_001077269		Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.1372C>G	2.37:g.175431882G>C	ENSP00000376330:p.Pro458Ala	Somatic		Capture	Illumina HiSeq	Phase_I	175140128	NM_001077269	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	Missense_Mutation	SNP	ENST00000392547.2	37	CCDS2260.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.517063	0.85495	.	.	ENSG00000115935	ENST00000392547;ENST00000392548;ENST00000272746;ENST00000359761;ENST00000392546;ENST00000409891	T;T;T;T;T	0.60424	0.84;1.03;0.84;0.84;0.19	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.79263	0.4416	M	0.80183	2.485	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.85130	0.997;0.997;0.994	T	0.79458	-0.1795	10	0.59425	D	0.04	.	20.3507	0.98813	0.0:0.0:1.0:0.0	.	458;458;458	O43516-3;O43516-2;O43516	.;.;WIPF1_HUMAN	A	458;314;458;458;458;458	ENSP00000376330:P458A;ENSP00000272746:P458A;ENSP00000352802:P458A;ENSP00000376329:P458A;ENSP00000386431:P458A	ENSP00000272746:P458A	P	-	1	0	WIPF1	175140128	1.000000	0.71417	0.995000	0.50966	0.887000	0.51463	7.875000	0.87205	2.808000	0.96608	0.655000	0.94253	CCG		0.453	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255453.1	NM_003387	
MTX2	10651	broad.mit.edu	37	2	177195386	177195386	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:177195386G>A	ENST00000249442.6	+	9	829	c.618G>A	c.(616-618)aaG>aaA	p.K206K	MTX2_ENST00000392529.2_Silent_p.K196K|MTX2_ENST00000443241.1_Silent_p.K150K	NM_006554.4	NP_006545.1	O75431	MTX2_HUMAN	metaxin 2	206					cellular protein metabolic process (GO:0044267)|mitochondrial transport (GO:0006839)|protein targeting to mitochondrion (GO:0006626)	mitochondrial outer membrane (GO:0005741)		p.K206K(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.00365)|Epithelial(96;0.0654)|all cancers(119;0.181)			TCTTCAATAAGCAGTAAGAAA	0.338																																					p.K206K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G618A	2						.						151.0	161.0	158.0					2																	177195386		2202	4299	6501	176903632	SO:0001819	synonymous_variant	10651	exon9			AF053551	CCDS2272.1	2q31.1	2012-02-07			ENSG00000128654	ENSG00000128654			7506	protein-coding gene	gene with protein product		608555				10381257, 17624330	Standard	NM_006554		Approved		uc002ukx.3	O75431	OTTHUMG00000132514	ENST00000249442.6:c.618G>A	2.37:g.177195386G>A		Somatic		Capture	Illumina HiSeq	Phase_I	176903632	NM_006554	A8JZZ4|Q53S50|Q53SQ2|Q5M7Z6|Q8IZ68	Silent	SNP	ENST00000249442.6	37	CCDS2272.1																																																																																				0.338	MTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255695.4	NM_006554	
HNRNPA3	220988	broad.mit.edu	37	2	178082570	178082570	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:178082570G>A	ENST00000392524.2	+	8	1195	c.958G>A	c.(958-960)Ggt>Agt	p.G320S	HNRNPA3_ENST00000411529.2_Missense_Mutation_p.G298S|HNRNPA3_ENST00000435711.1_Missense_Mutation_p.G320S			P51991	ROA3_HUMAN	heterogeneous nuclear ribonucleoprotein A3	320	Gly-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.G320S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|urinary_tract(1)	16						AAATTTTGGCGGTGGTAAGCA	0.408																																					p.G320S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G958A	2						.						90.0	82.0	85.0					2																	178082570		2203	4299	6502	177790816	SO:0001583	missense	220988	exon8			AF517524	CCDS2273.1	2q31.2	2013-02-12		2008-04-18	ENSG00000170144	ENSG00000170144		"""RNA binding motif (RRM) containing"""	24941	protein-coding gene	gene with protein product		605372		HNRPA3		11886857, 15776420	Standard	XM_005246380		Approved		uc002ulc.1	P51991	OTTHUMG00000132529	ENST00000392524.2:c.958G>A	2.37:g.178082570G>A	ENSP00000376309:p.Gly320Ser	Somatic		Capture	Illumina HiSeq	Phase_I	177790816	NM_194247	D3DPF4|Q53RW7|Q6URK5	Missense_Mutation	SNP	ENST00000392524.2	37	CCDS2273.1	.	.	.	.	.	.	.	.	.	.	g	13.37	2.215877	0.39201	.	.	ENSG00000170144	ENST00000392524;ENST00000411529;ENST00000416446;ENST00000420139;ENST00000435711	D;D;D	0.86432	-2.12;-2.12;-2.12	4.16	2.33	0.28932	.	0.284949	0.24633	N	0.036868	D	0.82632	0.5079	M	0.69523	2.12	0.28858	N	0.895679	B;B	0.29671	0.254;0.254	B;B	0.14578	0.011;0.011	T	0.71646	-0.4530	10	0.30078	T	0.28	.	10.2704	0.43479	0.1654:0.0:0.8346:0.0	.	298;320	B4DDB6;P51991	.;ROA3_HUMAN	S	320;298;264;265;320	ENSP00000376309:G320S;ENSP00000408487:G298S;ENSP00000416340:G320S	ENSP00000376309:G320S	G	+	1	0	HNRNPA3	177790816	1.000000	0.71417	0.754000	0.31244	0.746000	0.42486	3.938000	0.56583	0.364000	0.24374	0.536000	0.68110	GGT		0.408	HNRNPA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255729.3	NM_194247	
TTC30A	92104	broad.mit.edu	37	2	178483042	178483042	+	Missense_Mutation	SNP	G	G	A	rs148512972	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:178483042G>A	ENST00000355689.5	-	1	652	c.388C>T	c.(388-390)Cca>Tca	p.P130S	AC073834.3_ENST00000357045.4_RNA	NM_152275.3	NP_689488.3	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	130					cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)		p.P130S(1)		autonomic_ganglia(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			CTGGACCCTGGCAGATCGCCC	0.622																																					p.P130S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C388T	2						.	G	SER/PRO	0,4406		0,0,2203	95.0	101.0	99.0		388	4.1	1.0	2	dbSNP_134	99	7,8593	5.7+/-21.5	0,7,4293	yes	missense	TTC30A	NM_152275.3	74	0,7,6496	AA,AG,GG		0.0814,0.0,0.0538	benign	130/666	178483042	7,12999	2203	4300	6503	178191288	SO:0001583	missense	92104	exon1			AK024008	CCDS2276.1	2q31.2	2013-01-11			ENSG00000197557	ENSG00000197557		"""Tetratricopeptide (TTC) repeat domain containing"""	25853	protein-coding gene	gene with protein product						12477932	Standard	NM_152275		Approved	FLJ13946	uc002ulo.3	Q86WT1	OTTHUMG00000132528	ENST00000355689.5:c.388C>T	2.37:g.178483042G>A	ENSP00000347915:p.Pro130Ser	Somatic		Capture	Illumina HiSeq	Phase_I	178191288	NM_152275	A8K8N0|Q8IVP2	Missense_Mutation	SNP	ENST00000355689.5	37	CCDS2276.1	.	.	.	.	.	.	.	.	.	.	G	4.152	0.026636	0.08054	0.0	8.14E-4	ENSG00000197557	ENST00000355689	T	0.78246	-1.16	6.03	4.14	0.48551	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.363169	0.33834	N	0.004517	T	0.50633	0.1627	N	0.04297	-0.235	0.30125	N	0.805373	B	0.06786	0.001	B	0.06405	0.002	T	0.41378	-0.9512	10	0.10636	T	0.68	.	7.0443	0.25037	0.1512:0.2619:0.5869:0.0	.	130	Q86WT1	TT30A_HUMAN	S	130	ENSP00000347915:P130S	ENSP00000347915:P130S	P	-	1	0	TTC30A	178191288	0.998000	0.40836	0.983000	0.44433	0.261000	0.26267	0.937000	0.28951	0.795000	0.33922	-0.378000	0.06908	CCA		0.622	TTC30A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255728.2	NM_152275	
TTN	7273	broad.mit.edu	37	2	179396820	179396820	+	Missense_Mutation	SNP	C	C	T	rs373709706		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:179396820C>T	ENST00000591111.1	-	308	99823	c.99599G>A	c.(99598-99600)cGc>cAc	p.R33200H	TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R34841H|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R25776H|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R25901H|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R32273H|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R25968H			Q8WZ42	TITIN_HUMAN	titin	33200	Poly-Arg.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R32271H(1)|p.R25776H(1)|p.R25901H(1)|p.R25968H(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGACAGGGAGCGCCGTCGTCT	0.453																																					p.A25776T												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G77326A	2						.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4036		0,0,2018	99.0	92.0	94.0		77327,96818,77702,77903	5.6	1.0	2		94	1,8353		0,1,4176	no	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,29,29,29	0,1,6194	TT,TC,CC		0.012,0.0,0.0081	probably-damaging,probably-damaging,probably-damaging,probably-damaging	25776/26927,32273/33424,25901/27052,25968/27119	179396820	1,12389	2018	4177	6195	179105066	SO:0001583	missense	7273	exon186			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.99599G>A	2.37:g.179396820C>T	ENSP00000465570:p.Arg33200His	Somatic		Capture	Illumina HiSeq	Phase_I	179105066	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	21.1	4.092383	0.76756	0.0	1.2E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.80566	-1.39;-1.16;-1.18;-1.19	5.55	5.55	0.83447	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	D	0.84547	0.5496	N	0.24115	0.695	0.58432	D	0.999991	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	D	0.86646	0.1895	9	0.87932	D	0	.	19.5066	0.95118	0.0:1.0:0.0:0.0	.	25776;25901;25968;33200	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	32273;25776;25968;25901;25773	ENSP00000343764:R32273H;ENSP00000434586:R25776H;ENSP00000340554:R25968H;ENSP00000352154:R25901H	ENSP00000340554:R25968H	R	-	2	0	TTN	179105066	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.759000	0.68785	2.611000	0.88343	0.650000	0.86243	CGC		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179397571	179397571	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:179397571G>A	ENST00000591111.1	-	308	99072	c.98848C>T	c.(98848-98850)Cga>Tga	p.R32950*	TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.R34591*|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.R25526*|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.R25651*|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.R32023*|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.R25718*			Q8WZ42	TITIN_HUMAN	titin	32950					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R25718*(1)|p.R25651*(1)|p.R32021*(1)|p.R25526*(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CGCTTGGGTCGTTTCTGTACA	0.443																																					p.N25525N												.	.	4	Substitution - Nonsense(4)	large_intestine(4)	c.C76575T	2						.						106.0	101.0	103.0					2																	179397571		1978	4166	6144	179105817	SO:0001587	stop_gained	7273	exon186			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.98848C>T	2.37:g.179397571G>A	ENSP00000465570:p.Arg32950*	Somatic		Capture	Illumina HiSeq	Phase_I	179105817	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	72	114.218602	0.99999	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.81	3.33	0.38152	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.1335	0.59395	0.0:0.0:0.4507:0.5493	.	.	.	.	X	32023;25526;25718;25651;25523	.	ENSP00000340554:R25718X	R	-	1	2	TTN	179105817	0.970000	0.33590	0.861000	0.33841	0.929000	0.56500	0.966000	0.29331	1.040000	0.40099	-0.521000	0.04368	CGA		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179402473	179402473	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:179402473C>T	ENST00000591111.1	-	305	94762	c.94538G>A	c.(94537-94539)cGc>cAc	p.R31513H	TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R33154H|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R24089H|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R24214H|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R30586H|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R24281H			Q8WZ42	TITIN_HUMAN	titin	31513	Ig-like 140.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R24214H(1)|p.R24089H(1)|p.R24281H(1)|p.R30584H(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGTGTGTGTGCGTCCATCTGA	0.423																																					p.A24089T												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G72265A	2						.						70.0	70.0	70.0					2																	179402473		1946	4148	6094	179110719	SO:0001583	missense	7273	exon183			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.94538G>A	2.37:g.179402473C>T	ENSP00000465570:p.Arg31513His	Somatic		Capture	Illumina HiSeq	Phase_I	179110719	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	21.5	4.154125	0.78114	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	5.89	5.89	0.94794	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.77336	0.4115	L	0.39085	1.19	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.78132	-0.2323	9	0.87932	D	0	.	20.2562	0.98421	0.0:1.0:0.0:0.0	.	24089;24214;24281;31513	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	30586;24089;24281;24214;24086	ENSP00000343764:R30586H;ENSP00000434586:R24089H;ENSP00000340554:R24281H;ENSP00000352154:R24214H	ENSP00000340554:R24281H	R	-	2	0	TTN	179110719	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.797000	0.96272	0.563000	0.77884	CGC		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179426124	179426124	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:179426124T>C	ENST00000591111.1	-	276	80036	c.79812A>G	c.(79810-79812)gaA>gaG	p.E26604E	TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000589042.1_Silent_p.E28245E|TTN_ENST00000460472.2_Silent_p.E19180E|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000359218.5_Silent_p.E19305E|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Silent_p.E25677E|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.E19372E			Q8WZ42	TITIN_HUMAN	titin	26604	Fibronectin type-III 93. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E25675E(1)|p.E19372E(1)|p.E19180E(1)|p.E19305E(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGGGACTGGTTCACAAGATT	0.403																																					p.N19180S												.	.	4	Substitution - coding silent(4)	large_intestine(4)	c.A57539G	2						.						216.0	196.0	203.0					2																	179426124		1906	4136	6042	179134370	SO:0001819	synonymous_variant	7273	exon154			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.79812A>G	2.37:g.179426124T>C		Somatic		Capture	Illumina HiSeq	Phase_I	179134370	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179429213	179429213	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:179429213G>A	ENST00000591111.1	-	276	76947	c.76723C>T	c.(76723-76725)Cgc>Tgc	p.R25575C	TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R27216C|TTN_ENST00000460472.2_Missense_Mutation_p.R18151C|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R18276C|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R24648C|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R18343C			Q8WZ42	TITIN_HUMAN	titin	25575	Fibronectin type-III 86. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R18151C(2)|p.R24646C(2)|p.R18343C(1)|p.R18276C(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCATCCAGCGGCCATCAGGT	0.368																																					p.A18150A												.	.	6	Substitution - Missense(6)	large_intestine(4)|ovary(2)	c.C54450T	2						.						71.0	67.0	68.0					2																	179429213		1864	4107	5971	179137459	SO:0001583	missense	7273	exon154			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.76723C>T	2.37:g.179429213G>A	ENSP00000465570:p.Arg25575Cys	Somatic		Capture	Illumina HiSeq	Phase_I	179137459	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	13.36	2.213698	0.39102	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	6.16	5.28	0.74379	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.74928	0.3781	M	0.80422	2.495	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.79546	-0.1759	9	0.87932	D	0	.	17.1823	0.86858	0.0:0.0:0.8731:0.1269	.	18151;18276;18343;25575	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	24648;18151;18343;18276;18149	ENSP00000343764:R24648C;ENSP00000434586:R18151C;ENSP00000340554:R18343C;ENSP00000352154:R18276C	ENSP00000340554:R18343C	R	-	1	0	TTN	179137459	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	9.807000	0.99171	1.597000	0.50072	0.650000	0.86243	CGC		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179452471	179452471	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:179452471C>A	ENST00000591111.1	-	256	58866	c.58642G>T	c.(58642-58644)Gga>Tga	p.G19548*	TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.G21189*|TTN_ENST00000460472.2_Nonsense_Mutation_p.G12124*|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.G12249*|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.G18621*|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.G12316*			Q8WZ42	TITIN_HUMAN	titin	19548	Ig-like 109.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G12316*(1)|p.G12249*(1)|p.G18619*(1)|p.G12124*(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATAGGGCATCCTGCTCTCACT	0.438																																					p.Q12123H												.	.	4	Substitution - Nonsense(4)	large_intestine(4)	c.G36369T	2						.						57.0	55.0	56.0					2																	179452471		1925	4131	6056	179160717	SO:0001587	stop_gained	7273	exon134			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.58642G>T	2.37:g.179452471C>A	ENSP00000465570:p.Gly19548*	Somatic		Capture	Illumina HiSeq	Phase_I	179160717	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	61	58.283599	0.99989	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	6.01	6.01	0.97437	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.5211	0.99222	0.0:1.0:0.0:0.0	.	.	.	.	X	18621;12124;12316;12249;12122	.	ENSP00000340554:G12316X	G	-	1	0	TTN	179160717	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	5.978000	0.70501	2.861000	0.98227	0.650000	0.86243	GGA		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179456229	179456229	+	Missense_Mutation	SNP	G	G	A	rs376561549		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:179456229G>A	ENST00000591111.1	-	254	55524	c.55300C>T	c.(55300-55302)Cct>Tct	p.P18434S	TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P20075S|TTN_ENST00000460472.2_Missense_Mutation_p.P11010S|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P11135S|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P17507S|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P11202S			Q8WZ42	TITIN_HUMAN	titin	18434					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.P17505S(1)|p.P11135S(1)|p.P11202S(1)|p.P11010S(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACGGATGGAGGCACTGAAAAG	0.353																																					p.C11009C												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.C33027T	2						.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO	0,3708		0,0,1854	132.0	128.0	129.0		33604,33403,52519,33028	5.2	1.0	2		129	1,8185		0,1,4092	no	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	74,74,74,74	0,1,5946	AA,AG,GG		0.0122,0.0,0.0084	benign,benign,benign,benign	11202/27119,11135/27052,17507/33424,11010/26927	179456229	1,11893	1854	4093	5947	179164475	SO:0001583	missense	7273	exon132			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.55300C>T	2.37:g.179456229G>A	ENSP00000465570:p.Pro18434Ser	Somatic		Capture	Illumina HiSeq	Phase_I	179164475	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	13.20	2.166111	0.38217	0.0	1.22E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63744	-0.06;0.14;0.13;0.11	6.1	5.22	0.72569	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.50069	0.1594	L	0.28400	0.85	0.42626	D	0.993361	B;B;B;B	0.16166	0.016;0.016;0.016;0.016	B;B;B;B	0.12156	0.007;0.007;0.007;0.007	T	0.50389	-0.8834	9	0.87932	D	0	.	10.8166	0.46580	0.068:0.1308:0.8012:0.0	.	11010;11135;11202;18434	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	17507;11010;11202;11135;11008	ENSP00000343764:P17507S;ENSP00000434586:P11010S;ENSP00000340554:P11202S;ENSP00000352154:P11135S	ENSP00000340554:P11202S	P	-	1	0	TTN	179164475	0.999000	0.42202	1.000000	0.80357	0.981000	0.71138	2.226000	0.42963	1.582000	0.49881	0.650000	0.86243	CCT		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179466140	179466140	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:179466140T>C	ENST00000591111.1	-	237	50885	c.50661A>G	c.(50659-50661)aaA>aaG	p.K16887K	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Silent_p.K18528K|TTN_ENST00000460472.2_Silent_p.K9463K|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000359218.5_Silent_p.K9588K|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Silent_p.K15960K|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342175.6_Silent_p.K9655K			Q8WZ42	TITIN_HUMAN	titin	16887	Fibronectin type-III 22. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K9588K(1)|p.K9463K(1)|p.K15960K(1)|p.K9655K(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGGATTGACTTTGGTCCAGG	0.458																																					p.K9463K												.	.	4	Substitution - coding silent(4)	large_intestine(4)	c.A28389G	2						.						134.0	129.0	130.0					2																	179466140		1938	4136	6074	179174385	SO:0001819	synonymous_variant	7273	exon115			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.50661A>G	2.37:g.179466140T>C		Somatic		Capture	Illumina HiSeq	Phase_I	179174385	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CWC22	57703	broad.mit.edu	37	2	180815276	180815276	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:180815276G>A	ENST00000410053.3	-	19	2402	c.2103C>T	c.(2101-2103)agC>agT	p.S701S	CWC22_ENST00000295749.6_Silent_p.S701S	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	701	Ser-rich.			S -> G (in Ref. 4; AAH31216). {ECO:0000305}.	mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)	p.S701S(2)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						ATGAAGAGTCGCTCTCTTCAC	0.433																																					p.S701S												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C2103T	2						.						63.0	62.0	62.0					2																	180815276		1968	4177	6145	180523521	SO:0001819	synonymous_variant	57703	exon19				CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein b"""	615186	"""CWC22 spliceosome-associated protein homolog (S. cerevisiae)"""			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.2103C>T	2.37:g.180815276G>A		Somatic		Capture	Illumina HiSeq	Phase_I	180523521	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Silent	SNP	ENST00000410053.3	37	CCDS46465.1																																																																																				0.433	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943	
NAB1	4664	broad.mit.edu	37	2	191550284	191550284	+	Missense_Mutation	SNP	G	G	T	rs543055529		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:191550284G>T	ENST00000337386.5	+	8	1639	c.1178G>T	c.(1177-1179)aGg>aTg	p.R393M	NAB1_ENST00000545490.1_Missense_Mutation_p.R133M|AC006460.2_ENST00000411949.1_RNA|NAB1_ENST00000409581.1_Missense_Mutation_p.R393M|AC006460.2_ENST00000428032.1_RNA|NAB1_ENST00000357215.5_Missense_Mutation_p.R364M|NAB1_ENST00000409641.1_Missense_Mutation_p.R392M|AC006460.2_ENST00000421437.1_RNA	NM_005966.3	NP_005957.2	Q13506	NAB1_HUMAN	NGFI-A binding protein 1 (EGR1 binding protein 1)	393					endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of epidermis development (GO:0045682)|regulation of transcription, DNA-templated (GO:0006355)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.R393M(1)		kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0405)|all cancers(119;0.109)			GCCGAGAGGAGGTTGTCTGCA	0.478																																					p.R393M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1178T	2						.						75.0	70.0	72.0					2																	191550284		2203	4300	6503	191258529	SO:0001583	missense	4664	exon8				CCDS2307.1	2q32.3-q33	2008-05-23			ENSG00000138386	ENSG00000138386			7626	protein-coding gene	gene with protein product	"""EGR1 binding protein 1"""	600800				7624335, 8668170, 9418898	Standard	XM_005246579		Approved		uc002usb.3	Q13506	OTTHUMG00000132689	ENST00000337386.5:c.1178G>T	2.37:g.191550284G>T	ENSP00000336894:p.Arg393Met	Somatic		Capture	Illumina HiSeq	Phase_I	191258529	NM_005966	O75383|O75384|Q6GTU1|Q9UEV1	Missense_Mutation	SNP	ENST00000337386.5	37	CCDS2307.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.48|13.48	2.251067|2.251067	0.39797|0.39797	.|.	.|.	ENSG00000138386|ENSG00000138386	ENST00000434473|ENST00000409581;ENST00000337386;ENST00000357215;ENST00000409641;ENST00000545490	.|.	.|.	.|.	5.28|5.28	5.28|5.28	0.74379|0.74379	.|Nab1, C-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.61060|0.61060	0.2317|0.2317	N|N	0.24115|0.24115	0.695|0.695	0.48830|0.48830	D|D	0.999713|0.999713	.|D;D;D	.|0.61080	.|0.965;0.989;0.989	.|P;P;P	.|0.58077	.|0.66;0.832;0.832	T|T	0.64605|0.64605	-0.6368|-0.6368	5|9	.|0.62326	.|D	.|0.03	-20.3431|-20.3431	18.0822|18.0822	0.89444|0.89444	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|364;392;393	.|F8W8J7;B8ZZS2;Q13506	.|.;.;NAB1_HUMAN	D|M	145|393;393;364;392;133	.|.	.|ENSP00000336894:R393M	E|R	+|+	3|2	2|0	NAB1|NAB1	191258529|191258529	0.998000|0.998000	0.40836|0.40836	0.824000|0.824000	0.32777|0.32777	0.033000|0.033000	0.12548|0.12548	6.564000|6.564000	0.73969|0.73969	2.744000|2.744000	0.94065|0.94065	0.655000|0.655000	0.94253|0.94253	GAG|AGG		0.478	NAB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255986.1	NM_005966	
MYO1B	4430	broad.mit.edu	37	2	192255125	192255125	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:192255125C>T	ENST00000392318.3	+	18	2136	c.1889C>T	c.(1888-1890)gCa>gTa	p.A630V	MYO1B_ENST00000304164.4_Missense_Mutation_p.A630V|MYO1B_ENST00000439065.2_5'Flank|MYO1B_ENST00000392316.1_Missense_Mutation_p.A630V|MYO1B_ENST00000339514.4_Missense_Mutation_p.A630V	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	630	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.A630V(1)		NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			GTGCGGAGGGCAGGCTACGCC	0.483																																					p.A630V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1889T	2						.						106.0	101.0	102.0					2																	192255125		2203	4300	6503	191963370	SO:0001583	missense	4430	exon18			L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"""Myosins / Myosin superfamily : Class I"""	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.1889C>T	2.37:g.192255125C>T	ENSP00000376132:p.Ala630Val	Somatic		Capture	Illumina HiSeq	Phase_I	191963370	NM_012223	O43794|Q7Z6L5	Missense_Mutation	SNP	ENST00000392318.3	37	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.343877	0.82022	.	.	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316	D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43	5.45	5.45	0.79879	Myosin head, motor domain (2);	0.050911	0.85682	N	0.000000	D	0.92277	0.7550	M	0.92412	3.305	0.80722	D	1	B;B	0.16166	0.013;0.016	B;B	0.29862	0.108;0.101	D	0.90595	0.4540	10	0.87932	D	0	.	14.6674	0.68918	0.0:0.9288:0.0:0.0712	.	630;630	O43795;O43795-2	MYO1B_HUMAN;.	V	630	ENSP00000341903:A630V;ENSP00000376132:A630V;ENSP00000306382:A630V;ENSP00000376130:A630V	ENSP00000306382:A630V	A	+	2	0	MYO1B	191963370	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	5.936000	0.70153	2.838000	0.97847	0.655000	0.94253	GCA		0.483	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223	
HECW2	57520	broad.mit.edu	37	2	197172662	197172662	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:197172662C>T	ENST00000260983.3	-	11	2764	c.2582G>A	c.(2581-2583)cGg>cAg	p.R861Q	HECW2_ENST00000409111.1_Missense_Mutation_p.R505Q	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	861	Interaction with TP73.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R861Q(1)		biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						TCCTCACCGCCGGTTCAGCTG	0.498																																					p.R861Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2582A	2						.						89.0	83.0	85.0					2																	197172662		2203	4300	6503	196880907	SO:0001583	missense	57520	exon11			AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.2582G>A	2.37:g.197172662C>T	ENSP00000260983:p.Arg861Gln	Somatic		Capture	Illumina HiSeq	Phase_I	196880907	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	37	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	C	32	5.164053	0.94727	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	D;D	0.83992	-1.79;-1.79	5.17	4.27	0.50696	.	0.000000	0.85682	D	0.000000	D	0.89525	0.6740	M	0.72353	2.195	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	D	0.90184	0.4245	10	0.72032	D	0.01	.	14.2623	0.66092	0.0:0.9269:0.0:0.0731	.	861	Q9P2P5	HECW2_HUMAN	Q	505;861	ENSP00000386775:R505Q;ENSP00000260983:R861Q	ENSP00000260983:R861Q	R	-	2	0	HECW2	196880907	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.608000	0.67654	2.692000	0.91855	0.555000	0.69702	CGG		0.498	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760	
SF3B1	23451	broad.mit.edu	37	2	198266809	198266809	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:198266809G>A	ENST00000335508.6	-	15	2214	c.2123C>T	c.(2122-2124)gCc>gTc	p.A708V	SF3B1_ENST00000462613.1_5'UTR|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	708					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.A708V(1)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GGCAGCAATGGCCAAAGCACT	0.443			Mis		myelodysplastic syndrome																																p.A708V			Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2123T	2						.						92.0	88.0	90.0					2																	198266809		2203	4300	6503	197975054	SO:0001583	missense	23451	exon15			AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2123C>T	2.37:g.198266809G>A	ENSP00000335321:p.Ala708Val	Somatic		Capture	Illumina HiSeq	Phase_I	197975054	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	36	5.728276	0.96856	.	.	ENSG00000115524	ENST00000335508	T	0.70399	-0.48	6.02	6.02	0.97574	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.83991	0.5374	M	0.89534	3.04	0.80722	D	1	P	0.44521	0.837	P	0.49597	0.616	D	0.86160	0.1593	10	0.87932	D	0	.	20.5373	0.99239	0.0:0.0:1.0:0.0	.	708	O75533	SF3B1_HUMAN	V	708	ENSP00000335321:A708V	ENSP00000335321:A708V	A	-	2	0	SF3B1	197975054	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.287000	0.95975	2.857000	0.98124	0.650000	0.86243	GCC		0.443	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
BMPR2	659	broad.mit.edu	37	2	203384918	203384918	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:203384918C>T	ENST00000374580.4	+	7	1500	c.961C>T	c.(961-963)Cga>Tga	p.R321*	BMPR2_ENST00000374574.2_Nonsense_Mutation_p.R321*	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	321	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.R321*(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						AGAATTACCACGAGGAGGTAA	0.358																																					p.R321X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C961T	2	GRCh37	CM043449	BMPR2	M		.						77.0	74.0	75.0					2																	203384918		2203	4300	6503	203093163	SO:0001587	stop_gained	659	exon7			Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"""primary pulmonary hypertension 1"""	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.961C>T	2.37:g.203384918C>T	ENSP00000363708:p.Arg321*	Somatic		Capture	Illumina HiSeq	Phase_I	203093163	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Nonsense_Mutation	SNP	ENST00000374580.4	37	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	C	37	6.006334	0.97195	.	.	ENSG00000204217	ENST00000374580;ENST00000374574	.	.	.	5.14	4.22	0.49857	.	0.111183	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	15.1601	0.72778	0.1414:0.8586:0.0:0.0	.	.	.	.	X	321	.	ENSP00000363702:R321X	R	+	1	2	BMPR2	203093163	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.103000	0.41806	2.670000	0.90874	0.650000	0.86243	CGA		0.358	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204	
CYP20A1	57404	broad.mit.edu	37	2	204161497	204161497	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:204161497A>G	ENST00000356079.4	+	13	1378	c.1255A>G	c.(1255-1257)Acc>Gcc	p.T419A	CYP20A1_ENST00000461371.1_3'UTR|CYP20A1_ENST00000429815.2_Missense_Mutation_p.T427A	NM_177538.2	NP_803882.1	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A, polypeptide 1	419						integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.T419A(1)		cervix(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	11						ATATATGGTGACCACAGTACT	0.383																																					p.T419A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1255G	2						.						113.0	109.0	110.0					2																	204161497		2203	4300	6503	203869742	SO:0001583	missense	57404	exon13			AK021770	CCDS2357.1	2q33	2008-02-05			ENSG00000119004	ENSG00000119004		"""Cytochrome P450s"""	20576	protein-coding gene	gene with protein product							Standard	NM_177538		Approved	CYP-M	uc002uzv.4	Q6UW02	OTTHUMG00000132854	ENST00000356079.4:c.1255A>G	2.37:g.204161497A>G	ENSP00000348380:p.Thr419Ala	Somatic		Capture	Illumina HiSeq	Phase_I	203869742	NM_177538	Q4ZG61|Q8N4Q8|Q8WWA9|Q9HC04	Missense_Mutation	SNP	ENST00000356079.4	37	CCDS2357.1	.	.	.	.	.	.	.	.	.	.	A	7.897	0.733511	0.15574	.	.	ENSG00000119004	ENST00000356079;ENST00000421618;ENST00000429815	T;T	0.67523	-0.27;-0.27	5.63	-4.97	0.03029	.	0.350657	0.31809	N	0.007031	T	0.28797	0.0714	N	0.03115	-0.41	0.25987	N	0.982298	B;B	0.02656	0.0;0.0	B;B	0.09377	0.003;0.004	T	0.37619	-0.9698	10	0.08599	T	0.76	0.1731	5.9702	0.19349	0.1571:0.1358:0.5724:0.1346	.	427;419	E9PHG5;Q6UW02	.;CP20A_HUMAN	A	419;392;427	ENSP00000348380:T419A;ENSP00000407860:T427A	ENSP00000348380:T419A	T	+	1	0	CYP20A1	203869742	1.000000	0.71417	0.881000	0.34555	0.956000	0.61745	1.227000	0.32576	-0.815000	0.04346	0.482000	0.46254	ACC		0.383	CYP20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256328.3	NM_020674	
PLEKHM3	389072	broad.mit.edu	37	2	208811181	208811181	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:208811181A>G	ENST00000427836.2	-	4	2091	c.1602T>C	c.(1600-1602)agT>agC	p.S534S	PLEKHM3_ENST00000389247.4_Silent_p.S534S|PLEKHM3_ENST00000457206.1_Silent_p.S534S	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	534					intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)	p.S534S(2)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AATACCACCCACTGTAGTTGC	0.458																																					p.S534S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1602C	2						.						155.0	156.0	156.0					2																	208811181		1973	4166	6139	208519426	SO:0001819	synonymous_variant	389072	exon4			AK057612	CCDS42808.1	2q33.3	2013-01-10	2008-04-03	2008-04-03	ENSG00000178385	ENSG00000178385		"""Pleckstrin homology (PH) domain containing"""	34006	protein-coding gene	gene with protein product	"""differentiation associated protein"""		"""pleckstrin homology domain containing, family M, member 1-like"""	PLEKHM1L		19028694	Standard	NM_001080475		Approved	DAPR	uc002vcl.2	Q6ZWE6	OTTHUMG00000154781	ENST00000427836.2:c.1602T>C	2.37:g.208811181A>G		Somatic		Capture	Illumina HiSeq	Phase_I	208519426	NM_001080475	B9EKV2|Q8WW68	Silent	SNP	ENST00000427836.2	37	CCDS42808.1	.	.	.	.	.	.	.	.	.	.	A	11.07	1.530279	0.27387	.	.	ENSG00000178385	ENST00000447645	.	.	.	6.04	-9.47	0.00594	.	.	.	.	.	T	0.64382	0.2593	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73483	-0.3968	4	.	.	.	.	18.4198	0.90586	0.4093:0.0:0.5907:0.0	.	.	.	.	R	286	.	.	W	-	1	0	PLEKHM3	208519426	0.230000	0.23740	0.504000	0.27639	0.971000	0.66376	-0.155000	0.10115	-1.970000	0.01003	-0.371000	0.07208	TGG		0.458	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337036.1	NM_001080475	
PIKFYVE	200576	broad.mit.edu	37	2	209215524	209215524	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:209215524T>G	ENST00000264380.4	+	37	5622	c.5464T>G	c.(5464-5466)Tgt>Ggt	p.C1822G		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1822	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.C1822G(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						CAAGTTTTACTGTCGGCTCTA	0.413																																					p.C1822G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T5464G	2						.						117.0	117.0	117.0					2																	209215524		2203	4300	6503	208923769	SO:0001583	missense	200576	exon37			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.5464T>G	2.37:g.209215524T>G	ENSP00000264380:p.Cys1822Gly	Somatic		Capture	Illumina HiSeq	Phase_I	208923769	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.162313	0.78226	.	.	ENSG00000115020	ENST00000264380	T	0.30182	1.54	5.43	5.43	0.79202	Phosphatidylinositol-4-phosphate 5-kinase, core (1);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.106801	0.64402	D	0.000001	T	0.63010	0.2475	M	0.92169	3.28	0.80722	D	1	D	0.60575	0.988	D	0.65443	0.935	T	0.73183	-0.4063	10	0.87932	D	0	-14.2535	14.0486	0.64719	0.0:0.0:0.0:1.0	.	1822	Q9Y2I7	FYV1_HUMAN	G	1822	ENSP00000264380:C1822G	ENSP00000264380:C1822G	C	+	1	0	PIKFYVE	208923769	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.884000	0.87274	2.066000	0.61787	0.533000	0.62120	TGT		0.413	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
CPS1	1373	broad.mit.edu	37	2	211523354	211523354	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:211523354C>A	ENST00000233072.5	+	31	3894	c.3698C>A	c.(3697-3699)gCt>gAt	p.A1233D	CPS1_ENST00000451903.2_Missense_Mutation_p.A782D|CPS1_ENST00000430249.2_Missense_Mutation_p.A1239D	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1233	ATP-grasp 2.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)	p.A1233D(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	ATTGCAAAGGCTTTTGCCATC	0.403																																					p.A782D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2345A	2						.						121.0	114.0	116.0					2																	211523354		2203	4300	6503	211231599	SO:0001583	missense	1373	exon21			AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.3698C>A	2.37:g.211523354C>A	ENSP00000233072:p.Ala1233Asp	Somatic		Capture	Illumina HiSeq	Phase_I	211231599	NM_001122634	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.839249	0.91117	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.97114	-4.25;-4.25;-4.25	5.76	5.76	0.90799	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.000000	0.85682	D	0.000000	D	0.98298	0.9436	M	0.89785	3.06	0.80722	D	1	P;P	0.45634	0.863;0.863	P;P	0.51742	0.678;0.678	D	0.98662	1.0684	10	0.56958	D	0.05	-9.4802	19.9595	0.97236	0.0:1.0:0.0:0.0	.	1243;1233	Q59HF8;P31327	.;CPSM_HUMAN	D	1239;1241;1233;782	ENSP00000402608:A1239D;ENSP00000233072:A1233D;ENSP00000406136:A782D	ENSP00000233072:A1233D	A	+	2	0	CPS1	211231599	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.208000	0.77907	2.706000	0.92434	0.563000	0.77884	GCT		0.403	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
BARD1	580	broad.mit.edu	37	2	215646051	215646051	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:215646051C>G	ENST00000260947.4	-	4	681	c.547G>C	c.(547-549)Gtt>Ctt	p.V183L	BARD1_ENST00000471787.1_5'UTR|BARD1_ENST00000449967.2_Missense_Mutation_p.V39L	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	183					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.V183L(1)		NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CTTGGGGAAACAAATTCATAT	0.393									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.V183L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G547C	2						.						92.0	92.0	92.0					2																	215646051		2203	4300	6503	215354296	SO:0001583	missense	580	exon4	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"""Ankyrin repeat domain containing"""	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.547G>C	2.37:g.215646051C>G	ENSP00000260947:p.Val183Leu	Somatic		Capture	Illumina HiSeq	Phase_I	215354296	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	.	.	.	.	.	.	.	.	.	.	C	9.916	1.210773	0.22289	.	.	ENSG00000138376	ENST00000260947;ENST00000449967	T;T	0.73575	-0.76;-0.11	5.75	0.273	0.15650	.	0.700825	0.14202	N	0.334627	T	0.65354	0.2683	M	0.71581	2.175	0.29600	N	0.847767	B;B	0.31581	0.329;0.329	B;B	0.27170	0.077;0.077	T	0.55749	-0.8092	10	0.27785	T	0.31	-7.3138	5.6288	0.17497	0.1373:0.3982:0.0:0.4644	.	39;183	E7EUI3;Q99728	.;BARD1_HUMAN	L	183;39	ENSP00000260947:V183L;ENSP00000406752:V39L	ENSP00000260947:V183L	V	-	1	0	BARD1	215354296	0.948000	0.32251	0.878000	0.34440	0.074000	0.17049	-0.042000	0.12063	0.160000	0.19432	0.650000	0.86243	GTT		0.393	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465	
ATIC	471	broad.mit.edu	37	2	216214289	216214289	+	Missense_Mutation	SNP	G	G	A	rs149999349		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:216214289G>A	ENST00000236959.9	+	16	2016	c.1690G>A	c.(1690-1692)Ggt>Agt	p.G564S	ATIC_ENST00000540518.1_Missense_Mutation_p.G505S|ATIC_ENST00000435675.1_Missense_Mutation_p.G563S	NM_004044.6	NP_004035.2	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	564					'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|dihydrofolate metabolic process (GO:0046452)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	IMP cyclohydrolase activity (GO:0003937)|phosphoribosylaminoimidazolecarboxamide formyltransferase activity (GO:0004643)|protein homodimerization activity (GO:0042803)	p.G564S(1)	ATIC/ALK(24)	large_intestine(2)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	8		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)	GGCTCCCTCCGGTTCTGCTGC	0.483			T	ALK	ALCL																																p.G564S			Dom	yes		2	2q35	471	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1690A	2						.	G	SER/GLY	0,4406		0,0,2203	144.0	127.0	133.0		1690	6.2	0.9	2	dbSNP_134	133	1,8599	1.2+/-3.3	0,1,4299	no	missense	ATIC	NM_004044.6	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	564/593	216214289	1,13005	2203	4300	6503	215922534	SO:0001583	missense	471	exon16				CCDS2398.1	2q35	2010-04-27			ENSG00000138363	ENSG00000138363	2.1.2.3, 3.5.4.10		794	protein-coding gene	gene with protein product	"""phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase"""	601731				8567683, 9378707	Standard	NM_004044		Approved	PURH, AICARFT, IMPCHASE	uc002vex.4	P31939	OTTHUMG00000133023	ENST00000236959.9:c.1690G>A	2.37:g.216214289G>A	ENSP00000236959:p.Gly564Ser	Somatic		Capture	Illumina HiSeq	Phase_I	215922534	NM_004044	A8K202|E9PBU3|Q13856|Q53S28	Missense_Mutation	SNP	ENST00000236959.9	37	CCDS2398.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.977749	0.92982	0.0	1.16E-4	ENSG00000138363	ENST00000236959;ENST00000540518;ENST00000435675;ENST00000442048	D;D;D;D	0.94280	-3.39;-3.39;-3.39;-3.39	6.16	6.16	0.99307	AICAR transformylase domain (1);Cytidine deaminase-like (1);	0.000000	0.85682	D	0.000000	D	0.98021	0.9348	H	0.95043	3.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98136	1.0433	10	0.87932	D	0	-16.1112	20.8598	0.99761	0.0:0.0:1.0:0.0	.	563;564	E9PBU3;P31939	.;PUR9_HUMAN	S	564;505;563;79	ENSP00000236959:G564S;ENSP00000440523:G505S;ENSP00000415935:G563S;ENSP00000391399:G79S	ENSP00000236959:G564S	G	+	1	0	ATIC	215922534	1.000000	0.71417	0.915000	0.36163	0.274000	0.26718	9.750000	0.98875	2.937000	0.99478	0.650000	0.86243	GGT		0.483	ATIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256610.1	NM_004044	
FN1	2335	broad.mit.edu	37	2	216248846	216248846	+	Silent	SNP	G	G	A	rs374970848		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:216248846G>A	ENST00000359671.1	-	29	4783	c.4518C>T	c.(4516-4518)agC>agT	p.S1506S	FN1_ENST00000323926.6_Silent_p.S1597S|FN1_ENST00000490833.1_5'Flank|FN1_ENST00000354785.4_Silent_p.S1597S|FN1_ENST00000336916.4_Silent_p.S1506S|FN1_ENST00000421182.1_Silent_p.S1506S|FN1_ENST00000357867.4_Silent_p.S1506S|FN1_ENST00000345488.5_Silent_p.S1506S|FN1_ENST00000443816.1_Silent_p.S1506S|FN1_ENST00000446046.1_Silent_p.S1506S|FN1_ENST00000432072.2_Silent_p.S1597S|FN1_ENST00000357009.2_Silent_p.S1506S|FN1_ENST00000346544.3_Silent_p.S1506S|FN1_ENST00000356005.4_Silent_p.S1506S			P02751	FINC_HUMAN	fibronectin 1	1506	Cell-attachment.|Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)	p.S1506S(1)	FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	GTTTAAGGCCGCTGATGGTAG	0.493																																					p.S1506S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4518T	2						.	A	,,,,	0,4406		0,0,2203	121.0	112.0	115.0		4518,4518,4518,4518,4791	-5.3	0.0	2		115	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FN1	NM_002026.2,NM_212474.1,NM_212476.1,NM_212478.1,NM_212482.1	,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,	1506/2356,1506/2177,1506/2297,1506/2331,1597/2478	216248846	1,13005	2203	4300	6503	215957091	SO:0001819	synonymous_variant	2335	exon29				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.4518C>T	2.37:g.216248846G>A		Somatic		Capture	Illumina HiSeq	Phase_I	215957091	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	37																																																																																					0.493	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
TNS1	7145	broad.mit.edu	37	2	218678511	218678511	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:218678511C>T	ENST00000171887.4	-	26	4898	c.4446G>A	c.(4444-4446)ccG>ccA	p.P1482P	TNS1_ENST00000419504.1_Silent_p.P1469P|TNS1_ENST00000430930.1_Silent_p.P1461P	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1482	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.P1482P(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TGAAGGCCCCCGGCTCCTGGT	0.572																																					p.P1482P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4446A	2						.						58.0	58.0	58.0					2																	218678511		2203	4300	6503	218386756	SO:0001819	synonymous_variant	7145	exon26			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4446G>A	2.37:g.218678511C>T		Somatic		Capture	Illumina HiSeq	Phase_I	218386756	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																				0.572	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
PLCD4	84812	broad.mit.edu	37	2	219498480	219498480	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:219498480G>T	ENST00000450993.2	+	11	1941	c.1602G>T	c.(1600-1602)gaG>gaT	p.E534D	PLCD4_ENST00000417849.1_Missense_Mutation_p.E534D|PLCD4_ENST00000432688.1_Missense_Mutation_p.E566D|RP11-548H3.1_ENST00000607946.1_RNA	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	534	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.E534D(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		TCATCAAGGAGGCTGGTCAGG	0.502																																					p.E534D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1602T	2						.						48.0	44.0	46.0					2																	219498480		1901	4122	6023	219206724	SO:0001583	missense	84812	exon11			AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"""EF-hand domain containing"""	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.1602G>T	2.37:g.219498480G>T	ENSP00000388631:p.Glu534Asp	Somatic		Capture	Illumina HiSeq	Phase_I	219206724	NM_032726	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	37	CCDS46516.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.528837	0.27387	.	.	ENSG00000115556	ENST00000450993;ENST00000251959;ENST00000417849;ENST00000432688	T;T;T	0.67865	-0.29;-0.29;-0.29	5.4	0.323	0.15893	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.049463	0.85682	N	0.000000	T	0.44664	0.1304	L	0.33710	1.025	0.33336	D	0.569261	B	0.02656	0.0	B	0.08055	0.003	T	0.23013	-1.0200	10	0.34782	T	0.22	.	0.8582	0.01187	0.281:0.2172:0.3444:0.1574	.	534	Q9BRC7	PLCD4_HUMAN	D	534;534;534;566	ENSP00000388631:E534D;ENSP00000396942:E534D;ENSP00000396185:E566D	ENSP00000251959:E534D	E	+	3	2	PLCD4	219206724	0.993000	0.37304	0.999000	0.59377	0.854000	0.48673	0.716000	0.25836	0.108000	0.17862	-0.251000	0.11542	GAG		0.502	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1		
ANKZF1	55139	broad.mit.edu	37	2	220100475	220100475	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:220100475C>T	ENST00000323348.5	+	12	2023	c.1849C>T	c.(1849-1851)Cgg>Tgg	p.R617W	ANKZF1_ENST00000410034.3_Missense_Mutation_p.R617W|ANKZF1_ENST00000409849.1_Missense_Mutation_p.R407W|GLB1L_ENST00000497855.1_5'Flank	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	617						membrane (GO:0016020)	metal ion binding (GO:0046872)	p.R617W(2)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCAGGCTACACGGAAAAGGGA	0.542																																					p.R617W												.	.	2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.C1849T	2						.						76.0	90.0	85.0					2																	220100475		2153	4243	6396	219808719	SO:0001583	missense	55139	exon12			AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"""Zinc fingers, C2H2-type"", ""Ankyrin repeat domain containing"""	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.1849C>T	2.37:g.220100475C>T	ENSP00000321617:p.Arg617Trp	Somatic		Capture	Illumina HiSeq	Phase_I	219808719	NM_001042410	Q9NVZ4	Missense_Mutation	SNP	ENST00000323348.5	37	CCDS42821.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.637807	0.47049	.	.	ENSG00000163516	ENST00000323348;ENST00000409849;ENST00000410034	D;D;D	0.94862	-3.54;-3.54;-3.54	5.65	2.73	0.32206	.	0.060153	0.64402	D	0.000007	D	0.96827	0.8964	M	0.77820	2.39	0.35099	D	0.765079	D	0.89917	1.0	D	0.79108	0.992	D	0.99854	1.1075	10	0.87932	D	0	-19.6202	15.3342	0.74238	0.6136:0.3864:0.0:0.0	.	617	Q9H8Y5	ANKZ1_HUMAN	W	617;407;617	ENSP00000321617:R617W;ENSP00000386815:R407W;ENSP00000386337:R617W	ENSP00000321617:R617W	R	+	1	2	ANKZF1	219808719	0.990000	0.36364	0.404000	0.26397	0.593000	0.36681	1.756000	0.38390	0.402000	0.25451	-0.181000	0.13052	CGG		0.542	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089	
CCDC140	151278	broad.mit.edu	37	2	223168728	223168728	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:223168728G>A	ENST00000295226.1	+	2	491	c.107G>A	c.(106-108)cGc>cAc	p.R36H		NM_153038.1	NP_694583.1	Q96MF4	CC140_HUMAN	coiled-coil domain containing 140	36								p.R36H(1)		endometrium(4)|large_intestine(1)|prostate(1)	6		Renal(207;0.0376)		Epithelial(121;4.03e-10)|all cancers(144;1.8e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCCAACACCCGCGTTCCTCGA	0.567																																					p.R36H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G107A	2						.						49.0	52.0	51.0					2																	223168728		2203	4300	6503	222876972	SO:0001583	missense	151278	exon2			AK057009	CCDS2452.1	2q36.1	2008-02-05			ENSG00000163081	ENSG00000163081			26514	protein-coding gene	gene with protein product							Standard	NM_153038		Approved	FLJ32447	uc002vnb.1	Q96MF4	OTTHUMG00000133154	ENST00000295226.1:c.107G>A	2.37:g.223168728G>A	ENSP00000295226:p.Arg36His	Somatic		Capture	Illumina HiSeq	Phase_I	222876972	NM_153038		Missense_Mutation	SNP	ENST00000295226.1	37	CCDS2452.1	.	.	.	.	.	.	.	.	.	.	G	11.00	1.509698	0.27036	.	.	ENSG00000163081	ENST00000295226	.	.	.	3.23	0.081	0.14423	.	.	.	.	.	T	0.16896	0.0406	N	0.08118	0	0.09310	N	1	B	0.23490	0.086	B	0.15484	0.013	T	0.19192	-1.0313	8	0.87932	D	0	.	5.6466	0.17592	0.4327:0.0:0.5673:0.0	.	36	Q96MF4	CC140_HUMAN	H	36	.	ENSP00000295226:R36H	R	+	2	0	CCDC140	222876972	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.178000	0.03093	0.001000	0.14605	-0.345000	0.07892	CGC		0.567	CCDC140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256854.1	NM_153038	
DOCK10	55619	broad.mit.edu	37	2	225721664	225721664	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:225721664C>A	ENST00000258390.7	-	15	1788	c.1721G>T	c.(1720-1722)aGa>aTa	p.R574I	DOCK10_ENST00000409592.3_Missense_Mutation_p.R568I	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	574					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R574I(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TCTTGAGTCTCTGTCCACATT	0.313																																					p.R574I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1721T	2						.						102.0	97.0	99.0					2																	225721664		1827	4083	5910	225429908	SO:0001583	missense	55619	exon15			AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.1721G>T	2.37:g.225721664C>A	ENSP00000258390:p.Arg574Ile	Somatic		Capture	Illumina HiSeq	Phase_I	225429908	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.813088	0.70912	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.03242	4.0;4.0	5.53	5.53	0.82687	.	0.045969	0.85682	D	0.000000	T	0.12987	0.0315	M	0.83774	2.66	0.58432	D	0.999993	P;P	0.49253	0.921;0.756	P;B	0.47015	0.534;0.355	T	0.00752	-1.1581	10	0.56958	D	0.05	.	19.4442	0.94840	0.0:1.0:0.0:0.0	.	574;568	Q96BY6;B3FL70	DOC10_HUMAN;.	I	568;574	ENSP00000386694:R568I;ENSP00000258390:R574I	ENSP00000258390:R574I	R	-	2	0	DOCK10	225429908	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.683000	0.61679	2.589000	0.87451	0.579000	0.79373	AGA		0.313	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
DOCK10	55619	broad.mit.edu	37	2	225739401	225739401	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:225739401T>C	ENST00000258390.7	-	9	1066	c.999A>G	c.(997-999)ctA>ctG	p.L333L	DOCK10_ENST00000409592.3_Silent_p.L327L	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	333					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L333L(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		AGTCTGCGTGTAGGTTGTTCT	0.343																																					p.L333L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A999G	2						.						155.0	149.0	151.0					2																	225739401		1888	4113	6001	225447645	SO:0001819	synonymous_variant	55619	exon9			AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.999A>G	2.37:g.225739401T>C		Somatic		Capture	Illumina HiSeq	Phase_I	225447645	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	37	CCDS46528.1																																																																																				0.343	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
NYAP2	57624	broad.mit.edu	37	2	226378367	226378367	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:226378367A>G	ENST00000272907.6	+	3	915	c.502A>G	c.(502-504)Aaa>Gaa	p.K168E	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	168					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)			p.K168E(1)									TAAGAGCGGGAAAACCCCTGA	0.542																																					p.K168E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A502G	2						.						61.0	73.0	69.0					2																	226378367		2051	4205	6256	226086611	SO:0001583	missense	57624	exon3			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"""KIAA1486"""	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.502A>G	2.37:g.226378367A>G	ENSP00000272907:p.Lys168Glu	Somatic		Capture	Illumina HiSeq	Phase_I	226086611	NM_020864	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	A	13.26	2.185499	0.38609	.	.	ENSG00000144460	ENST00000272907	T	0.39229	1.09	5.46	4.26	0.50523	.	0.319284	0.29212	N	0.012812	T	0.33644	0.0870	L	0.53249	1.67	0.80722	D	1	B	0.26195	0.144	B	0.26094	0.066	T	0.12837	-1.0532	10	0.02654	T	1	-15.2508	12.6369	0.56689	0.8623:0.1377:0.0:0.0	.	168	Q9P242	K1486_HUMAN	E	168	ENSP00000272907:K168E	ENSP00000272907:K168E	K	+	1	0	KIAA1486	226086611	1.000000	0.71417	0.459000	0.27081	0.968000	0.65278	4.668000	0.61568	2.067000	0.61834	0.460000	0.39030	AAA		0.542	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864	
NYAP2	57624	broad.mit.edu	37	2	226446980	226446980	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:226446980G>A	ENST00000272907.6	+	4	1260	c.847G>A	c.(847-849)Gcc>Acc	p.A283T	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	283					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)			p.A283T(1)									GGGCCAAGACGCCAAATGTGA	0.557																																					p.A283T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G847A	2						.						103.0	109.0	107.0					2																	226446980		2109	4210	6319	226155224	SO:0001583	missense	57624	exon4			AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"""KIAA1486"""	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.847G>A	2.37:g.226446980G>A	ENSP00000272907:p.Ala283Thr	Somatic		Capture	Illumina HiSeq	Phase_I	226155224	NM_020864	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.631400	0.00813	.	.	ENSG00000144460	ENST00000272907	T	0.43294	0.95	5.51	-11.0	0.00169	.	0.628534	0.15497	N	0.259234	T	0.17492	0.0420	N	0.19112	0.55	0.27305	N	0.957469	B	0.25809	0.135	B	0.23716	0.048	T	0.43360	-0.9396	10	0.15499	T	0.54	-0.2572	8.1958	0.31396	0.0684:0.2833:0.4833:0.1651	.	283	Q9P242	K1486_HUMAN	T	283	ENSP00000272907:A283T	ENSP00000272907:A283T	A	+	1	0	KIAA1486	226155224	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.992000	0.03724	-6.038000	0.00007	-3.380000	0.00040	GCC		0.557	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864	
RHBDD1	84236	broad.mit.edu	37	2	227779033	227779033	+	Silent	SNP	C	C	T	rs138482669		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:227779033C>T	ENST00000341329.3	+	6	1064	c.822C>T	c.(820-822)ctC>ctT	p.L274L	RHBDD1_ENST00000392062.2_Silent_p.L274L|RHBDD1_ENST00000493526.1_3'UTR|RHBDD1_ENST00000409053.1_Silent_p.L108L	NM_032276.3	NP_115652.2	Q8TEB9	RHBL4_HUMAN	rhomboid domain containing 1	274	Ubiquitin-binding domain (UBD). {ECO:0000250}.				apoptotic process (GO:0006915)|cellular response to unfolded protein (GO:0034620)|cellular response to UV (GO:0034644)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|membrane protein intracellular domain proteolysis (GO:0031293)|membrane protein proteolysis (GO:0033619)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein processing (GO:0010954)|positive regulation of secretion (GO:0051047)|post-translational protein modification (GO:0043687)|spermatid differentiation (GO:0048515)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)	p.L274L(1)		breast(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		AAGAACAGCTCGAGAGAGCAT	0.473																																					p.L274L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C822T	2						.	C	,	0,4406		0,0,2203	89.0	90.0	90.0		822,822	0.8	1.0	2	dbSNP_134	90	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	RHBDD1	NM_001167608.1,NM_032276.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	274/316,274/316	227779033	1,13005	2203	4300	6503	227487277	SO:0001819	synonymous_variant	84236	exon8			AK074258	CCDS2464.1	2q36.3	2012-07-09			ENSG00000144468	ENSG00000144468			23081	protein-coding gene	gene with protein product						12838346	Standard	NM_032276		Approved	DKFZp547E052	uc002voi.3	Q8TEB9	OTTHUMG00000133178	ENST00000341329.3:c.822C>T	2.37:g.227779033C>T		Somatic		Capture	Illumina HiSeq	Phase_I	227487277	NM_001167608	Q495B9|Q53S43|Q5EBM8|Q6P5V8|Q8IV60|Q9H057	Silent	SNP	ENST00000341329.3	37	CCDS2464.1																																																																																				0.473	RHBDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256885.2		
TRIP12	9320	broad.mit.edu	37	2	230657813	230657813	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:230657813A>G	ENST00000283943.5	-	26	3970	c.3792T>C	c.(3790-3792)caT>caC	p.H1264H	TRIP12_ENST00000389044.4_Silent_p.H1312H|TRIP12_ENST00000389045.3_Silent_p.H994H	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1264					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)	p.H1264H(1)		breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		ATTTTAATTGATGTGTGTTGA	0.368																																					p.H1264H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3792C	2						.						88.0	88.0	88.0					2																	230657813		2203	4300	6503	230366057	SO:0001819	synonymous_variant	9320	exon26			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.3792T>C	2.37:g.230657813A>G		Somatic		Capture	Illumina HiSeq	Phase_I	230366057	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	37	CCDS33391.1																																																																																				0.368	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238	
SP110	3431	broad.mit.edu	37	2	231077600	231077600	+	Silent	SNP	C	C	T	rs201957445		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:231077600C>T	ENST00000358662.4	-	4	537	c.459G>A	c.(457-459)gcG>gcA	p.A153A	SP110_ENST00000338556.3_5'UTR|SP110_ENST00000540870.1_Silent_p.A159A|SP110_ENST00000258382.5_Silent_p.A153A|SP110_ENST00000392048.3_Silent_p.A153A|SP110_ENST00000258381.6_Silent_p.A153A|SP110_ENST00000486146.2_5'UTR	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	153					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.A153A(1)		breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		TGACTCTTGGCGCACAGGGTG	0.602																																					p.A153A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G459A	2						.						133.0	131.0	132.0					2																	231077600		2203	4300	6503	230785844	SO:0001819	synonymous_variant	3431	exon4			L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"""interferon-induced protein 41, 30kD"""	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.459G>A	2.37:g.231077600C>T		Somatic		Capture	Illumina HiSeq	Phase_I	230785844	NM_004510	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Silent	SNP	ENST00000358662.4	37	CCDS2474.1																																																																																				0.602	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
B3GNT7	93010	broad.mit.edu	37	2	232262990	232262990	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:232262990C>T	ENST00000287590.5	+	2	821	c.560C>T	c.(559-561)aCg>aTg	p.T187M		NM_145236.2	NP_660279.1	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	187					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)	p.T187M(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)	17		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		GAGGAGCGCACGCACTACCAG	0.682																																					p.T187M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C560T	2						.						42.0	48.0	46.0					2																	232262990		2057	4174	6231	231971234	SO:0001583	missense	93010	exon2			AK000770	CCDS46540.1	2q36.1	2013-02-21			ENSG00000156966	ENSG00000156966		"""Beta 3-glycosyltransferases"""	18811	protein-coding gene	gene with protein product		615313				12061784	Standard	NM_145236		Approved	beta3GnT7	uc002vrs.3	Q8NFL0	OTTHUMG00000153880	ENST00000287590.5:c.560C>T	2.37:g.232262990C>T	ENSP00000287590:p.Thr187Met	Somatic		Capture	Illumina HiSeq	Phase_I	231971234	NM_145236	B3KWY4|B7WNP0	Missense_Mutation	SNP	ENST00000287590.5	37	CCDS46540.1	.	.	.	.	.	.	.	.	.	.	T	7.570	0.666497	0.14710	.	.	ENSG00000156966	ENST00000287590	T	0.40756	1.02	5.2	1.21	0.21127	.	1.585360	0.02944	N	0.140826	T	0.25306	0.0615	N	0.04746	-0.17	0.09310	N	1	P	0.50272	0.933	B	0.42343	0.384	T	0.18840	-1.0324	10	0.52906	T	0.07	.	5.9495	0.19237	0.1329:0.6467:0.0:0.2204	.	187	Q8NFL0	B3GN7_HUMAN	M	187	ENSP00000287590:T187M	ENSP00000287590:T187M	T	+	2	0	B3GNT7	231971234	0.001000	0.12720	0.106000	0.21319	0.101000	0.19017	0.433000	0.21477	0.232000	0.21100	-0.755000	0.03482	ACG		0.682	B3GNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332827.1	NM_145236	
GIGYF2	26058	broad.mit.edu	37	2	233681732	233681732	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:233681732G>A	ENST00000409547.1	+	22	2671	c.2360G>A	c.(2359-2361)cGa>cAa	p.R787Q	GIGYF2_ENST00000409196.3_Missense_Mutation_p.R781Q|GIGYF2_ENST00000452341.2_Missense_Mutation_p.R618Q|GIGYF2_ENST00000373563.4_Missense_Mutation_p.R787Q|GIGYF2_ENST00000373566.3_Missense_Mutation_p.R809Q|GIGYF2_ENST00000409480.1_Missense_Mutation_p.R809Q|GIGYF2_ENST00000409451.3_Missense_Mutation_p.R808Q	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	787	Gln-rich.|Glu-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.R787Q(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		GAACTTGCCCGAAGGAAACAG	0.473																																					p.R781Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2342A	2						.						232.0	221.0	225.0					2																	233681732		2203	4300	6503	233389976	SO:0001583	missense	26058	exon19			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2360G>A	2.37:g.233681732G>A	ENSP00000386537:p.Arg787Gln	Somatic		Capture	Illumina HiSeq	Phase_I	233389976	NM_001103148	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.974210	0.53720	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000452341	T;T;T;T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.0	3.89	3.89	0.44902	.	0.000000	0.85682	D	0.000000	D	0.85358	0.5678	L	0.61218	1.895	0.54753	D	0.999985	D;D;D;D	0.89917	1.0;0.997;0.997;0.997	D;D;D;D	0.81914	0.995;0.953;0.953;0.953	D	0.84423	0.0572	10	0.33141	T	0.24	-8.8124	16.4263	0.83815	0.0:0.0:1.0:0.0	.	618;808;787;781	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	Q	809;787;809;787;781;808;781;618	ENSP00000362667:R809Q;ENSP00000362664:R787Q;ENSP00000386765:R809Q;ENSP00000386537:R787Q;ENSP00000387070:R781Q;ENSP00000387170:R808Q;ENSP00000410297:R781Q;ENSP00000411505:R618Q	ENSP00000362664:R787Q	R	+	2	0	GIGYF2	233389976	1.000000	0.71417	0.888000	0.34837	0.483000	0.33249	7.620000	0.83070	2.175000	0.68902	0.561000	0.74099	CGA		0.473	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
C2orf44	80304	broad.mit.edu	37	2	24261368	24261368	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:24261368T>C	ENST00000295148.4	-	2	1054	c.997A>G	c.(997-999)Aaa>Gaa	p.K333E	C2orf44_ENST00000406895.3_Missense_Mutation_p.K333E	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	333								p.K333E(1)	C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATAGTGACTTTTCTCGTCATG	0.393			T	ALK	NSCLC																																p.K333E			Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A997G	2						.						61.0	58.0	59.0					2																	24261368		2203	4300	6503	24114872	SO:0001583	missense	80304	exon2			AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.997A>G	2.37:g.24261368T>C	ENSP00000295148:p.Lys333Glu	Somatic		Capture	Illumina HiSeq	Phase_I	24114872	NM_025203	D6W532|Q8IYK0|Q9HBP5	Missense_Mutation	SNP	ENST00000295148.4	37	CCDS1705.1	.	.	.	.	.	.	.	.	.	.	T	18.03	3.533075	0.64972	.	.	ENSG00000163026	ENST00000295148;ENST00000406895	T;T	0.56941	0.43;0.43	5.38	5.38	0.77491	WD40/YVTN repeat-like-containing domain (1);	0.043639	0.85682	D	0.000000	T	0.70448	0.3225	M	0.75264	2.295	0.49915	D	0.999836	D;D	0.71674	0.998;0.998	D;D	0.63113	0.911;0.911	T	0.75007	-0.3469	10	0.87932	D	0	-18.2846	15.6933	0.77473	0.0:0.0:0.0:1.0	.	333;333	Q9H6R7-2;Q9H6R7	.;CB044_HUMAN	E	333	ENSP00000295148:K333E;ENSP00000385816:K333E	ENSP00000295148:K333E	K	-	1	0	C2orf44	24114872	1.000000	0.71417	0.478000	0.27316	0.704000	0.40688	7.698000	0.84413	2.181000	0.69327	0.533000	0.62120	AAA		0.393	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203	
GIGYF2	26058	broad.mit.edu	37	2	233721555	233721555	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:233721555G>A	ENST00000409547.1	+	31	4196	c.3885G>A	c.(3883-3885)acG>acA	p.T1295T	GIGYF2_ENST00000409196.3_Silent_p.T1289T|GIGYF2_ENST00000373563.4_Silent_p.T1295T|GIGYF2_ENST00000373566.3_Silent_p.T1317T|GIGYF2_ENST00000409480.1_Silent_p.T1317T|GIGYF2_ENST00000409451.3_Silent_p.T1316T	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1295					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.T1295T(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		AAATCGAGACGTTGGATGACT	0.502																																					p.T1289T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3867A	2						.						184.0	168.0	173.0					2																	233721555		2203	4300	6503	233429799	SO:0001819	synonymous_variant	26058	exon28			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.3885G>A	2.37:g.233721555G>A		Somatic		Capture	Illumina HiSeq	Phase_I	233429799	NM_001103148	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Silent	SNP	ENST00000409547.1	37	CCDS33401.1																																																																																				0.502	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
MATN3	4148	broad.mit.edu	37	2	20200211	20200211	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:20200211delT	ENST00000407540.3	-	5	1221	c.1159delA	c.(1159-1161)acafs	p.T387fs	AC079145.4_ENST00000416575.1_RNA|MATN3_ENST00000421259.2_Frame_Shift_Del_p.T345fs	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	387	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)	p.T387fs*10(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCTGAACATGTTTTTTTATCT	0.403																																					p.T387fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1159delA	2						.						75.0	71.0	72.0					2																	20200211		1845	4100	5945	20063692	SO:0001589	frameshift_variant	4148	exon5			AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.1159delA	2.37:g.20200211delT	ENSP00000383894:p.Thr387fs	Somatic		Capture	Illumina HiSeq	Phase_I	20063692	NM_002381	B2CPU0|Q4ZG02	Frame_Shift_Del	DEL	ENST00000407540.3	37	CCDS46226.1																																																																																				0.403	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381	
POMC	5443	broad.mit.edu	37	2	25383987	25383987	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:25383987delT	ENST00000405623.1	-	3	1222	c.767delA	c.(766-768)aacfs	p.N256fs	POMC_ENST00000264708.3_Frame_Shift_Del_p.N256fs|POMC_ENST00000395826.2_Frame_Shift_Del_p.N256fs|RP11-509E16.1_ENST00000567599.1_lincRNA|POMC_ENST00000380794.1_Frame_Shift_Del_p.N256fs			P01189	COLI_HUMAN	proopiomelanocortin	256					cell-cell signaling (GO:0007267)|cellular pigmentation (GO:0033059)|cellular protein metabolic process (GO:0044267)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|negative regulation of tumor necrosis factor production (GO:0032720)|neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of appetite (GO:0032098)|regulation of blood pressure (GO:0008217)|regulation of corticosterone secretion (GO:2000852)|regulation of glycogen metabolic process (GO:0070873)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|peroxisomal matrix (GO:0005782)|secretory granule (GO:0030141)|secretory granule lumen (GO:0034774)	G-protein coupled receptor binding (GO:0001664)|hormone activity (GO:0005179)|receptor binding (GO:0005102)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)	p.N256fs*>12(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(1)	12	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Loperamide(DB00836)	GATGATGGCGTTTTTGAACAG	0.637																																					p.N256fs	Colon(110;1515 1566 8452 10082 43216)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.767delA	2						.						45.0	47.0	46.0					2																	25383987		2203	4300	6503	25237491	SO:0001589	frameshift_variant	5443	exon4				CCDS1717.1	2p23	2013-02-25	2008-07-31		ENSG00000115138	ENSG00000115138		"""Endogenous ligands"""	9201	protein-coding gene	gene with protein product	"""adrenocorticotropin"", ""beta-lipotropin"", ""alpha-melanocyte stimulating hormone"", ""beta-melanocyte stimulating hormone"", ""beta-endorphin"", ""adrenocorticotropic hormone"", ""opiomelanocortin prepropeptide"""	176830				6254047, 9620771	Standard	NM_001035256		Approved	MSH, POC, CLIP, ACTH, NPP, LPH	uc002rfz.1	P01189	OTTHUMG00000094764	ENST00000405623.1:c.767delA	2.37:g.25383987delT	ENSP00000384092:p.Asn256fs	Somatic		Capture	Illumina HiSeq	Phase_I	25237491	NM_001035256	P78442|Q53T23|Q9UD39|Q9UD40	Frame_Shift_Del	DEL	ENST00000405623.1	37	CCDS1717.1																																																																																				0.637	POMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211573.3	NM_001035256	
DNMT3A	1788	broad.mit.edu	37	2	25505431	25505431	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:25505431delC	ENST00000264709.3	-	4	664	c.327delG	c.(325-327)gggfs	p.G109fs	DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.G109fs|DNMT3A_ENST00000406659.3_Frame_Shift_Del_p.G109fs	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	109					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.Q110fs*14(2)|p.Q110fs*52(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CGCCCTTCTGCCCCCCAGCAG	0.657			"""Mis, F, N, S"""		AML																																p.G109fs			Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	.	3	Insertion - Frameshift(2)|Deletion - Frameshift(1)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(1)	c.327delG	2						.						30.0	36.0	34.0					2																	25505431		2202	4299	6501	25358935	SO:0001589	frameshift_variant	1788	exon4				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.327delG	2.37:g.25505431delC	ENSP00000264709:p.Gly109fs	Somatic		Capture	Illumina HiSeq	Phase_I	25358935	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Del	DEL	ENST00000264709.3	37	CCDS33157.1																																																																																				0.657	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552	
OTOF	9381	broad.mit.edu	37	2	26725284	26725284	+	Silent	SNP	C	C	A	rs141271513		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:26725284C>A	ENST00000272371.2	-	7	720	c.594G>T	c.(592-594)gcG>gcT	p.A198A	OTOF_ENST00000403946.3_Silent_p.A198A	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	198					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)	p.A198A(1)		NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTCCAGCACCGCCGGTTCAT	0.527																																					p.A198A	GBM(102;732 1451 20652 24062 31372)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G594T	2						.						78.0	65.0	69.0					2																	26725284		2203	4300	6503	26578788	SO:0001819	synonymous_variant	9381	exon7			AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.594G>T	2.37:g.26725284C>A		Somatic		Capture	Illumina HiSeq	Phase_I	26578788	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																				0.527	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
TCF23	150921	broad.mit.edu	37	2	27373167	27373167	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:27373167C>T	ENST00000296096.5	+	2	529	c.399C>T	c.(397-399)ggC>ggT	p.G133G		NM_175769.2	NP_786951.1	Q7RTU1	TCF23_HUMAN	transcription factor 23	133					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	nucleus (GO:0005634)		p.G133G(1)		large_intestine(2)|lung(11)|prostate(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCACACTCGGCCACGAGTTGC	0.652																																					p.G133G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C399T	2						.						106.0	114.0	111.0					2																	27373167		2203	4300	6503	27226671	SO:0001819	synonymous_variant	150921	exon2			AC013403	CCDS33163.1	2p23.3	2013-05-21			ENSG00000163792	ENSG00000163792		"""Basic helix-loop-helix proteins"""	18602	protein-coding gene	gene with protein product		609635				11701948, 10652346	Standard	NM_175769		Approved	OUT, bHLHa24	uc010ylg.2	Q7RTU1	OTTHUMG00000152031	ENST00000296096.5:c.399C>T	2.37:g.27373167C>T		Somatic		Capture	Illumina HiSeq	Phase_I	27226671	NM_175769	B2RNZ3	Silent	SNP	ENST00000296096.5	37	CCDS33163.1																																																																																				0.652	TCF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324980.1	NM_175769	
SLC5A6	8884	broad.mit.edu	37	2	27427677	27427677	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:27427677G>A	ENST00000310574.3	-	8	1330	c.857C>T	c.(856-858)aCg>aTg	p.T286M	SLC5A6_ENST00000408041.1_Missense_Mutation_p.T286M|SLC5A6_ENST00000461319.1_5'Flank	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	286					biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)	p.T286M(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	AGCCTTCTCCGTGCGGGAACT	0.607																																					p.T286M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C857T	2						.						78.0	70.0	72.0					2																	27427677		2203	4300	6503	27281181	SO:0001583	missense	8884	exon8			AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"""Solute carriers"""	11041	protein-coding gene	gene with protein product		604024	"""solute carrier family 5 (sodium-dependent vitamin transporter), member 6"""			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.857C>T	2.37:g.27427677G>A	ENSP00000310208:p.Thr286Met	Somatic		Capture	Illumina HiSeq	Phase_I	27281181	NM_021095	B2RB85|D6W549|Q969Y5	Missense_Mutation	SNP	ENST00000310574.3	37	CCDS1740.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.365785	0.82463	.	.	ENSG00000138074	ENST00000310574;ENST00000408041	D;D	0.88046	-2.33;-2.33	5.45	4.54	0.55810	.	0.061271	0.64402	D	0.000004	D	0.93762	0.8006	M	0.91612	3.225	0.53688	D	0.999978	D	0.69078	0.997	P	0.62491	0.903	D	0.94819	0.7985	10	0.87932	D	0	.	14.1351	0.65281	0.0:0.15:0.85:0.0	.	286	Q9Y289	SC5A6_HUMAN	M	286	ENSP00000310208:T286M;ENSP00000384853:T286M	ENSP00000310208:T286M	T	-	2	0	SLC5A6	27281181	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	6.358000	0.73055	2.550000	0.86006	0.655000	0.94253	ACG		0.607	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095	
CAD	790	broad.mit.edu	37	2	27454962	27454962	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:27454962C>T	ENST00000403525.1	+	16	2470	c.2326C>T	c.(2326-2328)Cga>Tga	p.R776*	CAD_ENST00000264705.4_Nonsense_Mutation_p.R839*|CAD_ENST00000464159.1_3'UTR			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)	p.R839*(1)		NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTTCCTGCACCGAATGAAGCG	0.552																																					p.R839X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2515T	2						.						117.0	101.0	107.0					2																	27454962		2203	4300	6503	27308466	SO:0001587	stop_gained	790	exon17			D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.2326C>T	2.37:g.27454962C>T	ENSP00000384510:p.Arg776*	Somatic		Capture	Illumina HiSeq	Phase_I	27308466	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Nonsense_Mutation	SNP	ENST00000403525.1	37		.	.	.	.	.	.	.	.	.	.	C	38	6.831546	0.97869	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	.	.	.	5.38	1.17	0.20885	.	0.228629	0.42548	D	0.000683	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-7.8184	8.2873	0.31937	0.6582:0.26:0.0:0.0818	.	.	.	.	X	839;776	.	ENSP00000264705:R839X	R	+	1	2	CAD	27308466	1.000000	0.71417	0.932000	0.37286	0.485000	0.33311	1.816000	0.38992	0.364000	0.24374	-0.182000	0.12963	CGA		0.552	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		
GTF3C2	2976	broad.mit.edu	37	2	27551030	27551030	+	Silent	SNP	C	C	T	rs375864086		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:27551030C>T	ENST00000359541.2	-	17	2712	c.2283G>A	c.(2281-2283)ccG>ccA	p.P761P	GTF3C2_ENST00000264720.3_Silent_p.P761P|MPV17_ENST00000357186.6_5'Flank			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	761					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)		p.P761P(2)		central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTCCTGATACGGTATCAGAT	0.443																																					p.P761P												.	.	2	Substitution - coding silent(2)	urinary_tract(1)|large_intestine(1)	c.G2283A	2						.	C	,	0,4406		0,0,2203	78.0	75.0	76.0		2283,2283	-10.7	0.9	2		76	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	GTF3C2	NM_001035521.1,NM_001521.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	761/912,761/912	27551030	1,13005	2203	4300	6503	27404534	SO:0001819	synonymous_variant	2976	exon17			D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"""General transcription factors"", ""WD repeat domain containing"""	4665	protein-coding gene	gene with protein product		604883	"""general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"""			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.2283G>A	2.37:g.27551030C>T		Somatic		Capture	Illumina HiSeq	Phase_I	27404534	NM_001035521	D6W557|Q16632|Q9BWI7	Silent	SNP	ENST00000359541.2	37	CCDS1749.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.087|7.087	0.571360|0.571360	0.13623|0.13623	0.0|0.0	1.16E-4|1.16E-4	ENSG00000115207|ENSG00000115207	ENST00000454704;ENST00000415683|ENST00000457098	.|.	.|.	.|.	5.34|5.34	-10.7|-10.7	0.00240|0.00240	.|.	.|.	.|.	.|.	.|.	T|T	0.35038|0.35038	0.0918|0.0918	.|.	.|.	.|.	0.54753|0.54753	D|D	0.999981|0.999981	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.45833|0.45833	-0.9234|-0.9234	4|4	.|.	.|.	.|.	-9.9413|-9.9413	4.145|4.145	0.10212|0.10212	0.0917:0.3422:0.3643:0.2018|0.0917:0.3422:0.3643:0.2018	.|.	.|.	.|.	.|.	H|I	270;184|55	.|.	.|.	R|V	-|-	2|1	0|0	GTF3C2|GTF3C2	27404534|27404534	0.147000|0.147000	0.22687|0.22687	0.866000|0.866000	0.34008|0.34008	0.955000|0.955000	0.61496|0.61496	-1.304000|-1.304000	0.02741|0.02741	-1.458000|-1.458000	0.01916|0.01916	-1.114000|-1.114000	0.02060|0.02060	CGT|GTA		0.443	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2		
SNX17	9784	broad.mit.edu	37	2	27595509	27595509	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:27595509C>T	ENST00000233575.2	+	3	380	c.158C>T	c.(157-159)gCc>gTc	p.A53V	EIF2B4_ENST00000451130.2_5'Flank|EIF2B4_ENST00000493344.2_5'Flank|EIF2B4_ENST00000445933.2_5'Flank|SNX17_ENST00000543024.1_Intron|EIF2B4_ENST00000347454.4_5'Flank|SNX17_ENST00000537606.1_Missense_Mutation_p.A28V|SNX17_ENST00000542478.1_5'UTR	NM_001267059.1|NM_001267061.1|NM_014748.3	NP_001253988.1|NP_001253990.1|NP_055563.1	Q15036	SNX17_HUMAN	sorting nexin 17	53	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				cholesterol catabolic process (GO:0006707)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|receptor-mediated endocytosis (GO:0006898)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)	low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol binding (GO:0035091)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)	p.A53V(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAGTATGGGGCCAATGTGCTT	0.443																																					p.A53V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C158T	2						.						115.0	107.0	110.0					2																	27595509		2203	4300	6503	27449013	SO:0001583	missense	9784	exon3			D31764	CCDS1750.1, CCDS58704.1	2p23-p22	2008-05-21			ENSG00000115234	ENSG00000115234		"""Sorting nexins"""	14979	protein-coding gene	gene with protein product		605963				12169628, 15769472	Standard	NM_014748		Approved	KIAA0064	uc002rkg.2	Q15036	OTTHUMG00000097781	ENST00000233575.2:c.158C>T	2.37:g.27595509C>T	ENSP00000233575:p.Ala53Val	Somatic		Capture	Illumina HiSeq	Phase_I	27449013	NM_014748	B4DQM7|Q53HN7|Q6IAS3	Missense_Mutation	SNP	ENST00000233575.2	37	CCDS1750.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.193921	0.38707	.	.	ENSG00000115234	ENST00000233575;ENST00000537606	T;T	0.40225	1.04;1.04	5.46	5.46	0.80206	Phox homologous domain (5);	0.155442	0.64402	D	0.000014	T	0.34774	0.0909	L	0.39898	1.24	0.80722	D	1	B;B;B;B	0.23990	0.095;0.023;0.043;0.032	B;B;B;B	0.23018	0.015;0.004;0.043;0.006	T	0.09618	-1.0666	10	0.35671	T	0.21	-10.6092	12.9142	0.58197	0.1624:0.8376:0.0:0.0	.	28;41;33;53	B4DQM7;B4DTB8;B4DQ37;Q15036	.;.;.;SNX17_HUMAN	V	53;28	ENSP00000233575:A53V;ENSP00000439208:A28V	ENSP00000233575:A53V	A	+	2	0	SNX17	27449013	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.640000	0.54350	2.547000	0.85894	0.561000	0.74099	GCC		0.443	SNX17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215024.1	NM_014748	
FOSL2	2355	broad.mit.edu	37	2	28634797	28634797	+	Splice_Site	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:28634797G>T	ENST00000264716.4	+	4	1326	c.463G>T	c.(463-465)Gag>Tag	p.E155*	FOSL2_ENST00000379619.1_Nonsense_Mutation_p.E147*|FOSL2_ENST00000545753.1_Splice_Site_p.E116*	NM_005253.3	NP_005244.1	P15408	FOSL2_HUMAN	FOS-like antigen 2	155	bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				cell death (GO:0008219)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E155*(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)					TCCGTGGCAGGAGACAGAGGA	0.542																																					p.E155X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G463T	2						.						39.0	44.0	42.0					2																	28634797		2203	4300	6503	28488301	SO:0001630	splice_region_variant	2355	exon4				CCDS1766.1	2p23.3	2013-01-10			ENSG00000075426	ENSG00000075426		"""basic leucine zipper proteins"""	3798	protein-coding gene	gene with protein product		601575					Standard	NM_005253		Approved	FRA2, FLJ23306	uc002rma.3	P15408	OTTHUMG00000097832	ENST00000264716.4:c.463-1G>T	2.37:g.28634797G>T		Somatic		Capture	Illumina HiSeq	Phase_I	28488301	NM_005253	B2RD58|B3KP27|B4DYV4|Q6FG46	Nonsense_Mutation	SNP	ENST00000264716.4	37	CCDS1766.1	.	.	.	.	.	.	.	.	.	.	G	36	5.897418	0.97081	.	.	ENSG00000075426	ENST00000379619;ENST00000264716;ENST00000436647;ENST00000545753	.	.	.	5.08	5.08	0.68730	.	0.151274	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-4.2495	19.3591	0.94428	0.0:0.0:1.0:0.0	.	.	.	.	X	147;155;116;116	.	ENSP00000264716:E155X	E	+	1	0	FOSL2	28488301	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	9.658000	0.98594	2.746000	0.94184	0.650000	0.86243	GAG		0.542	FOSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215116.2	NM_005253	Nonsense_Mutation
EHD3	30845	broad.mit.edu	37	2	31467249	31467249	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:31467249G>A	ENST00000322054.5	+	2	622	c.337G>A	c.(337-339)Gcc>Acc	p.A113T	EHD3_ENST00000541626.1_Missense_Mutation_p.A113T	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	113	Dynamin-type G.				blood coagulation (GO:0007596)|endocytic recycling (GO:0032456)|protein homooligomerization (GO:0051260)|protein targeting to plasma membrane (GO:0072661)|regulation of cardiac muscle cell membrane potential (GO:0086036)	cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)	p.A113T(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					CCCTGGGAACGCCCTGGTGGT	0.562																																					p.A113T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G337A	2						.						116.0	89.0	98.0					2																	31467249		2203	4300	6503	31320753	SO:0001583	missense	30845	exon2			AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016		"""EF-hand domain containing"""	3244	protein-coding gene	gene with protein product		605891		PAST3		10673336	Standard	NM_014600		Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.337G>A	2.37:g.31467249G>A	ENSP00000327116:p.Ala113Thr	Somatic		Capture	Illumina HiSeq	Phase_I	31320753	NM_014600	B4DFR5|D6W574|Q8N514|Q9NZB3	Missense_Mutation	SNP	ENST00000322054.5	37	CCDS1774.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.982851	0.93044	.	.	ENSG00000013016	ENST00000541626;ENST00000322054	D;D	0.95272	-3.66;-3.66	5.7	5.7	0.88788	Dynamin, GTPase domain (1);	0.000000	0.85682	D	0.000000	D	0.94608	0.8262	N	0.16567	0.415	0.80722	D	1	D;D	0.76494	0.987;0.999	P;D	0.76071	0.821;0.987	D	0.93990	0.7266	10	0.33141	T	0.24	-23.698	19.8471	0.96713	0.0:0.0:1.0:0.0	.	113;113	B4DFR5;Q9NZN3	.;EHD3_HUMAN	T	113	ENSP00000440685:A113T;ENSP00000327116:A113T	ENSP00000327116:A113T	A	+	1	0	EHD3	31320753	1.000000	0.71417	0.859000	0.33776	0.904000	0.53231	9.476000	0.97823	2.688000	0.91661	0.655000	0.94253	GCC		0.562	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216810.1	NM_014600	
DPY30	84661	broad.mit.edu	37	2	32264371	32264371	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:32264371A>G	ENST00000342166.5	-	3	176	c.61T>C	c.(61-63)Tac>Cac	p.Y21H	DPY30_ENST00000295066.3_Missense_Mutation_p.Y21H			Q9C005	DPY30_HUMAN	dpy-30 homolog (C. elegans)	21					endosomal transport (GO:0016197)|histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)	p.Y21H(1)		large_intestine(2)	2	Acute lymphoblastic leukemia(172;0.155)					GTGAGACCGTACTCAGAGTGA	0.493																																					p.Y21H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T61C	2						.						153.0	154.0	154.0					2																	32264371		2203	4300	6503	32117875	SO:0001583	missense	84661	exon3				CCDS1777.1	2p22.3	2013-09-09			ENSG00000162961	ENSG00000162961			24590	protein-coding gene	gene with protein product		612032				12477932	Standard	XM_006712117		Approved	Saf19, HDPY-30, Cps25	uc002roa.1	Q9C005	OTTHUMG00000128457	ENST00000342166.5:c.61T>C	2.37:g.32264371A>G	ENSP00000345837:p.Tyr21His	Somatic		Capture	Illumina HiSeq	Phase_I	32117875	NM_032574	D6W578	Missense_Mutation	SNP	ENST00000342166.5	37	CCDS1777.1	.	.	.	.	.	.	.	.	.	.	A	16.40	3.113621	0.56398	.	.	ENSG00000162961	ENST00000342166;ENST00000295066	.	.	.	5.92	5.92	0.95590	.	0.053759	0.85682	D	0.000000	T	0.46795	0.1411	.	.	.	0.58432	D	0.999999	P	0.48911	0.917	B	0.43478	0.421	T	0.35475	-0.9787	8	0.18276	T	0.48	-11.0574	16.0277	0.80555	1.0:0.0:0.0:0.0	.	21	Q9C005	DPY30_HUMAN	H	21	.	ENSP00000295066:Y21H	Y	-	1	0	DPY30	32117875	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	7.864000	0.87037	2.274000	0.75844	0.533000	0.62120	TAC		0.493	DPY30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250255.2	NM_032574	
BIRC6	57448	broad.mit.edu	37	2	32740194	32740194	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:32740194C>A	ENST00000421745.2	+	55	10840	c.10706C>A	c.(10705-10707)cCt>cAt	p.P3569H		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3569					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.P3569H(1)|p.P3541H(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					ATTACCCCTCCTCCAGTGCAA	0.413																																					p.P3569H	Pancreas(94;175 1509 16028 18060 45422)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C10706A	2						.						101.0	97.0	98.0					2																	32740194		2203	4300	6503	32593698	SO:0001583	missense	57448	exon55			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.10706C>A	2.37:g.32740194C>A	ENSP00000393596:p.Pro3569His	Somatic		Capture	Illumina HiSeq	Phase_I	32593698	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	26.0	4.698959	0.88830	.	.	ENSG00000115760	ENST00000421745	T	0.78481	-1.18	5.68	5.68	0.88126	.	0.207593	0.43110	D	0.000602	D	0.84754	0.5542	L	0.50333	1.59	0.80722	D	1	D	0.67145	0.996	P	0.61533	0.89	D	0.85618	0.1262	10	0.87932	D	0	.	19.7934	0.96469	0.0:1.0:0.0:0.0	.	3569	Q9NR09	BIRC6_HUMAN	H	3569	ENSP00000393596:P3569H	ENSP00000393596:P3569H	P	+	2	0	BIRC6	32593698	1.000000	0.71417	0.993000	0.49108	0.979000	0.70002	3.248000	0.51430	2.678000	0.91216	0.585000	0.79938	CCT		0.413	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
TTC27	55622	broad.mit.edu	37	2	32927971	32927971	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:32927971C>T	ENST00000317907.4	+	10	1448	c.1217C>T	c.(1216-1218)gCa>gTa	p.A406V		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	406								p.A406V(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						GTGGAACGGGCAATGAGGCAG	0.443																																					p.A356V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1067T	2						.						115.0	103.0	107.0					2																	32927971		2203	4300	6503	32781475	SO:0001583	missense	55622	exon10			BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"""Tetratricopeptide (TTC) repeat domain containing"""	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1217C>T	2.37:g.32927971C>T	ENSP00000313953:p.Ala406Val	Somatic		Capture	Illumina HiSeq	Phase_I	32781475	NM_001193509	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	37	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.480044	0.84747	.	.	ENSG00000018699	ENST00000317907;ENST00000438654	T	0.33216	1.42	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.43942	0.1270	M	0.83953	2.67	0.80722	D	1	P	0.35575	0.51	B	0.36289	0.221	T	0.49341	-0.8950	10	0.72032	D	0.01	-14.2455	18.8499	0.92224	0.0:1.0:0.0:0.0	.	406	Q6P3X3	TTC27_HUMAN	V	406;48	ENSP00000313953:A406V	ENSP00000313953:A406V	A	+	2	0	TTC27	32781475	1.000000	0.71417	0.992000	0.48379	0.960000	0.62799	6.717000	0.74707	2.736000	0.93811	0.655000	0.94253	GCA		0.443	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735	
FAM98A	25940	broad.mit.edu	37	2	33810416	33810416	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:33810416G>A	ENST00000238823.8	-	8	1124	c.984C>T	c.(982-984)ggC>ggT	p.G328G	FAM98A_ENST00000441530.2_Silent_p.G133G|FAM98A_ENST00000403368.1_3'UTR|FAM98A_ENST00000498340.1_5'Flank			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	329							poly(A) RNA binding (GO:0044822)	p.G328G(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1)	24	all_hematologic(175;0.115)					GCTGCTGGGGGCCATCTTGCC	0.587																																					p.G328G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C984T	2						.						58.0	53.0	55.0					2																	33810416		2203	4300	6503	33663920	SO:0001819	synonymous_variant	25940	exon8				CCDS33179.1	2p22.3	2006-11-29		2005-11-20	ENSG00000119812	ENSG00000119812			24520	protein-coding gene	gene with protein product						12477932	Standard	NM_015475		Approved	DKFZP564F0522	uc002rpa.1	Q8NCA5	OTTHUMG00000152152	ENST00000238823.8:c.984C>T	2.37:g.33810416G>A		Somatic		Capture	Illumina HiSeq	Phase_I	33663920	NM_015475	B2RNA2|Q9Y3Y6	Silent	SNP	ENST00000238823.8	37	CCDS33179.1																																																																																				0.587	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475	
DHX57	90957	broad.mit.edu	37	2	39090518	39090518	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:39090518G>A	ENST00000295373.6	-	3	494	c.368C>T	c.(367-369)gCt>gTt	p.A123V	DHX57_ENST00000479345.2_5'UTR|AC018693.6_ENST00000442829.1_RNA	NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	123							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.A123V(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TCCAGCATCAGCATCTTGTTC	0.403																																					p.A123V	Melanoma(191;1090 2095 4375 23729 47341)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C368T	2						.						126.0	123.0	124.0					2																	39090518		2203	4300	6503	38944022	SO:0001583	missense	90957	exon3			AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.368C>T	2.37:g.39090518G>A	ENSP00000295373:p.Ala123Val	Somatic		Capture	Illumina HiSeq	Phase_I	38944022	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	.	.	.	.	.	.	.	.	.	.	G	10.91	1.484110	0.26598	.	.	ENSG00000163214	ENST00000295373;ENST00000355320;ENST00000417233	T	0.02446	4.29	5.68	3.89	0.44902	.	0.247869	0.28566	N	0.014895	T	0.01489	0.0048	N	0.08118	0	0.09310	N	1	P;B	0.34587	0.458;0.146	B;B	0.31869	0.137;0.038	T	0.49978	-0.8881	10	0.15952	T	0.53	.	6.9681	0.24635	0.3774:0.0:0.6226:0.0	.	123;123	Q6P158-2;Q6P158	.;DHX57_HUMAN	V	123;21;21	ENSP00000295373:A123V	ENSP00000295373:A123V	A	-	2	0	DHX57	38944022	0.900000	0.30661	0.352000	0.25734	0.990000	0.78478	2.499000	0.45372	0.755000	0.32990	-0.291000	0.09656	GCT		0.403	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
SLC8A1	6546	broad.mit.edu	37	2	40342512	40342512	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:40342512C>A	ENST00000403092.1	-	11	2836	c.2803G>T	c.(2803-2805)Ggt>Tgt	p.G935C	SLC8A1_ENST00000542756.1_Missense_Mutation_p.G930C|SLC8A1-AS1_ENST00000593848.1_RNA|SLC8A1-AS1_ENST00000597385.1_RNA|SLC8A1_ENST00000402441.1_Missense_Mutation_p.G899C|SLC8A1-AS1_ENST00000435515.1_RNA|SLC8A1_ENST00000408028.2_Missense_Mutation_p.G927C|SLC8A1-AS1_ENST00000597170.1_RNA|SLC8A1_ENST00000405269.1_Missense_Mutation_p.G899C|SLC8A1-AS1_ENST00000598247.1_RNA|SLC8A1-AS1_ENST00000599740.1_RNA|SLC8A1_ENST00000406391.2_Missense_Mutation_p.G899C|SLC8A1_ENST00000332839.4_Missense_Mutation_p.G935C|SLC8A1-AS1_ENST00000596532.1_RNA|SLC8A1_ENST00000406785.2_Missense_Mutation_p.G899C|SLC8A1_ENST00000405901.3_Missense_Mutation_p.G930C|SLC8A1-AS1_ENST00000599956.1_RNA|SLC8A1-AS1_ENST00000593878.1_RNA|SLC8A1_ENST00000542024.1_Missense_Mutation_p.G899C|SLC8A1-AS1_ENST00000444629.1_RNA|SLC8A1-AS1_ENST00000601679.1_RNA|SLC8A1-AS1_ENST00000599268.1_RNA			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	935					blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|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 the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.G935C(1)		NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	CCCAGCTCACCTCCGATTTCT	0.552																																					p.G930C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2788T	2						.						64.0	64.0	64.0					2																	40342512		2203	4300	6503	40196016	SO:0001583	missense	6546	exon9				CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"""Solute carriers"""	11068	protein-coding gene	gene with protein product	"""Na+/Ca++ exchanger"""	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.2803G>T	2.37:g.40342512C>A	ENSP00000384763:p.Gly935Cys	Somatic		Capture	Illumina HiSeq	Phase_I	40196016	NM_001112800	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	37	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.998865	0.74818	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	T;T;T;T;T;T;T;T;T;T	0.34667	1.36;1.41;1.41;1.41;1.36;1.36;1.41;1.36;1.36;1.35	5.94	5.94	0.96194	Sodium/calcium exchanger membrane region (1);	0.000000	0.85682	D	0.000000	T	0.69495	0.3117	M	0.91038	3.17	0.80722	D	1	P;D;D;D	0.89917	0.938;0.999;1.0;0.999	P;D;D;D	0.91635	0.656;0.972;0.999;0.984	T	0.75371	-0.3341	10	0.72032	D	0.01	.	17.8596	0.88777	0.0:1.0:0.0:0.0	.	899;922;930;935	P32418-2;P32418-3;F6VPY9;P32418	.;.;.;NAC1_HUMAN	C	899;935;930;935;930;899;899;935;927;922;899;899	ENSP00000383886:G899C;ENSP00000440727:G930C;ENSP00000384763:G935C;ENSP00000385678:G930C;ENSP00000385188:G899C;ENSP00000385535:G899C;ENSP00000332931:G935C;ENSP00000384908:G927C;ENSP00000385811:G899C;ENSP00000443515:G899C	ENSP00000332931:G935C	G	-	1	0	SLC8A1	40196016	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.711000	0.84669	2.820000	0.97059	0.650000	0.86243	GGT		0.552	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097	
OXER1	165140	broad.mit.edu	37	2	42990277	42990277	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:42990277C>T	ENST00000378661.2	-	1	1124	c.1043G>A	c.(1042-1044)aGt>aAt	p.S348N		NM_148962.4	NP_683765.1	Q8TDS5	OXER1_HUMAN	oxoeicosanoid (OXE) receptor 1	348					G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cAMP biosynthetic process (GO:0030817)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050648)|5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050647)|5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050646)|G-protein coupled receptor activity (GO:0004930)	p.S348N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10						GTCCAGGACACTGTTGAGGTA	0.652																																					p.S348N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1043A	2						.						53.0	61.0	58.0					2																	42990277		2203	4300	6503	42843781	SO:0001583	missense	165140	exon1			AB083055	CCDS1810.1	2p22.1	2012-08-10			ENSG00000162881	ENSG00000162881		"""GPCR / Class A : Leukotriene receptors"""	24884	protein-coding gene	gene with protein product	"""5-oxo-ETE acid G-protein-coupled receptor 1"""					12065583, 15001665	Standard	NM_148962		Approved	GPCR, TG1019, GPR170	uc002rss.3	Q8TDS5	OTTHUMG00000128643	ENST00000378661.2:c.1043G>A	2.37:g.42990277C>T	ENSP00000367930:p.Ser348Asn	Somatic		Capture	Illumina HiSeq	Phase_I	42843781	NM_148962	Q86WP7|Q8NGW4	Missense_Mutation	SNP	ENST00000378661.2	37	CCDS1810.1	.	.	.	.	.	.	.	.	.	.	C	13.95	2.388922	0.42308	.	.	ENSG00000162881	ENST00000378661	T	0.79554	-1.28	4.46	3.55	0.40652	GPCR, rhodopsin-like superfamily (1);	0.831573	0.09920	U	0.738621	D	0.88492	0.6451	M	0.70842	2.15	0.33711	D	0.61581	D	0.89917	1.0	D	0.91635	0.999	D	0.86063	0.1533	10	0.54805	T	0.06	.	11.2173	0.48833	0.1849:0.815:0.0:0.0	.	348	Q8TDS5	OXER1_HUMAN	N	348	ENSP00000367930:S348N	ENSP00000367930:S348N	S	-	2	0	OXER1	42843781	0.891000	0.30450	0.104000	0.21259	0.087000	0.18053	2.112000	0.41892	0.808000	0.34231	0.655000	0.94253	AGT		0.652	OXER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250514.1	NM_148962	
LRPPRC	10128	broad.mit.edu	37	2	44190783	44190784	+	Frame_Shift_Del	DEL	TA	TA	-	rs35035668	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	TA	TA	TA	-	TA	TA	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:44190783_44190784delTA	ENST00000260665.7	-	12	1488_1489	c.1431_1432delTA	c.(1429-1434)tatacafs	p.T478fs	LRPPRC_ENST00000409659.1_Frame_Shift_Del_p.T478fs|LRPPRC_ENST00000409946.1_Frame_Shift_Del_p.T478fs	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	478			T -> A (in dbSNP:rs35035668).		mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.T478fs*8(1)		breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				ACATAATCTGTATATGTTTCCT	0.351																																					p.477_478del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1431_1432del	2						.																																			44044288	SO:0001589	frameshift_variant	10128	exon12			M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.1431_1432delTA	2.37:g.44190785_44190786delTA	ENSP00000260665:p.Thr478fs	Somatic		Capture	Illumina HiSeq	Phase_I	44044287	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Frame_Shift_Del	DEL	ENST00000260665.7	37	CCDS33189.1																																																																																				0.351	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
CAMKMT	79823	broad.mit.edu	37	2	44993593	44993593	+	Missense_Mutation	SNP	C	C	T	rs201075899		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:44993593C>T	ENST00000378494.3	+	10	831	c.787C>T	c.(787-789)Cgc>Tgc	p.R263C		NM_024766.4	NP_079042.1	Q7Z624	CMKMT_HUMAN	calmodulin-lysine N-methyltransferase	263						Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	calmodulin-lysine N-methyltransferase activity (GO:0018025)	p.R263C(1)		breast(2)|large_intestine(3)|lung(5)	10						ATTTGCCCCACGCCGAGGGAA	0.368													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19642	0.0		0.0	False		,,,				2504	0.0				p.R263C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C787T	2						.						91.0	87.0	88.0					2																	44993593		2203	4300	6503	44847097	SO:0001583	missense	79823	exon10				CCDS1820.1	2p21	2011-06-22	2011-03-10	2011-03-10	ENSG00000143919	ENSG00000143919	2.1.1.60		26276	protein-coding gene	gene with protein product	"""CaM KMT"""	609559	"""chromosome 2 open reading frame 34"""	C2orf34		20975703	Standard	NM_024766		Approved	CLNMT	uc002rum.3	Q7Z624	OTTHUMG00000128761	ENST00000378494.3:c.787C>T	2.37:g.44993593C>T	ENSP00000367755:p.Arg263Cys	Somatic		Capture	Illumina HiSeq	Phase_I	44847097	NM_024766	Q4ZG15|Q53SS6|Q8N6P5|Q9H5G8	Missense_Mutation	SNP	ENST00000378494.3	37	CCDS1820.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	17.88	3.496438	0.64186	.	.	ENSG00000143919	ENST00000378494	T	0.07800	3.16	5.47	5.47	0.80525	.	0.701912	0.14850	N	0.294740	T	0.20047	0.0482	L	0.46157	1.445	0.80722	D	1	D	0.76494	0.999	P	0.54815	0.761	T	0.00453	-1.1730	10	0.56958	D	0.05	-1.5934	19.3513	0.94387	0.0:1.0:0.0:0.0	.	263	Q7Z624	CMKMT_HUMAN	C	263	ENSP00000367755:R263C	ENSP00000367755:R263C	R	+	1	0	CAMKMT	44847097	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.150000	0.50662	2.571000	0.86741	0.650000	0.86243	CGC		0.368	CAMKMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250678.2	NM_024766	
TTC7A	57217	broad.mit.edu	37	2	47233183	47233183	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:47233183C>T	ENST00000319190.5	+	9	1556	c.1188C>T	c.(1186-1188)taC>taT	p.Y396Y	TTC7A_ENST00000394850.2_Silent_p.Y396Y|TTC7A_ENST00000409245.1_Silent_p.Y362Y|TTC7A_ENST00000263737.6_Silent_p.Y42Y|TTC7A_ENST00000461601.1_3'UTR	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	396					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)			p.Y396Y(1)		breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GGGGACAGTACGTCATGCTCT	0.607																																					p.Y396Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1188T	2						.						143.0	108.0	120.0					2																	47233183		2203	4300	6503	47086687	SO:0001819	synonymous_variant	57217	exon9			AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"""Tetratricopeptide (TTC) repeat domain containing"""	19750	protein-coding gene	gene with protein product		609332	"""tetratricopeptide repeat domain 7"""	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.1188C>T	2.37:g.47233183C>T		Somatic		Capture	Illumina HiSeq	Phase_I	47086687	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	De_novo_Start_InFrame	SNP	ENST00000319190.5	37	CCDS33193.1																																																																																				0.607	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927	
STON1	11037	broad.mit.edu	37	2	48807797	48807797	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:48807797T>C	ENST00000406226.1	+	3	220	c.25T>C	c.(25-27)Tgg>Cgg	p.W9R	STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.W9R|STON1_ENST00000404752.1_Missense_Mutation_p.W9R|STON1_ENST00000309835.3_Missense_Mutation_p.W9R|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.W9R|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.W9R|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.W9R|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.W9R	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	9					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)		p.W9R(2)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TCCAGGCAAATGGGTCACCTT	0.373																																					p.W9R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T25C	2						.						93.0	88.0	90.0					2																	48807797		2203	4300	6503	48661301	SO:0001583	missense	286749	exon1			AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.25T>C	2.37:g.48807797T>C	ENSP00000384615:p.Trp9Arg	Somatic		Capture	Illumina HiSeq	Phase_I	48661301	NM_001198594	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Missense_Mutation	SNP	ENST00000406226.1	37	CCDS1841.1	.	.	.	.	.	.	.	.	.	.	T	17.63	3.436198	0.62955	.	.	ENSG00000243244;ENSG00000243244;ENSG00000243244;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781	ENST00000404752;ENST00000406226;ENST00000309835;ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751	T;T;T;T;T;T;T;T	0.34472	1.6;1.6;1.6;1.41;1.36;1.41;1.41;1.61	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.58250	0.2109	M	0.63843	1.955	0.51012	D	0.999901	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.998	T	0.61267	-0.7097	10	0.87932	D	0	.	15.79	0.78350	0.0:0.0:0.0:1.0	.	9;9;9	A8MXJ1;Q53S48;Q9Y6Q2	.;.;STON1_HUMAN	R	9	ENSP00000385273:W9R;ENSP00000384615:W9R;ENSP00000310969:W9R;ENSP00000385499:W9R;ENSP00000385701:W9R;ENSP00000378236:W9R;ENSP00000311493:W9R;ENSP00000378234:W9R	ENSP00000310969:W9R	W	+	1	0	STON1-GTF2A1L;STON1	48661301	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.140000	0.77322	2.371000	0.80710	0.533000	0.62120	TGG		0.373	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
GTF2A1L	11036	broad.mit.edu	37	2	48847998	48847998	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:48847998C>A	ENST00000403751.3	+	2	67	c.30C>A	c.(28-30)ctC>ctA	p.L10L	STON1-GTF2A1L_ENST00000309827.2_Silent_p.L714L|STON1-GTF2A1L_ENST00000394751.3_Silent_p.L714L|STON1-GTF2A1L_ENST00000405008.1_Silent_p.L714L|GTF2A1L_ENST00000468326.1_3'UTR|STON1-GTF2A1L_ENST00000394754.1_Silent_p.L714L|GTF2A1L_ENST00000430487.2_Intron|STON1-GTF2A1L_ENST00000402114.2_Silent_p.L714L	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	10					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.L714L(1)		lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGCCTAAACTCTACAGATCTG	0.274																																					p.L10L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C30A	2						.						49.0	50.0	49.0					2																	48847998		2203	4299	6502	48701502	SO:0001819	synonymous_variant	286749	exon2			AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"""TFIIA alpha/beta like factor"""	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.30C>A	2.37:g.48847998C>A		Somatic		Capture	Illumina HiSeq	Phase_I	48701502	NM_006872	B4DY14|Q53FD9|Q5D050	Silent	SNP	ENST00000403751.3	37	CCDS46281.1																																																																																				0.274	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872	
GPR75-ASB3	100302652	broad.mit.edu	37	2	53897736	53897736	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:53897736C>T	ENST00000263634.3	-	10	1595	c.1461G>A	c.(1459-1461)caG>caA	p.Q487Q	GPR75-ASB3_ENST00000482829.1_5'UTR|GPR75-ASB3_ENST00000352846.3_Silent_p.Q525Q|GPR75-ASB3_ENST00000406687.1_Silent_p.Q414Q|GPR75-ASB3_ENST00000394717.2_Silent_p.Q414Q|ASB3_ENST00000406625.2_Silent_p.Q522Q	NM_016115.4	NP_057199.1			GPR75-ASB3 readthrough									p.Q487Q(1)									GAAGTGGCAGCTGACTAATAT	0.428																																					p.Q487Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1461A	2						.						75.0	73.0	74.0					2																	53897736		2203	4300	6503	53751240	SO:0001819	synonymous_variant	51130	exon10				CCDS54361.1	2p16	2013-01-23			ENSG00000115239	ENSG00000115239			40043	other	readthrough							Standard	NM_001164165		Approved				OTTHUMG00000129279	ENST00000263634.3:c.1461G>A	2.37:g.53897736C>T		Somatic		Capture	Illumina HiSeq	Phase_I	53751240	NM_016115		Silent	SNP	ENST00000263634.3	37	CCDS1846.1																																																																																				0.428	GPR75-ASB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251402.3		
PSME4	23198	broad.mit.edu	37	2	54115120	54115120	+	Silent	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:54115120A>C	ENST00000404125.1	-	39	4450	c.4395T>G	c.(4393-4395)ctT>ctG	p.L1465L	PSME4_ENST00000421748.2_Silent_p.L609L|PSME4_ENST00000476586.1_5'Flank	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1465					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)	p.L1351L(1)		breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			GTAGTACATAAAGTCGACTAA	0.413																																					p.L1465L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T4395G	2						.						98.0	89.0	92.0					2																	54115120		2203	4300	6503	53968624	SO:0001819	synonymous_variant	23198	exon39			D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.4395T>G	2.37:g.54115120A>C		Somatic		Capture	Illumina HiSeq	Phase_I	53968624	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	37	CCDS33197.2																																																																																				0.413	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
EFEMP1	2202	broad.mit.edu	37	2	56102153	56102153	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:56102153C>T	ENST00000394555.2	-	8	1363	c.928G>A	c.(928-930)Gtc>Atc	p.V310I	EFEMP1_ENST00000355426.3_Missense_Mutation_p.V310I|EFEMP1_ENST00000424836.2_Missense_Mutation_p.V172I|EFEMP1_ENST00000394554.1_Missense_Mutation_p.V310I	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	310	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.|Mediates interaction with TIMP3.				epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)	p.V310I(1)		NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GGTTCATTGACACATTGATAT	0.383																																					p.V310I	GBM(92;934 1319 7714 28760 40110)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G928A	2						.						140.0	119.0	126.0					2																	56102153		2203	4300	6503	55955657	SO:0001583	missense	2202	exon9			U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"""Fibulins"""	3218	protein-coding gene	gene with protein product	"""fibulin 3"""	601548	"""fibrillin-like"", ""EGF-containing fibulin-like extracellular matrix protein 1"""	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.928G>A	2.37:g.56102153C>T	ENSP00000378058:p.Val310Ile	Somatic		Capture	Illumina HiSeq	Phase_I	55955657	NM_001039348	A8K3I4|B4DW75|D6W5D2|Q541U7	Missense_Mutation	SNP	ENST00000394555.2	37	CCDS1857.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.250460	0.59212	.	.	ENSG00000115380	ENST00000394555;ENST00000394554;ENST00000405693;ENST00000424836;ENST00000355426	D;D;D;D	0.95656	-2.25;-2.25;-3.77;-2.25	5.66	5.66	0.87406	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.219140	0.31507	N	0.007534	D	0.94295	0.8167	N	0.05414	-0.055	0.58432	D	0.999999	D;B	0.56035	0.974;0.084	D;B	0.73380	0.98;0.021	D	0.92097	0.5685	10	0.14252	T	0.57	.	19.79	0.96453	0.0:1.0:0.0:0.0	.	172;310	B4DW75;Q12805	.;FBLN3_HUMAN	I	310;310;166;172;310	ENSP00000378058:V310I;ENSP00000378057:V310I;ENSP00000399145:V172I;ENSP00000347596:V310I	ENSP00000347596:V310I	V	-	1	0	EFEMP1	55955657	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.200000	0.42724	2.680000	0.91292	0.478000	0.44815	GTC		0.383	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2		
VRK2	7444	broad.mit.edu	37	2	58313492	58313492	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:58313492G>A	ENST00000435505.2	+	8	1020	c.275G>A	c.(274-276)cGc>cAc	p.R92H	VRK2_ENST00000340157.4_Missense_Mutation_p.R92H|VRK2_ENST00000412104.2_Missense_Mutation_p.R92H|VRK2_ENST00000417641.2_Missense_Mutation_p.R92H|VRK2_ENST00000440705.2_Missense_Mutation_p.R69H			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	92	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R92L(1)|p.R92H(1)		endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						TGGATAGAACGCAAACAACTT	0.279																																					p.R92H												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G275A	2						.						106.0	120.0	115.0					2																	58313492		2203	4294	6497	58166996	SO:0001583	missense	7444	exon5			AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.275G>A	2.37:g.58313492G>A	ENSP00000408002:p.Arg92His	Somatic		Capture	Illumina HiSeq	Phase_I	58166996	NM_001130483	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Missense_Mutation	SNP	ENST00000435505.2	37	CCDS1859.1	.	.	.	.	.	.	.	.	.	.	G	9.725	1.160722	0.21538	.	.	ENSG00000028116	ENST00000435505;ENST00000417641;ENST00000423109;ENST00000412104;ENST00000340157;ENST00000394539;ENST00000440705	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	5.33	1.35	0.21983	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.092300	0.06725	N	0.775607	T	0.21387	0.0515	N	0.04636	-0.2	0.09310	N	1	B;B;B	0.09022	0.001;0.0;0.002	B;B;B	0.01281	0.0;0.0;0.0	T	0.22243	-1.0222	10	0.41790	T	0.15	0.0107	6.1896	0.20516	0.4948:0.0:0.1509:0.3544	.	92;92;92	Q86Y07-2;Q86Y07-5;Q86Y07	.;.;VRK2_HUMAN	H	92;92;96;92;92;92;69	ENSP00000408002:R92H;ENSP00000402375:R92H;ENSP00000404156:R92H;ENSP00000342381:R92H;ENSP00000398323:R69H	ENSP00000342381:R92H	R	+	2	0	VRK2	58166996	0.011000	0.17503	0.159000	0.22649	0.938000	0.57974	-0.285000	0.08410	0.028000	0.15324	-0.302000	0.09304	CGC		0.279	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296	
BCL11A	53335	broad.mit.edu	37	2	60689438	60689438	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:60689438G>A	ENST00000335712.6	-	4	836	c.609C>T	c.(607-609)caC>caT	p.H203H	BCL11A_ENST00000358510.4_Silent_p.H169H|BCL11A_ENST00000356842.4_Silent_p.H203H|BCL11A_ENST00000538214.1_Silent_p.H169H|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000359629.5_Silent_p.H203H|BCL11A_ENST00000537768.1_Silent_p.H51H	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	203	Required for nuclear body formation and for SUMO1 recruitment. {ECO:0000250}.				B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)	p.H203H(8)		NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			GGGGACTTCCGTGTTCGCTTT	0.488			T	IGH@	B-CLL																																p.H203H			Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	.	8	Substitution - coding silent(8)	lung(3)|endometrium(3)|large_intestine(2)	c.C609T	2						.						100.0	97.0	98.0					2																	60689438		2203	4300	6503	60542942	SO:0001819	synonymous_variant	53335	exon4			AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"""Zinc fingers, C2H2-type"""	13221	protein-coding gene	gene with protein product		606557	"""ecotropic viral integration site 9"""	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.609C>T	2.37:g.60689438G>A		Somatic		Capture	Illumina HiSeq	Phase_I	60542942	NM_138559	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Silent	SNP	ENST00000335712.6	37	CCDS1862.1																																																																																				0.488	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893	
EHBP1	23301	broad.mit.edu	37	2	63206352	63206353	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	GA	GA	GA	-	GA	GA	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:63206352_63206353delGA	ENST00000263991.5	+	16	3077_3078	c.2595_2596delGA	c.(2593-2598)ctgagafs	p.R866fs	EHBP1_ENST00000405289.1_Frame_Shift_Del_p.R831fs|EHBP1_ENST00000405015.3_Frame_Shift_Del_p.R831fs|EHBP1_ENST00000431489.1_Frame_Shift_Del_p.R831fs|EHBP1_ENST00000354487.3_Frame_Shift_Del_p.R831fs|EHBP1_ENST00000496857.1_3'UTR	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	866						cytoplasm (GO:0005737)|membrane (GO:0016020)		p.R868fs*22(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			GTCGGCAGCTGAGAGAGAGAGC	0.426																																					p.830_831del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2490_2491del	2						.																																			63059857	SO:0001589	frameshift_variant	23301	exon14			AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.2595_2596delGA	2.37:g.63206360_63206361delGA	ENSP00000263991:p.Arg866fs	Somatic		Capture	Illumina HiSeq	Phase_I	63059856	NM_001142614	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Frame_Shift_Del	DEL	ENST00000263991.5	37	CCDS1872.1																																																																																				0.426	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252	
SPRED2	200734	broad.mit.edu	37	2	65540790	65540790	+	Missense_Mutation	SNP	C	C	T	rs147302571		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:65540790C>T	ENST00000356388.4	-	6	1291	c.1102G>A	c.(1102-1104)Gat>Aat	p.D368N	SPRED2_ENST00000443619.2_Missense_Mutation_p.D365N	NM_181784.2	NP_861449.2	Q7Z698	SPRE2_HUMAN	sprouty-related, EVH1 domain containing 2	368	SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)	p.D368N(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						TCGCTAGTATCGCACGAGCAA	0.572																																					p.D368N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1102A	2						.						87.0	85.0	86.0					2																	65540790		2203	4300	6503	65394294	SO:0001583	missense	200734	exon6			AF052178	CCDS33211.1, CCDS46308.1	2p14	2003-06-02			ENSG00000198369	ENSG00000198369			17722	protein-coding gene	gene with protein product		609292					Standard	NM_181784		Approved	Spred-2, FLJ21897, FLJ31917	uc002sdr.4	Q7Z698	OTTHUMG00000152737	ENST00000356388.4:c.1102G>A	2.37:g.65540790C>T	ENSP00000348753:p.Asp368Asn	Somatic		Capture	Illumina HiSeq	Phase_I	65394294	NM_181784	A1L3V4|B7Z5K7|D6W5F7|E9PEP0|Q2NKX6	Missense_Mutation	SNP	ENST00000356388.4	37	CCDS33211.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.837340	0.91117	.	.	ENSG00000198369	ENST00000356388;ENST00000443619;ENST00000452315	T;T;T	0.63913	-0.07;-0.07;-0.07	5.4	4.51	0.55191	.	0.000000	0.85682	D	0.000000	T	0.78972	0.4368	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.82057	-0.0646	10	0.72032	D	0.01	-10.185	16.158	0.81680	0.0:0.8663:0.1337:0.0	.	365;368	E9PEP0;Q7Z698	.;SPRE2_HUMAN	N	368;365;383	ENSP00000348753:D368N;ENSP00000393697:D365N;ENSP00000390595:D383N	ENSP00000348753:D368N	D	-	1	0	SPRED2	65394294	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.818000	0.86416	1.262000	0.44165	0.655000	0.94253	GAT		0.572	SPRED2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327632.1		
DYSF	8291	broad.mit.edu	37	2	71766292	71766292	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:71766292G>A	ENST00000258104.3	+	16	1680	c.1403G>A	c.(1402-1404)cGc>cAc	p.R468H	DYSF_ENST00000409651.1_Missense_Mutation_p.R500H|DYSF_ENST00000409744.1_Missense_Mutation_p.R469H|DYSF_ENST00000413539.2_Missense_Mutation_p.R499H|DYSF_ENST00000409582.3_Missense_Mutation_p.R499H|DYSF_ENST00000410041.1_Missense_Mutation_p.R500H|DYSF_ENST00000410020.3_Missense_Mutation_p.R500H|DYSF_ENST00000394120.2_Missense_Mutation_p.R469H|DYSF_ENST00000409366.1_Missense_Mutation_p.R469H|DYSF_ENST00000429174.2_Missense_Mutation_p.R468H|DYSF_ENST00000409762.1_Missense_Mutation_p.R499H	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	468	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.R468H(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						TCTAGGGACCGCCTGACTCAC	0.552																																					p.R500H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1499A	2						.						148.0	125.0	133.0					2																	71766292		2203	4300	6503	71619800	SO:0001583	missense	8291	exon17			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1403G>A	2.37:g.71766292G>A	ENSP00000258104:p.Arg468His	Somatic		Capture	Illumina HiSeq	Phase_I	71619800	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.996373	0.74818	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	T;T;T;T;T;T;T;T;T;T;T	0.70631	-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5;-0.5	5.05	5.05	0.67936	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.054859	0.64402	D	0.000001	D	0.87297	0.6142	M	0.92555	3.32	0.47245	D	0.999362	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.998;0.998;0.998;0.996;0.997;0.997;0.997;0.993;0.998;0.997;1.0;0.993;0.996;0.997	D	0.88162	0.2858	10	0.42905	T	0.14	-23.904	16.309	0.82862	0.0:0.0:1.0:0.0	.	500;500;469;469;500;469;499;468;499;499;468;468;469;468	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	H	499;499;499;468;468;500;469;469;469;500;500	ENSP00000407046:R499H;ENSP00000387137:R499H;ENSP00000386547:R499H;ENSP00000398305:R468H;ENSP00000258104:R468H;ENSP00000386683:R500H;ENSP00000377678:R469H;ENSP00000386285:R469H;ENSP00000386512:R469H;ENSP00000386881:R500H;ENSP00000386617:R500H	ENSP00000258104:R468H	R	+	2	0	DYSF	71619800	1.000000	0.71417	1.000000	0.80357	0.537000	0.34900	7.805000	0.86005	2.786000	0.95864	0.563000	0.77884	CGC		0.552	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
DYSF	8291	broad.mit.edu	37	2	71838468	71838468	+	Missense_Mutation	SNP	G	G	A	rs573666770		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:71838468G>A	ENST00000258104.3	+	37	4274	c.3997G>A	c.(3997-3999)Gcc>Acc	p.A1333T	DYSF_ENST00000409651.1_Missense_Mutation_p.A1365T|DYSF_ENST00000409744.1_Missense_Mutation_p.A1320T|DYSF_ENST00000413539.2_Missense_Mutation_p.A1364T|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409582.3_Missense_Mutation_p.A1350T|DYSF_ENST00000410041.1_Missense_Mutation_p.A1351T|DYSF_ENST00000410020.3_Missense_Mutation_p.A1351T|DYSF_ENST00000394120.2_Missense_Mutation_p.A1334T|DYSF_ENST00000409366.1_Missense_Mutation_p.A1334T|DYSF_ENST00000429174.2_Missense_Mutation_p.A1333T|DYSF_ENST00000409762.1_Missense_Mutation_p.A1350T	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1333					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.A1333T(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CCAGCGTACCGCCATCGAGGT	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		17193	0.0		0.001	False		,,,				2504	0.0				p.A1365T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4093A	2						.						49.0	45.0	46.0					2																	71838468		2203	4300	6503	71691976	SO:0001583	missense	8291	exon38			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.3997G>A	2.37:g.71838468G>A	ENSP00000258104:p.Ala1333Thr	Somatic		Capture	Illumina HiSeq	Phase_I	71691976	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	19.10	3.761731	0.69763	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	T;T;T;T;T;T;T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41;-1.41;-1.41;-1.41;-1.41;-1.41;-1.41	4.66	4.66	0.58398	C2 calcium/lipid-binding domain, CaLB (1);	0.110607	0.64402	D	0.000009	D	0.89192	0.6645	M	0.86028	2.79	0.50813	D	0.999895	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.71674	0.991;0.991;0.984;0.984;0.984;0.995;0.995;0.99;0.998;0.984;0.98;0.966;0.984;0.991;0.973	P;P;P;P;P;D;D;P;D;P;P;P;P;P;P	0.66847	0.83;0.871;0.721;0.721;0.721;0.918;0.918;0.882;0.947;0.721;0.812;0.551;0.721;0.871;0.53	D	0.88186	0.2874	10	0.27785	T	0.31	-24.4787	15.4144	0.74952	0.0:0.0:1.0:0.0	.	76;1365;1351;1334;1320;1351;1320;1350;1319;1364;1350;1333;1319;1334;1333	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	T	1364;1350;1350;1333;1333;1365;1334;1320;1334;1351;1351	ENSP00000407046:A1364T;ENSP00000387137:A1350T;ENSP00000386547:A1350T;ENSP00000398305:A1333T;ENSP00000258104:A1333T;ENSP00000386683:A1365T;ENSP00000377678:A1334T;ENSP00000386285:A1320T;ENSP00000386512:A1334T;ENSP00000386881:A1351T;ENSP00000386617:A1351T	ENSP00000258104:A1333T	A	+	1	0	DYSF	71691976	1.000000	0.71417	0.869000	0.34112	0.882000	0.50991	7.974000	0.88039	2.324000	0.78689	0.561000	0.74099	GCC		0.667	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
CCT7	10574	broad.mit.edu	37	2	73471735	73471735	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:73471735G>A	ENST00000258091.5	+	6	651	c.510G>A	c.(508-510)caG>caA	p.Q170Q	CCT7_ENST00000540468.1_Silent_p.Q83Q|CCT7_ENST00000538797.1_Silent_p.Q42Q|CCT7_ENST00000473786.1_3'UTR|CCT7_ENST00000539919.1_Silent_p.Q126Q|CCT7_ENST00000398422.2_Intron|CCT7_ENST00000537131.1_Silent_p.Q70Q	NM_006429.3	NP_006420.1	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 (eta)	170					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)	p.Q170Q(1)		breast(1)|cervix(1)|endometrium(1)|lung(3)|stomach(1)	7						TGATCTCCCAGCAGAAAGCTT	0.498																																					p.Q126Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G378A	2						.						57.0	57.0	57.0					2																	73471735		2048	4211	6259	73325243	SO:0001819	synonymous_variant	10574	exon7			AF026292	CCDS42696.1, CCDS46336.1, CCDS54366.1, CCDS54367.1	2p13.2	2011-09-02			ENSG00000135624	ENSG00000135624		"""Heat Shock Proteins / Chaperonins"""	1622	protein-coding gene	gene with protein product		605140				9819444	Standard	NM_006429		Approved	Ccth, Nip7-1	uc002siz.3	Q99832	OTTHUMG00000152765	ENST00000258091.5:c.510G>A	2.37:g.73471735G>A		Somatic		Capture	Illumina HiSeq	Phase_I	73325243	NM_001166285	A8K7E6|A8MWI8|B7WNW9|B7Z4T9|B7Z4Z7|O14871|Q6FI26	Silent	SNP	ENST00000258091.5	37	CCDS46336.1																																																																																				0.498	CCT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327714.2		
EGR4	1961	broad.mit.edu	37	2	73518831	73518831	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:73518831C>T	ENST00000545030.1	-	2	1598	c.1524G>A	c.(1522-1524)acG>acA	p.T508T	EGR4_ENST00000436467.2_Silent_p.T405T	NM_001965.3	NP_001956.3	Q05215	EGR4_HUMAN	early growth response 4	508					cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T405T(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GTTTGTGGCCCGTGTGGATGC	0.672																																					p.T508T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1524A	2						.						57.0	53.0	55.0					2																	73518831		2203	4299	6502	73372339	SO:0001819	synonymous_variant	1961	exon2				CCDS1925.2	2p13	2013-01-08			ENSG00000135625	ENSG00000135625		"""Zinc fingers, C2H2-type"""	3241	protein-coding gene	gene with protein product		128992				1584812	Standard	NM_001965		Approved	NGFI-C, PAT133	uc010yrj.2	Q05215	OTTHUMG00000129774	ENST00000545030.1:c.1524G>A	2.37:g.73518831C>T		Somatic		Capture	Illumina HiSeq	Phase_I	73372339	NM_001965	B2RAE3|G3V1T5|Q2Z1P5	Silent	SNP	ENST00000545030.1	37	CCDS1925.2																																																																																				0.672	EGR4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001965	
ACTG2	72	broad.mit.edu	37	2	74128464	74128464	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:74128464T>C	ENST00000409624.1	+	3	669	c.26T>C	c.(25-27)cTc>cCc	p.L9P	ACTG2_ENST00000345517.3_Missense_Mutation_p.L9P|ACTG2_ENST00000409731.3_Missense_Mutation_p.L9P|ACTG2_ENST00000409918.1_Missense_Mutation_p.L9P			P63267	ACTH_HUMAN	actin, gamma 2, smooth muscle, enteric	9					muscle contraction (GO:0006936)	blood microparticle (GO:0072562)|cell periphery (GO:0071944)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.L9P(1)		large_intestine(3)|lung(14)|skin(1)	18						ACCACCGCGCTCGTGTGTGAC	0.617																																					p.L9P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T26C	2						.						67.0	58.0	61.0					2																	74128464		2203	4300	6503	73981972	SO:0001583	missense	72	exon2				CCDS1930.1, CCDS56124.1	2p13.1	2008-05-20			ENSG00000163017	ENSG00000163017			145	protein-coding gene	gene with protein product		102545		ACTL3, ACTA3		1710027, 1673027	Standard	NM_001199893		Approved	ACTSG	uc002sjw.3	P63267	OTTHUMG00000129813	ENST00000409624.1:c.26T>C	2.37:g.74128464T>C	ENSP00000386857:p.Leu9Pro	Somatic		Capture	Illumina HiSeq	Phase_I	73981972	NM_001615	B2R7E7|B4E315|D6W5H8|E9PG30|P12718|Q504R1|Q6FI22	Missense_Mutation	SNP	ENST00000409624.1	37	CCDS1930.1	.	.	.	.	.	.	.	.	.	.	T	11.93	1.784559	0.31593	.	.	ENSG00000163017	ENST00000409731;ENST00000345517;ENST00000409918;ENST00000442912;ENST00000409624	D;D;D;D;D	0.97976	-4.64;-4.64;-3.77;-3.77;-4.64	3.93	3.93	0.45458	.	0.000000	0.53938	D	0.000047	D	0.99064	0.9679	H	0.97023	3.925	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.989	D;D;D	0.83275	0.985;0.977;0.996	D	0.98997	1.0810	10	0.87932	D	0	.	12.1854	0.54236	0.0:0.0:0.0:1.0	.	9;9;9	E9PG30;B8ZZJ2;P63267	.;.;ACTH_HUMAN	P	9	ENSP00000386929:L9P;ENSP00000295137:L9P;ENSP00000387182:L9P;ENSP00000410020:L9P;ENSP00000386857:L9P	ENSP00000295137:L9P	L	+	2	0	ACTG2	73981972	1.000000	0.71417	0.277000	0.24703	0.253000	0.25986	7.792000	0.85828	1.785000	0.52413	0.254000	0.18369	CTC		0.617	ACTG2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328086.1	NM_001615	
PCGF1	84759	broad.mit.edu	37	2	74729940	74729940	+	IGR	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:74729940delC	ENST00000233630.6	-	0	1792				RP11-523H20.3_ENST00000606287.1_RNA|PCGF1_ENST00000480844.2_5'Flank|LBX2_ENST00000341396.2_Intron|LBX2_ENST00000550249.1_Intron|LBX2-AS1_ENST00000603175.1_RNA|LBX2_ENST00000460508.3_Frame_Shift_Del_p.G16fs|LBX2-AS1_ENST00000548978.2_RNA	NM_032673.2	NP_116062.2	Q9BSM1	PCGF1_HUMAN	polycomb group ring finger 1						histone H2A monoubiquitination (GO:0035518)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)	p.G16fs*99(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(2)	12						ACACTTTTCTCCCCCCAACTC	0.632																																					p.G16fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.47delG	2						.						46.0	52.0	50.0					2																	74729940		2203	4300	6503	74583448	SO:0001628	intergenic_variant	85474	exon1			AF087884	CCDS1946.2	2p13.1	2013-01-09			ENSG00000115289	ENSG00000115289		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	17615	protein-coding gene	gene with protein product		610231				11287196	Standard	NM_032673		Approved	NSPC1, RNF68, MGC10882	uc002slz.3	Q9BSM1	OTTHUMG00000129954		2.37:g.74729940delC		Somatic		Capture	Illumina HiSeq	Phase_I	74583448	NM_001009812	Q7Z506	Frame_Shift_Del	DEL	ENST00000233630.6	37	CCDS1946.2																																																																																				0.632	PCGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252216.1	NM_032673	
LRRTM4	80059	broad.mit.edu	37	2	77746270	77746270	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:77746270C>T	ENST00000409093.1	-	3	1061	c.725G>A	c.(724-726)cGc>cAc	p.R242H	LRRTM4_ENST00000409884.1_Missense_Mutation_p.R242H|LRRTM4_ENST00000409911.1_Missense_Mutation_p.R243H|LRRTM4_ENST00000409282.1_Missense_Mutation_p.R243H|LRRTM4_ENST00000409088.3_Missense_Mutation_p.R242H			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	242					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|regulation of presynaptic membrane organization (GO:1901629)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)		p.R242H(2)		autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64				Colorectal(11;0.059)		GCTAATGGAGCGAATCCTGTT	0.448																																					p.R242H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G725A	2						.						57.0	54.0	55.0					2																	77746270		1891	4099	5990	77599778	SO:0001583	missense	80059	exon3			AK122612	CCDS46346.1, CCDS46347.1, CCDS74530.1	2p12	2008-02-05			ENSG00000176204	ENSG00000176204			19411	protein-coding gene	gene with protein product		610870				12676565	Standard	NM_024993		Approved	FLJ12568	uc002snr.3	Q86VH4	OTTHUMG00000152842	ENST00000409093.1:c.725G>A	2.37:g.77746270C>T	ENSP00000386357:p.Arg242His	Somatic		Capture	Illumina HiSeq	Phase_I	77599778	NM_024993	Q4FZ98|Q6UXJ7	Missense_Mutation	SNP	ENST00000409093.1	37	CCDS46346.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.853202	0.51270	.	.	ENSG00000176204	ENST00000409911;ENST00000409884;ENST00000409093;ENST00000409088;ENST00000409282	T;T;T;T;T	0.59224	0.28;0.28;0.28;0.28;0.28	5.93	5.93	0.95920	.	0.133674	0.50627	D	0.000114	T	0.66036	0.2749	N	0.25031	0.7	0.44570	D	0.997532	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74348	0.97;0.949;0.983	T	0.68112	-0.5495	10	0.62326	D	0.03	.	18.9104	0.92481	0.0:1.0:0.0:0.0	.	243;242;242	Q4KMX1;Q86VH4-2;Q86VH4	.;.;LRRT4_HUMAN	H	243;242;242;242;243	ENSP00000387228:R243H;ENSP00000387297:R242H;ENSP00000386357:R242H;ENSP00000386236:R242H;ENSP00000386286:R243H	ENSP00000386236:R242H	R	-	2	0	LRRTM4	77599778	0.966000	0.33281	1.000000	0.80357	0.997000	0.91878	1.999000	0.40806	2.798000	0.96311	0.655000	0.94253	CGC		0.448	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993	
CTNNA2	1496	broad.mit.edu	37	2	80101436	80101436	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:80101436G>A	ENST00000402739.4	+	5	825	c.820G>A	c.(820-822)Ggc>Agc	p.G274S	CTNNA2_ENST00000466387.1_Missense_Mutation_p.G274S|CTNNA2_ENST00000496558.1_Missense_Mutation_p.G274S|CTNNA2_ENST00000541047.1_Missense_Mutation_p.G274S|CTNNA2_ENST00000540488.1_Missense_Mutation_p.G274S|CTNNA2_ENST00000361291.4_Missense_Mutation_p.G308S	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	274					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)	p.G274S(2)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CACGGGCATCGGCGAGCTGGC	0.527																																					p.G274S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G820A	2						.						41.0	45.0	44.0					2																	80101436		2018	4167	6185	79954944	SO:0001583	missense	1496	exon6				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.820G>A	2.37:g.80101436G>A	ENSP00000384638:p.Gly274Ser	Somatic		Capture	Illumina HiSeq	Phase_I	79954944	NM_004389	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	37		.	.	.	.	.	.	.	.	.	.	G	36	5.753580	0.96890	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2;1.2	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.67878	0.2940	M	0.87682	2.9	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.957;0.959	T	0.71859	-0.4465	10	0.62326	D	0.03	.	19.8737	0.96861	0.0:0.0:1.0:0.0	.	274;274;274	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	S	274;274;308;274;274;274	ENSP00000418191:G274S;ENSP00000419295:G274S;ENSP00000355398:G308S;ENSP00000384638:G274S;ENSP00000444675:G274S;ENSP00000441705:G274S	ENSP00000355398:G308S	G	+	1	0	CTNNA2	79954944	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.693000	0.91896	0.650000	0.86243	GGC		0.527	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
MRPS5	64969	broad.mit.edu	37	2	95770424	95770424	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:95770424G>A	ENST00000272418.2	-	7	932	c.724C>T	c.(724-726)Cgt>Tgt	p.R242C		NM_031902.3	NP_114108.1	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	242	S5 DRBM. {ECO:0000255|PROSITE- ProRule:PRU00268}.				translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.R242C(2)		central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						ACCAAGACACGGATCGATTTC	0.483																																					p.R242C												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C724T	2						.						181.0	155.0	164.0					2																	95770424		2203	4300	6503	95134151	SO:0001583	missense	64969	exon7			AB049940	CCDS2010.1	2p11.2-q11.2	2012-09-13			ENSG00000144029	ENSG00000144029		"""Mitochondrial ribosomal proteins / small subunits"""	14498	protein-coding gene	gene with protein product	"""mitochondrial 28S ribosomal protein S5"""	611972					Standard	NM_031902		Approved	MRP-S5, S5mt	uc002sub.3	P82675	OTTHUMG00000130394	ENST00000272418.2:c.724C>T	2.37:g.95770424G>A	ENSP00000272418:p.Arg242Cys	Somatic		Capture	Illumina HiSeq	Phase_I	95134151	NM_031902	Q4ZFY5|Q96LJ6|Q9BWI4|Q9BYC4	Missense_Mutation	SNP	ENST00000272418.2	37	CCDS2010.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.119346	0.56505	.	.	ENSG00000144029	ENST00000272418	.	.	.	5.09	5.09	0.68999	Ribosomal protein S5, N-terminal, conserved site (1);Ribosomal protein S5, N-terminal (2);Double-stranded RNA-binding-like (1);	0.043472	0.85682	D	0.000000	T	0.80177	0.4575	M	0.88842	2.985	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.69824	0.966;0.959	T	0.82916	-0.0220	9	0.62326	D	0.03	-8.4749	11.4446	0.50116	0.0:0.0:0.8199:0.1801	.	242;242	B4DIW8;P82675	.;RT05_HUMAN	C	242	.	ENSP00000272418:R242C	R	-	1	0	MRPS5	95134151	1.000000	0.71417	0.917000	0.36280	0.361000	0.29550	4.588000	0.60999	2.530000	0.85305	0.491000	0.48974	CGT		0.483	MRPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252772.1	NM_031902	
ZNF514	84874	broad.mit.edu	37	2	95815327	95815327	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:95815327T>C	ENST00000295208.2	-	5	1365	c.903A>G	c.(901-903)tcA>tcG	p.S301S	ZNF514_ENST00000411425.1_Silent_p.S301S|MRPS5_ENST00000475040.1_5'Flank	NM_032788.1	NP_116177.1	Q96K75	ZN514_HUMAN	zinc finger protein 514	301					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S301S(1)		large_intestine(4)|lung(6)|urinary_tract(1)	11						TAATAAGGGATGAAGTGTGAC	0.458																																					p.S301S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A903G	2						.						66.0	70.0	69.0					2																	95815327		2203	4300	6503	95179054	SO:0001819	synonymous_variant	84874	exon5			AL832263	CCDS2011.1	2q11.2	2013-01-08			ENSG00000144026	ENSG00000144026		"""Zinc fingers, C2H2-type"", ""-"""	25894	protein-coding gene	gene with protein product							Standard	NM_032788		Approved	FLJ14457	uc002sue.1	Q96K75	OTTHUMG00000130391	ENST00000295208.2:c.903A>G	2.37:g.95815327T>C		Somatic		Capture	Illumina HiSeq	Phase_I	95179054	NM_032788	Q5JPJ3	Silent	SNP	ENST00000295208.2	37	CCDS2011.1																																																																																				0.458	ZNF514-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252769.1	NM_032788	
TMEM127	55654	broad.mit.edu	37	2	96920587	96920587	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:96920587G>A	ENST00000258439.3	-	3	649	c.393C>T	c.(391-393)ttC>ttT	p.F131F	TMEM127_ENST00000432959.1_Silent_p.F131F|TMEM127_ENST00000435268.1_Silent_p.F47F	NM_001193304.2|NM_017849.3	NP_001180233.1|NP_060319.1	O75204	TM127_HUMAN	transmembrane protein 127	131					negative regulation of cell proliferation (GO:0008285)|negative regulation of TOR signaling (GO:0032007)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.F131F(1)		endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	5						GGATATGGGCGAAGGCATAGC	0.577																																					p.F131F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C393T	2						.						158.0	152.0	154.0					2																	96920587		2203	4300	6503	96284314	SO:0001819	synonymous_variant	55654	exon3			AK000514	CCDS2018.1	2q11.2	2014-09-17			ENSG00000135956	ENSG00000135956			26038	protein-coding gene	gene with protein product		613403				10493829	Standard	NM_017849		Approved	FLJ20507, FLJ22257	uc002svr.3	O75204	OTTHUMG00000130454	ENST00000258439.3:c.393C>T	2.37:g.96920587G>A		Somatic		Capture	Illumina HiSeq	Phase_I	96284314	NM_017849	D3DXH0	Silent	SNP	ENST00000258439.3	37	CCDS2018.1																																																																																				0.577	TMEM127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252845.3	NM_017849	
NCAPH	23397	broad.mit.edu	37	2	97009880	97009880	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:97009880T>C	ENST00000240423.4	+	6	676	c.633T>C	c.(631-633)gcT>gcC	p.A211A	NCAPH_ENST00000455200.1_Silent_p.A200A|NCAPH_ENST00000427946.1_Silent_p.A75A	NM_001281710.1|NM_001281711.1|NM_015341.3	NP_001268639.1|NP_001268640.1|NP_056156.2	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H	211					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.A211A(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(717;0.0221)				CCAAAAAGGCTGTAAAGCCAA	0.418																																					p.A211A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T633C	2						.						104.0	94.0	97.0					2																	97009880		2203	4300	6503	96373607	SO:0001819	synonymous_variant	23397	exon6			BC024211	CCDS2021.1, CCDS62960.1	2q11.2	2008-02-05	2006-09-04	2006-09-04	ENSG00000121152	ENSG00000121152			1112	protein-coding gene	gene with protein product		602332	"""barren (Drosophila) homolog"", ""barren homolog (Drosophila)"", ""barren homolog 1 (Drosophila)"""	BRRN1		9417923	Standard	NM_015341		Approved	CAP-H, hCAP-H	uc002svz.1	Q15003	OTTHUMG00000130451	ENST00000240423.4:c.633T>C	2.37:g.97009880T>C		Somatic		Capture	Illumina HiSeq	Phase_I	96373607	NM_015341	B4E189|Q8TB87	Silent	SNP	ENST00000240423.4	37	CCDS2021.1																																																																																				0.418	NCAPH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252842.2	NM_015341	
TMEM131	23505	broad.mit.edu	37	2	98377084	98377084	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:98377084C>T	ENST00000186436.5	-	38	5308	c.5080G>A	c.(5080-5082)Gct>Act	p.A1694T		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	1694	Ser-rich.					integral component of membrane (GO:0016021)		p.A1581T(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						TCAACAGGAGCGTGTGAAATG	0.478																																					p.A1694T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5080A	2						.						92.0	95.0	94.0					2																	98377084		1976	4156	6132	97743516	SO:0001583	missense	23505	exon38			AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.5080G>A	2.37:g.98377084C>T	ENSP00000186436:p.Ala1694Thr	Somatic		Capture	Illumina HiSeq	Phase_I	97743516	NM_015348		Missense_Mutation	SNP	ENST00000186436.5	37	CCDS46368.1	.	.	.	.	.	.	.	.	.	.	C	4.385	0.071122	0.08436	.	.	ENSG00000075568	ENST00000186436	T	0.27720	1.65	5.21	1.43	0.22495	.	0.629715	0.16777	N	0.199967	T	0.08935	0.0221	N	0.01874	-0.695	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17048	-1.0382	10	0.10636	T	0.68	-4.8149	5.0704	0.14604	0.0:0.168:0.152:0.68	.	1694;74	Q92545;Q0P631	TM131_HUMAN;.	T	1694	ENSP00000186436:A1694T	ENSP00000186436:A1694T	A	-	1	0	TMEM131	97743516	1.000000	0.71417	0.964000	0.40570	0.708000	0.40852	0.898000	0.28404	0.432000	0.26286	0.643000	0.83706	GCT		0.478	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542	
CNGA3	1261	broad.mit.edu	37	2	99013013	99013013	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:99013013delC	ENST00000272602.2	+	7	1419	c.1380delC	c.(1378-1380)ctcfs	p.L460fs	CNGA3_ENST00000409937.1_Frame_Shift_Del_p.L464fs|CNGA3_ENST00000393504.1_Frame_Shift_Del_p.L460fs|CNGA3_ENST00000436404.2_Frame_Shift_Del_p.L442fs			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	460					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	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.P461fs*4(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						TCAAGAGCCTCCCAGACAAGC	0.577																																					p.L460fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1380delC	2						.						62.0	58.0	59.0					2																	99013013		2203	4300	6503	98379445	SO:0001589	frameshift_variant	1261	exon8			S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.1380delC	2.37:g.99013013delC	ENSP00000272602:p.Leu460fs	Somatic		Capture	Illumina HiSeq	Phase_I	98379445	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Frame_Shift_Del	DEL	ENST00000272602.2	37	CCDS2034.1																																																																																				0.577	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298	
NCKAP5	344148	broad.mit.edu	37	2	133543031	133543031	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:133543031delG	ENST00000409261.1	-	14	1726	c.1353delC	c.(1351-1353)cccfs	p.P451fs	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000317721.6_Frame_Shift_Del_p.P451fs	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	451								p.C452fs*21(1)		NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CTGTTTTGCAGGGGGGATACT	0.463																																					p.P451fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1353delC	2						.						54.0	52.0	53.0					2																	133543031		1854	4097	5951	133259501	SO:0001589	frameshift_variant	344148	exon14			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.1353delC	2.37:g.133543031delG	ENSP00000387128:p.Pro451fs	Somatic		Capture	Illumina HiSeq	Phase_I	133259501	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Frame_Shift_Del	DEL	ENST00000409261.1	37	CCDS46418.1																																																																																				0.463	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
TTN	7273	broad.mit.edu	37	2	179486062	179486062	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:179486062delT	ENST00000591111.1	-	196	40684	c.40460delA	c.(40459-40461)aacfs	p.N13487fs	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Del_p.N15128fs|TTN_ENST00000460472.2_Frame_Shift_Del_p.N6063fs|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.N6188fs|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.N12560fs|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.N6255fs|TTN-AS1_ENST00000604956.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13487	Ig-like 91.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.N12560fs*49(1)|p.N6063fs*49(1)|p.N6255fs*49(1)|p.N6188fs*49(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TATTTCAAGGTTTTGAGGCTT	0.358																																					p.N6063fs												.	.	4	Deletion - Frameshift(4)	large_intestine(4)	c.18188delA	2						.						77.0	67.0	70.0					2																	179486062		1801	4067	5868	179194307	SO:0001589	frameshift_variant	7273	exon74			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.40460delA	2.37:g.179486062delT	ENSP00000465570:p.Asn13487fs	Somatic		Capture	Illumina HiSeq	Phase_I	179194307	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	37																																																																																					0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179536771	179536771	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:179536771delT	ENST00000591111.1	-	151	34256	c.34032delA	c.(34030-34032)aaafs	p.K11344fs	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Del_p.K11718fs|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.K10417fs|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	11344	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V10418fs*4(1)|p.V21fs*4(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCCTATGAACTTTTTCAACTC	0.328																																					p.K10417fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.31251delA	2						.						92.0	93.0	93.0					2																	179536771		1813	4065	5878	179245016	SO:0001589	frameshift_variant	7273	exon150			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.34032delA	2.37:g.179536771delT	ENSP00000465570:p.Lys11344fs	Somatic		Capture	Illumina HiSeq	Phase_I	179245016	NM_133378	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	37																																																																																					0.328	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
OSGEPL1	64172	broad.mit.edu	37	2	190626331	190626331	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:190626331delA	ENST00000264151.5	-	2	138	c.36delT	c.(34-36)tttfs	p.F12fs	OSGEPL1-AS1_ENST00000523895.1_RNA|RP11-455J20.3_ENST00000608680.1_RNA|OSGEPL1_ENST00000519810.1_Frame_Shift_Del_p.F12fs|OSGEPL1_ENST00000522700.1_Frame_Shift_Del_p.F12fs|OSGEPL1-AS1_ENST00000521819.1_RNA|OSGEPL1-AS1_ENST00000520651.1_RNA	NM_022353.2	NP_071748.2			O-sialoglycoprotein endopeptidase-like 1									p.F12fs*12(1)		large_intestine(2)|upper_aerodigestive_tract(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0293)|all cancers(119;0.0831)			TTGATGGTTTAAAAAAAACTC	0.269																																					p.F12fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.36delT	2						.						21.0	21.0	21.0					2																	190626331		1787	4043	5830	190334576	SO:0001589	frameshift_variant	64172	exon2			AJ295148	CCDS46472.1	2q32	2011-08-12			ENSG00000128694	ENSG00000128694			23075	protein-coding gene	gene with protein product						19578062	Standard	NM_022353		Approved	Qri7	uc002uqz.1	Q9H4B0	OTTHUMG00000164096	ENST00000264151.5:c.36delT	2.37:g.190626331delA	ENSP00000264151:p.Phe12fs	Somatic		Capture	Illumina HiSeq	Phase_I	190334576	NM_022353		Frame_Shift_Del	DEL	ENST00000264151.5	37	CCDS46472.1																																																																																				0.269	OSGEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377257.1	NM_022353	
DNAH7	56171	broad.mit.edu	37	2	196722321	196722321	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:196722321delT	ENST00000312428.6	-	44	8294	c.8194delA	c.(8194-8196)attfs	p.I2732fs		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2732	Stalk. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.I2732fs*15(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						AAATCCTCAATTTTTTTCCCT	0.433																																					p.I2732fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.8194delA	2						.																																			196430566	SO:0001589	frameshift_variant	56171	exon44			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.8194delA	2.37:g.196722321delT	ENSP00000311273:p.Ile2732fs	Somatic		Capture	Illumina HiSeq	Phase_I	196430566	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Frame_Shift_Del	DEL	ENST00000312428.6	37	CCDS42794.1																																																																																				0.433	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
PGAP1	80055	broad.mit.edu	37	2	197757100	197757101	+	Frame_Shift_Del	DEL	TT	TT	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	TT	TT	TT	-	TT	TT	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:197757100_197757101delTT	ENST00000354764.4	-	9	1172_1173	c.1058_1059delAA	c.(1057-1059)aaafs	p.K353fs	PGAP1_ENST00000409188.1_Intron|PGAP1_ENST00000409475.1_Frame_Shift_Del_p.K353fs|PGAP1_ENST00000485830.1_Intron	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	353					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)	p.K353fs*13(1)		breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						ATTTGGACACTTTTACTAGAAC	0.297																																					p.353_353del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1058_1059del	2						.																																			197465346	SO:0001589	frameshift_variant	80055	exon9				CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"""GPI inositol-deacylase"""	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.1058_1059delAA	2.37:g.197757102_197757103delTT	ENSP00000346809:p.Lys353fs	Somatic		Capture	Illumina HiSeq	Phase_I	197465345	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Frame_Shift_Del	DEL	ENST00000354764.4	37	CCDS2318.1																																																																																				0.297	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	
ABCB6	10058	broad.mit.edu	37	2	220081103	220081103	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:220081103delC	ENST00000265316.3	-	4	1269	c.953delG	c.(952-954)ggtfs	p.G319fs	ABCB6_ENST00000439002.2_Frame_Shift_Del_p.G273fs	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	319	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)	p.G318fs*9(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCAGTGCCACCCCCCTGGAG	0.572																																					p.G318fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.953delG	2						.						95.0	101.0	99.0					2																	220081103		2203	4300	6503	219789347	SO:0001589	frameshift_variant	10058	exon4			AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"""ATP binding cassette transporters / subfamily B"""	47	protein-coding gene	gene with protein product	"""ATP-binding cassette half-transporter"""	605452	"""ATP-binding cassette, sub-family B (MDR/TAP), member 6"""			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.953delG	2.37:g.220081103delC	ENSP00000265316:p.Gly319fs	Somatic		Capture	Illumina HiSeq	Phase_I	219789347	NM_005689	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Frame_Shift_Del	DEL	ENST00000265316.3	37	CCDS2436.1																																																																																				0.572	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689	
PSMD1	5707	broad.mit.edu	37	2	231931680	231931680	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:231931680delA	ENST00000308696.6	+	5	527	c.365delA	c.(364-366)gaafs	p.E122fs	PSMD1_ENST00000373635.4_Frame_Shift_Del_p.E122fs|PSMD1_ENST00000409643.1_Frame_Shift_Del_p.E122fs	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	122					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)	p.K124fs*11(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	CCTGAAGGAGAAAAAAAACCA	0.363																																					p.E122fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.365delA	2						.						70.0	61.0	64.0					2																	231931680		2203	4300	6503	231639924	SO:0001589	frameshift_variant	5707	exon5			D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"""Proteasome (prosome, macropain) subunits"""	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.365delA	2.37:g.231931680delA	ENSP00000309474:p.Glu122fs	Somatic		Capture	Illumina HiSeq	Phase_I	231639924	NM_002807	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Frame_Shift_Del	DEL	ENST00000308696.6	37	CCDS2482.1																																																																																				0.363	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2		
RBM44	375316	broad.mit.edu	37	2	238725977	238725977	+	Frame_Shift_Del	DEL	A	A	-	rs368429538		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:238725977delA	ENST00000409864.1	+	3	672	c.418delA	c.(418-420)aaafs	p.K141fs	RBM44_ENST00000316997.4_Frame_Shift_Del_p.K141fs|RBM44_ENST00000444524.2_Intron			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	140						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)	p.E142fs*57(2)		breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		TGAAGTGCAGAAAAAAGAGGA	0.308																																					p.K140fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.418delA	2						.						23.0	23.0	23.0					2																	238725977		1792	4059	5851	238390716	SO:0001589	frameshift_variant	375316	exon3			AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"""RNA binding motif (RRM) containing"""	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.418delA	2.37:g.238725977delA	ENSP00000386727:p.Lys141fs	Somatic		Capture	Illumina HiSeq	Phase_I	238390716	NM_001080504	A0AUW3	Frame_Shift_Del	DEL	ENST00000409864.1	37	CCDS46554.1																																																																																				0.308	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504	
AQP12A	375318	broad.mit.edu	37	2	241631398	241631398	+	Missense_Mutation	SNP	G	G	A	rs149487583	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr2:241631398G>A	ENST00000337801.4	+	1	137	c.68G>A	c.(67-69)cGg>cAg	p.R23Q	AQP12A_ENST00000429564.1_Missense_Mutation_p.R23Q|AC011298.2_ENST00000407635.2_lincRNA	NM_198998.2	NP_945349.1	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	23						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.R23Q(1)		endometrium(2)|kidney(3)|large_intestine(2)|lung(7)	14		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		GCGGCCAGGCGGGCCTCCAAG	0.687																																					p.R23Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G68A	2						.		GLN/ARG	3,4343		0,3,2170	47.0	55.0	52.0		68	2.4	0.8	2	dbSNP_134	52	13,8561		0,13,4274	no	missense	AQP12A	NM_198998.1	43	0,16,6444	AA,AG,GG		0.1516,0.069,0.1238	probably-damaging	23/296	241631398	16,12904	2173	4287	6460	241280071	SO:0001583	missense	375318	exon1			AB040748		2q37.3	2013-06-03	2005-05-26	2005-05-26	ENSG00000184945	ENSG00000184945		"""Ion channels / Aquaporins"""	19941	protein-coding gene	gene with protein product		609789	"""aquaporin 12"""	AQP12			Standard	NM_198998		Approved		uc002vzu.3	Q8IXF9	OTTHUMG00000183906	ENST00000337801.4:c.68G>A	2.37:g.241631398G>A	ENSP00000337144:p.Arg23Gln	Somatic		Capture	Illumina HiSeq	Phase_I	241280071	NM_198998		Missense_Mutation	SNP	ENST00000337801.4	37		75	0.034340659340659344	13	0.026422764227642278	19	0.052486187845303865	20	0.03496503496503497	23	0.030343007915567283	.	15.69	2.907241	0.52333	6.9E-4	0.001516	ENSG00000184945	ENST00000337801;ENST00000429564	T;T	0.11169	2.8;2.8	2.43	2.43	0.29744	.	0.556195	0.18450	N	0.140848	T	0.02267	0.0070	M	0.62723	1.935	0.30015	N	0.814819	D	0.65815	0.995	P	0.48677	0.586	T	0.03249	-1.1056	10	0.28530	T	0.3	0.0022	10.6008	0.45365	0.0:0.0:1.0:0.0	.	23	Q8IXF9	AQ12A_HUMAN	Q	23	ENSP00000337144:R23Q;ENSP00000405899:R23Q	ENSP00000337144:R23Q	R	+	2	0	AQP12A	241280071	0.914000	0.31030	0.831000	0.32960	0.328000	0.28507	1.176000	0.31957	1.382000	0.46385	0.186000	0.17326	CGG		0.687	AQP12A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257185.2	NM_198998	
GPR128	84873	broad.mit.edu	37	3	100365541	100365541	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:100365541C>T	ENST00000273352.3	+	10	1507	c.1239C>T	c.(1237-1239)aaC>aaT	p.N413N	SNORA31_ENST00000517180.1_RNA|GPR128_ENST00000475887.1_Silent_p.N118N	NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	413	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.N413N(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						GCCGCTGCAACCATACTACTA	0.428																																					p.N413N	Pancreas(87;185 1975 7223 18722)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1239T	3						.						85.0	87.0	87.0					3																	100365541		2203	4300	6503	101848231	SO:0001819	synonymous_variant	84873	exon10			AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"""-"", ""GPCR / Class B : Orphans"""	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.1239C>T	3.37:g.100365541C>T		Somatic		Capture	Illumina HiSeq	Phase_I	101848231	NM_032787	Q14D94|Q86SQ2	Silent	SNP	ENST00000273352.3	37	CCDS2938.1																																																																																				0.428	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1		
IMPG2	50939	broad.mit.edu	37	3	100972560	100972560	+	Missense_Mutation	SNP	C	C	T	rs199986912		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:100972560C>T	ENST00000193391.7	-	11	1406	c.1219G>A	c.(1219-1221)Gca>Aca	p.A407T		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	407					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)	p.A407T(1)		NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	GACGGCGTTGCCTGAAGACTT	0.398																																					p.A407T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1219A	3						.						92.0	83.0	86.0					3																	100972560		2203	4300	6503	102455250	SO:0001583	missense	50939	exon11			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.1219G>A	3.37:g.100972560C>T	ENSP00000193391:p.Ala407Thr	Somatic		Capture	Illumina HiSeq	Phase_I	102455250	NM_016247	A8MWT5|Q9UKD4|Q9UKK5	Missense_Mutation	SNP	ENST00000193391.7	37	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	C	12.26	1.883908	0.33255	.	.	ENSG00000081148	ENST00000193391	T	0.23348	1.91	5.77	1.87	0.25490	.	0.932755	0.09099	N	0.848771	T	0.13243	0.0321	N	0.19112	0.55	0.20764	N	0.999855	B;B	0.17852	0.024;0.013	B;B	0.10450	0.005;0.005	T	0.39210	-0.9625	10	0.09843	T	0.71	0.0037	4.7395	0.13005	0.2749:0.52:0.1327:0.0724	.	407;407	F1T0J3;Q9BZV3	.;IMPG2_HUMAN	T	407	ENSP00000193391:A407T	ENSP00000193391:A407T	A	-	1	0	IMPG2	102455250	0.003000	0.15002	0.309000	0.25155	0.991000	0.79684	-0.225000	0.09151	0.123000	0.18342	0.655000	0.94253	GCA		0.398	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3		
ALCAM	214	broad.mit.edu	37	3	105266292	105266292	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:105266292A>G	ENST00000306107.5	+	11	1799	c.1299A>G	c.(1297-1299)atA>atG	p.I433M	ALCAM_ENST00000486979.2_Missense_Mutation_p.I382M|ALCAM_ENST00000472644.2_Missense_Mutation_p.I433M|ALCAM_ENST00000389927.4_Missense_Mutation_p.I155M	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	433	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)	p.I433M(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CTAAAACAATAATCTGCCATG	0.348																																					p.I433M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1299G	3						.						76.0	72.0	73.0					3																	105266292		2203	4298	6501	106748982	SO:0001583	missense	214	exon11			AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.1299A>G	3.37:g.105266292A>G	ENSP00000305988:p.Ile433Met	Somatic		Capture	Illumina HiSeq	Phase_I	106748982	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Missense_Mutation	SNP	ENST00000306107.5	37	CCDS33810.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.28|11.28	1.591631|1.591631	0.28357|0.28357	.|.	.|.	ENSG00000170017|ENSG00000170017	ENST00000306107;ENST00000472644;ENST00000486979;ENST00000389927|ENST00000465413	T;T;T;T|.	0.13307|.	3.9;3.9;3.9;2.6|.	5.61|5.61	-2.35|-2.35	0.06684|0.06684	Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.105242|.	0.64402|.	D|.	0.000003|.	T|T	0.40743|0.40743	0.1129|0.1129	L|L	0.34521|0.34521	1.04|1.04	0.39898|0.39898	D|D	0.973862|0.973862	D;P;P|.	0.58970|.	0.984;0.942;0.942|.	P;P;P|.	0.62184|.	0.899;0.867;0.867|.	T|T	0.25152|0.25152	-1.0140|-1.0140	10|5	0.72032|.	D|.	0.01|.	-17.1487|-17.1487	6.9685|6.9685	0.24637|0.24637	0.4479:0.1586:0.0:0.3935|0.4479:0.1586:0.0:0.3935	.|.	155;433;433|.	Q6ZS95;B4DTU0;Q13740|.	.;.;CD166_HUMAN|.	M|D	433;433;382;155|194	ENSP00000305988:I433M;ENSP00000419236:I433M;ENSP00000418213:I382M;ENSP00000374577:I155M|.	ENSP00000305988:I433M|.	I|N	+|+	3|1	3|0	ALCAM|ALCAM	106748982|106748982	0.989000|0.989000	0.36119|0.36119	0.986000|0.986000	0.45419|0.45419	0.238000|0.238000	0.25445|0.25445	0.190000|0.190000	0.17057|0.17057	-0.477000|-0.477000	0.06832|0.06832	-3.057000|-3.057000	0.00068|0.00068	ATA|AAT		0.348	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
QTRTD1	79691	broad.mit.edu	37	3	113795743	113795743	+	Missense_Mutation	SNP	C	C	T	rs376673299		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:113795743C>T	ENST00000493014.1	+	3	450	c.382C>T	c.(382-384)Cgc>Tgc	p.R128C	QTRTD1_ENST00000485050.1_Missense_Mutation_p.R246C|QTRTD1_ENST00000281273.4_Missense_Mutation_p.R234C|QTRTD1_ENST00000479882.1_Missense_Mutation_p.R111C	NM_001256836.1	NP_001243765.1			queuine tRNA-ribosyltransferase domain containing 1									p.R234C(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|skin(2)	10						GGCTAGACTACGCTTGCTGTC	0.577													C|||	1	0.000199681	0.0	0.0	5008	,	,		19328	0.0		0.0	False		,,,				2504	0.001				p.R234C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C700T	3						.	C	CYS/ARG	0,4406		0,0,2203	80.0	65.0	70.0		700	1.8	0.8	3		70	1,8599	1.2+/-3.3	0,1,4299	no	missense	QTRTD1	NM_024638.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	234/416	113795743	1,13005	2203	4300	6503	115278433	SO:0001583	missense	79691	exon7			AK023022	CCDS33828.1, CCDS58846.1, CCDS58845.1, CCDS58844.1	3q13.31	2010-11-16			ENSG00000151576	ENSG00000151576			25771	protein-coding gene	gene with protein product						12477932	Standard	NM_024638		Approved	FLJ12960	uc003eaz.4	Q9H974	OTTHUMG00000159336	ENST00000493014.1:c.382C>T	3.37:g.113795743C>T	ENSP00000419169:p.Arg128Cys	Somatic		Capture	Illumina HiSeq	Phase_I	115278433	NM_024638		Missense_Mutation	SNP	ENST00000493014.1	37	CCDS58845.1	.	.	.	.	.	.	.	.	.	.	C	7.483	0.648997	0.14516	0.0	1.16E-4	ENSG00000151576	ENST00000485050;ENST00000281273;ENST00000479882;ENST00000493014	.	.	.	5.71	1.8	0.24995	.	0.761563	0.12945	N	0.426261	T	0.42720	0.1215	L	0.58510	1.815	0.25067	N	0.99102	B;P;B	0.44877	0.0;0.845;0.001	B;P;B	0.46975	0.0;0.533;0.0	T	0.25502	-1.0130	9	0.51188	T	0.08	-0.0265	6.3781	0.21519	0.2008:0.547:0.0:0.2522	.	128;111;234	B7Z472;B7Z5R2;Q9H974	.;.;QTRD1_HUMAN	C	246;234;111;128	.	ENSP00000281273:R234C	R	+	1	0	QTRTD1	115278433	0.938000	0.31826	0.835000	0.33067	0.034000	0.12701	0.333000	0.19768	0.088000	0.17205	-0.797000	0.03246	CGC		0.577	QTRTD1-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000354711.1	NM_024638	
ARHGAP31	57514	broad.mit.edu	37	3	119121244	119121244	+	Splice_Site	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:119121244G>T	ENST00000264245.4	+	10	2177	c.1645G>T	c.(1645-1647)Gct>Tct	p.A549S		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	549					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)	p.A549S(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						GACTTCTGCAGGTAAGTAGAG	0.483																																					p.A549S	Pancreas(7;176 297 5394 51128 51241)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1645T	3						.						20.0	22.0	21.0					3																	119121244		1798	4007	5805	120603934	SO:0001630	splice_region_variant	57514	exon10				CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"""Rho GTPase activating proteins"""	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.1645+1G>T	3.37:g.119121244G>T		Somatic		Capture	Illumina HiSeq	Phase_I	120603934	NM_020754	Q9ULL6	Missense_Mutation	SNP	ENST00000264245.4	37	CCDS43135.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.550495	0.65311	.	.	ENSG00000031081	ENST00000264245;ENST00000543280	T	0.07021	3.23	5.11	5.11	0.69529	.	0.102804	0.42964	D	0.000635	T	0.09686	0.0238	L	0.56769	1.78	0.34422	D	0.697593	P	0.46784	0.884	B	0.35813	0.211	T	0.29150	-1.0021	10	0.30854	T	0.27	.	15.8432	0.78868	0.0:0.0:1.0:0.0	.	549	Q2M1Z3	RHG31_HUMAN	S	549	ENSP00000264245:A549S	ENSP00000264245:A549S	A	+	1	0	ARHGAP31	120603934	1.000000	0.71417	0.998000	0.56505	0.810000	0.45777	3.922000	0.56462	2.657000	0.90304	0.655000	0.94253	GCT		0.483	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2		Missense_Mutation
POLQ	10721	broad.mit.edu	37	3	121200503	121200503	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:121200503G>A	ENST00000264233.5	-	19	6255	c.6127C>T	c.(6127-6129)Cga>Tga	p.R2043*		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2043					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.R2178*(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		GCTCTGTATCGCCCAGAATGC	0.463								DNA polymerases (catalytic subunits)																													p.R2043X	Pancreas(152;907 1925 26081 31236 36904)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C6127T	3						.						82.0	83.0	83.0					3																	121200503		2203	4300	6503	122683193	SO:0001587	stop_gained	10721	exon19			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.6127C>T	3.37:g.121200503G>A	ENSP00000264233:p.Arg2043*	Somatic		Capture	Illumina HiSeq	Phase_I	122683193	NM_199420	O95160|Q6VMB5	Nonsense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	G	48	14.364681	0.99792	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	.	.	.	5.05	-0.635	0.11512	.	0.108387	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6343	0.76937	0.0:0.0:0.4154:0.5846	.	.	.	.	X	1666;2043;2179	.	ENSP00000264233:R2043X	R	-	1	2	POLQ	122683193	1.000000	0.71417	0.955000	0.39395	0.987000	0.75469	1.604000	0.36804	-0.020000	0.14032	0.650000	0.86243	CGA		0.463	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
POLQ	10721	broad.mit.edu	37	3	121208011	121208011	+	Missense_Mutation	SNP	C	C	A	rs3218640	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:121208011C>A	ENST00000264233.5	-	16	3895	c.3767G>T	c.(3766-3768)gGa>gTa	p.G1256V		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1256					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.G1391V(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TATATCATCTCCTAATGCCTG	0.348								DNA polymerases (catalytic subunits)																													p.G1256V	Pancreas(152;907 1925 26081 31236 36904)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3767T	3						.						175.0	181.0	179.0					3																	121208011		2203	4300	6503	122690701	SO:0001583	missense	10721	exon16			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.3767G>T	3.37:g.121208011C>A	ENSP00000264233:p.Gly1256Val	Somatic		Capture	Illumina HiSeq	Phase_I	122690701	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.389579	0.25118	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.51817	0.69	5.15	1.41	0.22369	.	0.621947	0.16971	N	0.192099	T	0.51041	0.1651	L	0.32530	0.975	0.58432	P	9.000000000036756E-6	D;D	0.89917	0.998;1.0	P;D	0.77557	0.905;0.99	T	0.57871	-0.7736	9	0.52906	T	0.07	.	6.5155	0.22246	0.0:0.5533:0.0:0.4467	.	1256;428	O75417;O75417-2	DPOLQ_HUMAN;.	V	879;1256;1392	ENSP00000264233:G1256V	ENSP00000264233:G1256V	G	-	2	0	POLQ	122690701	0.003000	0.15002	0.042000	0.18584	0.346000	0.29079	0.086000	0.14935	0.441000	0.26529	-0.251000	0.11542	GGA		0.348	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
PARP14	54625	broad.mit.edu	37	3	122433187	122433187	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:122433187G>A	ENST00000474629.2	+	12	4177	c.3911G>A	c.(3910-3912)gGa>gAa	p.G1304E		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1304	Macro 3. {ECO:0000255|PROSITE- ProRule:PRU00490}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.G1304E(1)|p.G1141E(1)		NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		GTAATTGGTGGAAATGATGTC	0.408																																					p.G1304E												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3911A	3						.						66.0	62.0	64.0					3																	122433187		1843	4096	5939	123915877	SO:0001583	missense	54625	exon12			AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.3911G>A	3.37:g.122433187G>A	ENSP00000418194:p.Gly1304Glu	Somatic		Capture	Illumina HiSeq	Phase_I	123915877	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.364661	0.41902	.	.	ENSG00000173193	ENST00000474629;ENST00000398162;ENST00000398157	T	0.21543	2.0	5.51	2.6	0.31112	Appr-1-p processing (3);	0.208076	0.35495	N	0.003177	T	0.16342	0.0393	N	0.19112	0.55	0.28975	N	0.889011	D;B	0.64830	0.994;0.211	P;B	0.54460	0.753;0.241	T	0.06267	-1.0836	10	0.02654	T	1	.	9.021	0.36200	0.0:0.2689:0.4541:0.2771	.	1304;1304	Q460N5-4;Q460N5	.;PAR14_HUMAN	E	1304;1223;300	ENSP00000418194:G1304E	ENSP00000381224:G300E	G	+	2	0	PARP14	123915877	0.005000	0.15991	0.958000	0.39756	0.851000	0.48451	1.557000	0.36299	0.370000	0.24538	0.561000	0.74099	GGA		0.408	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
ADCY5	111	broad.mit.edu	37	3	123008639	123008639	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:123008639A>G	ENST00000462833.1	-	19	4702	c.3490T>C	c.(3490-3492)Tac>Cac	p.Y1164H	ADCY5_ENST00000309879.5_Missense_Mutation_p.Y814H|ADCY5_ENST00000491190.1_Missense_Mutation_p.Y822H	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	1164	Guanylate cyclase 2. {ECO:0000255|PROSITE-ProRule:PRU00099}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.Y1164H(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		TCATTGATGTACTTCATCTGG	0.582																																					p.Y1164H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3490C	3						.						165.0	147.0	153.0					3																	123008639		2203	4300	6503	124491329	SO:0001583	missense	111	exon19			U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"""Adenylate cyclases"""	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.3490T>C	3.37:g.123008639A>G	ENSP00000419361:p.Tyr1164His	Somatic		Capture	Illumina HiSeq	Phase_I	124491329	NM_183357	B7Z8A6|Q7RTV7|Q8NFM3	Missense_Mutation	SNP	ENST00000462833.1	37	CCDS3022.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.822922	0.32237	.	.	ENSG00000173175	ENST00000462833;ENST00000491190;ENST00000309879	T;T;T	0.80653	-1.4;-1.4;-1.4	5.13	5.13	0.70059	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.242522	0.30374	N	0.009777	T	0.65015	0.2651	N	0.05124	-0.11	0.49687	D	0.999819	B;B	0.23806	0.015;0.091	B;B	0.32022	0.035;0.139	T	0.61327	-0.7085	10	0.14252	T	0.57	.	15.1105	0.72351	1.0:0.0:0.0:0.0	.	1164;822	O95622;B3KWA8	ADCY5_HUMAN;.	H	1164;822;814	ENSP00000419361:Y1164H;ENSP00000418537:Y822H;ENSP00000308685:Y814H	ENSP00000308685:Y814H	Y	-	1	0	ADCY5	124491329	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.903000	0.63272	2.151000	0.67156	0.454000	0.30748	TAC		0.582	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048	
ITGB5	3693	broad.mit.edu	37	3	124492725	124492725	+	Silent	SNP	G	G	A	rs144048165	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:124492725G>A	ENST00000296181.4	-	11	2024	c.1728C>T	c.(1726-1728)tgC>tgT	p.C576C	ITGB5_ENST00000461306.1_5'UTR	NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	576	Cysteine-rich tandem repeats.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)	p.C576C(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		AACCTGCATGGCACTTGCATT	0.547													G|||	11	0.00219649	0.0076	0.0014	5008	,	,		23863	0.0		0.0	False		,,,				2504	0.0				p.C576C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1728T	3						.	G		34,4372	40.0+/-72.8	1,32,2170	93.0	76.0	81.0		1728	5.2	1.0	3	dbSNP_134	81	0,8600		0,0,4300	no	coding-synonymous	ITGB5	NM_002213.3		1,32,6470	AA,AG,GG		0.0,0.7717,0.2614		576/800	124492725	34,12972	2203	4300	6503	125975415	SO:0001819	synonymous_variant	3693	exon11			J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"""Integrins"""	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.1728C>T	3.37:g.124492725G>A		Somatic		Capture	Illumina HiSeq	Phase_I	125975415	NM_002213	B0LPF8|B2RD70	Silent	SNP	ENST00000296181.4	37	CCDS3030.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	10.47	1.358664	0.24598	0.007717	0.0	ENSG00000082781	ENST00000481591	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	T	0.54240	0.1846	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56238	-0.8012	4	.	.	.	.	11.3302	0.49470	0.0823:0.0:0.9177:0.0	.	.	.	.	V	266	.	.	A	-	2	0	ITGB5	125975415	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.784000	0.47774	2.705000	0.92388	0.655000	0.94253	GCC		0.547	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213	
CAND2	23066	broad.mit.edu	37	3	12858079	12858079	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:12858079C>T	ENST00000456430.2	+	10	1689	c.1648C>T	c.(1648-1650)Cgg>Tgg	p.R550W	CAND2_ENST00000295989.5_Missense_Mutation_p.R457W	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	550					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)		p.R457W(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GGAGCTGGTGCGGGCCCTGTG	0.617																																					p.R550W	GBM(43;676 868 1633 6395 37496)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1648T	3						.						27.0	32.0	30.0					3																	12858079		2061	4201	6262	12833079	SO:0001583	missense	23066	exon10				CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1648C>T	3.37:g.12858079C>T	ENSP00000387641:p.Arg550Trp	Somatic		Capture	Illumina HiSeq	Phase_I	12833079	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.411482	0.42817	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	D;D	0.89681	-2.55;-2.55	5.12	1.92	0.25849	Armadillo-like helical (1);Armadillo-type fold (1);	0.385071	0.23633	N	0.046108	D	0.90501	0.7024	L	0.54323	1.7	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.59012	0.772;0.85	D	0.89906	0.4048	10	0.87932	D	0	-31.0625	11.7857	0.52041	0.68:0.3199:0.0:0.0	.	550;457	O75155;O75155-2	CAND2_HUMAN;.	W	457;550	ENSP00000295989:R457W;ENSP00000387641:R550W	ENSP00000295989:R457W	R	+	1	2	CAND2	12833079	1.000000	0.71417	0.944000	0.38274	0.272000	0.26649	3.897000	0.56273	0.533000	0.28675	-0.310000	0.09108	CGG		0.617	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
ZXDC	79364	broad.mit.edu	37	3	126185027	126185027	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:126185027T>A	ENST00000389709.3	-	5	1465	c.1412A>T	c.(1411-1413)cAc>cTc	p.H471L	ZXDC_ENST00000336332.5_Missense_Mutation_p.H471L	NM_025112.4	NP_079388.3	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C	471					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|LRR domain binding (GO:0030275)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H471L(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(1)	17				GBM - Glioblastoma multiforme(114;0.155)		TCTGACCATGTGCGCCTTCAT	0.582																																					p.H471L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A1412T	3						.						79.0	87.0	84.0					3																	126185027		2144	4259	6403	127667717	SO:0001583	missense	79364	exon5			AK023923	CCDS43145.1, CCDS43146.1	3q21.3	2014-02-12			ENSG00000070476	ENSG00000070476		"""Zinc fingers, C2H2-type"""	28160	protein-coding gene	gene with protein product		615746				8619474, 9110174	Standard	XM_005247757		Approved	MGC11349, FLJ13861	uc003eiv.3	Q2QGD7	OTTHUMG00000162754	ENST00000389709.3:c.1412A>T	3.37:g.126185027T>A	ENSP00000374359:p.His471Leu	Somatic		Capture	Illumina HiSeq	Phase_I	127667717	NM_025112	C5J0H9|Q6DKI8|Q7L3L1|Q8NAU2	Missense_Mutation	SNP	ENST00000389709.3	37	CCDS43145.1	.	.	.	.	.	.	.	.	.	.	T	19.98	3.927869	0.73327	.	.	ENSG00000070476	ENST00000389709;ENST00000336332	T;T	0.35048	1.33;1.33	5.23	5.23	0.72850	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.56124	0.1964	M	0.62723	1.935	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.73708	0.967;0.981	T	0.59773	-0.7391	10	0.87932	D	0	-19.2914	13.3472	0.60580	0.0:0.0:0.0:1.0	.	471;471	Q2QGD7-2;Q2QGD7	.;ZXDC_HUMAN	L	471	ENSP00000374359:H471L;ENSP00000337694:H471L	ENSP00000337694:H471L	H	-	2	0	ZXDC	127667717	1.000000	0.71417	0.062000	0.19696	0.459000	0.32528	7.751000	0.85126	2.095000	0.63458	0.482000	0.46254	CAC		0.582	ZXDC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370327.2	NM_025112	
RHO	6010	broad.mit.edu	37	3	129251457	129251457	+	Missense_Mutation	SNP	G	G	A	rs150250946		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:129251457G>A	ENST00000296271.3	+	4	872	c.778G>A	c.(778-780)Gct>Act	p.A260T		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	260					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)	p.A260T(2)		breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	CATGGTCATCGCTTTCCTGAT	0.602																																					p.A260T	Esophageal Squamous(118;214 1623 30842 43234 46940)											.	.	2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	c.G778A	3						.	G	THR/ALA	0,4406		0,0,2203	227.0	163.0	185.0		778	4.6	0.0	3	dbSNP_134	185	2,8598	2.2+/-6.3	0,2,4298	no	missense	RHO	NM_000539.3	58	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	260/349	129251457	2,13004	2203	4300	6503	130734147	SO:0001583	missense	6010	exon4			AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"""GPCR / Class A : Opsin receptors"""	10012	protein-coding gene	gene with protein product	"""opsin 2, rod pigment"""	180380	"""retinitis pigmentosa 4, autosomal dominant"""	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.778G>A	3.37:g.129251457G>A	ENSP00000296271:p.Ala260Thr	Somatic		Capture	Illumina HiSeq	Phase_I	130734147	NM_000539	Q16414|Q2M249	Missense_Mutation	SNP	ENST00000296271.3	37	CCDS3063.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.781297	0.49891	0.0	2.33E-4	ENSG00000163914	ENST00000296271	T	0.72394	-0.65	5.51	4.55	0.56014	GPCR, rhodopsin-like superfamily (1);	0.426739	0.26149	N	0.026057	T	0.69806	0.3152	M	0.85299	2.745	0.31181	N	0.702011	P	0.35656	0.514	B	0.22601	0.04	T	0.75662	-0.3240	10	0.87932	D	0	.	12.937	0.58320	0.0:0.0:0.4963:0.5037	.	260	P08100	OPSD_HUMAN	T	260	ENSP00000296271:A260T	ENSP00000296271:A260T	A	+	1	0	RHO	130734147	0.753000	0.28349	0.030000	0.17652	0.991000	0.79684	1.724000	0.38064	1.112000	0.41740	0.561000	0.74099	GCT		0.602	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539	
BFSP2	8419	broad.mit.edu	37	3	133185748	133185748	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:133185748A>G	ENST00000302334.2	+	5	1057	c.968A>G	c.(967-969)aAc>aGc	p.N323S	BFSP2_ENST00000511434.1_3'UTR	NM_003571.2	NP_003562.1	Q13515	BFSP2_HUMAN	beaded filament structural protein 2, phakinin	323	Rod.				cell maturation (GO:0048469)|intermediate filament cytoskeleton organization (GO:0045104)|lens fiber cell development (GO:0070307)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)	p.N323S(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|urinary_tract(1)	13						GAGTTACACAACACTTCGTGC	0.562																																					p.N323S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A968G	3						.						86.0	81.0	83.0					3																	133185748		2203	4300	6503	134668438	SO:0001583	missense	8419	exon5			U48224	CCDS33859.1	3q22.1	2013-01-16			ENSG00000170819	ENSG00000170819		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1041	protein-coding gene	gene with protein product		603212					Standard	NM_003571		Approved	CP47, CP49, LIFL-L, phakinin	uc003epn.1	Q13515	OTTHUMG00000159719	ENST00000302334.2:c.968A>G	3.37:g.133185748A>G	ENSP00000304987:p.Asn323Ser	Somatic		Capture	Illumina HiSeq	Phase_I	134668438	NM_003571	Q14D32|Q9HBW5	Missense_Mutation	SNP	ENST00000302334.2	37	CCDS33859.1	.	.	.	.	.	.	.	.	.	.	A	10.96	1.498702	0.26861	.	.	ENSG00000170819	ENST00000302334	D	0.88509	-2.39	5.74	3.37	0.38596	Filament (1);	0.600404	0.16424	N	0.215034	T	0.81702	0.4878	N	0.25647	0.755	0.25239	N	0.989768	B	0.14012	0.009	B	0.12837	0.008	T	0.72033	-0.4412	10	0.87932	D	0	-14.2662	9.8381	0.40982	0.8618:0.0:0.1382:0.0	.	323	Q13515	BFSP2_HUMAN	S	323	ENSP00000304987:N323S	ENSP00000304987:N323S	N	+	2	0	BFSP2	134668438	1.000000	0.71417	0.803000	0.32268	0.990000	0.78478	5.638000	0.67861	0.457000	0.26962	0.459000	0.35465	AAC		0.562	BFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357031.1		
TF	7018	broad.mit.edu	37	3	133494355	133494355	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:133494355C>A	ENST00000402696.3	+	15	2251	c.1766C>A	c.(1765-1767)cCt>cAt	p.P589H	TF_ENST00000264998.3_Missense_Mutation_p.P462H	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	589	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.		P -> S (in allele TF*C2; dbSNP:rs1049296). {ECO:0000269|PubMed:11702220, ECO:0000269|PubMed:11703331, ECO:0000269|PubMed:9272172, ECO:0000269|Ref.5}.		blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)	p.P589H(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	ACCAGGAAACCTGTGGAGGAG	0.493																																					p.P589H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1766A	3						.						182.0	179.0	180.0					3																	133494355		2203	4300	6503	134977045	SO:0001583	missense	7018	exon15				CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.1766C>A	3.37:g.133494355C>A	ENSP00000385834:p.Pro589His	Somatic		Capture	Illumina HiSeq	Phase_I	134977045	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Missense_Mutation	SNP	ENST00000402696.3	37	CCDS3080.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.427498	0.43122	.	.	ENSG00000091513	ENST00000402696;ENST00000264998	T;T	0.08720	3.06;3.06	5.01	1.89	0.25635	.	1.463040	0.03931	N	0.285272	T	0.39655	0.1086	H	0.94423	3.535	0.09310	N	1	P	0.48589	0.912	P	0.57204	0.815	T	0.40608	-0.9554	10	0.87932	D	0	-0.967	13.8587	0.63545	0.3978:0.6022:0.0:0.0	.	589	P02787	TRFE_HUMAN	H	589;462	ENSP00000385834:P589H;ENSP00000264998:P462H	ENSP00000264998:P462H	P	+	2	0	TF	134977045	0.000000	0.05858	0.043000	0.18650	0.014000	0.08584	0.238000	0.18004	0.662000	0.31006	-0.310000	0.09108	CCT		0.493	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
CEP63	80254	broad.mit.edu	37	3	134226075	134226075	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:134226075C>T	ENST00000337090.3	+	3	342	c.169C>T	c.(169-171)Cgt>Tgt	p.R57C	CEP63_ENST00000332047.5_Missense_Mutation_p.R57C|CEP63_ENST00000513612.2_Missense_Mutation_p.R57C|CEP63_ENST00000354446.3_Missense_Mutation_p.R57C|CEP63_ENST00000606977.1_Missense_Mutation_p.R57C|CEP63_ENST00000504013.1_3'UTR|CEP63_ENST00000383229.3_Missense_Mutation_p.R57C			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	57					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)		p.R57C(1)		kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CTTGAAAATCCGTGAACAGGA	0.368																																					p.R57C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C169T	3						.						116.0	114.0	114.0					3																	134226075		2203	4300	6503	135708765	SO:0001583	missense	80254	exon3			AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.169C>T	3.37:g.134226075C>T	ENSP00000336524:p.Arg57Cys	Somatic		Capture	Illumina HiSeq	Phase_I	135708765	NM_001042383	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	37	CCDS3086.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.293884	0.60086	.	.	ENSG00000182923	ENST00000332047;ENST00000354446;ENST00000511574;ENST00000337090;ENST00000383229;ENST00000512894;ENST00000513612	T;T;T;T;T;T;T	0.26223	1.78;1.78;1.78;1.78;1.78;1.75;1.78	5.07	5.07	0.68467	.	0.196730	0.41823	D	0.000809	T	0.49064	0.1535	M	0.71581	2.175	0.49798	D	0.999821	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.978;0.987;0.992	T	0.49818	-0.8899	10	0.72032	D	0.01	-8.1035	12.6732	0.56878	0.1653:0.8347:0.0:0.0	.	57;57;57;57	Q96MT8;Q96MT8-2;Q96MT8-4;Q96MT8-3	CEP63_HUMAN;.;.;.	C	57	ENSP00000328382:R57C;ENSP00000346432:R57C;ENSP00000424626:R57C;ENSP00000336524:R57C;ENSP00000372716:R57C;ENSP00000423225:R57C;ENSP00000426129:R57C	ENSP00000328382:R57C	R	+	1	0	CEP63	135708765	0.989000	0.36119	0.999000	0.59377	0.451000	0.32288	2.456000	0.44997	2.508000	0.84585	0.655000	0.94253	CGT		0.368	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180	
MSL2	55167	broad.mit.edu	37	3	135870407	135870407	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:135870407G>T	ENST00000309993.2	-	2	2048	c.1316C>A	c.(1315-1317)cCt>cAt	p.P439H	MSL2_ENST00000434835.2_Missense_Mutation_p.P365H	NM_018133.3	NP_060603.2	Q9HCI7	MSL2_HUMAN	male-specific lethal 2 homolog (Drosophila)	439	Lys-rich.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.P439H(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	18						ATGATGACTAGGAATCTTTTC	0.383																																					p.P439H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1316A	3						.						100.0	104.0	103.0					3																	135870407		2203	4300	6503	137353097	SO:0001583	missense	55167	exon2			AK001408	CCDS33861.1, CCDS46922.1	3q22.2	2008-10-29	2008-10-29	2008-10-29	ENSG00000174579	ENSG00000174579		"""RING-type (C3HC4) zinc fingers"""	25544	protein-coding gene	gene with protein product	"""male-specific lethal-2 homolog (Drosophila)"""	614802	"""ring finger protein 184"", ""male-specific lethal 2-like 1 (Drosophila)"""	RNF184, MSL2L1		16227571, 16543150	Standard	NM_018133		Approved	FLJ10546, KIAA1585, msl-2	uc003eqx.1	Q9HCI7	OTTHUMG00000159793	ENST00000309993.2:c.1316C>A	3.37:g.135870407G>T	ENSP00000311827:p.Pro439His	Somatic		Capture	Illumina HiSeq	Phase_I	137353097	NM_018133	B4DYL4|G5E9I1|Q0D2P1|Q8NDB4|Q9NVS4	Missense_Mutation	SNP	ENST00000309993.2	37	CCDS33861.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.854821	0.32791	.	.	ENSG00000174579	ENST00000309993;ENST00000434835	.	.	.	5.65	3.88	0.44766	.	0.160839	0.56097	D	0.000031	T	0.55561	0.1928	L	0.51422	1.61	0.43430	D	0.995594	P	0.49447	0.924	P	0.47015	0.534	T	0.52290	-0.8595	9	0.36615	T	0.2	-7.4701	11.8193	0.52228	0.1417:0.0:0.8583:0.0	.	439	Q9HCI7	MSL2_HUMAN	H	439;365	.	ENSP00000311827:P439H	P	-	2	0	MSL2	137353097	1.000000	0.71417	0.997000	0.53966	0.980000	0.70556	7.660000	0.83776	0.757000	0.33036	-0.222000	0.12452	CCT		0.383	MSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357347.1	NM_018133	
ARMC8	25852	broad.mit.edu	37	3	137964044	137964044	+	Intron	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:137964044C>T	ENST00000469044.1	+	12	1405				ARMC8_ENST00000489213.1_Missense_Mutation_p.R343C|ARMC8_ENST00000470821.1_Missense_Mutation_p.R385C|ARMC8_ENST00000538260.1_Intron|ARMC8_ENST00000491704.1_Intron|ARMC8_ENST00000471453.1_Missense_Mutation_p.R371C|ARMC8_ENST00000461822.1_Intron|ARMC8_ENST00000485396.1_Intron|ARMC8_ENST00000393058.3_Intron|ARMC8_ENST00000358441.2_Missense_Mutation_p.R371C|ARMC8_ENST00000481646.1_Intron	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8									p.R371C(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						GGGAGAGGGGCGTCCCCCAGT	0.512																																					p.R371C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1111T	3						.						54.0	52.0	53.0					3																	137964044		2203	4300	6503	139446734	SO:0001627	intron_variant	25852	exon13				CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"""Armadillo repeat containing"""	24999	protein-coding gene	gene with protein product	"""GID complex subunit 5, VID28 homolog (S. cerevisiae)"""					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.1134+19C>T	3.37:g.137964044C>T		Somatic		Capture	Illumina HiSeq	Phase_I	139446734	NM_213654	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Missense_Mutation	SNP	ENST00000469044.1	37		.	.	.	.	.	.	.	.	.	.	C	16.11	3.030377	0.54790	.	.	ENSG00000114098	ENST00000358441;ENST00000489213;ENST00000471453;ENST00000470821	T;T;T;T	0.37411	1.91;1.2;1.91;1.91	5.42	5.42	0.78866	.	.	.	.	.	T	0.34629	0.0904	N	0.08118	0	0.80722	D	1	D;D	0.59767	0.986;0.986	P;P	0.58210	0.835;0.835	T	0.21895	-1.0232	8	.	.	.	.	16.7031	0.85364	0.0:1.0:0.0:0.0	.	385;371	G5E9V6;Q8IUR7-6	.;.	C	371;343;371;385	ENSP00000351221:R371C;ENSP00000418412:R343C;ENSP00000420440:R371C;ENSP00000418405:R385C	.	R	+	1	0	ARMC8	139446734	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	3.135000	0.50546	2.522000	0.85027	0.650000	0.86243	CGT		0.512	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396	
PXYLP1	92370	broad.mit.edu	37	3	141011377	141011377	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:141011377A>G	ENST00000286353.4	+	6	910	c.773A>G	c.(772-774)cAg>cGg	p.Q258R	ACPL2_ENST00000504264.1_Missense_Mutation_p.Q241R|RP11-438D8.2_ENST00000507698.1_RNA|ACPL2_ENST00000393007.1_Missense_Mutation_p.Q242R|ACPL2_ENST00000508812.1_Missense_Mutation_p.Q249R|ACPL2_ENST00000502783.1_Missense_Mutation_p.Q220R|ACPL2_ENST00000393010.2_Missense_Mutation_p.Q258R	NM_001037172.1|NM_001282728.1	NP_001032249.1|NP_001269657.1	Q8TE99	PXYP1_HUMAN		258						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)	p.Q258R(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(2)	23						GAAAAGGAGCAGCGTCGTCAG	0.512																																					p.Q258R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A773G	3						.						62.0	67.0	65.0					3																	141011377		2203	4300	6503	142494067	SO:0001583	missense	92370	exon8																														ENST00000286353.4:c.773A>G	3.37:g.141011377A>G	ENSP00000286353:p.Gln258Arg	Somatic		Capture	Illumina HiSeq	Phase_I	142494067	NM_152282	D3DNF5|Q49AJ2|W0TR04	Missense_Mutation	SNP	ENST00000286353.4	37	CCDS3116.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.528097	0.85706	.	.	ENSG00000155893	ENST00000286353;ENST00000502783;ENST00000393010;ENST00000504264;ENST00000508812;ENST00000393007;ENST00000332228	T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.47801	0.1465	M	0.65320	2	0.80722	D	1	D;D	0.69078	0.98;0.997	P;D	0.66979	0.9;0.948	T	0.36553	-0.9743	10	0.14252	T	0.57	.	13.7867	0.63115	1.0:0.0:0.0:0.0	.	241;258	B7Z3R9;Q8TE99	.;ACPL2_HUMAN	R	258;220;258;241;249;242;66	ENSP00000286353:Q258R;ENSP00000422558:Q220R;ENSP00000376733:Q258R;ENSP00000426877:Q241R;ENSP00000422901:Q249R;ENSP00000376731:Q242R	ENSP00000286353:Q258R	Q	+	2	0	ACPL2	142494067	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.154000	0.94694	2.197000	0.70478	0.454000	0.30748	CAG		0.512	ACPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359533.2		
GFM1	85476	broad.mit.edu	37	3	158409190	158409190	+	Silent	SNP	C	C	T	rs149049400	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:158409190C>T	ENST00000486715.1	+	18	2547	c.2190C>T	c.(2188-2190)gaC>gaT	p.D730D	RP11-379F4.7_ENST00000607624.1_lincRNA|GFM1_ENST00000264263.5_Silent_p.D749D	NM_024996.5	NP_079272.4			G elongation factor, mitochondrial 1									p.D730D(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|urinary_tract(2)	22			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			CACAAGAAGACGTCATTAATA	0.368													C|||	3	0.000599042	0.0	0.0	5008	,	,		17858	0.0		0.003	False		,,,				2504	0.0				p.D730D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2190T	3						.	C		0,4406		0,0,2203	106.0	108.0	108.0		2190	-9.8	0.0	3	dbSNP_134	108	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	GFM1	NM_024996.5		0,7,6496	TT,TC,CC		0.0814,0.0,0.0538		730/752	158409190	7,12999	2203	4300	6503	159891884	SO:0001819	synonymous_variant	85476	exon18			AF309777	CCDS33885.1	3q25	2008-02-05			ENSG00000168827	ENSG00000168827			13780	protein-coding gene	gene with protein product		606639	"""G translation elongation factor, mitochondrial"""			11374907, 11735030	Standard	NM_024996		Approved	EFGM, GFM, EGF1	uc003fce.3	Q96RP9	OTTHUMG00000158804	ENST00000486715.1:c.2190C>T	3.37:g.158409190C>T		Somatic		Capture	Illumina HiSeq	Phase_I	159891884	NM_024996		Silent	SNP	ENST00000486715.1	37	CCDS33885.1																																																																																				0.368	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996	
SAMD7	344658	broad.mit.edu	37	3	169644797	169644797	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:169644797C>T	ENST00000428432.2	+	6	1136	c.747C>T	c.(745-747)gcC>gcT	p.A249A	SAMD7_ENST00000335556.3_Silent_p.A249A	NM_182610.2	NP_872416.1	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	249								p.A249A(1)		NS(1)|biliary_tract(1)|breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)			CAGCTCTTGCCAACACCTGTG	0.517																																					p.A249A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C747T	3						.						101.0	99.0	100.0					3																	169644797		2203	4300	6503	171127491	SO:0001819	synonymous_variant	344658	exon6			BX537903	CCDS3209.1	3q26.31	2013-01-10			ENSG00000187033	ENSG00000187033		"""Sterile alpha motif (SAM) domain containing"""	25394	protein-coding gene	gene with protein product							Standard	NM_182610		Approved	DKFZp686E1583	uc003fgd.3	Q7Z3H4	OTTHUMG00000158730	ENST00000428432.2:c.747C>T	3.37:g.169644797C>T		Somatic		Capture	Illumina HiSeq	Phase_I	171127491	NM_182610		Silent	SNP	ENST00000428432.2	37	CCDS3209.1																																																																																				0.517	SAMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351959.1	NM_182610	
TBC1D5	9779	broad.mit.edu	37	3	17255828	17255828	+	Silent	SNP	G	G	A	rs142834175		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:17255828G>A	ENST00000253692.7	-	18	3287	c.1623C>T	c.(1621-1623)agC>agT	p.S541S	TBC1D5_ENST00000429383.4_Silent_p.S541S|TBC1D5_ENST00000414318.2_5'UTR|TBC1D5_ENST00000429924.2_Silent_p.S515S|TBC1D5_ENST00000446818.2_Silent_p.S563S	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	541						retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)	p.S541S(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						AACTCTCAACGCTTGGAGATG	0.398																																					p.S541S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1623T	3						.	G	,,	0,4406		0,0,2203	62.0	63.0	63.0		1623,1689,1623	2.1	1.0	3	dbSNP_134	63	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	TBC1D5	NM_001134380.1,NM_001134381.1,NM_014744.2	,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,	541/796,563/818,541/796	17255828	2,13004	2203	4300	6503	17230832	SO:0001819	synonymous_variant	9779	exon18			D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.1623C>T	3.37:g.17255828G>A		Somatic		Capture	Illumina HiSeq	Phase_I	17230832	NM_001134380	A6NP25|C9JP52	Silent	SNP	ENST00000253692.7	37	CCDS33714.1																																																																																				0.398	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744	
PHC3	80012	broad.mit.edu	37	3	169815061	169815061	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:169815061G>A	ENST00000494943.1	-	15	2977	c.2909C>T	c.(2908-2910)gCc>gTc	p.A970V	PHC3_ENST00000495893.2_Missense_Mutation_p.A982V			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	970	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.A951V(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			GATCTTCAGGGCTGGGCCTAG	0.428																																					p.A982V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2945T	3						.						281.0	280.0	280.0					3																	169815061		2053	4235	6288	171297755	SO:0001583	missense	80012	exon15				CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889		"""Sterile alpha motif (SAM) domain containing"""	15682	protein-coding gene	gene with protein product	"""early development regulator 3"", ""polyhomeotic like 3"""		"""polyhomeotic like 3 (Drosophila)"""			12167701, 12384788	Standard	NM_024947		Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000494943.1:c.2909C>T	3.37:g.169815061G>A	ENSP00000420271:p.Ala970Val	Somatic		Capture	Illumina HiSeq	Phase_I	171297755	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Missense_Mutation	SNP	ENST00000494943.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.388512|5.388512	0.95988|0.95988	.|.	.|.	ENSG00000173889|ENSG00000173889	ENST00000494943;ENST00000495893|ENST00000484068	T;T|.	0.53423|.	0.62;0.62|.	5.68|5.68	5.68|5.68	0.88126|0.88126	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);|.	0.000000|.	0.64402|.	D|.	0.000001|.	D|D	0.86477|0.86477	0.5942|0.5942	M|M	0.91717|0.91717	3.235|3.235	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.91635|.	0.988;0.999|.	D|D	0.88669|0.88669	0.3194|0.3194	10|5	0.87932|.	D|.	0|.	-11.6914|-11.6914	19.7918|19.7918	0.96461|0.96461	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	970;982|.	Q8NDX5;Q8NDX5-7|.	PHC3_HUMAN;.|.	V|S	970;982|148	ENSP00000420271:A970V;ENSP00000420294:A982V|.	ENSP00000420271:A970V|.	A|P	-|-	2|1	0|0	PHC3|PHC3	171297755|171297755	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.414000|9.414000	0.97362|0.97362	2.677000|2.677000	0.91161|0.91161	0.591000|0.591000	0.81541|0.81541	GCC|CCC		0.428	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947	
GHSR	2693	broad.mit.edu	37	3	172166123	172166123	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:172166123G>A	ENST00000241256.2	-	1	123	c.81C>T	c.(79-81)aaC>aaT	p.N27N	GHSR_ENST00000427970.1_Silent_p.N27N	NM_198407.2	NP_940799.1	Q92847	GHSR_HUMAN	growth hormone secretagogue receptor	27					actin polymerization or depolymerization (GO:0008154)|adult feeding behavior (GO:0008343)|cellular response to insulin stimulus (GO:0032869)|decidualization (GO:0046697)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone secretion (GO:0030252)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin secretion (GO:0046676)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of appetite (GO:0032100)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of hindgut contraction (GO:0043134)|regulation of synapse assembly (GO:0051963)|response to food (GO:0032094)|response to hormone (GO:0009725)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|growth hormone secretagogue receptor activity (GO:0001616)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)	p.N27N(2)		biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	33	Ovarian(172;0.00143)|Breast(254;0.197)		Lung(28;3.93e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			CCAGCGAGTCGTTGCCGGGGG	0.682																																					p.N27N	Esophageal Squamous(93;641 1401 20883 29581 34638)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C81T	3						.						24.0	25.0	25.0					3																	172166123		2201	4300	6501	173648817	SO:0001819	synonymous_variant	2693	exon1			AY429112	CCDS3218.1, CCDS46959.1	3q26.31	2012-08-08			ENSG00000121853	ENSG00000121853		"""GPCR / Class A : Ghrelin receptors"""	4267	protein-coding gene	gene with protein product		601898				8688086	Standard	NM_198407		Approved		uc003fib.2	Q92847	OTTHUMG00000156946	ENST00000241256.2:c.81C>T	3.37:g.172166123G>A		Somatic		Capture	Illumina HiSeq	Phase_I	173648817	NM_198407	Q14D12|Q6ISR8|Q92848|Q96RJ7	Silent	SNP	ENST00000241256.2	37	CCDS3218.1																																																																																				0.682	GHSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346728.1	NM_004122	
ZNF639	51193	broad.mit.edu	37	3	179051159	179051159	+	Missense_Mutation	SNP	A	A	G	rs367684429		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:179051159A>G	ENST00000326361.3	+	7	852	c.407A>G	c.(406-408)gAa>gGa	p.E136G	ZNF639_ENST00000484866.1_Missense_Mutation_p.E136G|ZNF639_ENST00000466663.1_3'UTR|ZNF639_ENST00000496856.1_Missense_Mutation_p.E136G	NM_016331.1	NP_057415.1	Q9UID6	ZN639_HUMAN	zinc finger protein 639	136					negative regulation by host of viral transcription (GO:0043922)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|transcription, DNA-templated (GO:0006351)|viral entry into host cell (GO:0046718)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein self-association (GO:0043621)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.E136G(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(10)|urinary_tract(1)	16	all_cancers(143;7.9e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			CACACTGCTGAAGATGTTCCA	0.403																																					p.E136G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A407G	3						.						67.0	64.0	65.0					3																	179051159		2203	4300	6503	180533853	SO:0001583	missense	51193	exon7			BC020500	CCDS3227.1	3q27.1	2010-03-26			ENSG00000121864	ENSG00000121864		"""Zinc fingers, C2H2-type"""	30950	protein-coding gene	gene with protein product	"""zinc finger amplified in esophageal squamous cell carcinomas 1"""					14522885	Standard	NM_016331		Approved	ANC-2H01, ZASC1	uc003fjr.1	Q9UID6	OTTHUMG00000157439	ENST00000326361.3:c.407A>G	3.37:g.179051159A>G	ENSP00000325634:p.Glu136Gly	Somatic		Capture	Illumina HiSeq	Phase_I	180533853	NM_016331	A9X3Z9|D3DNR3	Missense_Mutation	SNP	ENST00000326361.3	37	CCDS3227.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.961382	0.74016	.	.	ENSG00000121864	ENST00000496856;ENST00000491818;ENST00000481587;ENST00000326361;ENST00000466264;ENST00000484866	T;T;T;T	0.04119	3.7;3.7;4.3;3.7	5.87	5.87	0.94306	.	0.067511	0.64402	D	0.000012	T	0.14141	0.0342	L	0.34521	1.04	0.45172	D	0.998189	D	0.71674	0.998	D	0.72982	0.979	T	0.00934	-1.1509	10	0.72032	D	0.01	.	16.5764	0.84681	1.0:0.0:0.0:0.0	.	136	Q9UID6	ZN639_HUMAN	G	136	ENSP00000417740:E136G;ENSP00000325634:E136G;ENSP00000419650:E136G;ENSP00000418766:E136G	ENSP00000325634:E136G	E	+	2	0	ZNF639	180533853	1.000000	0.71417	0.993000	0.49108	0.994000	0.84299	6.278000	0.72614	2.371000	0.80710	0.533000	0.62120	GAA		0.403	ZNF639-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348855.1	NM_016331	
PEX5L	51555	broad.mit.edu	37	3	179525599	179525599	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:179525599G>A	ENST00000467460.1	-	14	1869	c.1539C>T	c.(1537-1539)cgC>cgT	p.R513R	PEX5L_ENST00000467440.2_5'UTR|PEX5L_ENST00000468741.1_Silent_p.R321R|PEX5L_ENST00000485199.1_Silent_p.R478R|PEX5L_ENST00000476138.1_Silent_p.R470R|PEX5L_ENST00000263962.8_Silent_p.R511R|PEX5L_ENST00000464614.1_Silent_p.R405R|PEX5L_ENST00000465751.1_Silent_p.R489R|PEX5L_ENST00000472994.1_Silent_p.R454R|PEX5L_ENST00000392649.3_Silent_p.R405R	NM_001256751.1|NM_016559.2	NP_001243680.1|NP_057643.1	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	513					maintenance of protein location (GO:0045185)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of membrane potential (GO:0042391)	cytosol (GO:0005829)|dendrite (GO:0030425)|peroxisomal membrane (GO:0005778)|receptor complex (GO:0043235)	peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|small GTPase binding (GO:0031267)	p.R513R(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			TCGCCCCGAGGCGGTTCCATA	0.517																																					p.R513R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1539T	3						.						92.0	100.0	97.0					3																	179525599		2203	4300	6503	181008293	SO:0001819	synonymous_variant	51555	exon14			AJ245503	CCDS3236.1, CCDS58861.1, CCDS58862.1, CCDS58863.1, CCDS58864.1, CCDS58865.1, CCDS58866.1, CCDS58867.1	3q27.1	2013-01-10			ENSG00000114757	ENSG00000114757		"""Tetratricopeptide (TTC) repeat domain containing"""	30024	protein-coding gene	gene with protein product		611058				11463335	Standard	NM_016559		Approved	PEX5R, PXR2	uc003fki.2	Q8IYB4	OTTHUMG00000157363	ENST00000467460.1:c.1539C>T	3.37:g.179525599G>A		Somatic		Capture	Illumina HiSeq	Phase_I	181008293	NM_016559	B7Z2A5|B7Z305|B7Z318|B7Z5Z5|B7Z8P2|E7EUV8|E7EUZ0|E9PEC1|E9PH97|Q9NQD1|Q9P2U3|Q9P2U4	Silent	SNP	ENST00000467460.1	37	CCDS3236.1																																																																																				0.517	PEX5L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348577.1	NM_016559	
SOX2	6657	broad.mit.edu	37	3	181430376	181430376	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:181430376C>T	ENST00000325404.1	+	1	655	c.228C>T	c.(226-228)ggC>ggT	p.G76G	SOX2_ENST00000431565.2_Silent_p.G76G	NM_003106.3	NP_003097.1	P48431	SOX2_HUMAN	SRY (sex determining region Y)-box 2	76					adenohypophysis development (GO:0021984)|cell cycle arrest (GO:0007050)|cerebral cortex development (GO:0021987)|chromatin organization (GO:0006325)|detection of mechanical stimulus involved in equilibrioception (GO:0050973)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|diencephalon morphogenesis (GO:0048852)|endodermal cell fate specification (GO:0001714)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|eye development (GO:0001654)|forebrain development (GO:0030900)|forebrain neuron differentiation (GO:0021879)|glial cell fate commitment (GO:0021781)|inner ear development (GO:0048839)|inner ear morphogenesis (GO:0042472)|lens induction in camera-type eye (GO:0060235)|lung alveolus development (GO:0048286)|male genitalia development (GO:0030539)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate commitment (GO:0048663)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|osteoblast differentiation (GO:0001649)|pigment biosynthetic process (GO:0046148)|pituitary gland development (GO:0021983)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|response to growth factor (GO:0070848)|response to retinoic acid (GO:0032526)|response to wounding (GO:0009611)|retina morphogenesis in camera-type eye (GO:0060042)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|miRNA binding (GO:0035198)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.G76G(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|skin(1)	10	all_cancers(143;1.22e-16)|Ovarian(172;0.0283)		all cancers(12;1.82e-48)|Epithelial(37;9.85e-40)|OV - Ovarian serous cystadenocarcinoma(80;7.37e-23)|Lung(8;2.01e-21)|GBM - Glioblastoma multiforme(1;2.13e-08)			AGCGCCTGGGCGCCGAGTGGA	0.607			A		"""NSCLC, oesophageal squamous carcinoma"""		MICROPHTHALMIA AND ESOPHAGEAL ATRESIA SYNDROME																														p.G76G			Dom	yes		3	3q26.3-q27	6657	SRY (sex determining region Y)-box 2	yes	E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C228T	3						.						41.0	45.0	44.0					3																	181430376		2203	4300	6503	182913070	SO:0001819	synonymous_variant	6657	exon1			BC013923	CCDS3239.1	3q26.3-q27	2014-09-17						"""SRY (sex determining region Y)-boxes"""	11195	protein-coding gene	gene with protein product		184429				7849401	Standard	NM_003106		Approved		uc003fkx.3	P48431		ENST00000325404.1:c.228C>T	3.37:g.181430376C>T		Somatic		Capture	Illumina HiSeq	Phase_I	182913070	NM_003106	Q14537	Silent	SNP	ENST00000325404.1	37	CCDS3239.1																																																																																				0.607	SOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350419.1	NM_003106	
KLHL6	89857	broad.mit.edu	37	3	183225871	183225871	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:183225871C>A	ENST00000341319.3	-	3	920	c.885G>T	c.(883-885)agG>agT	p.R295S		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	295					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)			p.R295S(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			GGTGGTACATCCTGGCTTCCT	0.527																																					p.R295S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G885T	3						.						88.0	81.0	83.0					3																	183225871		2203	4300	6503	184708565	SO:0001583	missense	89857	exon3			AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.885G>T	3.37:g.183225871C>A	ENSP00000341342:p.Arg295Ser	Somatic		Capture	Illumina HiSeq	Phase_I	184708565	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	C	14.30	2.495393	0.44352	.	.	ENSG00000172578	ENST00000341319	T	0.74106	-0.81	5.24	2.45	0.29901	.	0.096353	0.64402	D	0.000002	T	0.65165	0.2665	L	0.55103	1.725	0.54753	D	0.999988	P	0.36282	0.546	B	0.34873	0.191	T	0.64214	-0.6460	10	0.56958	D	0.05	.	7.6054	0.28100	0.0:0.6406:0.0:0.3594	.	295	Q8WZ60	KLHL6_HUMAN	S	295	ENSP00000341342:R295S	ENSP00000341342:R295S	R	-	3	2	KLHL6	184708565	0.980000	0.34600	1.000000	0.80357	0.999000	0.98932	0.255000	0.18333	0.852000	0.35287	0.655000	0.94253	AGG		0.527	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
AP2M1	1173	broad.mit.edu	37	3	183899603	183899603	+	Splice_Site	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:183899603G>A	ENST00000292807.5	+	8	975	c.827G>A	c.(826-828)aGg>aAg	p.R276K	AP2M1_ENST00000439647.1_Splice_Site_p.R274K|AP2M1_ENST00000461733.1_3'UTR|EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000382456.3_Splice_Site_p.R274K|AP2M1_ENST00000411763.2_Splice_Site_p.R301K	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	276	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.R276K(1)		endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GAGCTTATGAGGTGCCATTGG	0.527																																					p.R274K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G821A	3						.						80.0	82.0	82.0					3																	183899603		2151	4262	6413	185382297	SO:0001630	splice_region_variant	1173	exon7			U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"""clathrin-associated/assembly/adaptor protein, medium 1"", ""plasma membrane adaptor AP-2 50kDA protein"", ""clathrin coat adaptor protein AP50"", ""clathrin adaptor complex AP2, mu subunit"", ""HA2 50 kDA subunit"", ""clathrin assembly protein complex 2 medium chain"", ""AP-2 mu 2 chain"""	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.827+1G>A	3.37:g.183899603G>A		Somatic		Capture	Illumina HiSeq	Phase_I	185382297	NM_001025205	A6NE12|D3DNT1|P20172|P53679	Missense_Mutation	SNP	ENST00000292807.5	37	CCDS43177.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.596922	0.46318	.	.	ENSG00000161203	ENST00000382456;ENST00000411763;ENST00000292807;ENST00000540821;ENST00000539646;ENST00000439647;ENST00000432591	T;T;T;T;T	0.19938	2.11;2.11;2.11;2.11;2.11	5.14	5.14	0.70334	Clathrin adaptor, mu subunit, conserved site (1);Clathrin adaptor, mu subunit, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.15565	0.0375	N	0.20483	0.58	0.80722	D	1	B;B;B;B;B	0.12630	0.003;0.001;0.006;0.005;0.005	B;B;B;B;B	0.19148	0.024;0.005;0.009;0.014;0.005	T	0.09037	-1.0693	10	0.13470	T	0.59	.	18.8078	0.92045	0.0:0.0:1.0:0.0	.	166;146;276;301;274	B7Z4N2;B4DTI4;Q96CW1;E9PFW3;Q96CW1-2	.;.;AP2M1_HUMAN;.;.	K	274;301;276;216;261;274;205	ENSP00000371894:R274K;ENSP00000403362:R301K;ENSP00000292807:R276K;ENSP00000409081:R274K;ENSP00000395438:R205K	ENSP00000292807:R276K	R	+	2	0	AP2M1	185382297	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.251000	0.95483	2.677000	0.91161	0.655000	0.94253	AGG		0.527	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068	Missense_Mutation
ALG3	10195	broad.mit.edu	37	3	183963058	183963058	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:183963058G>A	ENST00000397676.3	-	4	563	c.533C>T	c.(532-534)gCc>gTc	p.A178V	ALG3_ENST00000418734.2_Missense_Mutation_p.A122V|ALG3_ENST00000463495.1_5'Flank|EIF2B5_ENST00000444495.1_Intron|ALG3_ENST00000445626.2_Missense_Mutation_p.A130V|ALG3_ENST00000455059.1_Missense_Mutation_p.A138V	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase	178					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)|dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity (GO:0052925)	p.A178V(1)		kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CAGCACCATGGCCACTGGGTC	0.547																																					p.A130V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C389T	3						.						34.0	38.0	37.0					3																	183963058		2018	4183	6201	185445752	SO:0001583	missense	10195	exon4			BC002839	CCDS46967.1, CCDS46968.1	3q27.3	2013-02-26	2013-02-26		ENSG00000214160	ENSG00000214160	2.4.1.258	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	23056	protein-coding gene	gene with protein product	"""carbohydrate deficient glycoprotein syndrome type IV"", ""dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase"", ""dol-P-Man dependent alpha-1,3- mannosyltransferase"""	608750	"""asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-mannosyltransferase)"", ""asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)"""			1058125	Standard	NM_005787		Approved	NOT56L, Not56, CDGS4, D16Ertd36e	uc003fne.2	Q92685	OTTHUMG00000156823	ENST00000397676.3:c.533C>T	3.37:g.183963058G>A	ENSP00000380793:p.Ala178Val	Somatic		Capture	Illumina HiSeq	Phase_I	185445752	NM_001006941	A8JZZ6|Q9BT71	Missense_Mutation	SNP	ENST00000397676.3	37	CCDS46968.1	.	.	.	.	.	.	.	.	.	.	G	33	5.265636	0.95399	.	.	ENSG00000214160	ENST00000418734;ENST00000397676;ENST00000445626;ENST00000455059	D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36	5.14	5.14	0.70334	.	0.000000	0.85682	U	0.000000	D	0.95711	0.8605	M	0.91872	3.25	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.999;1.0;1.0	D	0.96651	0.9481	10	0.87932	D	0	-10.419	17.5931	0.88003	0.0:0.0:1.0:0.0	.	70;130;122;138;178	B4DMZ7;A8JZZ6;B4DS50;C9J7S5;Q92685	.;.;.;.;ALG3_HUMAN	V	122;178;130;138	ENSP00000402976:A122V;ENSP00000380793:A178V;ENSP00000402744:A130V;ENSP00000397613:A138V	ENSP00000380793:A178V	A	-	2	0	ALG3	185445752	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.869000	0.99810	2.378000	0.81104	0.462000	0.41574	GCC		0.547	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787	
EPHB3	2049	broad.mit.edu	37	3	184298942	184298942	+	Silent	SNP	C	C	T	rs551443278		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:184298942C>T	ENST00000330394.2	+	14	3173	c.2721C>T	c.(2719-2721)agC>agT	p.S907S	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	907					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)	p.S907S(1)		breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			TCATTGCCAGCGCTCAGTCTG	0.577													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18366	0.0		0.0	False		,,,				2504	0.0				p.S907S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2721T	3						.						85.0	96.0	92.0					3																	184298942		2203	4300	6503	185781636	SO:0001819	synonymous_variant	2049	exon14			X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.2721C>T	3.37:g.184298942C>T		Somatic		Capture	Illumina HiSeq	Phase_I	185781636	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																				0.577	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
TRA2B	6434	broad.mit.edu	37	3	185643392	185643392	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:185643392G>A	ENST00000453386.2	-	3	468	c.193C>T	c.(193-195)Cga>Tga	p.R65*	TRA2B_ENST00000382191.4_5'UTR|TRA2B_ENST00000471134.1_5'Flank	NM_004593.2	NP_004584.1	P62995	TRA2B_HUMAN	transformer 2 beta homolog (Drosophila)	65	Arg/Ser-rich (RS1 domain).				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R65R(1)|p.R65*(1)		breast(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(3)|prostate(1)|urinary_tract(1)	18						TAATGCCTTCGGGAGCTTCTT	0.463																																					p.R65X												.	.	2	Substitution - Nonsense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.C193T	3						.						96.0	94.0	94.0					3																	185643392		2203	4300	6503	187126086	SO:0001587	stop_gained	6434	exon3			AF057159	CCDS33905.1, CCDS58872.1	3q26.2-q27	2014-06-13	2009-02-27	2009-02-27	ENSG00000136527	ENSG00000136527		"""RNA binding motif (RRM) containing"""	10781	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 156"""	602719	"""splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)"""	SFRS10		9790768	Standard	NM_004593		Approved	Htra2-beta, PPP1R156	uc003fpv.3	P62995	OTTHUMG00000156641	ENST00000453386.2:c.193C>T	3.37:g.185643392G>A	ENSP00000416959:p.Arg65*	Somatic		Capture	Illumina HiSeq	Phase_I	187126086	NM_004593	B4DVK2|D3DNU3|O15449|Q15815|Q64283	Nonsense_Mutation	SNP	ENST00000453386.2	37	CCDS33905.1	.	.	.	.	.	.	.	.	.	.	G	39	7.868912	0.98534	.	.	ENSG00000136527	ENST00000453386	.	.	.	6.17	4.35	0.52113	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-3.3171	10.1485	0.42778	0.0713:0.0:0.7873:0.1414	.	.	.	.	X	65	.	ENSP00000416959:R65X	R	-	1	2	TRA2B	187126086	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	6.636000	0.74299	0.894000	0.36317	0.655000	0.94253	CGA		0.463	TRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344984.1	NM_004593	
LPP	4026	broad.mit.edu	37	3	188592144	188592144	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:188592144C>T	ENST00000312675.4	+	11	1962	c.1716C>T	c.(1714-1716)tgC>tgT	p.C572C	LPP_ENST00000543006.1_Silent_p.C572C	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	572	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.C572C(1)	HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TCTAGGATTGCGGTGGTCTCC	0.483			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""																																p.C572C			Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1716T	3						.						187.0	165.0	173.0					3																	188592144		2203	4300	6503	190074838	SO:0001819	synonymous_variant	4026	exon11			AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1716C>T	3.37:g.188592144C>T		Somatic		Capture	Illumina HiSeq	Phase_I	190074838	NM_001167671	A1L4L6|D3DNV6|Q8NFX5	Silent	SNP	ENST00000312675.4	37	CCDS3291.1																																																																																				0.483	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
TP63	8626	broad.mit.edu	37	3	189586505	189586505	+	Splice_Site	SNP	C	C	T	rs576449010		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:189586505C>T	ENST00000264731.3	+	8	1218	c.1129C>T	c.(1129-1131)Ccg>Tcg	p.P377S	TP63_ENST00000382063.4_Splice_Site_p.P292S|TP63_ENST00000354600.5_Splice_Site_p.P283S|TP63_ENST00000437221.1_Splice_Site_p.P283S|TP63_ENST00000392461.3_Splice_Site_p.P283S|TP63_ENST00000456148.1_Intron|TP63_ENST00000440651.2_Intron|TP63_ENST00000418709.2_Splice_Site_p.P377S|TP63_ENST00000392463.2_Splice_Site_p.P283S|TP63_ENST00000320472.5_Splice_Site_p.P377S|TP63_ENST00000449992.1_Splice_Site_p.P198S|TP63_ENST00000392460.3_Splice_Site_p.P377S	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63	377	Interaction with HIPK2.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)	p.P377S(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		TACGAAGCGCCGTAAGTAGAT	0.488										HNSCC(45;0.13)			C|||	1	0.000199681	0.0	0.0	5008	,	,		20141	0.001		0.0	False		,,,				2504	0.0				p.P283S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C847T	3						.						124.0	118.0	120.0					3																	189586505		2203	4300	6503	191069199	SO:0001630	splice_region_variant	8626	exon6			AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282			15979	protein-coding gene	gene with protein product		603273	"""tumor protein p73-like"", ""tumor protein p53-like"", ""tumor protein p53-competing protein"""	TP73L, TP53L, TP53CP		9774969, 9662378, 11181441, 11181451	Standard	NM_003722		Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000264731.3:c.1129+1C>T	3.37:g.189586505C>T		Somatic		Capture	Illumina HiSeq	Phase_I	191069199	NM_001114980	O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	Missense_Mutation	SNP	ENST00000264731.3	37	CCDS3293.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.503638	0.44558	.	.	ENSG00000073282	ENST00000264731;ENST00000418709;ENST00000320472;ENST00000392460;ENST00000382063;ENST00000354600;ENST00000437221;ENST00000392463;ENST00000392461;ENST00000449992	D;D;D;D;D;D;D;D;D;D	0.99607	-5.96;-6.22;-6.21;-6.21;-6.26;-5.94;-6.2;-6.18;-6.18;-6.27	6.03	6.03	0.97812	.	0.113900	0.64402	D	0.000010	D	0.97980	0.9335	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B;B;B;B	0.30068	0.068;0.267;0.136;0.078;0.136;0.084;0.068;0.084;0.136	B;B;B;B;B;B;B;B;B	0.28784	0.04;0.094;0.04;0.027;0.04;0.018;0.04;0.018;0.04	D	0.98648	1.0678	9	.	.	.	-3.1155	17.7226	0.88356	0.0:1.0:0.0:0.0	.	198;377;283;283;283;283;377;377;377	Q9H3D4-10;Q9H3D4-7;Q9H3D4-4;Q9H3D4-2;Q9H3D4-6;C9D7C9;Q9H3D4-3;Q9H3D4;Q9H3D4-5	.;.;.;.;.;.;.;P63_HUMAN;.	S	377;377;377;377;292;283;283;283;283;198	ENSP00000264731:P377S;ENSP00000407144:P377S;ENSP00000317510:P377S;ENSP00000376253:P377S;ENSP00000371495:P292S;ENSP00000346614:P283S;ENSP00000392488:P283S;ENSP00000376256:P283S;ENSP00000376254:P283S;ENSP00000387839:P198S	.	P	+	1	0	TP63	191069199	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.977000	0.56874	2.854000	0.98071	0.655000	0.94253	CCG		0.488	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	NM_003722	Missense_Mutation
HES1	3280	broad.mit.edu	37	3	193855508	193855508	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:193855508A>G	ENST00000232424.3	+	4	565	c.329A>G	c.(328-330)tAc>tGc	p.Y110C		NM_005524.3	NP_005515.1	P30042	ES1_HUMAN	hes family bHLH transcription factor 1	0						mitochondrion (GO:0005739)		p.Y110C(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6	all_cancers(143;7.3e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;3.65e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;1.48e-05)		CTGGGGAAGTACCGAGCCGGC	0.667																																					p.Y110C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A329G	3						.						55.0	48.0	51.0					3																	193855508		2203	4300	6503	195338202	SO:0001583	missense	3280	exon4			L19314	CCDS3305.1	3q28-q29	2013-10-17	2013-10-17	2003-01-10	ENSG00000114315	ENSG00000114315		"""Basic helix-loop-helix proteins"""	5192	protein-coding gene	gene with protein product		139605	"""hairy homolog (Drosophila)"", ""hairy and enhancer of split 1, (Drosophila)"""	HRY		8020957	Standard	NM_005524		Approved	FLJ20408, HES-1, Hes1, bHLHb39	uc003ftq.2	Q14469	OTTHUMG00000155984	ENST00000232424.3:c.329A>G	3.37:g.193855508A>G	ENSP00000232424:p.Tyr110Cys	Somatic		Capture	Illumina HiSeq	Phase_I	195338202	NM_005524	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Missense_Mutation	SNP	ENST00000232424.3	37	CCDS3305.1	.	.	.	.	.	.	.	.	.	.	A	19.23	3.787156	0.70337	.	.	ENSG00000114315	ENST00000232424	T	0.62788	0.0	4.19	4.19	0.49359	Orange subgroup (1);Orange (2);	0.133844	0.52532	D	0.000073	D	0.82518	0.5054	M	0.92122	3.275	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86694	0.1925	10	0.87932	D	0	-15.0092	12.7699	0.57415	1.0:0.0:0.0:0.0	.	110	Q14469	HES1_HUMAN	C	110	ENSP00000232424:Y110C	ENSP00000232424:Y110C	Y	+	2	0	HES1	195338202	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.237000	0.95368	1.656000	0.50722	0.454000	0.30748	TAC		0.667	HES1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342632.1		
GP5	2814	broad.mit.edu	37	3	194118104	194118104	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:194118104C>T	ENST00000401815.1	-	1	979	c.908G>A	c.(907-909)cGc>cAc	p.R303H	GP5_ENST00000323007.3_Missense_Mutation_p.R303H			P40197	GPV_HUMAN	glycoprotein V (platelet)	303					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|negative regulation of platelet activation (GO:0010544)|platelet activation (GO:0030168)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.R303H(2)		breast(3)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(14)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	35	all_cancers(143;6.64e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;7.38e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.06e-05)		GGGCAGGGTGCGCAGCTGGGT	0.701																																					p.R303H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G908A	3						.						8.0	11.0	10.0					3																	194118104		2039	4110	6149	195599393	SO:0001583	missense	2814	exon2			L11238	CCDS3307.1	3q29	2008-02-01			ENSG00000178732	ENSG00000178732		"""CD molecules"""	4443	protein-coding gene	gene with protein product		173511				7690959	Standard	NM_004488		Approved	CD42d	uc003ftv.1	P40197	OTTHUMG00000150345	ENST00000401815.1:c.908G>A	3.37:g.194118104C>T	ENSP00000383931:p.Arg303His	Somatic		Capture	Illumina HiSeq	Phase_I	195599393	NM_004488	D1MER9	Missense_Mutation	SNP	ENST00000401815.1	37	CCDS3307.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.868826	0.51588	.	.	ENSG00000178732	ENST00000401815;ENST00000323007	T;T	0.25250	1.81;1.81	3.95	3.06	0.35304	.	0.420079	0.17732	N	0.163853	T	0.27063	0.0663	L	0.41356	1.27	0.09310	N	1	D	0.61697	0.99	P	0.47299	0.543	T	0.07829	-1.0752	10	0.51188	T	0.08	.	13.3584	0.60642	0.0:0.5095:0.4905:0.0	.	303	P40197	GPV_HUMAN	H	303	ENSP00000383931:R303H;ENSP00000319286:R303H	ENSP00000319286:R303H	R	-	2	0	GP5	195599393	0.000000	0.05858	0.602000	0.28890	0.921000	0.55340	0.310000	0.19356	0.927000	0.37143	0.455000	0.32223	CGC		0.701	GP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317710.1	NM_004488	
NRROS	375387	broad.mit.edu	37	3	196387060	196387060	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:196387060T>C	ENST00000328557.4	+	3	749	c.546T>C	c.(544-546)cgT>cgC	p.R182R		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	182					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R182R(1)									GCCTGGAGCGTCTCCGGGAGC	0.637																																					p.R182R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T546C	3						.						40.0	38.0	39.0					3																	196387060		2203	4298	6501	197871457	SO:0001819	synonymous_variant	375387	exon3			AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"""leucine rich repeat containing 33"""	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	ENST00000328557.4:c.546T>C	3.37:g.196387060T>C		Somatic		Capture	Illumina HiSeq	Phase_I	197871457	NM_198565		Silent	SNP	ENST00000328557.4	37	CCDS3319.1																																																																																				0.637	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565	
CHL1	10752	broad.mit.edu	37	3	432785	432785	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:432785A>G	ENST00000256509.2	+	22	3376	c.2734A>G	c.(2734-2736)Aac>Gac	p.N912D	CHL1_ENST00000397491.2_Missense_Mutation_p.N896D	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.N912D(1)		NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		CTTAGCCTATAACTCTAAAGG	0.378																																					p.N912D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2734G	3						.						90.0	96.0	94.0					3																	432785		2203	4300	6503	407785	SO:0001583	missense	10752	exon22			AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.2734A>G	3.37:g.432785A>G	ENSP00000256509:p.Asn912Asp	Somatic		Capture	Illumina HiSeq	Phase_I	407785	NM_006614	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.7|25.7	4.666244|4.666244	0.88251|0.88251	.|.	.|.	ENSG00000134121|ENSG00000134121	ENST00000445697|ENST00000256509;ENST00000397491	.|T;T	.|0.61859	.|0.07;0.07	5.75|5.75	5.75|5.75	0.90469|0.90469	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.80808|0.80808	0.4694|0.4694	M|M	0.89534|0.89534	3.04|3.04	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|1.0;1.0;0.999	D|D	0.85061|0.85061	0.0934|0.0934	5|10	.|0.87932	.|D	.|0	.|.	16.0374|16.0374	0.80640|0.80640	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|896;896;912	.|B3KX75;O00533;O00533-2	.|.;CHL1_HUMAN;.	M|D	98|912;896	.|ENSP00000256509:N912D;ENSP00000380628:N896D	.|ENSP00000256509:N912D	I|N	+|+	3|1	3|0	CHL1|CHL1	407785|407785	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.813000|0.813000	0.45954|0.45954	8.476000|8.476000	0.90421|0.90421	2.190000|2.190000	0.69967|0.69967	0.533000|0.533000	0.62120|0.62120	ATA|AAC		0.378	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
CPNE9	151835	broad.mit.edu	37	3	9768814	9768814	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:9768814G>T	ENST00000383832.3	+	20	1610	c.1420G>T	c.(1420-1422)Ggt>Tgt	p.G474C	CPNE9_ENST00000383831.3_Missense_Mutation_p.G474C	NM_153635.2	NP_705899.2	Q8IYJ1	CPNE9_HUMAN	copine family member IX	474	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.G474C(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	16	Medulloblastoma(99;0.227)					AGAGTTGGACGGTGATGATGT	0.602																																					p.G474C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1420T	3						.						219.0	217.0	218.0					3																	9768814		2119	4230	6349	9743814	SO:0001583	missense	151835	exon19				CCDS2574.2	3p25.3	2008-10-30			ENSG00000144550	ENSG00000144550			24336	protein-coding gene	gene with protein product						9430674	Standard	XM_006712990		Approved	KIAA4217	uc003bsd.3	Q8IYJ1	OTTHUMG00000128418	ENST00000383832.3:c.1420G>T	3.37:g.9768814G>T	ENSP00000373343:p.Gly474Cys	Somatic		Capture	Illumina HiSeq	Phase_I	9743814	NM_153635	A1L430|A6NDX6|A8MSP8	Missense_Mutation	SNP	ENST00000383832.3	37	CCDS2574.2	.	.	.	.	.	.	.	.	.	.	G	25.5	4.649660	0.87958	.	.	ENSG00000144550	ENST00000383832;ENST00000383831	T;T	0.26067	1.76;1.76	4.25	4.25	0.50352	von Willebrand factor, type A (2);	0.116409	0.56097	D	0.000023	T	0.60379	0.2264	M	0.92784	3.345	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.72200	-0.4362	10	0.59425	D	0.04	.	16.465	0.84076	0.0:0.0:1.0:0.0	.	474	Q8IYJ1	CPNE9_HUMAN	C	474	ENSP00000373343:G474C;ENSP00000373342:G474C	ENSP00000373342:G474C	G	+	1	0	CPNE9	9743814	1.000000	0.71417	0.961000	0.40146	0.951000	0.60555	9.100000	0.94213	2.191000	0.70037	0.467000	0.42956	GGT		0.602	CPNE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250205.4	NM_001033755	
TRIM71	131405	broad.mit.edu	37	3	32932999	32932999	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:32932999A>G	ENST00000383763.5	+	4	2366	c.2303A>G	c.(2302-2304)aAc>aGc	p.N768S		NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase	768					fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N768S(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GACTTCAACAACCACCGGCTC	0.602																																					p.N768S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2303G	3						.						30.0	32.0	31.0					3																	32932999		1928	4134	6062	32908003	SO:0001583	missense	131405	exon4				CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	32669	protein-coding gene	gene with protein product			"""tripartite motif-containing 71"", ""tripartite motif containing 71"""				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.2303A>G	3.37:g.32932999A>G	ENSP00000373272:p.Asn768Ser	Somatic		Capture	Illumina HiSeq	Phase_I	32908003	NM_001039111		Missense_Mutation	SNP	ENST00000383763.5	37	CCDS43060.1	.	.	.	.	.	.	.	.	.	.	A	19.35	3.811214	0.70797	.	.	ENSG00000206557	ENST00000383763	T	0.80033	-1.33	5.86	5.86	0.93980	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.90116	0.6912	M	0.88570	2.965	0.80722	D	1	D	0.56968	0.978	P	0.62014	0.897	D	0.91214	0.5001	10	0.52906	T	0.07	-53.852	15.067	0.72002	1.0:0.0:0.0:0.0	.	768	Q2Q1W2	LIN41_HUMAN	S	768	ENSP00000373272:N768S	ENSP00000373272:N768S	N	+	2	0	TRIM71	32908003	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.278000	0.95766	2.238000	0.73509	0.533000	0.62120	AAC		0.602	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111	
CLASP2	23122	broad.mit.edu	37	3	33617754	33617754	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:33617754C>T	ENST00000468888.2	-	24	2410	c.2364G>A	c.(2362-2364)ggG>ggA	p.G788G	CLASP2_ENST00000359576.5_Silent_p.G787G|CLASP2_ENST00000539981.1_Silent_p.G557G|CLASP2_ENST00000307312.7_Silent_p.G276G|CLASP2_ENST00000399362.4_Silent_p.G787G|CLASP2_ENST00000461133.3_Silent_p.G554G|CLASP2_ENST00000480013.1_Silent_p.G575G			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	575					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)	p.G787G(1)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						ATTGGCTGATCCCATAACCTG	0.453																																					p.G787G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2361A	3						.						80.0	78.0	78.0					3																	33617754		1929	4138	6067	33592758	SO:0001819	synonymous_variant	23122	exon24			AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.2364G>A	3.37:g.33617754C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33592758	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	37																																																																																					0.453	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044	
CLASP2	23122	broad.mit.edu	37	3	33626319	33626319	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:33626319G>A	ENST00000468888.2	-	22	2211	c.2165C>T	c.(2164-2166)gCc>gTc	p.A722V	CLASP2_ENST00000359576.5_Missense_Mutation_p.A721V|CLASP2_ENST00000539981.1_Missense_Mutation_p.A491V|CLASP2_ENST00000307312.7_Missense_Mutation_p.A210V|CLASP2_ENST00000399362.4_Missense_Mutation_p.A721V|CLASP2_ENST00000461133.3_Missense_Mutation_p.A488V|CLASP2_ENST00000480013.1_Missense_Mutation_p.A488V			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	488					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)	p.A721V(1)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						TTGTGCTGAGGCTGAATTGAC	0.483																																					p.A721V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2162T	3						.						80.0	80.0	80.0					3																	33626319		1916	4149	6065	33601323	SO:0001583	missense	23122	exon22			AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.2165C>T	3.37:g.33626319G>A	ENSP00000419974:p.Ala722Val	Somatic		Capture	Illumina HiSeq	Phase_I	33601323	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	37		.	.	.	.	.	.	.	.	.	.	G	18.01	3.528128	0.64860	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576;ENST00000307312;ENST00000539981;ENST00000480013;ENST00000461133	T;T;T	0.18174	2.23;2.23;2.25	5.65	5.65	0.86999	Armadillo-type fold (1);	0.242225	0.41938	D	0.000790	T	0.14917	0.0360	N	0.19112	0.55	0.43175	D	0.994985	B;B	0.31548	0.259;0.328	B;B	0.32864	0.08;0.154	T	0.07790	-1.0754	10	0.34782	T	0.22	-1.5403	19.7321	0.96186	0.0:0.0:1.0:0.0	.	488;721	O75122;F5H604	CLAP2_HUMAN;.	V	722;721;721;210;491;488;488	ENSP00000419974:A722V;ENSP00000382297:A721V;ENSP00000352581:A721V	ENSP00000304743:A210V	A	-	2	0	CLASP2	33601323	1.000000	0.71417	0.956000	0.39512	0.982000	0.71751	4.195000	0.58400	2.668000	0.90789	0.655000	0.94253	GCC		0.483	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044	
DCLK3	85443	broad.mit.edu	37	3	36780110	36780110	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:36780110G>A	ENST00000416516.2	-	2	531	c.41C>T	c.(40-42)gCt>gTt	p.A14V		NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	14						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A14V(1)		breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	48						TTCTTCTACAGCCACCTGAAT	0.552																																					p.A14V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C41T	3						.						140.0	140.0	140.0					3																	36780110		1939	4142	6081	36755114	SO:0001583	missense	85443	exon2			AB051552	CCDS43064.1	3p22.3	2007-04-02	2007-04-02	2007-04-02	ENSG00000163673	ENSG00000163673			19005	protein-coding gene	gene with protein product		613167	"""doublecortin and CaM kinase-like 3"""	DCAMKL3		11214970, 16869982	Standard	NM_033403		Approved	KIAA1765, DCDC3C	uc003cgi.2	Q9C098	OTTHUMG00000155805	ENST00000416516.2:c.41C>T	3.37:g.36780110G>A	ENSP00000394484:p.Ala14Val	Somatic		Capture	Illumina HiSeq	Phase_I	36755114	NM_033403		Missense_Mutation	SNP	ENST00000416516.2	37	CCDS43064.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.960462	0.53400	.	.	ENSG00000163673	ENST00000416516	T	0.74737	-0.87	5.04	5.04	0.67666	.	.	.	.	.	T	0.59459	0.2195	L	0.29908	0.895	0.28435	N	0.917081	P	0.37636	0.603	B	0.32762	0.152	T	0.54649	-0.8262	9	0.32370	T	0.25	.	9.6031	0.39617	0.1592:0.0:0.8408:0.0	.	14	Q9C098	DCLK3_HUMAN	V	14	ENSP00000394484:A14V	ENSP00000394484:A14V	A	-	2	0	DCLK3	36755114	1.000000	0.71417	0.930000	0.37139	0.970000	0.65996	3.703000	0.54808	2.494000	0.84150	0.655000	0.94253	GCT		0.552	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355	
EPM2AIP1	9852	broad.mit.edu	37	3	37034438	37034438	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:37034438C>T	ENST00000322716.5	-	1	357	c.131G>A	c.(130-132)cGc>cAc	p.R44H	MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000539477.1_5'Flank|MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000536378.1_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	44					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)		p.R44H(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						TACGATGAGGCGGCGACAGAC	0.662																																					p.R44H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G131A	3						.						32.0	38.0	36.0					3																	37034438		2046	4185	6231	37009442	SO:0001583	missense	9852	exon1			AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.131G>A	3.37:g.37034438C>T	ENSP00000406027:p.Arg44His	Somatic		Capture	Illumina HiSeq	Phase_I	37009442	NM_014805	O94866|Q9H3L3	Missense_Mutation	SNP	ENST00000322716.5	37	CCDS46790.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.912092	0.33721	.	.	ENSG00000178567	ENST00000322716	T	0.14266	2.52	5.09	4.16	0.48862	.	.	.	.	.	T	0.11879	0.0289	L	0.36672	1.1	0.29132	N	0.879574	B	0.09022	0.002	B	0.06405	0.002	T	0.08027	-1.0742	9	0.59425	D	0.04	-3.2249	8.5499	0.33444	0.0:0.8844:0.0:0.1156	.	44	Q7L775	EPMIP_HUMAN	H	44	ENSP00000406027:R44H	ENSP00000406027:R44H	R	-	2	0	EPM2AIP1	37009442	0.997000	0.39634	0.999000	0.59377	0.594000	0.36715	1.176000	0.31957	1.374000	0.46228	0.655000	0.94253	CGC		0.662	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805	
GOLGA4	2803	broad.mit.edu	37	3	37292888	37292888	+	Silent	SNP	G	G	A	rs201354584		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:37292888G>A	ENST00000361924.2	+	2	449	c.75G>A	c.(73-75)gcG>gcA	p.A25A	GOLGA4_ENST00000435830.2_3'UTR|GOLGA4_ENST00000444882.1_Silent_p.A25A|GOLGA4_ENST00000356847.4_Silent_p.A25A	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	25					Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)	p.A25A(2)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						AAATCTAGGCGTCCTCCAATT	0.388																																					p.A25A												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G75A	3						.						90.0	83.0	86.0					3																	37292888		2203	4300	6503	37267892	SO:0001819	synonymous_variant	2803	exon2			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.75G>A	3.37:g.37292888G>A		Somatic		Capture	Illumina HiSeq	Phase_I	37267892	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Silent	SNP	ENST00000361924.2	37	CCDS2666.1																																																																																				0.388	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	
SCN11A	11280	broad.mit.edu	37	3	38888839	38888839	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:38888839G>A	ENST00000302328.3	-	26	4920	c.4722C>T	c.(4720-4722)tgC>tgT	p.C1574C	SCN11A_ENST00000450244.1_Silent_p.C1574C|SCN11A_ENST00000456224.3_Silent_p.C1536C	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1574					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.C1574C(1)		NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CAGGGAGGTGGCAGTTTTCTG	0.443																																					p.C1574C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4722T	3						.						115.0	112.0	113.0					3																	38888839		2203	4300	6503	38863843	SO:0001819	synonymous_variant	11280	exon26			AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	protein-coding gene	gene with protein product		604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.4722C>T	3.37:g.38888839G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38863843	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	37	CCDS33737.1																																																																																				0.443	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	
SCN11A	11280	broad.mit.edu	37	3	38945502	38945502	+	Missense_Mutation	SNP	C	C	T	rs201421435		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:38945502C>T	ENST00000302328.3	-	12	1894	c.1696G>A	c.(1696-1698)Gtt>Att	p.V566I	SCN11A_ENST00000450244.1_Missense_Mutation_p.V566I|SCN11A_ENST00000456224.3_Missense_Mutation_p.V566I|SCN11A_ENST00000444237.2_Missense_Mutation_p.V566I	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	566					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.V566I(2)		NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ACCTTCTTAACGCACAGCCAC	0.502																																					p.V566I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1696A	3						.						169.0	142.0	151.0					3																	38945502		2203	4300	6503	38920506	SO:0001583	missense	11280	exon12			AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	protein-coding gene	gene with protein product		604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.1696G>A	3.37:g.38945502C>T	ENSP00000307599:p.Val566Ile	Somatic		Capture	Illumina HiSeq	Phase_I	38920506	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	C	0.069	-1.206332	0.01568	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.95724	-3.79;-3.79;-3.79;-3.66	5.58	-3.27	0.05048	.	0.863211	0.10490	N	0.668523	T	0.80042	0.4551	N	0.01140	-0.99	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.73895	-0.3838	10	0.07813	T	0.8	.	5.7901	0.18355	0.2656:0.4267:0.0:0.3077	.	566	Q9UI33	SCNBA_HUMAN	I	566	ENSP00000307599:V566I;ENSP00000400945:V566I;ENSP00000416757:V566I;ENSP00000408028:V566I	ENSP00000307599:V566I	V	-	1	0	SCN11A	38920506	0.000000	0.05858	0.001000	0.08648	0.284000	0.27059	-1.685000	0.01930	-0.898000	0.03906	-0.385000	0.06624	GTT		0.502	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	
TTC21A	199223	broad.mit.edu	37	3	39170627	39170627	+	Missense_Mutation	SNP	G	G	A	rs373913915		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:39170627G>A	ENST00000431162.2	+	15	2116	c.1982G>A	c.(1981-1983)cGc>cAc	p.R661H	TTC21A_ENST00000301819.6_Missense_Mutation_p.R662H|TTC21A_ENST00000440121.1_Missense_Mutation_p.R613H			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	661								p.R662H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GAAGAGAACCGCATCACCATT	0.512																																					p.R613H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1838A	3						.	G	HIS/ARG,HIS/ARG	0,4302		0,0,2151	93.0	94.0	94.0		1838,1982	5.8	1.0	3		94	1,8489		0,1,4244	no	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	29,29	0,1,6395	AA,AG,GG		0.0118,0.0,0.0078	probably-damaging,probably-damaging	613/1273,661/1321	39170627	1,12791	2151	4245	6396	39145631	SO:0001583	missense	199223	exon14			AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.1982G>A	3.37:g.39170627G>A	ENSP00000398211:p.Arg661His	Somatic		Capture	Illumina HiSeq	Phase_I	39145631	NM_001105513	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.869639	0.72065	0.0	1.18E-4	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.76968	-1.06;-0.18;-1.06	5.85	5.85	0.93711	Tetratricopeptide-like helical (1);	0.168035	0.42548	D	0.000699	D	0.89473	0.6725	M	0.87097	2.86	0.46849	D	0.999221	D;D;D	0.89917	1.0;1.0;1.0	D;D;P	0.68943	0.961;0.942;0.877	D	0.88984	0.3410	10	0.44086	T	0.13	-15.6685	18.9349	0.92582	0.0:0.0:1.0:0.0	.	613;662;661	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	H	662;644;661;613	ENSP00000301819:R662H;ENSP00000398211:R661H;ENSP00000410882:R613H	ENSP00000301819:R662H	R	+	2	0	TTC21A	39145631	1.000000	0.71417	1.000000	0.80357	0.240000	0.25518	6.291000	0.72719	2.773000	0.95371	0.655000	0.94253	CGC		0.512	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
TTC21A	199223	broad.mit.edu	37	3	39178786	39178786	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:39178786C>T	ENST00000431162.2	+	25	3513	c.3379C>T	c.(3379-3381)Cgg>Tgg	p.R1127W	TTC21A_ENST00000301819.6_Missense_Mutation_p.R1128W|TTC21A_ENST00000493856.1_3'UTR|TTC21A_ENST00000440121.1_Missense_Mutation_p.R1079W			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	1127								p.R1128W(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GACCCAGCTGCGGCTGCTGCA	0.612																																					p.R1079W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3235T	3						.						20.0	25.0	24.0					3																	39178786		2007	4165	6172	39153790	SO:0001583	missense	199223	exon24			AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.3379C>T	3.37:g.39178786C>T	ENSP00000398211:p.Arg1127Trp	Somatic		Capture	Illumina HiSeq	Phase_I	39153790	NM_001105513	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	C	15.63	2.889068	0.52014	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.65549	-0.16;-0.15;-0.04	4.27	0.844	0.18943	.	0.515223	0.16734	N	0.201713	T	0.69869	0.3159	M	0.85197	2.74	0.32852	D	0.506842	D;D;D	0.76494	0.999;0.998;0.997	P;P;P	0.53649	0.701;0.731;0.543	T	0.73600	-0.3931	10	0.49607	T	0.09	-11.9434	6.6687	0.23056	0.5078:0.2487:0.2435:0.0	.	1079;1128;1127	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	W	1128;1110;1127;1079	ENSP00000301819:R1128W;ENSP00000398211:R1127W;ENSP00000410882:R1079W	ENSP00000301819:R1128W	R	+	1	2	TTC21A	39153790	0.166000	0.22962	0.996000	0.52242	0.430000	0.31655	0.333000	0.19768	0.241000	0.21283	0.205000	0.17691	CGG		0.612	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
XIRP1	165904	broad.mit.edu	37	3	39228104	39228104	+	Missense_Mutation	SNP	G	G	A	rs187061436		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:39228104G>A	ENST00000340369.3	-	2	3061	c.2833C>T	c.(2833-2835)Cgg>Tgg	p.R945W	XIRP1_ENST00000396251.1_Missense_Mutation_p.R945W|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	945					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)	p.R945W(1)		breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		GGCTCCCACCGCAGACTGTGC	0.642													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15654	0.0		0.0	False		,,,				2504	0.0				p.R945W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2833T	3						.						31.0	34.0	33.0					3																	39228104		2203	4300	6503	39203108	SO:0001583	missense	165904	exon2			AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.2833C>T	3.37:g.39228104G>A	ENSP00000343140:p.Arg945Trp	Somatic		Capture	Illumina HiSeq	Phase_I	39203108	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	20.8	4.050093	0.75846	.	.	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.06294	3.32;3.67	5.03	4.15	0.48705	.	0.559978	0.18073	N	0.152553	T	0.15955	0.0384	L	0.51422	1.61	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.60541	0.876;0.736	T	0.00542	-1.1680	10	0.87932	D	0	.	11.184	0.48644	0.0:0.0:0.8162:0.1838	.	945;945	Q702N8;Q702N8-2	XIRP1_HUMAN;.	W	945	ENSP00000379550:R945W;ENSP00000343140:R945W	ENSP00000343140:R945W	R	-	1	2	XIRP1	39203108	0.996000	0.38824	0.995000	0.50966	0.969000	0.65631	3.983000	0.56916	1.258000	0.44101	0.655000	0.94253	CGG		0.642	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
TRAK1	22906	broad.mit.edu	37	3	42132962	42132962	+	Start_Codon_SNP	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:42132962A>G	ENST00000327628.5	+	1	401	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	TRAK1_ENST00000487159.1_Intron	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	1					endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.M1V(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						ATGTCTGCACATGGCATTGGT	0.572																																					p.M1V	GBM(44;195 884 22595 31865 41850)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1G	3						.						88.0	85.0	86.0					3																	42132962		1966	4134	6100	42107966	SO:0001582	initiator_codon_variant	22906	exon1				CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1A>G	3.37:g.42132962A>G	ENSP00000328998:p.Met1Val	Somatic		Capture	Illumina HiSeq	Phase_I	42107966	NM_001042646	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	A	14.27	2.486624	0.44249	.	.	ENSG00000182606	ENST00000327628;ENST00000543338	T	0.07114	3.22	4.17	4.17	0.49024	.	0.330375	0.26481	N	0.024128	T	0.10981	0.0268	.	.	.	0.80722	D	1	B;B	0.31435	0.323;0.323	B;B	0.38194	0.267;0.267	T	0.05386	-1.0888	9	0.87932	D	0	.	9.7826	0.40658	1.0:0.0:0.0:0.0	.	1;1	B7Z347;Q9UPV9	.;TRAK1_HUMAN	V	1	ENSP00000328998:M1V	ENSP00000328998:M1V	M	+	1	0	TRAK1	42107966	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.007000	0.57093	1.881000	0.54492	0.482000	0.46254	ATG		0.572	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	Missense_Mutation
TRAK1	22906	broad.mit.edu	37	3	42264857	42264857	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:42264857C>T	ENST00000327628.5	+	16	2890	c.2490C>T	c.(2488-2490)agC>agT	p.S830S	TRAK1_ENST00000396175.1_Silent_p.S772S|RNU4-78P_ENST00000410940.1_RNA|TRAK1_ENST00000487159.1_3'UTR	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	830					endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.S772S(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						TCCGCAGCAGCGAGAGCCAGA	0.577																																					p.S830S	GBM(44;195 884 22595 31865 41850)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2490T	3						.						48.0	53.0	51.0					3																	42264857		2034	4190	6224	42239861	SO:0001819	synonymous_variant	22906	exon16				CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.2490C>T	3.37:g.42264857C>T		Somatic		Capture	Illumina HiSeq	Phase_I	42239861	NM_001042646	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Silent	SNP	ENST00000327628.5	37	CCDS43072.1																																																																																				0.577	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
ZNF662	389114	broad.mit.edu	37	3	42950356	42950356	+	Missense_Mutation	SNP	C	C	A	rs201942800		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:42950356C>A	ENST00000541208.1	+	3	475	c.106C>A	c.(106-108)Cct>Act	p.P36T	ZNF662_ENST00000328199.6_Missense_Mutation_p.P96T|KRBOX1_ENST00000426937.1_5'UTR|ZNF662_ENST00000440367.2_Missense_Mutation_p.P36T|ZNF662_ENST00000430067.2_3'UTR|ZNF662_ENST00000422021.1_Missense_Mutation_p.P36T			Q6ZS27	ZN662_HUMAN	zinc finger protein 662	36	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P36T(1)		breast(2)|endometrium(1)|large_intestine(6)|lung(5)|upper_aerodigestive_tract(1)	15				KIRC - Kidney renal clear cell carcinoma(284;0.217)		GTGCTCGGTTCCTCGGGGAGC	0.552																																					p.P96T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C286A	3						.						76.0	81.0	79.0					3																	42950356		2203	4300	6503	42925360	SO:0001583	missense	389114	exon3			AK127779	CCDS2708.1, CCDS46807.1	3p22.1	2013-01-08			ENSG00000182983	ENSG00000182983		"""Zinc fingers, C2H2-type"", ""-"""	31930	protein-coding gene	gene with protein product							Standard	NM_207404		Approved	FLJ45880	uc003cmk.2	Q6ZS27	OTTHUMG00000133041	ENST00000541208.1:c.106C>A	3.37:g.42950356C>A	ENSP00000446208:p.Pro36Thr	Somatic		Capture	Illumina HiSeq	Phase_I	42925360	NM_001134656	A1A4T9|F8W7S8|Q6ZNF8|Q6ZQW8	Missense_Mutation	SNP	ENST00000541208.1	37	CCDS2708.1	.	.	.	.	.	.	.	.	.	.	C	5.856	0.342116	0.11069	.	.	ENSG00000182983	ENST00000440367;ENST00000328199;ENST00000541208;ENST00000422021	T;T;T	0.08102	3.13;3.24;3.13	3.08	2.18	0.27775	Krueppel-associated box (1);	.	.	.	.	T	0.05456	0.0144	L	0.28054	0.825	0.09310	N	1	B;B	0.16603	0.018;0.011	B;B	0.18263	0.021;0.009	T	0.45101	-0.9284	9	0.17369	T	0.5	.	5.7296	0.18032	0.225:0.5557:0.2192:0.0	.	96;36	F8W7S8;Q6ZS27	.;ZN662_HUMAN	T	36;96;36;36	ENSP00000405047:P36T;ENSP00000329264:P96T;ENSP00000446208:P36T	ENSP00000329264:P96T	P	+	1	0	ZNF662	42925360	0.000000	0.05858	0.006000	0.13384	0.043000	0.13939	-0.139000	0.10358	0.609000	0.30018	0.561000	0.74099	CCT		0.552	ZNF662-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256646.4	NM_207404	
NBEAL2	23218	broad.mit.edu	37	3	47041622	47041622	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:47041622delT	ENST00000450053.3	+	27	4212	c.4033delT	c.(4033-4035)tttfs	p.F1345fs	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Intron	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1345					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.Y1346fs*20(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CCCTGATGGCTTTTACCATGC	0.622																																					p.F1345fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.4033delT	3						.						139.0	147.0	144.0					3																	47041622		2077	4216	6293	47016626	SO:0001589	frameshift_variant	23218	exon27			AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.4033delT	3.37:g.47041622delT	ENSP00000415034:p.Phe1345fs	Somatic		Capture	Illumina HiSeq	Phase_I	47016626	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Frame_Shift_Del	DEL	ENST00000450053.3	37	CCDS46817.1																																																																																				0.622	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
CSPG5	10675	broad.mit.edu	37	3	47618505	47618505	+	Silent	SNP	G	G	A	rs373067610		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:47618505G>A	ENST00000383738.2	-	2	3109	c.1011C>T	c.(1009-1011)atC>atT	p.I337I	CSPG5_ENST00000465441.1_5'Flank|CSPG5_ENST00000264723.4_Silent_p.I337I|CSPG5_ENST00000456150.1_Silent_p.I199I	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	337					axon regeneration (GO:0031103)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)|regulation of growth (GO:0040008)|regulation of synaptic transmission (GO:0050804)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	growth factor activity (GO:0008083)	p.I337I(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	22				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GCCTGAGGGCGATGCTGCTGC	0.682													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16198	0.0		0.0	False		,,,				2504	0.0				p.I337I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1011T	3						.	G	,,,,	1,4405	2.1+/-5.4	0,1,2202	34.0	37.0	36.0		597,1011,1011,597,1011	-1.0	0.9	3		36	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CSPG5	NM_001206942.1,NM_001206943.1,NM_001206944.1,NM_001206945.1,NM_006574.3	,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,	199/402,337/567,337/478,199/429,337/540	47618505	1,13005	2203	4300	6503	47593509	SO:0001819	synonymous_variant	10675	exon2			AF059274	CCDS2757.1, CCDS56252.1, CCDS56253.1, CCDS74930.1	3p21.3	2008-07-18			ENSG00000114646	ENSG00000114646			2467	protein-coding gene	gene with protein product		606775				9950058	Standard	NM_006574		Approved	NGC	uc003crp.4	O95196	OTTHUMG00000133518	ENST00000383738.2:c.1011C>T	3.37:g.47618505G>A		Somatic		Capture	Illumina HiSeq	Phase_I	47593509	NM_006574	Q71M39|Q71M40	Silent	SNP	ENST00000383738.2	37	CCDS56253.1																																																																																				0.682	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574	
ATRIP	84126	broad.mit.edu	37	3	48501974	48501974	+	Silent	SNP	G	G	A	rs201062615		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:48501974G>A	ENST00000320211.3	+	8	1634	c.1521G>A	c.(1519-1521)ggG>ggA	p.G507G	ATRIP_ENST00000357105.6_Silent_p.G380G|ATRIP_ENST00000412052.1_Silent_p.G414G|ATRIP_ENST00000346691.4_Silent_p.G507G	NM_130384.2	NP_569055.1	Q8WXE1	ATRIP_HUMAN	ATR interacting protein	507					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.G507G(1)		central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)	22				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTGCTGCTGGGGAAGGAAACA	0.547								Other conserved DNA damage response genes																													p.G507G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1521A	3						.						86.0	90.0	89.0					3																	48501974		2203	4300	6503	48476978	SO:0001819	synonymous_variant	84126	exon8			AF451323	CCDS2767.1, CCDS2768.1, CCDS59449.1, CCDS59450.1	3p24.3-p22.1	2007-06-20			ENSG00000164053	ENSG00000164053			33499	protein-coding gene	gene with protein product		606605				11721054	Standard	NM_130384		Approved	FLJ12343, MGC20625, MGC21482, MGC26740	uc003ctf.2	Q8WXE1	OTTHUMG00000133532	ENST00000320211.3:c.1521G>A	3.37:g.48501974G>A		Somatic		Capture	Illumina HiSeq	Phase_I	48476978	NM_130384	A8K6A3|A8K714|B2RCE7|B4DU92|B5MEB7|Q69YK9|Q8NHQ2|Q8WUG7|Q96CL3|Q9HA30	Silent	SNP	ENST00000320211.3	37	CCDS2768.1																																																																																				0.547	ATRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257507.2	NM_130384	
COL7A1	1294	broad.mit.edu	37	3	48604343	48604343	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:48604343C>A	ENST00000328333.8	-	110	8330	c.8223G>T	c.(8221-8223)caG>caT	p.Q2741H	COL7A1_ENST00000454817.1_Missense_Mutation_p.Q2709H|COL7A1_ENST00000470076.1_5'Flank	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2741	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.Q2741H(1)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCCTTACCTTCTGGCCCTGAA	0.617																																					p.Q2741H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8223T	3						.						15.0	16.0	16.0					3																	48604343		2200	4297	6497	48579347	SO:0001583	missense	1294	exon110			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.8223G>T	3.37:g.48604343C>A	ENSP00000332371:p.Gln2741His	Somatic		Capture	Illumina HiSeq	Phase_I	48579347	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.582492	0.28180	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	D;D	0.94280	-3.39;-3.39	4.86	3.77	0.43336	.	0.000000	0.39341	N	0.001399	D	0.95108	0.8415	M	0.64997	1.995	0.31029	N	0.717624	D	0.89917	1.0	D	0.91635	0.999	D	0.92216	0.5780	10	0.33940	T	0.23	.	11.9901	0.53169	0.0:0.8999:0.0:0.1001	.	2741	Q02388	CO7A1_HUMAN	H	2741;2709	ENSP00000332371:Q2741H;ENSP00000412569:Q2709H	ENSP00000332371:Q2741H	Q	-	3	2	COL7A1	48579347	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	1.720000	0.38022	2.260000	0.74910	0.467000	0.42956	CAG		0.617	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
COL7A1	1294	broad.mit.edu	37	3	48612871	48612871	+	Frame_Shift_Del	DEL	G	G	-	rs375047225		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:48612871delG	ENST00000328333.8	-	73	6188	c.6081delC	c.(6079-6081)cccfs	p.P2027fs	COL7A1_ENST00000454817.1_Frame_Shift_Del_p.P1995fs	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2027	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P2029fs*177(1)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CGGAAGGCCCGGGGGGGCCCC	0.721																																					p.P2027fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.6081delC	3	GRCh37	CD961934	COL7A1	D		.			29,3811		4,21,1895	9.0	11.0	11.0			5.0	0.8	3		11	44,7720		3,38,3841	no	frameshift	COL7A1	NM_000094.3		7,59,5736	A1A1,A1R,RR		0.5667,0.7552,0.6291			48612871	73,11531	2081	4155	6236	48587875	SO:0001589	frameshift_variant	1294	exon73			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.6081delC	3.37:g.48612871delG	ENSP00000332371:p.Pro2027fs	Somatic		Capture	Illumina HiSeq	Phase_I	48587875	NM_000094	Q14054|Q16507	Frame_Shift_Del	DEL	ENST00000328333.8	37	CCDS2773.1																																																																																				0.721	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
QARS	5859	broad.mit.edu	37	3	49140834	49140834	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:49140834G>A	ENST00000306125.6	-	5	797	c.460C>T	c.(460-462)Cgg>Tgg	p.R154W	QARS_ENST00000414533.1_Missense_Mutation_p.R143W|QARS_ENST00000470225.1_5'Flank|QARS_ENST00000420147.2_Missense_Mutation_p.R172W			P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	154					brain development (GO:0007420)|gene expression (GO:0010467)|glutaminyl-tRNA aminoacylation (GO:0006425)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|glutamine-tRNA ligase activity (GO:0004819)	p.R154W(1)		breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	L-Glutamine(DB00130)	AGCACAGCCCGAGCCTCTCCT	0.522																																					p.R154W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C460T	3						.						112.0	104.0	107.0					3																	49140834		2203	4300	6503	49115838	SO:0001583	missense	5859	exon5			X76013	CCDS2788.1, CCDS63633.1	3p21.31	2011-07-01			ENSG00000172053	ENSG00000172053	6.1.1.18	"""Aminoacyl tRNA synthetases / Class I"""	9751	protein-coding gene	gene with protein product	"""glutamine tRNA ligase"""	603727				8078941, 10393422	Standard	NM_005051		Approved		uc003cvx.4	P47897	OTTHUMG00000156774	ENST00000306125.6:c.460C>T	3.37:g.49140834G>A	ENSP00000307567:p.Arg154Trp	Somatic		Capture	Illumina HiSeq	Phase_I	49115838	NM_005051	B4DWJ2	Missense_Mutation	SNP	ENST00000306125.6	37	CCDS2788.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.025864	0.75390	.	.	ENSG00000172053	ENST00000306125;ENST00000414533;ENST00000420147;ENST00000452739;ENST00000417025	T;T	0.26810	1.72;1.71	5.71	4.76	0.60689	Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.57562	0.2062	M	0.88450	2.955	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.65627	-0.6122	10	0.87932	D	0	-19.4633	15.5326	0.75977	0.0:0.0:0.7728:0.2272	.	172;143;154	B7Z840;B4DWJ2;P47897	.;.;SYQ_HUMAN	W	154;143;172;196;154	ENSP00000307567:R154W;ENSP00000390015:R143W	ENSP00000307567:R154W	R	-	1	2	QARS	49115838	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.812000	0.62613	2.686000	0.91538	0.650000	0.86243	CGG		0.522	QARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345689.2	NM_005051	
CAMKV	79012	broad.mit.edu	37	3	49897617	49897617	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:49897617C>A	ENST00000477224.1	-	10	1407	c.929G>T	c.(928-930)aGg>aTg	p.R310M	CAMKV_ENST00000463537.1_Missense_Mutation_p.R310M|CAMKV_ENST00000488336.1_Missense_Mutation_p.R310M|CAMKV_ENST00000467248.1_Missense_Mutation_p.R235M|CAMKV_ENST00000466940.1_Missense_Mutation_p.R267M|CAMKV_ENST00000296471.7_Missense_Mutation_p.R282M|CAMKV_ENST00000498324.1_5'Flank			Q8NCB2	CAMKV_HUMAN	CaM kinase-like vesicle-associated	310						cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)	p.R310M(1)		central_nervous_system(1)|large_intestine(2)|lung(2)|ovary(2)	7				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		CCACTTGGCCCTGGCAAAGTT	0.498																																					p.R310M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G929T	3						.						122.0	118.0	119.0					3																	49897617		2203	4300	6503	49872621	SO:0001583	missense	79012	exon10			BC017363	CCDS33762.1	3p21.31	2005-03-04			ENSG00000164076	ENSG00000164076			28788	protein-coding gene	gene with protein product		614993				12477932	Standard	XM_005265478		Approved	MGC8407, VACAMKL	uc003cxt.1	Q8NCB2	OTTHUMG00000158288	ENST00000477224.1:c.929G>T	3.37:g.49897617C>A	ENSP00000419195:p.Arg310Met	Somatic		Capture	Illumina HiSeq	Phase_I	49872621	NM_024046	A6NFD4|Q6FIB8|Q8NBS8|Q8NC85|Q8NDU4|Q8WTT8|Q9BQC9|Q9H0Q5	Missense_Mutation	SNP	ENST00000477224.1	37	CCDS33762.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.390402	0.82902	.	.	ENSG00000164076	ENST00000296471;ENST00000488336;ENST00000463537;ENST00000477224;ENST00000467248;ENST00000466940	T;T;T;T;T;T	0.69040	0.09;-0.3;1.06;-0.37;0.75;1.43	6.06	6.06	0.98353	Protein kinase-like domain (1);	0.000000	0.47093	D	0.000253	T	0.77987	0.4213	M	0.65498	2.005	0.49915	D	0.999834	D;D;D;D;D;D;D	0.71674	0.993;0.99;0.997;0.997;0.998;0.998;0.997	P;P;P;P;P;D;P	0.63597	0.77;0.825;0.825;0.862;0.885;0.916;0.825	T	0.79288	-0.1865	10	0.87932	D	0	.	12.6846	0.56940	0.0:0.9241:0.0:0.0759	.	267;273;310;235;282;310;310	E7ETR1;B4DMF2;B2RDF9;B4DM24;Q8NCB2-2;Q8NCB2-3;Q8NCB2	.;.;.;.;.;.;CAMKV_HUMAN	M	282;310;310;310;235;267	ENSP00000296471:R282M;ENSP00000418809:R310M;ENSP00000417614:R310M;ENSP00000419195:R310M;ENSP00000420053:R235M;ENSP00000420724:R267M	ENSP00000296471:R282M	R	-	2	0	CAMKV	49872621	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.916000	0.39986	2.882000	0.98803	0.655000	0.94253	AGG		0.498	CAMKV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350584.4	NM_024046	
MON1A	84315	broad.mit.edu	37	3	49948232	49948232	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:49948232C>T	ENST00000417270.1	-	5	1416	c.723G>A	c.(721-723)gcG>gcA	p.A241A	MON1A_ENST00000483022.1_5'Flank|CTD-2330K9.3_ENST00000419183.1_Intron|MON1A_ENST00000296473.3_Silent_p.A330A|MON1A_ENST00000455683.2_Silent_p.A168A			Q86VX9	MON1A_HUMAN	MON1 secretory trafficking family member A	233								p.A233A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GCAGCTCCTGCGCCAGCTCTT	0.597																																					p.A330A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G990A	3						.						41.0	41.0	41.0					3																	49948232		2203	4300	6503	49923236	SO:0001819	synonymous_variant	84315	exon4			AK074404	CCDS2808.2, CCDS46830.1	3p21.31	2013-08-21	2013-08-21		ENSG00000164077	ENSG00000164077			28207	protein-coding gene	gene with protein product		611464	"""MON1 homolog A (yeast)"""			12477932	Standard	NM_032355		Approved	MGC13272, SAND1	uc003cxz.3	Q86VX9	OTTHUMG00000156737	ENST00000417270.1:c.723G>A	3.37:g.49948232C>T		Somatic		Capture	Illumina HiSeq	Phase_I	49923236	NM_032355	B2RDQ1|G5E9N1|Q8NAV7|Q9BRF3	Silent	SNP	ENST00000417270.1	37																																																																																					0.597	MON1A-005	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000345538.2	NM_032355	
SEMA3F	6405	broad.mit.edu	37	3	50220873	50220873	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:50220873C>T	ENST00000002829.3	+	12	1593	c.1109C>T	c.(1108-1110)gCc>gTc	p.A370V	SEMA3F_ENST00000413852.1_Missense_Mutation_p.A271V|SEMA3F_ENST00000434342.1_Missense_Mutation_p.A339V	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	370	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)	p.A370V(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		CGAGGCTCTGCCGTGTGTGTC	0.622																																					p.A370V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1109T	3						.						81.0	70.0	74.0					3																	50220873		2203	4300	6503	50195877	SO:0001583	missense	6405	exon12			U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10728	protein-coding gene	gene with protein product	"""sema IV"""	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.1109C>T	3.37:g.50220873C>T	ENSP00000002829:p.Ala370Val	Somatic		Capture	Illumina HiSeq	Phase_I	50195877	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Missense_Mutation	SNP	ENST00000002829.3	37	CCDS2811.1	.	.	.	.	.	.	.	.	.	.	C	36	5.913825	0.97099	.	.	ENSG00000001617	ENST00000450338;ENST00000413852;ENST00000002829;ENST00000434342	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	5.45	5.45	0.79879	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.82006	0.4943	H	0.94345	3.525	0.80722	D	1	D;P	0.76494	0.999;0.909	P;P	0.62491	0.903;0.796	D	0.87285	0.2295	10	0.87932	D	0	.	18.8886	0.92389	0.0:1.0:0.0:0.0	.	339;370	C9JQ85;Q13275	.;SEM3F_HUMAN	V	339;271;370;339	ENSP00000398399:A339V;ENSP00000388931:A271V;ENSP00000002829:A370V;ENSP00000409859:A339V	ENSP00000002829:A370V	A	+	2	0	SEMA3F	50195877	1.000000	0.71417	0.969000	0.41365	0.976000	0.68499	7.652000	0.83633	2.542000	0.85734	0.511000	0.50034	GCC		0.622	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186	
DOCK3	1795	broad.mit.edu	37	3	51352550	51352550	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:51352550C>T	ENST00000266037.9	+	32	3416	c.3393C>T	c.(3391-3393)aaC>aaT	p.N1131N		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1131					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.N1131N(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		AAAATGGCAACTTCAAACAGG	0.483																																					p.L1118F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3352T	3						.						86.0	86.0	86.0					3																	51352550		1911	4123	6034	51327590	SO:0001819	synonymous_variant	1795	exon32			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"""dedicator of cyto-kinesis 3"""			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.3393C>T	3.37:g.51352550C>T		Somatic		Capture	Illumina HiSeq	Phase_I	51327590	NM_004947	O15017	Silent	SNP	ENST00000266037.9	37	CCDS46835.1																																																																																				0.483	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947	
RBM15B	29890	broad.mit.edu	37	3	51430451	51430451	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:51430451C>A	ENST00000323686.4	+	1	1721	c.1621C>A	c.(1621-1623)Cga>Aga	p.R541R		NM_013286.4	NP_037418.3	Q8NDT2	RB15B_HUMAN	RNA binding motif protein 15B	541					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R541R(1)|p.R541*(1)		endometrium(4)|large_intestine(5)|lung(3)	12				BRCA - Breast invasive adenocarcinoma(193;0.000224)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GTACTCAGACCGAGACCGGAC	0.607																																					p.R541R												.	.	2	Substitution - Nonsense(1)|Substitution - coding silent(1)	large_intestine(2)	c.C1621A	3						.						37.0	43.0	41.0					3																	51430451		2203	4300	6503	51405491	SO:0001819	synonymous_variant	29890	exon1			AL831838	CCDS33764.1	3p21.1	2013-02-12			ENSG00000179837	ENSG00000259956		"""RNA binding motif (RRM) containing"""	24303	protein-coding gene	gene with protein product		612602				16129689	Standard	NM_013286		Approved	HUMAGCGB, OTT3	uc003dbd.3	Q8NDT2	OTTHUMG00000156896	ENST00000323686.4:c.1621C>A	3.37:g.51430451C>A		Somatic		Capture	Illumina HiSeq	Phase_I	51405491	NM_013286	A4QPG7|Q6QE19|Q9BV96	Silent	SNP	ENST00000323686.4	37	CCDS33764.1																																																																																				0.607	RBM15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346489.1	NM_013286	
IQCF3	401067	broad.mit.edu	37	3	51864587	51864587	+	Missense_Mutation	SNP	C	C	T	rs369862122		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:51864587C>T	ENST00000456080.1	+	8	1400	c.235C>T	c.(235-237)Cgg>Tgg	p.R79W	IQCF3_ENST00000446775.1_Missense_Mutation_p.R79W|IQCF3_ENST00000440739.2_Missense_Mutation_p.R79W|IQCF3_ENST00000437810.2_Missense_Mutation_p.R79W|IQCF3_ENST00000462079.1_3'UTR|IQCF3_ENST00000444293.1_Missense_Mutation_p.A42V			P0C7M6	IQCF3_HUMAN	IQ motif containing F3	79								p.R79W(2)		endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CCGTCAGCGGCGGCAGGCCCT	0.632																																					p.R79W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C235T	3						.	C	TRP/ARG,TRP/ARG	0,4388		0,0,2194	66.0	80.0	75.0		235,235	2.8	0.0	3		75	2,8576		0,2,4287	no	missense,missense	IQCF3	NM_001085479.2,NM_001207023.1	101,101	0,2,6481	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging	79/155,79/155	51864587	2,12964	2194	4289	6483	51839627	SO:0001583	missense	401067	exon5			AK057432	CCDS46837.1	3p21.31	2008-06-12			ENSG00000229972	ENSG00000229972			31816	protein-coding gene	gene with protein product							Standard	NM_001085479		Approved		uc021wyz.1	P0C7M6	OTTHUMG00000156910	ENST00000456080.1:c.235C>T	3.37:g.51864587C>T	ENSP00000415609:p.Arg79Trp	Somatic		Capture	Illumina HiSeq	Phase_I	51839627	NM_001085479	B2RUV0	Missense_Mutation	SNP	ENST00000456080.1	37	CCDS46837.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	14.09|14.09	2.430613|2.430613	0.43122|0.43122	0.0|0.0	2.33E-4|2.33E-4	ENSG00000229972|ENSG00000229972	ENST00000444293|ENST00000456080;ENST00000437810;ENST00000446775;ENST00000440739	.|T;T;T;T	.|0.40225	.|1.04;1.04;1.04;1.04	4.72|4.72	2.75|2.75	0.32379|0.32379	.|.	.|.	.|.	.|.	.|.	T|T	0.39091|0.39091	0.1065|0.1065	M|M	0.64997|0.64997	1.995|1.995	0.09310|0.09310	N|N	1|1	.|P	.|0.48834	.|0.916	.|B	.|0.39876	.|0.312	T|T	0.24548|0.24548	-1.0157|-1.0157	6|9	0.87932|0.72032	D|D	0|0.01	.|.	9.8718|9.8718	0.41180|0.41180	0.4498:0.5502:0.0:0.0|0.4498:0.5502:0.0:0.0	.|.	.|79	.|P0C7M6	.|IQCF3_HUMAN	V|W	42|79	.|ENSP00000415609:R79W;ENSP00000409373:R79W;ENSP00000401767:R79W;ENSP00000402012:R79W	ENSP00000402530:A42V|ENSP00000409373:R79W	A|R	+|+	2|1	0|2	IQCF3|IQCF3	51839627|51839627	0.004000|0.004000	0.15560|0.15560	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	2.094000|2.094000	0.41719|0.41719	0.564000|0.564000	0.29238|0.29238	0.655000|0.655000	0.94253|0.94253	GCG|CGG		0.632	IQCF3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346579.2	NM_001085479	
RRP9	9136	broad.mit.edu	37	3	51970286	51970286	+	Missense_Mutation	SNP	C	C	T	rs376861276	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:51970286C>T	ENST00000232888.6	-	8	795	c.722G>A	c.(721-723)cGg>cAg	p.R241Q		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	241					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)	p.R241Q(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|skin(1)	21				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)		CACTGCATCCCGGTGTCCTGT	0.557													C|||	2	0.000399361	0.0	0.0	5008	,	,		18738	0.0		0.0	False		,,,				2504	0.002				p.R241Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G722A	3						.						127.0	119.0	122.0					3																	51970286		2203	4300	6503	51945326	SO:0001583	missense	9136	exon8			AJ001340	CCDS2837.1	3p21.31	2013-01-10	2008-02-26	2006-10-24	ENSG00000114767	ENSG00000114767		"""WD repeat domain containing"""	16829	protein-coding gene	gene with protein product			"""RNA, U3 small nucleolar interacting protein 2"""	RNU3IP2		9418896, 12032086	Standard	NM_004704		Approved	U3-55K	uc003dbw.2	O43818	OTTHUMG00000156930	ENST00000232888.6:c.722G>A	3.37:g.51970286C>T	ENSP00000232888:p.Arg241Gln	Somatic		Capture	Illumina HiSeq	Phase_I	51945326	NM_004704	B2R996|Q8IZ30	Missense_Mutation	SNP	ENST00000232888.6	37	CCDS2837.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.523135	0.85600	.	.	ENSG00000114767	ENST00000232888	T	0.59772	0.24	5.24	5.24	0.73138	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.053623	0.64402	D	0.000001	T	0.65375	0.2685	L	0.31120	0.905	0.58432	D	0.999999	D	0.76494	0.999	D	0.66602	0.945	T	0.64664	-0.6354	10	0.39692	T	0.17	-28.9097	18.4201	0.90587	0.0:1.0:0.0:0.0	.	241	O43818	U3IP2_HUMAN	Q	241	ENSP00000232888:R241Q	ENSP00000232888:R241Q	R	-	2	0	RRP9	51945326	0.990000	0.36364	0.998000	0.56505	0.807000	0.45602	1.241000	0.32743	2.458000	0.83093	0.655000	0.94253	CGG		0.557	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704	
STAB1	23166	broad.mit.edu	37	3	52536665	52536665	+	Missense_Mutation	SNP	G	G	A	rs201122593		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:52536665G>A	ENST00000321725.6	+	6	581	c.505G>A	c.(505-507)Gga>Aga	p.G169R		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	169	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)	p.G169R(1)		breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CTGTGTGCACGGAGTGTGCAA	0.607																																					p.G169R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G505A	3						.						100.0	83.0	89.0					3																	52536665		2203	4300	6503	52511705	SO:0001583	missense	23166	exon6			AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.505G>A	3.37:g.52536665G>A	ENSP00000312946:p.Gly169Arg	Somatic		Capture	Illumina HiSeq	Phase_I	52511705	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	37	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	G	18.77	3.695746	0.68386	.	.	ENSG00000010327	ENST00000321725	T	0.56275	0.47	4.47	4.47	0.54385	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000001	T	0.78635	0.4314	H	0.94771	3.58	0.43642	D	0.996049	D;D	0.89917	1.0;1.0	D;D	0.81914	0.994;0.995	D	0.84602	0.0673	10	0.87932	D	0	.	13.025	0.58810	0.0:0.0:1.0:0.0	.	169;169	Q9NY15;Q9NY15-2	STAB1_HUMAN;.	R	169	ENSP00000312946:G169R	ENSP00000312946:G169R	G	+	1	0	STAB1	52511705	1.000000	0.71417	0.182000	0.23118	0.183000	0.23260	3.942000	0.56614	2.210000	0.71456	0.561000	0.74099	GGA		0.607	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
ITIH1	3697	broad.mit.edu	37	3	52818484	52818484	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:52818484G>T	ENST00000273283.2	+	11	1422	c.1398G>T	c.(1396-1398)caG>caT	p.Q466H	ITIH1_ENST00000540715.1_Missense_Mutation_p.Q324H|ITIH1_ENST00000542827.1_Missense_Mutation_p.Q466H|ITIH1_ENST00000537050.1_Missense_Mutation_p.Q178H	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	466	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.Q466H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		ATGCCACCCAGCAGCTGCAGG	0.572																																					p.Q324H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G972T	3						.						104.0	98.0	100.0					3																	52818484		2203	4300	6503	52793524	SO:0001583	missense	3697	exon9				CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"""inter-alpha (globulin) inhibitor, H1 polypeptide"""			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.1398G>T	3.37:g.52818484G>T	ENSP00000273283:p.Gln466His	Somatic		Capture	Illumina HiSeq	Phase_I	52793524	NM_001166434	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.953539	0.53293	.	.	ENSG00000055957	ENST00000542827;ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133	T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;4.53;4.05	5.09	4.2	0.49525	von Willebrand factor, type A (2);	0.120840	0.56097	D	0.000030	T	0.82195	0.4984	L	0.50333	1.59	0.34083	D	0.659755	D;D;D	0.64830	0.991;0.985;0.994	P;P;D	0.66196	0.555;0.555;0.942	D	0.86800	0.1991	10	0.66056	D	0.02	-25.7836	9.8856	0.41260	0.1694:0.0:0.8306:0.0	.	324;67;466	F5H165;Q9P1C5;P19827	.;.;ITIH1_HUMAN	H	466;466;324;178;19	ENSP00000442584:Q466H;ENSP00000273283:Q466H;ENSP00000443973:Q324H;ENSP00000443847:Q178H;ENSP00000395836:Q19H	ENSP00000273283:Q466H	Q	+	3	2	ITIH1	52793524	0.013000	0.17824	1.000000	0.80357	0.807000	0.45602	-0.267000	0.08619	1.350000	0.45770	0.591000	0.81541	CAG		0.572	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
DCP1A	55802	broad.mit.edu	37	3	53326309	53326309	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:53326309G>A	ENST00000607628.1	-	7	1282	c.1173C>T	c.(1171-1173)agC>agT	p.S391S	DCP1A_ENST00000294241.6_Silent_p.S391S|Y_RNA_ENST00000384175.1_RNA|DCP1A_ENST00000606822.1_Silent_p.S353S|DCP1A_ENST00000480258.1_5'UTR	NM_018403.5	NP_060873.4	Q9NPI6	DCP1A_HUMAN	decapping mRNA 1A	391					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)	p.S391S(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)		GAAGATCAACGCTTGGGAGGG	0.547																																					p.S391S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1173T	3						.						192.0	189.0	190.0					3																	53326309		2038	4199	6237	53301349	SO:0001819	synonymous_variant	55802	exon7			AJ275986	CCDS74946.1	3p21.1	2013-05-02	2013-05-02		ENSG00000162290	ENSG00000272886			18714	protein-coding gene	gene with protein product		607010	"""DCP1 decapping enzyme homolog A (S. cerevisiae)"""				Standard	XM_005278360		Approved	HSA275986, SMIF, SMAD4IP1	uc021wzi.1	Q9NPI6	OTTHUMG00000158193	ENST00000607628.1:c.1173C>T	3.37:g.53326309G>A		Somatic		Capture	Illumina HiSeq	Phase_I	53301349	NM_018403	B4DHN9|U3KQM8	Silent	SNP	ENST00000607628.1	37																																																																																					0.547	DCP1A-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018403	
IL17RD	54756	broad.mit.edu	37	3	57131695	57131695	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:57131695A>G	ENST00000296318.7	-	12	2124	c.2036T>C	c.(2035-2037)aTg>aCg	p.M679T	IL17RD_ENST00000320057.5_Missense_Mutation_p.M535T|IL17RD_ENST00000427856.2_Missense_Mutation_p.M655T|IL17RD_ENST00000463523.1_Missense_Mutation_p.M535T	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	679					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.M535T(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)		GAGTCCTTCCATCAGTGGCAG	0.617																																					p.M679T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2036C	3						.						43.0	37.0	39.0					3																	57131695		2203	4300	6503	57106735	SO:0001583	missense	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.2036T>C	3.37:g.57131695A>G	ENSP00000296318:p.Met679Thr	Somatic		Capture	Illumina HiSeq	Phase_I	57106735	NM_017563	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Missense_Mutation	SNP	ENST00000296318.7	37	CCDS2880.2	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184014	0.78677	.	.	ENSG00000144730	ENST00000296318;ENST00000320057;ENST00000427856;ENST00000463523	T;T;T;T	0.12984	2.63;2.65;2.64;2.65	5.91	5.91	0.95273	.	0.038580	0.85682	D	0.000000	T	0.21307	0.0513	L	0.58101	1.795	0.80722	D	1	P;P;P	0.39665	0.682;0.546;0.675	B;B;B	0.41988	0.205;0.205;0.372	T	0.00651	-1.1626	10	0.87932	D	0	-22.4379	16.3483	0.83171	1.0:0.0:0.0:0.0	.	535;679;655	B4DXM5;Q8NFM7;Q8NFM7-3	.;I17RD_HUMAN;.	T	679;535;655;535	ENSP00000296318:M679T;ENSP00000322250:M535T;ENSP00000399209:M655T;ENSP00000417516:M535T	ENSP00000296318:M679T	M	-	2	0	IL17RD	57106735	1.000000	0.71417	0.992000	0.48379	0.788000	0.44548	8.784000	0.91818	2.254000	0.74563	0.533000	0.62120	ATG		0.617	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563	
APPL1	26060	broad.mit.edu	37	3	57301817	57301817	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:57301817A>G	ENST00000288266.3	+	20	2037	c.1890A>G	c.(1888-1890)gaA>gaG	p.E630E		NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	630	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)	p.E630E(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		TGCATGCTGAACTGGTAAGAA	0.453																																					p.E630E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1890G	3						.						127.0	121.0	123.0					3																	57301817		2203	4300	6503	57276857	SO:0001819	synonymous_variant	26060	exon20			AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"""Pleckstrin homology (PH) domain containing"""	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.1890A>G	3.37:g.57301817A>G		Somatic		Capture	Illumina HiSeq	Phase_I	57276857	NM_012096	Q9P2B9	Silent	SNP	ENST00000288266.3	37	CCDS2882.1																																																																																				0.453	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096	
ASB14	142686	broad.mit.edu	37	3	57312503	57312503	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:57312503A>G	ENST00000389601.3	-	9	1453	c.1333T>C	c.(1333-1335)Tat>Cat	p.Y445H	ASB14_ENST00000487349.1_Missense_Mutation_p.Y445H	NM_130387.5	NP_569058.1	A6NK59	ASB14_HUMAN	ankyrin repeat and SOCS box containing 14	445					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.Y160H(1)		central_nervous_system(1)|large_intestine(1)|lung(1)|skin(2)	5				KIRC - Kidney renal clear cell carcinoma(284;0.011)|Kidney(284;0.0127)		TCTGTGTCATACCCATAGTTC	0.423																																					p.Y160H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T478C	3						.						172.0	165.0	167.0					3																	57312503		2203	4300	6503	57287543	SO:0001583	missense	142686	exon1			AF403032	CCDS46856.1, CCDS46856.2	3p21.1	2013-01-10	2011-01-25			ENSG00000239388		"""Ankyrin repeat domain containing"""	19766	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 14"""			12076535	Standard	NM_130387		Approved	DKFZp313L0121	uc021wzs.1	A6NK59		ENST00000389601.3:c.1333T>C	3.37:g.57312503A>G	ENSP00000374252:p.Tyr445His	Somatic		Capture	Illumina HiSeq	Phase_I	57287543	NM_130387	C9JX97|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000389601.3	37		.	.	.	.	.	.	.	.	.	.	A	24.6	4.549539	0.86127	.	.	ENSG00000239388	ENST00000487349;ENST00000389601;ENST00000438870	T;T	0.68181	-0.25;-0.31	6.06	6.06	0.98353	.	.	.	.	.	T	0.81973	0.4936	M	0.75615	2.305	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.83416	0.0030	9	0.62326	D	0.03	.	16.6245	0.84952	1.0:0.0:0.0:0.0	.	445;160	C9JX97;A6NK59-2	.;.	H	445;445;281	ENSP00000419199:Y445H;ENSP00000374252:Y445H	ENSP00000374252:Y445H	Y	-	1	0	ASB14	57287543	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.892000	0.92491	2.323000	0.78572	0.528000	0.53228	TAT		0.423	ASB14-201	KNOWN	basic	protein_coding	protein_coding			
KCTD6	200845	broad.mit.edu	37	3	58487329	58487329	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:58487329C>A	ENST00000355076.6	+	2	1667	c.684C>A	c.(682-684)ttC>ttA	p.F228L	KCTD6_ENST00000404589.3_Missense_Mutation_p.F228L|KCTD6_ENST00000490264.1_Missense_Mutation_p.F228L	NM_153331.3	NP_699162.3	Q8NC69	KCTD6_HUMAN	potassium channel tetramerization domain containing 6	228					protein homooligomerization (GO:0051260)		ankyrin binding (GO:0030506)	p.F228L(1)		endometrium(1)|large_intestine(2)|lung(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(55;0.000177)|Kidney(10;0.00229)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.148)		ACTGGACTTTCTGTAGGCTAG	0.473																																					p.F228L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C684A	3						.						32.0	28.0	29.0					3																	58487329		2203	4300	6503	58462369	SO:0001583	missense	200845	exon2			AK074934	CCDS2891.1	3p21.2	2013-06-20	2013-06-20		ENSG00000168301	ENSG00000168301			22235	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 6"""			21472142	Standard	NM_153331		Approved	MGC27385, KCASH3	uc003dkj.4	Q8NC69	OTTHUMG00000159161	ENST00000355076.6:c.684C>A	3.37:g.58487329C>A	ENSP00000347188:p.Phe228Leu	Somatic		Capture	Illumina HiSeq	Phase_I	58462369	NM_153331	B3KNI5|Q8NBS6|Q8TCA6	Missense_Mutation	SNP	ENST00000355076.6	37	CCDS2891.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.700153	0.48307	.	.	ENSG00000168301	ENST00000404589;ENST00000490264;ENST00000355076	T;T;T	0.22539	1.95;1.95;1.95	5.45	4.58	0.56647	.	0.048075	0.85682	D	0.000000	T	0.11665	0.0284	N	0.08118	0	0.51012	D	0.999902	B	0.02656	0.0	B	0.01281	0.0	T	0.06991	-1.0796	10	0.44086	T	0.13	.	12.0541	0.53524	0.0:0.8561:0.0:0.1439	.	228	Q8NC69	KCTD6_HUMAN	L	228	ENSP00000384948:F228L;ENSP00000417490:F228L;ENSP00000347188:F228L	ENSP00000347188:F228L	F	+	3	2	KCTD6	58462369	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.616000	0.46376	1.302000	0.44855	0.591000	0.81541	TTC		0.473	KCTD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353591.1	NM_153331	
CADPS	8618	broad.mit.edu	37	3	62636540	62636540	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:62636540C>T	ENST00000383710.4	-	5	1534	c.1185G>A	c.(1183-1185)gtG>gtA	p.V395V	CADPS_ENST00000357948.3_Silent_p.V395V|CADPS_ENST00000283269.9_Silent_p.V395V|CADPS_ENST00000490353.2_Silent_p.V395V	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	395					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)	p.V395V(2)		breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		AGAAAGACAGCACGACATCTG	0.502																																					p.V395V												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1185A	3						.						98.0	86.0	90.0					3																	62636540		2203	4300	6503	62611580	SO:0001819	synonymous_variant	8618	exon5			U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.1185G>A	3.37:g.62636540C>T		Somatic		Capture	Illumina HiSeq	Phase_I	62611580	NM_183393	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	ENST00000383710.4	37	CCDS46858.1																																																																																				0.502	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	
MAGI1	9223	broad.mit.edu	37	3	65342782	65342782	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:65342782delG	ENST00000402939.2	-	23	3659	c.3660delC	c.(3658-3660)cccfs	p.P1220fs	RP11-88H12.2_ENST00000602316.1_RNA|MAGI1_ENST00000330909.8_Frame_Shift_Del_p.P1280fs	NM_001033057.1	NP_001028229.1	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	1249					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)	p.A1221fs*10(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		GACCGGTGGCGGGGCCGTGGC	0.627																																					p.P1278fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3833delC	3						.						33.0	41.0	39.0					3																	65342782		2197	4288	6485	65317822	SO:0001589	frameshift_variant	9223	exon25			AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000402939.2:c.3660delC	3.37:g.65342782delG	ENSP00000385450:p.Pro1220fs	Somatic		Capture	Illumina HiSeq	Phase_I	65317822	NM_015520	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Frame_Shift_Del	DEL	ENST00000402939.2	37	CCDS33780.1																																																																																				0.627	MAGI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349126.1	NM_004742	
EOGT	285203	broad.mit.edu	37	3	69058915	69058915	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:69058915C>A	ENST00000383701.3	-	4	825	c.83G>T	c.(82-84)aGc>aTc	p.S28I	EOGT_ENST00000540955.1_5'UTR|EOGT_ENST00000540764.1_5'Flank|EOGT_ENST00000295571.5_Missense_Mutation_p.S28I	NM_001278689.1	NP_001265618.1	Q5NDL2	EOGT_HUMAN	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	28					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)	protein N-acetylglucosaminyltransferase activity (GO:0016262)	p.S28I(1)									GCCTGGAATGCTGTGAGTATT	0.448																																					p.S28I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G83T	3						.						135.0	118.0	123.0					3																	69058915		2203	4300	6503	69141605	SO:0001583	missense	285203	exon4			AK091089	CCDS2908.1, CCDS63684.1	3p14.1	2013-10-11	2012-05-21	2012-05-21	ENSG00000163378	ENSG00000163378	2.4.1.255		28526	protein-coding gene	gene with protein product	"""AER61 glycosyltransferase"""	614789	"""chromosome 3 open reading frame 64"""	C3orf64		22310717	Standard	NM_001278689		Approved	AER61, FLJ33770	uc003dnk.3	Q5NDL2	OTTHUMG00000156279	ENST00000383701.3:c.83G>T	3.37:g.69058915C>A	ENSP00000373206:p.Ser28Ile	Somatic		Capture	Illumina HiSeq	Phase_I	69141605	NM_173654	A8K2U1|B4DFH5|L7X1M5|Q6MZY0|Q6P985|Q6ZTV0	Missense_Mutation	SNP	ENST00000383701.3	37		.	.	.	.	.	.	.	.	.	.	C	6.260	0.416160	0.11870	.	.	ENSG00000163378	ENST00000383701;ENST00000295571;ENST00000424374;ENST00000456376	.	.	.	5.48	1.21	0.21127	.	1.155530	0.06230	N	0.688526	T	0.35158	0.0922	L	0.36672	1.1	0.19945	N	0.999941	B;B	0.28026	0.198;0.115	B;B	0.31686	0.092;0.134	T	0.38824	-0.9643	9	0.48119	T	0.1	.	7.5848	0.27987	0.0:0.5896:0.2179:0.1925	.	28;28	Q5NDL2;Q5NDL2-3	AER61_HUMAN;.	I	28	.	ENSP00000295571:S28I	S	-	2	0	C3orf64	69141605	0.000000	0.05858	0.001000	0.08648	0.166000	0.22503	0.044000	0.13992	0.629000	0.30376	0.460000	0.39030	AGC		0.448	EOGT-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000343722.1	NM_173654	
LMOD3	56203	broad.mit.edu	37	3	69169038	69169038	+	Silent	SNP	G	G	A	rs537602397		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:69169038G>A	ENST00000420581.2	-	2	647	c.468C>T	c.(466-468)gaC>gaT	p.D156D	LMOD3_ENST00000475434.1_Silent_p.D156D|LMOD3_ENST00000489031.1_Silent_p.D156D	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	156	Glu-rich.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.D156D(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		ctccttcgtcgtcatcatcat	0.383													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20310	0.0		0.0	False		,,,				2504	0.0				p.D156D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C468T	3						.						125.0	111.0	116.0					3																	69169038		2016	4167	6183	69251728	SO:0001819	synonymous_variant	56203	exon2			AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.468C>T	3.37:g.69169038G>A		Somatic		Capture	Illumina HiSeq	Phase_I	69251728	NM_198271	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Silent	SNP	ENST00000420581.2	37	CCDS46862.1																																																																																				0.383	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529	
PDZRN3	23024	broad.mit.edu	37	3	73432689	73432689	+	Missense_Mutation	SNP	C	C	T	rs371515948		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:73432689C>T	ENST00000263666.4	-	10	3142	c.3028G>A	c.(3028-3030)Gat>Aat	p.D1010N	PDZRN3_ENST00000466780.1_Missense_Mutation_p.D667N|PDZRN3_ENST00000535920.1_Missense_Mutation_p.D732N|PDZRN3_ENST00000479530.1_Missense_Mutation_p.D727N|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000462146.2_Missense_Mutation_p.D667N	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	1010					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D1010N(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		TTCCTGTCATCGGCTGCTTGC	0.507																																					p.D1010N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3028A	3						.	C	ASN/ASP	2,4404	4.2+/-10.8	0,2,2201	214.0	213.0	213.0		3028	4.8	0.0	3		213	0,8600		0,0,4300	no	missense	PDZRN3	NM_015009.1	23	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	1010/1067	73432689	2,13004	2203	4300	6503	73515379	SO:0001583	missense	23024	exon10			AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.3028G>A	3.37:g.73432689C>T	ENSP00000263666:p.Asp1010Asn	Somatic		Capture	Illumina HiSeq	Phase_I	73515379	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	37	CCDS33789.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.04|11.04	1.520784|1.520784	0.27211|0.27211	4.54E-4|4.54E-4	0.0|0.0	ENSG00000121440|ENSG00000121440	ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530|ENST00000416926	T;T;T;T;T|.	0.75154|.	-0.91;-0.91;-0.91;-0.91;-0.91|.	5.66|5.66	4.79|4.79	0.61399|0.61399	.|.	0.210367|.	0.48767|.	D|.	0.000176|.	T|T	0.52885|0.52885	0.1762|0.1762	N|N	0.19112|0.19112	0.55|0.55	0.45607|0.45607	D|D	0.998547|0.998547	B;P;P;P|.	0.52061|.	0.311;0.881;0.47;0.95|.	B;B;B;B|.	0.39379|.	0.14;0.133;0.088;0.298|.	T|T	0.59322|0.59322	-0.7476|-0.7476	10|6	0.37606|0.87932	T|D	0.19|0	.|.	13.8131|13.8131	0.63274|0.63274	0.0:0.9261:0.0:0.0739|0.0:0.9261:0.0:0.0739	.|.	732;727;727;1010|.	F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7|.	.;.;.;PZRN3_HUMAN|.	N|Q	1010;732;667;667;727|729	ENSP00000263666:D1010N;ENSP00000442026:D732N;ENSP00000418168:D667N;ENSP00000418484:D667N;ENSP00000418624:D727N|.	ENSP00000263666:D1010N|ENSP00000392657:R729Q	D|R	-|-	1|2	0|0	PDZRN3|PDZRN3	73515379|73515379	1.000000|1.000000	0.71417|0.71417	0.041000|0.041000	0.18516|0.18516	0.008000|0.008000	0.06430|0.06430	7.580000|7.580000	0.82523|0.82523	1.385000|1.385000	0.46445|0.46445	0.655000|0.655000	0.94253|0.94253	GAT|CGA		0.507	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
PDZRN3	23024	broad.mit.edu	37	3	73433170	73433170	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:73433170delG	ENST00000263666.4	-	10	2661	c.2547delC	c.(2545-2547)cccfs	p.P849fs	PDZRN3_ENST00000466780.1_Frame_Shift_Del_p.P506fs|PDZRN3_ENST00000535920.1_Frame_Shift_Del_p.P571fs|PDZRN3_ENST00000479530.1_Frame_Shift_Del_p.P566fs|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000462146.2_Frame_Shift_Del_p.P506fs	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	849					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T850fs*37(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GGCTGGGCGTGGGGCTCCGGC	0.662																																					p.P849fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2547delC	3						.						41.0	46.0	44.0					3																	73433170		2202	4300	6502	73515860	SO:0001589	frameshift_variant	23024	exon10			AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2547delC	3.37:g.73433170delG	ENSP00000263666:p.Pro849fs	Somatic		Capture	Illumina HiSeq	Phase_I	73515860	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Frame_Shift_Del	DEL	ENST00000263666.4	37	CCDS33789.1																																																																																				0.662	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
CNTN3	5067	broad.mit.edu	37	3	74334456	74334456	+	Splice_Site	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:74334456G>A	ENST00000263665.6	-	19	2731	c.2704C>T	c.(2704-2706)Cct>Tct	p.P902S		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	902	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.P902S(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		ATATACTTACGCGTTTTCTTG	0.433																																					p.P902S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2704T	3						.						113.0	121.0	119.0					3																	74334456		2203	4300	6503	74417146	SO:0001630	splice_region_variant	5067	exon19			AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.2704+1C>T	3.37:g.74334456G>A		Somatic		Capture	Illumina HiSeq	Phase_I	74417146	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178894	0.78564	.	.	ENSG00000113805	ENST00000263665	T	0.54479	0.57	5.4	5.4	0.78164	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.70885	0.3275	M	0.87456	2.885	0.80722	D	1	D	0.64830	0.994	P	0.52424	0.698	T	0.75875	-0.3163	9	.	.	.	.	19.5306	0.95228	0.0:0.0:1.0:0.0	.	902	Q9P232	CNTN3_HUMAN	S	902	ENSP00000263665:P902S	.	P	-	1	0	CNTN3	74417146	1.000000	0.71417	0.423000	0.26634	0.507000	0.33981	9.446000	0.97590	2.665000	0.90641	0.655000	0.94253	CCT		0.433	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	Missense_Mutation
ARL13B	200894	broad.mit.edu	37	3	93699283	93699283	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:93699283G>A	ENST00000394222.3	+	1	291	c.16G>A	c.(16-18)Gcc>Acc	p.A6T	ARL13B_ENST00000471138.1_Missense_Mutation_p.A6T|ARL13B_ENST00000539730.1_5'UTR|ARL13B_ENST00000486562.1_3'UTR|ARL13B_ENST00000303097.7_Missense_Mutation_p.A6T|ARL13B_ENST00000535334.1_5'UTR	NM_001174150.1	NP_001167621.1	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 13B	6					cilium assembly (GO:0042384)|dorsal/ventral pattern formation (GO:0009953)|formation of radial glial scaffolds (GO:0021943)|heart looping (GO:0001947)|interneuron migration from the subpallium to the cortex (GO:0021830)|left/right axis specification (GO:0070986)|neural tube patterning (GO:0021532)|nonmotile primary cilium assembly (GO:0035058)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|intracellular (GO:0005622)|primary cilium (GO:0072372)	GTP binding (GO:0005525)	p.A6T(2)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(2)	10						CAGTCTGATGGCCAGTTGCTG	0.697																																					p.A6T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G16A	3						.						96.0	85.0	89.0					3																	93699283		2203	4300	6503	95181973	SO:0001583	missense	200894	exon1			AL713789	CCDS2924.1, CCDS2925.1, CCDS54615.1	3q11	2014-05-09	2005-11-18	2005-11-18	ENSG00000169379	ENSG00000169379		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	25419	protein-coding gene	gene with protein product		608922	"""ADP-ribosylation factor-like 2-like 1"""	ARL2L1		15314642, 18674751	Standard	NR_033427		Approved	DKFZp761H079, JBTS8	uc003drf.3	Q3SXY8	OTTHUMG00000159012	ENST00000394222.3:c.16G>A	3.37:g.93699283G>A	ENSP00000377769:p.Ala6Thr	Somatic		Capture	Illumina HiSeq	Phase_I	95181973	NM_001174150	D3DN29|G3V1S8|Q504W8|Q8TCL5	Missense_Mutation	SNP	ENST00000394222.3	37	CCDS2925.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.512926	0.64522	.	.	ENSG00000169379	ENST00000303097;ENST00000394222;ENST00000471138	T;T;T	0.71103	-0.54;0.08;0.08	5.07	5.07	0.68467	.	0.123548	0.53938	D	0.000047	T	0.68210	0.2976	N	0.17082	0.46	0.80722	D	1	D;B	0.54207	0.965;0.006	P;B	0.55871	0.786;0.011	T	0.72613	-0.4240	10	0.87932	D	0	-4.6968	14.1377	0.65297	0.0:0.0:1.0:0.0	.	6;6	Q3SXY8-2;Q3SXY8	.;AR13B_HUMAN	T	6	ENSP00000306225:A6T;ENSP00000377769:A6T;ENSP00000420780:A6T	ENSP00000306225:A6T	A	+	1	0	ARL13B	95181973	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	3.127000	0.50484	2.792000	0.96026	0.655000	0.94253	GCC		0.697	ARL13B-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352904.1	NM_182896	
STX19	415117	broad.mit.edu	37	3	93733816	93733816	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:93733816delT	ENST00000315099.2	-	2	554	c.298delA	c.(298-300)attfs	p.I100fs	ARL13B_ENST00000471138.1_Intron|ARL13B_ENST00000539730.1_Intron|ARL13B_ENST00000486562.1_Intron|ARL13B_ENST00000394222.3_Intron|ARL13B_ENST00000303097.7_Intron|ARL13B_ENST00000535334.1_Intron	NM_001001850.2	NP_001001850.1	Q8N4C7	STX19_HUMAN	syntaxin 19	100					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)		p.I100fs*10(1)		kidney(2)|large_intestine(2)|lung(4)|prostate(1)	9						TCTGCCTGAATTTTTATCTCC	0.353																																					p.I100fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.298delA	3						.						140.0	146.0	144.0					3																	93733816		2203	4300	6503	95216506	SO:0001589	frameshift_variant	415117	exon2			AF461456	CCDS33793.1	3q11	2005-12-30			ENSG00000178750	ENSG00000178750			19300	protein-coding gene	gene with protein product							Standard	NM_001001850		Approved	MGC21382	uc003drh.1	Q8N4C7	OTTHUMG00000159013	ENST00000315099.2:c.298delA	3.37:g.93733816delT	ENSP00000320679:p.Ile100fs	Somatic		Capture	Illumina HiSeq	Phase_I	95216506	NM_001001850		Frame_Shift_Del	DEL	ENST00000315099.2	37	CCDS33793.1																																																																																				0.353	STX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352909.1	NM_001001850	
CRYBG3	131544	broad.mit.edu	37	3	97614916	97614916	+	Missense_Mutation	SNP	G	G	A	rs371125970		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:97614916G>A	ENST00000182096.4	+	9	1908	c.1844G>A	c.(1843-1845)cGg>cAg	p.R615Q		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2563							carbohydrate binding (GO:0030246)	p.R615Q(2)		breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						TTGTCTTTCCGGTACTTACAA	0.368													G|||	1	0.000199681	0.0	0.0	5008	,	,		18223	0.0		0.001	False		,,,				2504	0.0				.												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	.	3						.	G	GLN/ARG	0,3666		0,0,1833	143.0	131.0	135.0		7688	5.7	1.0	3		135	1,8183		0,1,4091	no	missense	CRYBG3	XM_003118522.2	43	0,1,5924	AA,AG,GG		0.0122,0.0,0.0084	probably-damaging	2563/2971	97614916	1,11849	1833	4092	5925	99097606	SO:0001583	missense	131544	.					3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.1844G>A	3.37:g.97614916G>A	ENSP00000182096:p.Arg615Gln	Somatic		Capture	Illumina HiSeq	Phase_I	99097606	.	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Missense_Mutation	SNP	ENST00000182096.4	37		.	.	.	.	.	.	.	.	.	.	G	28.0	4.878573	0.91740	0.0	1.22E-4	ENSG00000080200	ENST00000182096	D	0.82344	-1.6	5.74	5.74	0.90152	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.098517	0.46442	D	0.000291	D	0.90459	0.7012	M	0.73430	2.235	0.80722	D	1	D	0.76494	0.999	D	0.64237	0.923	D	0.90805	0.4697	10	0.66056	D	0.02	.	18.6893	0.91577	0.0:0.0:1.0:0.0	.	615	Q68DQ2	CRBG3_HUMAN	Q	615	ENSP00000182096:R615Q	ENSP00000182096:R615Q	R	+	2	0	CRYBG3	99097606	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.738000	0.74822	2.723000	0.93209	0.655000	0.94253	CGG		0.368	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605	
OR5H14	403273	broad.mit.edu	37	3	97868314	97868314	+	Missense_Mutation	SNP	C	C	A	rs540702892		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:97868314C>A	ENST00000437310.1	+	1	145	c.85C>A	c.(85-87)Ctg>Atg	p.L29M	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	29						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L29M(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						ACCCCTGTTCCTGGCATTCTT	0.418																																					p.L29M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C85A	3						.						88.0	92.0	91.0					3																	97868314		2202	4279	6481	99351004	SO:0001583	missense	403273	exon1				CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"""GPCR / Class A : Olfactory receptors"""	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.85C>A	3.37:g.97868314C>A	ENSP00000401706:p.Leu29Met	Somatic		Capture	Illumina HiSeq	Phase_I	99351004	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	37	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	C	6.916	0.538610	0.13250	.	.	ENSG00000236032	ENST00000437310	T	0.00455	7.31	2.49	-0.49	0.12049	.	0.000000	0.32819	N	0.005607	T	0.00552	0.0018	L	0.52905	1.665	0.09310	N	1	D	0.63046	0.992	D	0.65233	0.933	T	0.53514	-0.8428	10	0.52906	T	0.07	.	3.4201	0.07391	0.0:0.4244:0.2084:0.3672	.	29	A6NHG9	O5H14_HUMAN	M	29	ENSP00000401706:L29M	ENSP00000401706:L29M	L	+	1	2	OR5H14	99351004	0.000000	0.05858	0.639000	0.29394	0.390000	0.30446	-2.307000	0.01132	-0.310000	0.08766	0.195000	0.17529	CTG		0.418	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1		
ZBTB20	26137	broad.mit.edu	37	3	114058003	114058003	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:114058003delG	ENST00000474710.1	-	5	2253	c.2075delC	c.(2074-2076)cctfs	p.P692fs	ZBTB20_ENST00000464560.1_Frame_Shift_Del_p.P619fs|ZBTB20_ENST00000471418.1_Frame_Shift_Del_p.P619fs|ZBTB20_ENST00000393785.2_Frame_Shift_Del_p.P619fs|ZBTB20_ENST00000481632.1_Frame_Shift_Del_p.P619fs|ZBTB20_ENST00000462705.1_Frame_Shift_Del_p.P619fs|ZBTB20_ENST00000357258.3_Frame_Shift_Del_p.P619fs	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	692						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.P619fs*43(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		TGTGCCTGCAGGGGGGGTCCC	0.632																																					p.P619fs	NSCLC(69;748 1344 9802 11203 30933)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1856delC	3						.						56.0	55.0	55.0					3																	114058003		2203	4300	6503	115540693	SO:0001589	frameshift_variant	26137	exon12			AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	13503	protein-coding gene	gene with protein product		606025	"""zinc finger protein 288"""	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.2075delC	3.37:g.114058003delG	ENSP00000419153:p.Pro692fs	Somatic		Capture	Illumina HiSeq	Phase_I	115540693	NM_001164343	Q63HP6|Q8N6R5|Q9Y410	Frame_Shift_Del	DEL	ENST00000474710.1	37	CCDS54626.1																																																																																				0.632	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642	
B3GALNT1	8706	broad.mit.edu	37	3	160803879	160803879	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:160803879delT	ENST00000392781.2	-	8	1411	c.664delA	c.(664-666)accfs	p.T222fs	B3GALNT1_ENST00000392779.2_Frame_Shift_Del_p.T222fs|B3GALNT1_ENST00000392780.1_Frame_Shift_Del_p.T222fs|B3GALNT1_ENST00000320474.4_Frame_Shift_Del_p.T222fs|B3GALNT1_ENST00000488170.1_Frame_Shift_Del_p.T222fs|B3GALNT1_ENST00000473285.1_Frame_Shift_Del_p.T222fs|B3GALNT1_ENST00000417187.1_Intron	NM_001038628.1	NP_001033717.1	O75752	B3GL1_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	222					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity (GO:0047273)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)	p.T222fs*23(1)		breast(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13			LUSC - Lung squamous cell carcinoma(72;4.41e-05)|Lung(72;4.61e-05)			GAAATATGGGTTTTTTGGTAA	0.363																																					p.T222fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.664delA	3						.						35.0	37.0	36.0					3																	160803879		2201	4295	6496	162286573	SO:0001589	frameshift_variant	8706	exon4			Y15062	CCDS3193.1	3q25	2014-07-18	2006-06-14	2006-05-09	ENSG00000169255	ENSG00000169255	2.4.1.79	"""Blood group antigens"", ""Beta 3-glycosyltransferases"""	918	protein-coding gene	gene with protein product	"""globoside synthase"", ""P antigen synthase"""	603094	"""UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 (Globoside blood group)"", ""UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1 (Globoside blood group)"""	B3GALT3		9582303, 10993897	Standard	XM_005247861		Approved	beta3Gal-T3, galT3, P1, GLOB	uc003fdv.3	O75752	OTTHUMG00000159064	ENST00000392781.2:c.664delA	3.37:g.160803879delT	ENSP00000376532:p.Thr222fs	Somatic		Capture	Illumina HiSeq	Phase_I	162286573	NM_033168	D3DNM4|Q3Y531|Q6IAI5|Q8NFM8|Q8NFM9|Q9HA06	Frame_Shift_Del	DEL	ENST00000392781.2	37	CCDS3193.1																																																																																				0.363	B3GALNT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353125.1	NM_033167	
SLITRK3	22865	broad.mit.edu	37	3	164907334	164907334	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:164907334delA	ENST00000475390.1	-	2	1728	c.1285delT	c.(1285-1287)tggfs	p.W429fs	SLITRK3_ENST00000241274.3_Frame_Shift_Del_p.W429fs			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	429					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.W429fs*30(1)|p.W429fs*36(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						GAAAAATTCCAAAAATCAGAA	0.388										HNSCC(40;0.11)																											p.W429fs												.	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(1)|pancreas(1)	c.1285delT	3						.						48.0	50.0	49.0					3																	164907334		2203	4300	6503	166390028	SO:0001589	frameshift_variant	22865	exon2			AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1285delT	3.37:g.164907334delA	ENSP00000420091:p.Trp429fs	Somatic		Capture	Illumina HiSeq	Phase_I	166390028	NM_014926	Q1RMY6	Frame_Shift_Del	DEL	ENST00000475390.1	37	CCDS3197.1																																																																																				0.388	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926	
MECOM	2122	broad.mit.edu	37	3	168833257	168833257	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:168833257delT	ENST00000464456.1	-	7	3039	c.1839delA	c.(1837-1839)aaafs	p.K613fs	MECOM_ENST00000392736.3_Frame_Shift_Del_p.K613fs|MECOM_ENST00000494292.1_Frame_Shift_Del_p.K801fs|MECOM_ENST00000472280.1_Frame_Shift_Del_p.K614fs|MECOM_ENST00000264674.3_Frame_Shift_Del_p.K678fs|MECOM_ENST00000468789.1_Frame_Shift_Del_p.K613fs|MECOM_ENST00000433243.2_Frame_Shift_Del_p.K614fs|MECOM_ENST00000460814.1_Frame_Shift_Del_p.K613fs	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	22					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G614fs*30(2)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CGTTGCTTCCTTTTTTTCCCC	0.498																																					p.K678fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.2034delA	3						.						121.0	110.0	114.0					3																	168833257		2203	4300	6503	170315951	SO:0001589	frameshift_variant	2122	exon8			S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.1839delA	3.37:g.168833257delT	ENSP00000419770:p.Lys613fs	Somatic		Capture	Illumina HiSeq	Phase_I	170315951	NM_001105077	Q13466|Q6FH90	Frame_Shift_Del	DEL	ENST00000464456.1	37	CCDS54669.1																																																																																				0.498	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
ATP11B	23200	broad.mit.edu	37	3	182602674	182602674	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:182602674delT	ENST00000323116.5	+	22	2903	c.2643delT	c.(2641-2643)tatfs	p.Y881fs		NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	881					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.Y884fs*30(1)		breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			TTGTACAGTATTTTTTTTATA	0.269																																					p.Y881fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2643delT	3						.						60.0	64.0	63.0					3																	182602674		2202	4298	6500	184085368	SO:0001589	frameshift_variant	23200	exon22			AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"""ATPases / P-type"""	13553	protein-coding gene	gene with protein product		605869	"""ATPase, Class VI, type 11B"""			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.2643delT	3.37:g.182602674delT	ENSP00000321195:p.Tyr881fs	Somatic		Capture	Illumina HiSeq	Phase_I	184085368	NM_014616	Q96FN1|Q9UKK7	Frame_Shift_Del	DEL	ENST00000323116.5	37	CCDS33896.1																																																																																				0.269	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616	
YEATS2	55689	broad.mit.edu	37	3	183508697	183508697	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:183508697delC	ENST00000305135.5	+	21	3221	c.3026delC	c.(3025-3027)accfs	p.T1009fs		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1009					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)	p.T1011fs*25(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			AAGGCTGCCACCCCCACCGTC	0.562																																					p.T1009fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3026delC	3						.						99.0	109.0	106.0					3																	183508697		2056	4200	6256	184991391	SO:0001589	frameshift_variant	55689	exon21			AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.3026delC	3.37:g.183508697delC	ENSP00000306983:p.Thr1009fs	Somatic		Capture	Illumina HiSeq	Phase_I	184991391	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Frame_Shift_Del	DEL	ENST00000305135.5	37	CCDS43175.1																																																																																				0.562	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023	
ABCC5	10057	broad.mit.edu	37	3	183665257	183665257	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:183665257delA	ENST00000334444.6	-	23	3509	c.3269delT	c.(3268-3270)ttgfs	p.L1090fs	ABCC5_ENST00000265586.6_Frame_Shift_Del_p.L1047fs	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	1090	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	ACACGTAAACAAAAAAAAAGG	0.532																																					p.L1090fs												.	.	0			c.3269delT	3						.						49.0	58.0	55.0					3																	183665257		1969	4159	6128	185147951	SO:0001589	frameshift_variant	10057	exon23			AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"""ATP binding cassette transporters / subfamily C"""	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.3269delT	3.37:g.183665257delA	ENSP00000333926:p.Leu1090fs	Germline		Capture	Illumina HiSeq	Phase_I	185147951	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Frame_Shift_Del	DEL	ENST00000334444.6	37	CCDS43176.1																																																																																				0.532	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	
NRROS	375387	broad.mit.edu	37	3	196388100	196388100	+	Missense_Mutation	SNP	C	C	T	rs536832751		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr3:196388100C>T	ENST00000328557.4	+	3	1789	c.1586C>T	c.(1585-1587)gCg>gTg	p.A529V		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	529					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A529V(1)									AGCTTTATGGCGTTGGACTTC	0.582													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18817	0.0		0.0	False		,,,				2504	0.0				p.A529V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1586T	3						.						126.0	124.0	125.0					3																	196388100		2203	4300	6503	197872497	SO:0001583	missense	375387	exon3			AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"""leucine rich repeat containing 33"""	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	ENST00000328557.4:c.1586C>T	3.37:g.196388100C>T	ENSP00000328625:p.Ala529Val	Somatic		Capture	Illumina HiSeq	Phase_I	197872497	NM_198565		Missense_Mutation	SNP	ENST00000328557.4	37	CCDS3319.1	.	.	.	.	.	.	.	.	.	.	C	3.437	-0.114973	0.06881	.	.	ENSG00000174004	ENST00000328557	T	0.53206	0.63	5.97	3.56	0.40772	.	0.288824	0.37095	N	0.002260	T	0.26593	0.0650	N	0.08118	0	0.21105	N	0.99979	B	0.25105	0.118	B	0.17979	0.02	T	0.10497	-1.0627	10	0.28530	T	0.3	.	13.024	0.58804	0.5803:0.4197:0.0:0.0	.	529	Q86YC3	LRC33_HUMAN	V	529	ENSP00000328625:A529V	ENSP00000328625:A529V	A	+	2	0	LRRC33	197872497	0.827000	0.29292	0.011000	0.14972	0.016000	0.09150	4.567000	0.60850	0.495000	0.27882	-0.266000	0.10368	GCG		0.582	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565	
GPRIN3	285513	broad.mit.edu	37	4	90169267	90169268	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:90169267_90169268insT	ENST00000609438.1	-	2	2512_2513	c.1994_1995insA	c.(1993-1995)aagfs	p.K665fs	GPRIN3_ENST00000333209.4_Frame_Shift_Ins_p.K665fs	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	665								p.Q666fs*23(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CGCCAAGCTGCTTTTTCTTATC	0.554																																					p.K665fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1995_1996insA	4						.																																			90388291	SO:0001589	frameshift_variant	285513	exon2			AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.1995dupA	4.37:g.90169272_90169272dupT	ENSP00000476603:p.Lys665fs	Somatic		Capture	Illumina HiSeq	Phase_I	90388290	NM_198281	Q8IVE4	Frame_Shift_Ins	INS	ENST00000609438.1	37	CCDS34030.1																																																																																				0.554	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281	
MANBA	4126	broad.mit.edu	37	4	103611760	103611760	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:103611760A>G	ENST00000226578.4	-	6	941	c.842T>C	c.(841-843)aTt>aCt	p.I281T	MANBA_ENST00000505239.1_Missense_Mutation_p.I224T	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	281					cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)	p.I281T(1)		cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		TACCTTGCTAATGTTCACAAA	0.398																																					p.I281T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T842C	4						.						246.0	216.0	226.0					4																	103611760		2203	4300	6503	103830808	SO:0001583	missense	4126	exon6				CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.842T>C	4.37:g.103611760A>G	ENSP00000226578:p.Ile281Thr	Somatic		Capture	Illumina HiSeq	Phase_I	103830808	NM_005908	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	.	.	.	.	.	.	.	.	.	.	A	11.69	1.713475	0.30413	.	.	ENSG00000109323	ENST00000226578;ENST00000505239	T;T	0.55413	0.52;0.52	4.65	4.65	0.58169	.	0.052109	0.85682	D	0.000000	T	0.67757	0.2927	M	0.78916	2.43	0.43218	D	0.995096	P;D	0.58970	0.852;0.984	B;P	0.59115	0.353;0.852	T	0.71290	-0.4637	10	0.51188	T	0.08	-17.3238	12.8253	0.57716	1.0:0.0:0.0:0.0	.	224;281	E9PFW2;O00462	.;MANBA_HUMAN	T	281;224	ENSP00000226578:I281T;ENSP00000427322:I224T	ENSP00000226578:I281T	I	-	2	0	MANBA	103830808	1.000000	0.71417	0.998000	0.56505	0.383000	0.30230	5.695000	0.68279	1.948000	0.56530	0.528000	0.53228	ATT		0.398	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2		
TACR3	6870	broad.mit.edu	37	4	104510952	104510952	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:104510952C>T	ENST00000304883.2	-	5	1425	c.1285G>A	c.(1285-1287)Gca>Aca	p.A429T	RP11-297P16.3_ENST00000502936.1_RNA|RP11-297P16.3_ENST00000512401.1_RNA	NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	429					aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)	p.A429T(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		CTTGGCGTTGCTCTTTTCTTC	0.517																																					p.A429T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1285A	4						.						226.0	211.0	216.0					4																	104510952		2203	4300	6503	104730401	SO:0001583	missense	6870	exon5			M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"""GPCR / Class A : Tachykinin receptors"""	11528	protein-coding gene	gene with protein product	"""neurokinin beta receptor"""	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.1285G>A	4.37:g.104510952C>T	ENSP00000303325:p.Ala429Thr	Somatic		Capture	Illumina HiSeq	Phase_I	104730401	NM_001059	Q0P510	Missense_Mutation	SNP	ENST00000304883.2	37	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	C	9.170	1.020798	0.19433	.	.	ENSG00000169836	ENST00000304883	T	0.64260	-0.09	5.54	3.78	0.43462	.	0.453024	0.21862	N	0.068002	T	0.52805	0.1757	L	0.50919	1.6	0.31757	N	0.633787	B	0.18013	0.025	B	0.18561	0.022	T	0.55535	-0.8126	10	0.26408	T	0.33	.	10.1296	0.42672	0.135:0.7933:0.0:0.0717	.	429	P29371	NK3R_HUMAN	T	429	ENSP00000303325:A429T	ENSP00000303325:A429T	A	-	1	0	TACR3	104730401	0.702000	0.27816	0.066000	0.19879	0.021000	0.10359	2.068000	0.41471	1.322000	0.45245	-0.282000	0.10007	GCA		0.517	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059	
INTS12	57117	broad.mit.edu	37	4	106607849	106607849	+	Splice_Site	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:106607849C>A	ENST00000451321.2	-	6	1283	c.804G>T	c.(802-804)aaG>aaT	p.K268N	INTS12_ENST00000394735.1_Splice_Site_p.K268N|INTS12_ENST00000340139.5_Splice_Site_p.K268N	NM_001142471.1	NP_001135943.1	Q96CB8	INT12_HUMAN	integrator complex subunit 12	268					snRNA processing (GO:0016180)	integrator complex (GO:0032039)	zinc ion binding (GO:0008270)	p.K268N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(123;5.12e-07)		TCTACTATACCTTGACTTCTG	0.279																																					p.K268N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G804T	4						.						85.0	84.0	85.0					4																	106607849		2203	4300	6503	106827298	SO:0001630	splice_region_variant	57117	exon6				CCDS3671.1	4q24	2013-01-28	2006-03-15	2006-03-15	ENSG00000138785	ENSG00000138785		"""Zinc fingers, PHD-type"""	25067	protein-coding gene	gene with protein product	"""hypothetical nuclear factor SBBI22"""	611355	"""PHD finger protein 22"""	PHF22		16239144	Standard	NM_020395		Approved	SBBI22, INT12	uc010ilr.3	Q96CB8	OTTHUMG00000131215	ENST00000451321.2:c.804+1G>T	4.37:g.106607849C>A		Somatic		Capture	Illumina HiSeq	Phase_I	106827298	NM_001142471	B2RC48|Q3B6Z3|Q9HD71	Missense_Mutation	SNP	ENST00000451321.2	37	CCDS3671.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.044903	0.93685	.	.	ENSG00000138785	ENST00000394735;ENST00000340139;ENST00000451321	T;T;T	0.55234	0.53;0.53;0.53	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.65207	0.2669	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.58640	-0.7601	9	.	.	.	-14.9994	20.6593	0.99626	0.0:1.0:0.0:0.0	.	268	Q96CB8	INT12_HUMAN	N	268	ENSP00000378221:K268N;ENSP00000340737:K268N;ENSP00000415433:K268N	.	K	-	3	2	INTS12	106827298	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.319000	0.79040	2.885000	0.99019	0.655000	0.94253	AAG		0.279	INTS12-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318624.1	NM_020395	Missense_Mutation
DKK2	27123	broad.mit.edu	37	4	107845203	107845203	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:107845203G>A	ENST00000285311.3	-	4	1393	c.688C>T	c.(688-690)Cgt>Tgt	p.R230C	DKK2_ENST00000510463.1_Missense_Mutation_p.R184C|DKK2_ENST00000513208.1_Missense_Mutation_p.R130C	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	230	DKK-type Cys-2.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)		p.R230C(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		CAGTCGCAACGCTGGAAAATT	0.483																																					p.R230C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C688T	4						.						158.0	145.0	149.0					4																	107845203		2203	4300	6503	108064652	SO:0001583	missense	27123	exon4			AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"""dickkopf (Xenopus laevis) homolog 2"", ""dickkopf 2 homolog (Xenopus laevis)"""			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.688C>T	4.37:g.107845203G>A	ENSP00000285311:p.Arg230Cys	Somatic		Capture	Illumina HiSeq	Phase_I	108064652	NM_014421	A0AVE9|B2R6S7|Q9UIU3	Missense_Mutation	SNP	ENST00000285311.3	37	CCDS3675.1	.	.	.	.	.	.	.	.	.	.	G	19.01	3.742934	0.69418	.	.	ENSG00000155011	ENST00000285311;ENST00000513208;ENST00000510463	T;T;T	0.57907	0.37;0.5;0.52	5.64	3.79	0.43588	.	0.000000	0.85682	D	0.000000	T	0.71945	0.3400	M	0.81341	2.54	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.77040	-0.2735	10	0.87932	D	0	-11.8314	13.5124	0.61519	0.0:0.0:0.5801:0.4199	.	230	Q9UBU2	DKK2_HUMAN	C	230;130;184	ENSP00000285311:R230C;ENSP00000421255:R130C;ENSP00000423797:R184C	ENSP00000285311:R230C	R	-	1	0	DKK2	108064652	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	4.419000	0.59835	1.320000	0.45209	0.585000	0.79938	CGT		0.483	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4		
SEC24B	10427	broad.mit.edu	37	4	110431263	110431263	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:110431263T>C	ENST00000265175.5	+	8	1827	c.1772T>C	c.(1771-1773)cTa>cCa	p.L591P	SEC24B_ENST00000504968.2_Missense_Mutation_p.L621P|SEC24B_ENST00000399100.2_Missense_Mutation_p.L556P	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	591					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)	p.L591P(1)|p.L556P(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		TTCAGAGACCTAACGGTAAAG	0.313																																					p.L591P												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1772C	4						.						98.0	81.0	86.0					4																	110431263		1815	4073	5888	110650712	SO:0001583	missense	10427	exon8			AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"""SEC24 (S. cerevisiae) related gene family, member B"", ""SEC24 family, member B (S. cerevisiae)"""			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.1772T>C	4.37:g.110431263T>C	ENSP00000265175:p.Leu591Pro	Somatic		Capture	Illumina HiSeq	Phase_I	110650712	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Missense_Mutation	SNP	ENST00000265175.5	37	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	T	19.75	3.886445	0.72410	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	T;T;T	0.26810	1.71;1.71;1.71	5.47	5.47	0.80525	Zinc finger, Sec23/Sec24-type (1);	0.158979	0.43260	D	0.000595	T	0.48822	0.1521	M	0.73598	2.24	0.80722	D	1	D;P;D;D;D	0.89917	1.0;0.527;0.999;1.0;0.999	D;B;D;D;D	0.72982	0.966;0.119;0.932;0.979;0.954	T	0.52351	-0.8587	10	0.87932	D	0	-13.1193	10.76	0.46259	0.1417:0.0:0.0:0.8583	.	505;190;621;556;591	B4DTM6;B4E2E1;B7ZKM8;O95487-2;O95487	.;.;.;.;SC24B_HUMAN	P	621;556;591	ENSP00000428564:L621P;ENSP00000382051:L556P;ENSP00000265175:L591P	ENSP00000265175:L591P	L	+	2	0	SEC24B	110650712	1.000000	0.71417	0.994000	0.49952	0.992000	0.81027	5.962000	0.70364	2.083000	0.62718	0.460000	0.39030	CTA		0.313	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2		
CFI	3426	broad.mit.edu	37	4	110662061	110662061	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:110662061C>T	ENST00000394634.2	-	13	1947	c.1740G>A	c.(1738-1740)caG>caA	p.Q580Q	CFI_ENST00000394635.3_Silent_p.Q588Q|CFI_ENST00000512148.1_Silent_p.Q573Q	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	580					complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.Q580Q(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|skin(2)|stomach(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		ATACATTGTACTGAGAAATAA	0.348																																					p.Q580Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1740A	4						.						82.0	87.0	85.0					4																	110662061		2203	4300	6503	110881510	SO:0001819	synonymous_variant	3426	exon13			J02770	CCDS34049.1	4q25	2014-09-17	2006-02-10	2006-02-10		ENSG00000205403	3.4.21.45	"""Complement system"""	5394	protein-coding gene	gene with protein product	"""Konglutinogen-activating factor"", ""C3b-inactivator"""	217030	"""I factor (complement)"""	IF		2956252	Standard	NM_000204		Approved	FI, C3b-INA, KAF	uc003hzr.4	P05156		ENST00000394634.2:c.1740G>A	4.37:g.110662061C>T		Somatic		Capture	Illumina HiSeq	Phase_I	110881510	NM_000204	O60442	Silent	SNP	ENST00000394634.2	37	CCDS34049.1																																																																																				0.348	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204	
ANK2	287	broad.mit.edu	37	4	114276050	114276050	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:114276050A>G	ENST00000357077.4	+	38	6329	c.6276A>G	c.(6274-6276)atA>atG	p.I2092M	ANK2_ENST00000510275.2_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.I2059M|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000394537.3_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2092					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.I2092M(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)		GCCACAAAATACCTGAACCTG	0.478																																					p.I2092M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A6276G	4						.						69.0	72.0	71.0					4																	114276050		2203	4300	6503	114495499	SO:0001583	missense	287	exon38			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.6276A>G	4.37:g.114276050A>G	ENSP00000349588:p.Ile2092Met	Somatic		Capture	Illumina HiSeq	Phase_I	114495499	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	A	3.522	-0.097533	0.07010	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.66995	-0.23;-0.24	5.65	-6.88	0.01665	.	0.734274	0.12233	N	0.487257	T	0.34483	0.0899	N	0.14661	0.345	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.001;0.003	T	0.19647	-1.0299	9	.	.	.	.	1.971	0.03406	0.2892:0.1805:0.3535:0.1769	.	2059;2092	Q01484;Q01484-4	ANK2_HUMAN;.	M	2092;2059	ENSP00000349588:I2092M;ENSP00000264366:I2059M	.	I	+	3	3	ANK2	114495499	0.000000	0.05858	0.001000	0.08648	0.158000	0.22134	-0.032000	0.12266	-1.155000	0.02822	0.460000	0.39030	ATA		0.478	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
NDNF	79625	broad.mit.edu	37	4	121957482	121957482	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:121957482T>C	ENST00000379692.4	-	4	2170	c.1644A>G	c.(1642-1644)atA>atG	p.I548M	NDNF_ENST00000506900.1_5'Flank	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	548	Fibronectin type-III 2.				cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)	p.I548M(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						CCCCATGTCCTATGACATAAA	0.388																																					p.I548M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1644G	4						.						122.0	125.0	124.0					4																	121957482		2203	4300	6503	122176932	SO:0001583	missense	79625	exon4			BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 31"""	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.1644A>G	4.37:g.121957482T>C	ENSP00000369014:p.Ile548Met	Somatic		Capture	Illumina HiSeq	Phase_I	122176932	NM_024574	A8K0Q0|Q6UWE5|Q9H5P7	Missense_Mutation	SNP	ENST00000379692.4	37	CCDS3717.2	.	.	.	.	.	.	.	.	.	.	T	8.509	0.866097	0.17250	.	.	ENSG00000173376	ENST00000379692	T	0.54675	0.56	6.03	-4.94	0.03057	.	0.236146	0.50627	D	0.000119	T	0.21267	0.0512	N	0.12746	0.255	0.34941	D	0.750284	B	0.02656	0.0	B	0.11329	0.006	T	0.01570	-1.1322	10	0.29301	T	0.29	-16.0456	1.0718	0.01623	0.3372:0.1238:0.1532:0.3857	.	548	Q8TB73	NDNF_HUMAN	M	548	ENSP00000369014:I548M	ENSP00000369014:I548M	I	-	3	3	NDNF	122176932	0.697000	0.27767	0.984000	0.44739	0.996000	0.88848	-0.148000	0.10219	-0.396000	0.07703	0.533000	0.62120	ATA		0.388	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2	NM_024574	
KIAA1109	84162	broad.mit.edu	37	4	123128369	123128369	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:123128369G>A	ENST00000264501.4	+	16	1976	c.1603G>A	c.(1603-1605)Gct>Act	p.A535T	KIAA1109_ENST00000388738.3_Missense_Mutation_p.A535T|KIAA1109_ENST00000455637.1_Missense_Mutation_p.A535T|KIAA1109_ENST00000495260.1_3'UTR			Q2LD37	K1109_HUMAN	KIAA1109	535					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A535T(2)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AATGATTTGGGCTGCTAATCA	0.318																																					p.A535T												.	.	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	c.G1603A	4						.						104.0	97.0	99.0					4																	123128369		1817	4077	5894	123347819	SO:0001583	missense	84162	exon14			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.1603G>A	4.37:g.123128369G>A	ENSP00000264501:p.Ala535Thr	Somatic		Capture	Illumina HiSeq	Phase_I	123347819	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.2|28.2	4.898838|4.898838	0.91962|0.91962	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000424425	T;T;T|.	0.23147|.	2.51;2.51;1.92|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	0.910588|.	0.08906|.	N|.	0.876568|.	T|T	0.68723|0.68723	0.3032|0.3032	L|L	0.43152|0.43152	1.355|1.355	0.58432|0.58432	D|D	0.999999|0.999999	D|.	0.69078|.	0.997|.	D|.	0.77004|.	0.989|.	T|T	0.63449|0.63449	-0.6635|-0.6635	10|5	0.15952|.	T|.	0.53|.	.|.	19.7657|19.7657	0.96340|0.96340	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	535|.	Q2LD37|.	K1109_HUMAN|.	T|D	535|367	ENSP00000264501:A535T;ENSP00000373390:A535T;ENSP00000389925:A535T|.	ENSP00000264501:A535T|.	A|G	+|+	1|2	0|0	KIAA1109|KIAA1109	123347819|123347819	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.394000|9.394000	0.97261|0.97261	2.649000|2.649000	0.89929|0.89929	0.655000|0.655000	0.94253|0.94253	GCT|GGC		0.318	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
FAT4	79633	broad.mit.edu	37	4	126238577	126238577	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:126238577C>T	ENST00000394329.3	+	1	1024	c.1011C>T	c.(1009-1011)gcC>gcT	p.A337A		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	337	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.A337A(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						CTGGGCGCGCCGAGGCGCTGA	0.617											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A337A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1011T	4						.						29.0	37.0	34.0					4																	126238577		2091	4217	6308	126458027	SO:0001819	synonymous_variant	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.1011C>T	4.37:g.126238577C>T		Somatic	1548	Capture	Illumina HiSeq	Phase_I	126458027	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.617	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FAT4	79633	broad.mit.edu	37	4	126372303	126372303	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:126372303T>G	ENST00000394329.3	+	9	10145	c.10132T>G	c.(10132-10134)Ttt>Gtt	p.F3378V	FAT4_ENST00000335110.5_Missense_Mutation_p.F1676V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3378	Cadherin 32. {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.F3378V(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						GGCCAAGAACTTTGGCAGCAT	0.403																																					p.F3378V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T10132G	4						.						162.0	157.0	159.0					4																	126372303		2203	4300	6503	126591753	SO:0001583	missense	79633	exon9			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.10132T>G	4.37:g.126372303T>G	ENSP00000377862:p.Phe3378Val	Somatic		Capture	Illumina HiSeq	Phase_I	126591753	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	T	0.732	-0.779435	0.02929	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01599	4.74;4.74	5.27	2.65	0.31530	Cadherin (4);Cadherin-like (1);	0.000000	0.35646	U	0.003073	T	0.00967	0.0032	N	0.02539	-0.55	0.27962	N	0.936733	B;B;B	0.23249	0.001;0.009;0.082	B;B;B	0.21708	0.0;0.003;0.036	T	0.47262	-0.9131	10	0.18710	T	0.47	.	12.8941	0.58089	0.0:0.0:0.4993:0.5007	.	1676;3378;3378	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	V	3378;1676	ENSP00000377862:F3378V;ENSP00000335169:F1676V	ENSP00000335169:F1676V	F	+	1	0	FAT4	126591753	0.654000	0.27367	0.968000	0.41197	0.075000	0.17131	1.181000	0.32017	0.828000	0.34709	-0.313000	0.08912	TTT		0.403	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FAT4	79633	broad.mit.edu	37	4	126372832	126372832	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:126372832C>A	ENST00000394329.3	+	9	10674	c.10661C>A	c.(10660-10662)gCc>gAc	p.A3554D	FAT4_ENST00000335110.5_Missense_Mutation_p.A1852D	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3554	Cadherin 34. {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.A3554D(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						ACAGGTCCTGCCACCAGTTAT	0.493																																					p.A3554D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C10661A	4						.						116.0	117.0	117.0					4																	126372832		2203	4300	6503	126592282	SO:0001583	missense	79633	exon9			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.10661C>A	4.37:g.126372832C>A	ENSP00000377862:p.Ala3554Asp	Somatic		Capture	Illumina HiSeq	Phase_I	126592282	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	15.80	2.941395	0.53079	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.37411	1.2;1.2	5.91	5.04	0.67666	Cadherin (4);Cadherin-like (1);	0.000000	0.34110	U	0.004256	T	0.41351	0.1155	N	0.17872	0.535	0.80722	D	1	P;D;D	0.89917	0.946;1.0;1.0	P;D;D	0.91635	0.507;0.999;0.998	T	0.17501	-1.0367	10	0.06494	T	0.89	.	16.1731	0.81831	0.1343:0.8657:0.0:0.0	.	1852;3554;3554	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	D	3554;1852	ENSP00000377862:A3554D;ENSP00000335169:A1852D	ENSP00000335169:A1852D	A	+	2	0	FAT4	126592282	1.000000	0.71417	0.995000	0.50966	0.221000	0.24807	7.662000	0.83803	1.443000	0.47586	0.655000	0.94253	GCC		0.493	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FAT4	79633	broad.mit.edu	37	4	126411803	126411804	+	Missense_Mutation	DNP	CT	CT	TC	rs200391966		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	CT	CT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:126411803_126411804CT>TC	ENST00000394329.3	+	17	13839_13840	c.13826_13827CT>TC	c.(13825-13827)cCT>cTC	p.P4609L	FAT4_ENST00000335110.5_Missense_Mutation_p.P2850L	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4609					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.P4609>?(1)|p.P4552>?(1)		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						CCCAGCGCCCCTTTGGCATCTC	0.48																																					.												.	.	2	Complex(2)	large_intestine(2)	c.13826_13827TC	4						.																																			126631254	SO:0001583	missense	79633	exon17			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	Exception_encountered	4.37:g.126411803_126411804delinsTC	ENSP00000377862:p.Pro4609Leu	Somatic		Capture	Illumina HiSeq	Phase_I	126631253	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	DNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.480	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
MFSD8	256471	broad.mit.edu	37	4	128854140	128854140	+	Splice_Site	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:128854140G>A	ENST00000296468.3	-	9	990	c.863C>T	c.(862-864)aCc>aTc	p.T288I	MFSD8_ENST00000541133.1_3'UTR|MFSD8_ENST00000513559.1_Splice_Site_p.T243I|MFSD8_ENST00000515130.1_5'UTR	NM_152778.2	NP_689991.1	Q8NHS3	MFSD8_HUMAN	major facilitator superfamily domain containing 8	288					cell death (GO:0008219)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)		p.T288I(1)		cervix(2)|endometrium(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)	23						TAAAACTTACGTTTCAAAAAG	0.328																																					p.T288I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C863T	4						.						125.0	123.0	124.0					4																	128854140		2203	4300	6503	129073590	SO:0001630	splice_region_variant	256471	exon9			AK074564	CCDS3736.1	4q28.2	2014-09-17			ENSG00000164073	ENSG00000164073			28486	protein-coding gene	gene with protein product		611124	"""ceroid-lipofuscinosis, neuronal 7, late infantile, variant"""	CLN7		17564970	Standard	NM_152778		Approved	MGC33302	uc003ifp.3	Q8NHS3	OTTHUMG00000133303	ENST00000296468.3:c.863+1C>T	4.37:g.128854140G>A		Somatic		Capture	Illumina HiSeq	Phase_I	129073590	NM_152778	B2RDM1|B7Z205|Q8N2P3	Missense_Mutation	SNP	ENST00000296468.3	37	CCDS3736.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.432016	0.62844	.	.	ENSG00000164073	ENST00000296468;ENST00000513559	T;T	0.58940	0.3;0.3	4.55	4.55	0.56014	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.75788	0.3897	M	0.75615	2.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.77376	-0.2611	9	.	.	.	-15.2695	17.5171	0.87777	0.0:0.0:1.0:0.0	.	250;288	B7Z280;Q8NHS3	.;MFSD8_HUMAN	I	288;243	ENSP00000296468:T288I;ENSP00000425000:T243I	.	T	-	2	0	MFSD8	129073590	1.000000	0.71417	1.000000	0.80357	0.586000	0.36452	7.514000	0.81750	2.352000	0.79861	0.585000	0.79938	ACC		0.328	MFSD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257097.1	NM_152778	Missense_Mutation
SCLT1	132320	broad.mit.edu	37	4	129805652	129805652	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:129805652T>G	ENST00000281142.5	-	21	2550	c.2047A>C	c.(2047-2049)Atg>Ctg	p.M683L	SCLT1_ENST00000503215.1_Missense_Mutation_p.M279L|SCLT1_ENST00000502495.1_5'UTR|SCLT1_ENST00000439369.2_Missense_Mutation_p.M170L|SCLT1_ENST00000434680.1_Missense_Mutation_p.M302L	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	683					cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)	p.M683L(2)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						TCCAGATTCATCAGGGAGGCT	0.353																																					p.M683L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A2047C	4						.						64.0	68.0	67.0					4																	129805652		2203	4300	6503	130025102	SO:0001583	missense	132320	exon21			AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466			26406	protein-coding gene	gene with protein product		611399				15797711	Standard	XM_005262732		Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.2047A>C	4.37:g.129805652T>G	ENSP00000281142:p.Met683Leu	Somatic		Capture	Illumina HiSeq	Phase_I	130025102	NM_144643	A4QN04|Q0VAH2|Q6P2M4	Missense_Mutation	SNP	ENST00000281142.5	37	CCDS3740.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.327824	0.41197	.	.	ENSG00000151466	ENST00000281142;ENST00000434680;ENST00000439369;ENST00000503215	T	0.43294	0.95	4.73	3.5	0.40072	.	0.147080	0.64402	D	0.000013	T	0.23846	0.0577	N	0.24115	0.695	0.09310	N	1	B;B;B;B	0.20671	0.005;0.047;0.047;0.004	B;B;B;B	0.18561	0.015;0.022;0.022;0.009	T	0.07673	-1.0760	9	.	.	.	-4.7725	6.2784	0.20993	0.0:0.1884:0.0:0.8116	.	170;302;683;279	Q96NL6-3;Q96NL6-2;Q96NL6;D6RBP0	.;.;SCLT1_HUMAN;.	L	683;302;170;279	ENSP00000281142:M683L	.	M	-	1	0	SCLT1	130025102	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.768000	0.26590	1.999000	0.58509	0.459000	0.35465	ATG		0.353	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643	
PCDH18	54510	broad.mit.edu	37	4	138442723	138442723	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:138442723C>T	ENST00000344876.4	-	4	3254	c.2868G>A	c.(2866-2868)acG>acA	p.T956T	PCDH18_ENST00000507846.1_Silent_p.T735T|PCDH18_ENST00000510305.1_Silent_p.T167T|PCDH18_ENST00000511115.1_Silent_p.T136T|PCDH18_ENST00000412923.2_Silent_p.T955T	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	956	Interaction with DAB1. {ECO:0000250}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T956T(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					GCTGGGGTTGCGTTGGGAATT	0.517																																					p.T956T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2868A	4						.						129.0	124.0	126.0					4																	138442723		2203	4300	6503	138662173	SO:0001819	synonymous_variant	54510	exon4			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"""Cadherins / Protocadherins : Non-clustered"""	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2868G>A	4.37:g.138442723C>T		Somatic		Capture	Illumina HiSeq	Phase_I	138662173	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Silent	SNP	ENST00000344876.4	37	CCDS34064.1																																																																																				0.517	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035	
ELF2	1998	broad.mit.edu	37	4	139981778	139981778	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:139981778A>G	ENST00000394235.2	-	9	1323	c.821T>C	c.(820-822)gTa>gCa	p.V274A	ELF2_ENST00000515489.1_5'Flank|ELF2_ENST00000358635.3_Missense_Mutation_p.V226A|ELF2_ENST00000379549.2_Missense_Mutation_p.V197A|ELF2_ENST00000265495.4_Missense_Mutation_p.V274A|ELF2_ENST00000379550.1_Missense_Mutation_p.V286A|ELF2_ENST00000510408.1_Missense_Mutation_p.V214A	NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)									p.V274A(1)		endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					GAACTGATATACAAGCCTCTG	0.363																																					p.V226A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T677C	4						.						97.0	97.0	97.0					4																	139981778		2203	4300	6503	140201228	SO:0001583	missense	1998	exon6			AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381			3317	protein-coding gene	gene with protein product						8756667	Standard	NM_201999		Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.821T>C	4.37:g.139981778A>G	ENSP00000377782:p.Val274Ala	Somatic		Capture	Illumina HiSeq	Phase_I	140201228	NM_006874		Missense_Mutation	SNP	ENST00000394235.2	37	CCDS3744.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.394244	0.83011	.	.	ENSG00000109381	ENST00000358635;ENST00000394235;ENST00000379550;ENST00000265495;ENST00000379549;ENST00000540754;ENST00000510408;ENST00000420916;ENST00000512627	T;T;T;T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81;1.81;1.81;1.81	5.72	5.72	0.89469	.	0.054066	0.64402	D	0.000001	T	0.47967	0.1474	L	0.58969	1.84	0.80722	D	1	P;D;P;D;D	0.89917	0.756;0.998;0.597;0.999;1.0	P;D;P;D;D	0.91635	0.499;0.995;0.585;0.997;0.999	T	0.36016	-0.9765	9	.	.	.	.	16.0102	0.80396	1.0:0.0:0.0:0.0	.	89;274;197;214;226	B7Z8R4;Q15723-1;E9PCX3;B7Z720;Q15723-3	.;.;.;.;.	A	226;274;286;274;197;89;214;197;185	ENSP00000351458:V226A;ENSP00000377782:V274A;ENSP00000368868:V286A;ENSP00000265495:V274A;ENSP00000368867:V197A;ENSP00000426997:V214A;ENSP00000397796:V197A;ENSP00000426087:V185A	.	V	-	2	0	ELF2	140201228	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	7.400000	0.79949	2.190000	0.69967	0.533000	0.62120	GTA		0.363	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874	
MAML3	55534	broad.mit.edu	37	4	140812012	140812012	+	Missense_Mutation	SNP	C	C	T	rs376616820		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:140812012C>T	ENST00000509479.2	-	2	1434	c.578G>A	c.(577-579)cGa>cAa	p.R193Q	MAML3_ENST00000327122.5_Missense_Mutation_p.R37Q|MAML3_ENST00000398940.1_5'Flank	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)									p.R193Q(2)		breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					AATGTCCTTTCGAATTCGTTT	0.468																																					p.R193Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G578A	4						.	C	GLN/ARG	0,3994		0,0,1997	72.0	70.0	70.0		578	5.3	1.0	4		70	1,8331		0,1,4165	no	missense	MAML3	NM_018717.4	43	0,1,6162	TT,TC,CC		0.012,0.0,0.0081	probably-damaging	193/1139	140812012	1,12325	1997	4166	6163	141031462	SO:0001583	missense	55534	exon2			AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.578G>A	4.37:g.140812012C>T	ENSP00000421180:p.Arg193Gln	Somatic		Capture	Illumina HiSeq	Phase_I	141031462	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.862549	0.91511	0.0	1.2E-4	ENSG00000196782	ENST00000509479;ENST00000327122	T	0.28454	1.61	5.3	5.3	0.74995	.	0.000000	0.64402	D	0.000001	T	0.58133	0.2101	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.60885	-0.7174	10	0.59425	D	0.04	.	18.973	0.92722	0.0:1.0:0.0:0.0	.	193	Q96JK9	MAML3_HUMAN	Q	193;37	ENSP00000421180:R193Q	ENSP00000313316:R37Q	R	-	2	0	MAML3	141031462	1.000000	0.71417	0.996000	0.52242	0.940000	0.58332	5.674000	0.68117	2.469000	0.83416	0.585000	0.79938	CGA		0.468	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
USP38	84640	broad.mit.edu	37	4	144134767	144134767	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:144134767G>A	ENST00000307017.4	+	9	2144	c.1638G>A	c.(1636-1638)caG>caA	p.Q546Q	USP38_ENST00000510377.1_Silent_p.Q546Q	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	546	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)	p.Q546Q(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					TGAAAGTTCAGGCCTCACACA	0.373																																					p.Q546Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1638A	4						.						36.0	36.0	36.0					4																	144134767		2203	4300	6503	144354217	SO:0001819	synonymous_variant	84640	exon9			AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"""Ubiquitin-specific peptidases"""	20067	protein-coding gene	gene with protein product			"""ubiquitin specific protease 38"""			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.1638G>A	4.37:g.144134767G>A		Somatic		Capture	Illumina HiSeq	Phase_I	144354217	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Silent	SNP	ENST00000307017.4	37	CCDS3758.1																																																																																				0.373	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557	
USP38	84640	broad.mit.edu	37	4	144135040	144135040	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:144135040A>G	ENST00000307017.4	+	9	2417	c.1911A>G	c.(1909-1911)tcA>tcG	p.S637S	USP38_ENST00000510377.1_Silent_p.S637S	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	637	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)	p.S637S(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					CAGCATCATCACCCAGTATAC	0.448																																					p.S637S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1911G	4						.						153.0	165.0	161.0					4																	144135040		2203	4300	6503	144354490	SO:0001819	synonymous_variant	84640	exon9			AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"""Ubiquitin-specific peptidases"""	20067	protein-coding gene	gene with protein product			"""ubiquitin specific protease 38"""			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.1911A>G	4.37:g.144135040A>G		Somatic		Capture	Illumina HiSeq	Phase_I	144354490	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Silent	SNP	ENST00000307017.4	37	CCDS3758.1																																																																																				0.448	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557	
POU4F2	5458	broad.mit.edu	37	4	147561722	147561722	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:147561722G>A	ENST00000281321.3	+	2	1240	c.992G>A	c.(991-993)cGc>cAc	p.R331H	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	331					axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R331H(1)		NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					AAGTCCCACCGCGAGAAGCTC	0.582																																					p.R331H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G992A	4						.						74.0	77.0	76.0					4																	147561722		2203	4300	6503	147781172	SO:0001583	missense	5458	exon2			U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9219	protein-coding gene	gene with protein product		113725	"""POU domain, class 4, transcription factor 2"", ""POU domain class 4, transcription factor 2"""	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.992G>A	4.37:g.147561722G>A	ENSP00000281321:p.Arg331His	Somatic		Capture	Illumina HiSeq	Phase_I	147781172	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Missense_Mutation	SNP	ENST00000281321.3	37	CCDS34074.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.390788	0.82902	.	.	ENSG00000151615	ENST00000281321	D	0.83591	-1.74	5.49	5.49	0.81192	Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.90978	0.7163	M	0.81682	2.555	0.80722	D	1	D	0.76494	0.999	P	0.62184	0.899	D	0.91778	0.5433	10	0.72032	D	0.01	.	19.37	0.94480	0.0:0.0:1.0:0.0	.	331	Q12837	PO4F2_HUMAN	H	331	ENSP00000281321:R331H	ENSP00000281321:R331H	R	+	2	0	POU4F2	147781172	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	9.841000	0.99482	2.595000	0.87683	0.561000	0.74099	CGC		0.582	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575	
GATB	5188	broad.mit.edu	37	4	152600991	152600991	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:152600991T>G	ENST00000515812.1	-	10	1277	c.1261A>C	c.(1261-1263)Aca>Cca	p.T421P	PET112_ENST00000263985.6_Missense_Mutation_p.T462P|PET112_ENST00000507592.1_5'UTR|RP11-164P12.3_ENST00000514269.1_RNA														p.T462P(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						GAAGAAATTGTTCTGCTGTCC	0.493																																					p.T462P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1384C	4						.						197.0	193.0	195.0					4																	152600991		2203	4300	6503	152820441	SO:0001583	missense	5188	exon11																														ENST00000515812.1:c.1261A>C	4.37:g.152600991T>G	ENSP00000426859:p.Thr421Pro	Somatic		Capture	Illumina HiSeq	Phase_I	152820441	NM_004564		Missense_Mutation	SNP	ENST00000515812.1	37		.	.	.	.	.	.	.	.	.	.	T	7.729	0.698892	0.15106	.	.	ENSG00000059691	ENST00000263985;ENST00000515812	T;T	0.48522	0.82;0.81	5.69	3.94	0.45596	Asn/Gln amidotransferase (2);Aspartyl/glutamyl-tRNA amidotransferase subunit B-related (1);	0.627824	0.16250	N	0.222749	T	0.49098	0.1537	M	0.78223	2.4	0.09310	N	0.999998	B	0.20550	0.046	B	0.26693	0.072	T	0.51474	-0.8701	10	0.87932	D	0	0.872	7.9431	0.29969	0.0:0.7477:0.0:0.2523	.	462	O75879	GATB_HUMAN	P	462;421	ENSP00000263985:T462P;ENSP00000426859:T421P	ENSP00000263985:T462P	T	-	1	0	PET112	152820441	0.000000	0.05858	0.025000	0.17156	0.219000	0.24729	0.371000	0.20450	1.376000	0.46267	-0.248000	0.11899	ACA		0.493	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1		
GATB	5188	broad.mit.edu	37	4	152609907	152609907	+	Silent	SNP	G	G	A	rs376818767		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:152609907G>A	ENST00000515812.1	-	9	1099	c.1083C>T	c.(1081-1083)gtC>gtT	p.V361V	PET112_ENST00000263985.6_Silent_p.V402V|PET112_ENST00000507592.1_5'Flank														p.V402V(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						CCAGTAGGCCGACTTCGTTCT	0.398																																					p.V402V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1206T	4						.	G		1,4405	2.1+/-5.4	0,1,2202	90.0	92.0	91.0		1206	3.2	1.0	4		91	0,8600		0,0,4300	no	coding-synonymous	PET112	NM_004564.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		402/558	152609907	1,13005	2203	4300	6503	152829357	SO:0001819	synonymous_variant	5188	exon10																														ENST00000515812.1:c.1083C>T	4.37:g.152609907G>A		Somatic		Capture	Illumina HiSeq	Phase_I	152829357	NM_004564		Silent	SNP	ENST00000515812.1	37																																																																																					0.398	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1		
FGA	2243	broad.mit.edu	37	4	155508049	155508049	+	Nonsense_Mutation	SNP	G	G	A	rs140911890		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:155508049G>A	ENST00000302053.3	-	5	610	c.532C>T	c.(532-534)Cga>Tga	p.R178*	FGA_ENST00000403106.3_Nonsense_Mutation_p.R178*	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	178					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)	p.R178*(2)		NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	CGACAAGATCGGATCTTAATA	0.398																																					p.R178X	NSCLC(143;340 1922 20892 22370 48145)											.	.	2	Substitution - Nonsense(2)	large_intestine(1)|endometrium(1)	c.C532T	4	GRCh37	CM067990	FGA	M	rs140911890	.	G	stop/ARG,stop/ARG	0,4406		0,0,2203	77.0	78.0	78.0		532,532	5.3	1.0	4	dbSNP_134	78	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained	FGA	NM_000508.3,NM_021871.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	178/867,178/645	155508049	1,13005	2203	4300	6503	155727499	SO:0001587	stop_gained	2243	exon5				CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3661	protein-coding gene	gene with protein product		134820	"""fibrinogen, A alpha polypeptide"""				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.532C>T	4.37:g.155508049G>A	ENSP00000306361:p.Arg178*	Somatic		Capture	Illumina HiSeq	Phase_I	155727499	NM_021871	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Nonsense_Mutation	SNP	ENST00000302053.3	37	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	G	31	5.103508	0.94245	0.0	1.16E-4	ENSG00000171560	ENST00000302053;ENST00000403106;ENST00000457487	.	.	.	6.17	5.31	0.75309	.	0.121346	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.4222	0.83766	0.0:0.0:0.8585:0.1415	.	.	.	.	X	178	.	ENSP00000306361:R178X	R	-	1	2	FGA	155727499	1.000000	0.71417	1.000000	0.80357	0.459000	0.32528	6.211000	0.72182	1.555000	0.49500	0.655000	0.94253	CGA		0.398	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508	
FAM198B	51313	broad.mit.edu	37	4	159091831	159091831	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:159091831C>T	ENST00000296530.8	-	2	1318	c.697G>A	c.(697-699)Gca>Aca	p.A233T	FAM198B_ENST00000393807.5_Missense_Mutation_p.A233T|FAM198B_ENST00000592057.1_Missense_Mutation_p.A233T|FAM198B_ENST00000585682.1_Missense_Mutation_p.A233T|RP11-597D13.9_ENST00000505532.1_RNA|RP11-597D13.9_ENST00000514381.1_RNA|RP11-597D13.9_ENST00000503611.1_RNA|FAM198B_ENST00000589306.1_Intron|RP11-597D13.9_ENST00000509463.1_RNA	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	233						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.A233T(2)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(14)|skin(2)|urinary_tract(1)	26						CGGAGCCCTGCCACTGCGCTG	0.652											OREG0016378	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A233T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G697A	4						.						41.0	46.0	44.0					4																	159091831		2201	4300	6501	159311281	SO:0001583	missense	51313	exon2				CCDS3798.1, CCDS34087.1	4q32.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000164125	ENSG00000164125			25312	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 18"""	C4orf18		12975309	Standard	NM_001031700		Approved	FLJ38155, DKFZp434L142	uc003ipr.4	Q6UWH4	OTTHUMG00000161537	ENST00000296530.8:c.697G>A	4.37:g.159091831C>T	ENSP00000296530:p.Ala233Thr	Somatic	1798	Capture	Illumina HiSeq	Phase_I	159311281	NM_001128424	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	Missense_Mutation	SNP	ENST00000296530.8	37	CCDS3798.1	.	.	.	.	.	.	.	.	.	.	C	0.939	-0.710304	0.03230	.	.	ENSG00000164125	ENST00000337222;ENST00000296530;ENST00000393807;ENST00000417442	T;T	0.28454	1.61;1.61	4.71	3.85	0.44370	.	0.562976	0.18205	N	0.148384	T	0.17831	0.0428	L	0.37630	1.12	0.09310	N	1	P;B;B	0.37276	0.589;0.009;0.003	B;B;B	0.28011	0.085;0.005;0.005	T	0.11155	-1.0599	10	0.12103	T	0.63	-30.6906	9.283	0.37740	0.289:0.5709:0.1401:0.0	.	233;233;233	Q6UWH4-3;Q6UWH4-2;Q6UWH4	.;.;F198B_HUMAN	T	233	ENSP00000296530:A233T;ENSP00000377396:A233T	ENSP00000296530:A233T	A	-	1	0	FAM198B	159311281	0.000000	0.05858	0.654000	0.29608	0.137000	0.21094	0.013000	0.13310	1.152000	0.42452	0.563000	0.77884	GCA		0.652	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1	NM_001031700, NM_016613	
FNIP2	57600	broad.mit.edu	37	4	159789396	159789396	+	Silent	SNP	C	C	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:159789396C>G	ENST00000264433.6	+	13	1683	c.1608C>G	c.(1606-1608)acC>acG	p.T536T	FNIP2_ENST00000379346.3_Silent_p.T559T	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	536					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.T536T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		ACCAGCTGACCTGGAGTGGCA	0.488																																					p.T536T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1608G	4						.						88.0	90.0	90.0					4																	159789396		2068	4221	6289	160008846	SO:0001819	synonymous_variant	57600	exon13			AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 1"""	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.1608C>G	4.37:g.159789396C>G		Somatic		Capture	Illumina HiSeq	Phase_I	160008846	NM_020840	Q05DC3|Q96I31|Q9H994	Silent	SNP	ENST00000264433.6	37	CCDS47155.1																																																																																				0.488	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840	
FSTL5	56884	broad.mit.edu	37	4	162841612	162841612	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:162841612G>T	ENST00000306100.5	-	4	789	c.353C>A	c.(352-354)gCt>gAt	p.A118D	FSTL5_ENST00000427802.2_Missense_Mutation_p.A117D|FSTL5_ENST00000379164.4_Missense_Mutation_p.A117D|FSTL5_ENST00000536695.1_Missense_Mutation_p.A117D	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	118	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.A118D(1)		central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TTTCAGGCAAGCAGCTCTGTG	0.418																																					p.A118D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C353A	4						.						148.0	133.0	138.0					4																	162841612		2203	4300	6503	163061062	SO:0001583	missense	56884	exon4			BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.353C>A	4.37:g.162841612G>T	ENSP00000305334:p.Ala118Asp	Somatic		Capture	Illumina HiSeq	Phase_I	163061062	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	37	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004437	0.93287	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.04809	3.55;3.55;3.55;3.55	5.86	5.86	0.93980	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.056955	0.64402	D	0.000001	T	0.28566	0.0707	M	0.89968	3.075	0.80722	D	1	D;D;D	0.69078	0.982;0.997;0.993	P;D;P	0.65323	0.824;0.934;0.883	T	0.02901	-1.1096	10	0.87932	D	0	.	19.5509	0.95319	0.0:0.0:1.0:0.0	.	117;117;118	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	D	118;117;117;117	ENSP00000305334:A118D;ENSP00000368462:A117D;ENSP00000389270:A117D;ENSP00000440409:A117D	ENSP00000305334:A118D	A	-	2	0	FSTL5	163061062	1.000000	0.71417	0.923000	0.36655	0.989000	0.77384	9.420000	0.97426	2.937000	0.99478	0.650000	0.86243	GCT		0.418	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
MARCH1	55016	broad.mit.edu	37	4	165118324	165118324	+	Intron	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:165118324C>A	ENST00000503008.1	-	2	864				MARCH1_ENST00000508725.1_Intron|MARCH1_ENST00000514618.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase						antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Q180H(1)		endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				cttccACTACCTGAGCATCTT	0.557																																					p.Q180H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G540T	4						.						163.0	134.0	144.0					4																	165118324		2203	4300	6503	165337774	SO:0001627	intron_variant	23520	exon1			AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	26077	protein-coding gene	gene with protein product		613331	"""membrane-associated ring finger (C3HC4) 1"""			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.113-85510G>T	4.37:g.165118324C>A		Somatic		Capture	Illumina HiSeq	Phase_I	165337774	NM_012403	D3DP29|Q9NWR0	Missense_Mutation	SNP	ENST00000503008.1	37	CCDS54814.1																																																																																				0.557	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923	
NCAPG	64151	broad.mit.edu	37	4	17835941	17835941	+	Missense_Mutation	SNP	T	T	C	rs146806366		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:17835941T>C	ENST00000251496.2	+	14	2080	c.1904T>C	c.(1903-1905)gTc>gCc	p.V635A		NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	635					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)		p.V635A(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		ATTGATGATGTCACAATAAAA	0.284																																					p.V635A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1904C	4						.	T	ALA/VAL	0,4406		0,0,2203	61.0	61.0	61.0		1904	4.5	1.0	4	dbSNP_134	61	1,8599	1.2+/-3.3	0,1,4299	no	missense	NCAPG	NM_022346.3	64	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	635/1016	17835941	1,13005	2203	4300	6503	17445039	SO:0001583	missense	64151	exon14			AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"""chromosome condensation protein G"""	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.1904T>C	4.37:g.17835941T>C	ENSP00000251496:p.Val635Ala	Somatic		Capture	Illumina HiSeq	Phase_I	17445039	NM_022346	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000251496.2	37	CCDS3424.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.090722	0.36855	0.0	1.16E-4	ENSG00000109805	ENST00000251496;ENST00000510063	T;T	0.60548	0.18;0.18	5.72	4.53	0.55603	Armadillo-type fold (1);	0.307905	0.34676	N	0.003777	T	0.45276	0.1334	L	0.43152	1.355	0.34901	D	0.746534	B	0.19445	0.036	B	0.19666	0.026	T	0.48115	-0.9063	10	0.08381	T	0.77	-8.4617	11.9812	0.53121	0.0:0.0693:0.0:0.9307	.	635	Q9BPX3	CND3_HUMAN	A	635;200	ENSP00000251496:V635A;ENSP00000425625:V200A	ENSP00000251496:V635A	V	+	2	0	NCAPG	17445039	0.987000	0.35691	1.000000	0.80357	0.997000	0.91878	3.085000	0.50151	2.188000	0.69820	0.477000	0.44152	GTC		0.284	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346	
CLCN3	1182	broad.mit.edu	37	4	170641111	170641111	+	Missense_Mutation	SNP	C	C	T	rs372151295		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:170641111C>T	ENST00000513761.1	+	13	2979	c.2420C>T	c.(2419-2421)aCg>aTg	p.T807M	CLCN3_ENST00000360642.3_Missense_Mutation_p.T780M|CLCN3_ENST00000347613.4_Silent_p.D832D|CLCN3_ENST00000504131.2_Missense_Mutation_p.T790M	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	807	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)	p.D832D(1)		breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		ATGGCCCAGACGGCAAACCAA	0.408																																					p.T807M												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2420T	4						.						78.0	82.0	80.0					4																	170641111		2203	4300	6503	170877686	SO:0001583	missense	1182	exon13			X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"""Ion channels / Chloride channels : Voltage-sensitive"""	2021	protein-coding gene	gene with protein product		600580	"""chloride channel 3"""				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.2420C>T	4.37:g.170641111C>T	ENSP00000424603:p.Thr807Met	Somatic		Capture	Illumina HiSeq	Phase_I	170877686	NM_001829	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Missense_Mutation	SNP	ENST00000513761.1	37	CCDS34101.1	.	.	.	.	.	.	.	.	.	.	C	0.800	-0.755694	0.03019	.	.	ENSG00000109572	ENST00000513761;ENST00000360642;ENST00000504131	D;D;D	0.85773	-2.03;-2.03;-2.03	5.39	4.36	0.52297	Cystathionine beta-synthase, core (1);	.	.	.	.	T	0.68174	0.2972	.	.	.	0.25379	N	0.988632	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.51348	-0.8717	8	0.07482	T	0.82	-7.513	9.8954	0.41316	0.0:0.785:0.0:0.215	.	780;790;807	B7Z932;B9EGJ9;P51790	.;.;CLCN3_HUMAN	M	807;780;790	ENSP00000424603:T807M;ENSP00000353857:T780M;ENSP00000424540:T790M	ENSP00000353857:T780M	T	+	2	0	CLCN3	170877686	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.007000	0.57093	2.512000	0.84698	0.563000	0.77884	ACG		0.408	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2		
TENM3	55714	broad.mit.edu	37	4	183713563	183713563	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:183713563A>G	ENST00000511685.1	+	26	5861	c.5738A>G	c.(5737-5739)aAc>aGc	p.N1913S	TENM3_ENST00000406950.2_Missense_Mutation_p.N1913S			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1913					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.N1913S(1)									TACTACCGCAACATATACAAC	0.542																																					p.N1913S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A5738G	4						.						68.0	72.0	70.0					4																	183713563		2023	4178	6201	183950557	SO:0001583	missense	55714	exon25			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5738A>G	4.37:g.183713563A>G	ENSP00000424226:p.Asn1913Ser	Somatic		Capture	Illumina HiSeq	Phase_I	183950557	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	A	18.68	3.676443	0.67928	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.86432	-2.12;-2.12	5.04	5.04	0.67666	.	.	.	.	.	D	0.92371	0.7579	M	0.79805	2.47	0.80722	D	1	D	0.63880	0.993	D	0.65443	0.935	D	0.90993	0.4836	9	0.23302	T	0.38	.	14.9375	0.70967	1.0:0.0:0.0:0.0	.	1913	Q9P273	TEN3_HUMAN	S	1913	ENSP00000424226:N1913S;ENSP00000385276:N1913S	ENSP00000385276:N1913S	N	+	2	0	ODZ3	183950557	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.107000	0.94261	2.108000	0.64289	0.482000	0.46254	AAC		0.542	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
CENPU	79682	broad.mit.edu	37	4	185622005	185622005	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:185622005G>A	ENST00000281453.5	-	11	1025	c.955C>T	c.(955-957)Cgt>Tgt	p.R319C	MLF1IP_ENST00000541971.1_Missense_Mutation_p.R319C|MLF1IP_ENST00000506535.1_Intron	NM_024629.3	NP_078905.2												p.R319C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		TCAATCATACGCTGCCTTTTC	0.383																																					p.R319C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C955T	4						.						179.0	158.0	165.0					4																	185622005		2203	4300	6503	185858999	SO:0001583	missense	79682	exon11																														ENST00000281453.5:c.955C>T	4.37:g.185622005G>A	ENSP00000281453:p.Arg319Cys	Somatic		Capture	Illumina HiSeq	Phase_I	185858999	NM_024629		Missense_Mutation	SNP	ENST00000281453.5	37	CCDS3838.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.958372	0.53400	.	.	ENSG00000151725	ENST00000281453;ENST00000541971	T;T	0.33654	1.4;1.4	4.94	3.05	0.35203	.	0.549745	0.17852	N	0.159831	T	0.34454	0.0898	M	0.63843	1.955	0.51233	D	0.999918	P	0.41420	0.749	B	0.39465	0.3	T	0.29274	-1.0017	10	0.87932	D	0	-9.3399	8.5043	0.33177	0.2054:0.0:0.7946:0.0	.	319	Q71F23	CENPU_HUMAN	C	319	ENSP00000281453:R319C;ENSP00000445862:R319C	ENSP00000281453:R319C	R	-	1	0	MLF1IP	185858999	0.947000	0.32204	0.990000	0.47175	0.731000	0.41821	2.606000	0.46291	1.295000	0.44724	0.563000	0.77884	CGT		0.383	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2		
CFAP97	57587	broad.mit.edu	37	4	186085257	186085257	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:186085257C>T	ENST00000458385.2	-	4	1516	c.1397G>A	c.(1396-1398)cGc>cAc	p.R466H		NM_020827.1	NP_065878.1	Q9P2B7	K1430_HUMAN		466										endometrium(3)|kidney(2)|large_intestine(5)|upper_aerodigestive_tract(1)	11		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)		GCCCATATTGCGATGATAGTC	0.383																																					p.R466H												.	.	0			c.G1397A	4						.						164.0	157.0	159.0					4																	186085257		1904	4128	6032	186322251	SO:0001583	missense	57587	exon4																														ENST00000458385.2:c.1397G>A	4.37:g.186085257C>T	ENSP00000409964:p.Arg466His	Somatic		Capture	Illumina HiSeq	Phase_I	186322251	NM_020827	B3KRP7|D3DP60|Q05CU1|Q4W5M4|Q8N6E7|Q9UF45	Missense_Mutation	SNP	ENST00000458385.2	37	CCDS47168.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.723502	0.89298	.	.	ENSG00000164323	ENST00000458385	T	0.40476	1.03	5.48	5.48	0.80851	.	.	.	.	.	T	0.54615	0.1869	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.56619	-0.7949	9	0.72032	D	0.01	-4.1902	17.4901	0.87701	0.0:1.0:0.0:0.0	.	466	Q9P2B7	K1430_HUMAN	H	466	ENSP00000409964:R466H	ENSP00000409964:R466H	R	-	2	0	KIAA1430	186322251	1.000000	0.71417	0.998000	0.56505	0.866000	0.49608	5.277000	0.65586	2.724000	0.93272	0.655000	0.94253	CGC		0.383	KIAA1430-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360717.2		
GAK	2580	broad.mit.edu	37	4	860923	860923	+	Frame_Shift_Del	DEL	G	G	-	rs201137296		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:860923delG	ENST00000314167.4	-	21	2803	c.2693delC	c.(2692-2694)ccgfs	p.P898fs	GAK_ENST00000511163.1_Frame_Shift_Del_p.P819fs|GAK_ENST00000509566.1_5'UTR	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	898					cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.P898fs*47(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		GCAGGCCTGCGGGGGTACAGC	0.716																																					p.P898fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2693delC	4						.						17.0	20.0	19.0					4																	860923		2194	4290	6484	850923	SO:0001589	frameshift_variant	2580	exon21			D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.2693delC	4.37:g.860923delG	ENSP00000314499:p.Pro898fs	Somatic		Capture	Illumina HiSeq	Phase_I	850923	NM_005255	Q5U4P5|Q9BVY6	Frame_Shift_Del	DEL	ENST00000314167.4	37	CCDS3340.1																																																																																				0.716	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
IDUA	3425	broad.mit.edu	37	4	998096	998096	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:998096G>A	ENST00000247933.4	+	14	1965	c.1877G>A	c.(1876-1878)tGg>tAg	p.W626*	IDUA_ENST00000514224.1_Nonsense_Mutation_p.W494*|IDUA_ENST00000453894.1_Nonsense_Mutation_p.W648*	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	626			W -> R (in MPS1H/S). {ECO:0000269|PubMed:7550242}.		carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)	p.W626*(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CTGGACTACTGGGCCCGACCA	0.657																																					p.W626X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1877A	4						.						55.0	62.0	60.0					4																	998096		2203	4300	6503	988096	SO:0001587	stop_gained	3425	exon14			M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.1877G>A	4.37:g.998096G>A	ENSP00000247933:p.Trp626*	Somatic		Capture	Illumina HiSeq	Phase_I	988096	NM_000203	B3KWK6	Nonsense_Mutation	SNP	ENST00000247933.4	37	CCDS3343.1	.	.	.	.	.	.	.	.	.	.	G	43	10.065245	0.99329	.	.	ENSG00000127415	ENST00000247933;ENST00000453894;ENST00000514224	.	.	.	5.55	5.55	0.83447	.	0.123427	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.8344	17.0455	0.86501	0.0:0.0:1.0:0.0	.	.	.	.	X	626;648;494	.	ENSP00000247933:W626X	W	+	2	0	IDUA	988096	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.020000	0.64066	2.641000	0.89580	0.555000	0.69702	TGG		0.657	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
NOP14	8602	broad.mit.edu	37	4	2949306	2949306	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:2949306G>A	ENST00000314262.6	-	10	1494	c.1446C>T	c.(1444-1446)ggC>ggT	p.G482G	NOP14-AS1_ENST00000515194.1_RNA|NOP14_ENST00000416614.2_Silent_p.G482G|NOP14-AS1_ENST00000503709.1_RNA|NOP14_ENST00000502735.1_Silent_p.G482G|NOP14-AS1_ENST00000505731.1_RNA|NOP14-AS1_ENST00000507702.1_RNA|NOP14_ENST00000398071.4_Silent_p.G482G	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	482					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)	p.G482G(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						TAGCCAAATCGCCAACGTATT	0.448																																					p.G482G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1446T	4						.						142.0	130.0	134.0					4																	2949306		2203	4300	6503	2919104	SO:0001819	synonymous_variant	8602	exon10			AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"""NOP14 homolog (S. cerevisiae)"""	611526	"""chromosome 4 open reading frame 9"", ""nucleolar protein 14"", ""nucleolar protein 14 homolog (yeast)"", ""NOP14 nucleolar protein homolog (yeast)"""	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.1446C>T	4.37:g.2949306G>A		Somatic		Capture	Illumina HiSeq	Phase_I	2919104	NM_003703	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Silent	SNP	ENST00000314262.6	37	CCDS33945.1																																																																																				0.448	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703	
RGS12	6002	broad.mit.edu	37	4	3430412	3430412	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:3430412A>G	ENST00000344733.5	+	16	4443	c.3539A>G	c.(3538-3540)cAg>cGg	p.Q1180R	RGS12_ENST00000306648.7_Intron|RGS12_ENST00000336727.3_Missense_Mutation_p.Q1180R|RGS12_ENST00000382788.3_Missense_Mutation_p.Q1180R|RGS12_ENST00000338806.4_Missense_Mutation_p.Q532R|RGS12_ENST00000538395.1_Intron	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	1180					positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)	p.Q1180R(1)		autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		AAAAAATATCAGAAAATTAAT	0.328																																					p.Q1180R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3539G	4						.						44.0	49.0	47.0					4																	3430412		2202	4300	6502	3400210	SO:0001583	missense	6002	exon16			AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"""Regulators of G-protein signaling"""	9994	protein-coding gene	gene with protein product		602512	"""regulator of G-protein signalling 12"""			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.3539A>G	4.37:g.3430412A>G	ENSP00000339381:p.Gln1180Arg	Somatic		Capture	Illumina HiSeq	Phase_I	3400210	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	37	CCDS3366.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.144472	0.77888	.	.	ENSG00000159788	ENST00000344733;ENST00000336727;ENST00000382788;ENST00000338806	T;T;T;T	0.35421	1.62;1.62;1.62;1.31	4.86	4.86	0.63082	.	0.057348	0.64402	D	0.000001	T	0.44973	0.1319	M	0.70595	2.14	0.80722	D	1	P;B;P;P	0.50528	0.936;0.178;0.894;0.936	P;B;B;P	0.48921	0.595;0.171;0.391;0.595	T	0.38735	-0.9647	10	0.23302	T	0.38	-39.5622	13.9468	0.64089	1.0:0.0:0.0:0.0	.	522;532;1180;1180	O14924-2;O14924-3;O14924;O14924-4	.;.;RGS12_HUMAN;.	R	1180;1180;1180;532	ENSP00000339381:Q1180R;ENSP00000338509:Q1180R;ENSP00000372238:Q1180R;ENSP00000342133:Q532R	ENSP00000338509:Q1180R	Q	+	2	0	RGS12	3400210	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.801000	0.75170	1.945000	0.56424	0.533000	0.62120	CAG		0.328	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926	
EVC2	132884	broad.mit.edu	37	4	5586405	5586405	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:5586405G>A	ENST00000344408.5	-	17	3055	c.3002C>T	c.(3001-3003)gCa>gTa	p.A1001V	EVC2_ENST00000310917.2_Missense_Mutation_p.A921V|EVC2_ENST00000344938.1_Missense_Mutation_p.A1001V	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	1001					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.A1001V(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						CATCTCAGATGCACTCAGCTC	0.622																																					p.A921V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2762T	4						.						52.0	51.0	52.0					4																	5586405		2203	4300	6503	5637306	SO:0001583	missense	132884	exon17			AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.3002C>T	4.37:g.5586405G>A	ENSP00000342144:p.Ala1001Val	Somatic		Capture	Illumina HiSeq	Phase_I	5637306	NM_001166136	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	G	7.695	0.691847	0.15039	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.74315	-0.83;-0.82;-0.83	4.8	-6.97	0.01616	.	0.265072	0.38111	N	0.001801	T	0.42765	0.1217	N	0.14661	0.345	0.09310	N	1	B	0.29716	0.255	B	0.22152	0.038	T	0.29305	-1.0016	10	0.34782	T	0.22	-1.2426	4.5783	0.12245	0.2294:0.0807:0.5427:0.1472	.	1001	Q86UK5	LBN_HUMAN	V	1001;921;1001	ENSP00000339954:A1001V;ENSP00000311683:A921V;ENSP00000342144:A1001V	ENSP00000311683:A921V	A	-	2	0	EVC2	5637306	0.000000	0.05858	0.002000	0.10522	0.046000	0.14306	-0.506000	0.06359	-0.798000	0.04444	-0.484000	0.04775	GCA		0.622	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
GBA3	57733	broad.mit.edu	37	4	22820387	22820387	+	RNA	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:22820387G>A	ENST00000503442.1	+	0	421				GBA3_ENST00000511446.2_RNA|GBA3_ENST00000508264.1_RNA|GBA3_ENST00000508166.1_RNA	NM_001128432.2	NP_001121904.1	Q9H227	GBA3_HUMAN	glucosidase, beta, acid 3 (gene/pseudogene)						carbohydrate metabolic process (GO:0005975)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide catabolic process (GO:0046477)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	beta-galactosidase activity (GO:0004565)|beta-glucosidase activity (GO:0008422)|glycosylceramidase activity (GO:0017042)	p.W417*(1)		breast(1)|kidney(2)|large_intestine(4)|lung(20)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						ATTGTGCATGGTCTCTTCTGG	0.413																																					p.W110X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G330A	4						.						85.0	75.0	78.0					4																	22820387		1863	4101	5964	22429485			57733	exon3			AB017913		4p15.2	2013-05-09	2013-05-09		ENSG00000249948	ENSG00000249948	3.2.1.21		19069	protein-coding gene	gene with protein product	"""klotho-related protein"""	606619	"""glucosidase, beta, acid 3 (cytosolic)"""			11389701	Standard	NM_020973		Approved	GLUC, KLrP	uc031sdv.1	Q9H227	OTTHUMG00000160448		4.37:g.22820387G>A		Somatic		Capture	Illumina HiSeq	Phase_I	22429485	NM_001128432	Q32LY7|Q3MIH4|Q53GG8|Q6NSF4|Q8NHT8|Q9H3T4|Q9H4C6	Nonsense_Mutation	SNP	ENST00000503442.1	37																																																																																					0.413	GBA3-003	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000360620.2		
GBA3	57733	broad.mit.edu	37	4	22820531	22820531	+	RNA	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:22820531T>G	ENST00000503442.1	+	0	565				GBA3_ENST00000511446.2_RNA|GBA3_ENST00000508264.1_RNA|GBA3_ENST00000508166.1_RNA	NM_001128432.2	NP_001121904.1	Q9H227	GBA3_HUMAN	glucosidase, beta, acid 3 (gene/pseudogene)						carbohydrate metabolic process (GO:0005975)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide catabolic process (GO:0046477)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	beta-galactosidase activity (GO:0004565)|beta-glucosidase activity (GO:0008422)|glycosylceramidase activity (GO:0017042)			breast(1)|kidney(2)|large_intestine(4)|lung(20)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						ACAATGGCCTTGAAGCACATC	0.473																																					p.L158L												.	.	0			c.T474G	4						.						80.0	69.0	73.0					4																	22820531		1920	4127	6047	22429629			57733	exon3			AB017913		4p15.2	2013-05-09	2013-05-09		ENSG00000249948	ENSG00000249948	3.2.1.21		19069	protein-coding gene	gene with protein product	"""klotho-related protein"""	606619	"""glucosidase, beta, acid 3 (cytosolic)"""			11389701	Standard	NM_020973		Approved	GLUC, KLrP	uc031sdv.1	Q9H227	OTTHUMG00000160448		4.37:g.22820531T>G		Somatic		Capture	Illumina HiSeq	Phase_I	22429629	NM_001128432	Q32LY7|Q3MIH4|Q53GG8|Q6NSF4|Q8NHT8|Q9H3T4|Q9H4C6	Silent	SNP	ENST00000503442.1	37																																																																																					0.473	GBA3-003	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000360620.2		
TBC1D1	23216	broad.mit.edu	37	4	38117555	38117555	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:38117555C>T	ENST00000261439.4	+	16	3137	c.2782C>T	c.(2782-2784)Cca>Tca	p.P928S	TBC1D1_ENST00000407365.1_3'UTR|TBC1D1_ENST00000508802.1_Missense_Mutation_p.P1022S	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	928	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)	p.P928S(1)		NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						ACAGTATCGGCCAGACATGAT	0.408																																					p.P928S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2782T	4						.						104.0	102.0	103.0					4																	38117555		2203	4300	6503	37793950	SO:0001583	missense	23216	exon16			AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.2782C>T	4.37:g.38117555C>T	ENSP00000261439:p.Pro928Ser	Somatic		Capture	Illumina HiSeq	Phase_I	37793950	NM_015173	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	37	CCDS33972.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.1|28.1	4.889002|4.889002	0.91814|0.91814	.|.	.|.	ENSG00000065882|ENSG00000065882	ENST00000510573|ENST00000508802;ENST00000261439;ENST00000454732	.|T;T	.|0.11385	.|2.78;2.78	5.29|5.29	5.29|5.29	0.74685|0.74685	.|Rab-GAP/TBC domain (4);	.|0.000000	.|0.56097	.|D	.|0.000024	T|T	0.33000|0.33000	0.0848|0.0848	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.71674	.|0.97;0.998;0.998	.|D;D;D	.|0.79784	.|0.944;0.993;0.973	T|T	0.01666|0.01666	-1.1300|-1.1300	5|10	.|0.72032	.|D	.|0.01	-26.0681|-26.0681	19.3015|19.3015	0.94145|0.94145	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1022;660;928	.|E9PGH8;Q6PJJ8;Q86TI0	.|.;.;TBCD1_HUMAN	V|S	615|1022;928;192	.|ENSP00000423651:P1022S;ENSP00000261439:P928S	.|ENSP00000261439:P928S	A|P	+|+	2|1	0|0	TBC1D1|TBC1D1	37793950|37793950	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.408000|7.408000	0.80041|0.80041	2.644000|2.644000	0.89710|0.89710	0.561000|0.561000	0.74099|0.74099	GCC|CCA		0.408	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
TLR1	7096	broad.mit.edu	37	4	38799382	38799382	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:38799382A>G	ENST00000502213.2	-	3	1300	c.1071T>C	c.(1069-1071)aaT>aaC	p.N357N	TLR1_ENST00000308979.2_Silent_p.N357N			Q15399	TLR1_HUMAN	toll-like receptor 1	357					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.N357N(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						TTAAGAGATTATTGGAAAAAT	0.363																																					p.N357N	GBM(5;216 373 40795 46382)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1071C	4						.						49.0	51.0	51.0					4																	38799382		2203	4300	6503	38475777	SO:0001819	synonymous_variant	7096	exon4			U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1071T>C	4.37:g.38799382A>G		Somatic		Capture	Illumina HiSeq	Phase_I	38475777	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	37	CCDS33973.1																																																																																				0.363	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
KLHL5	51088	broad.mit.edu	37	4	39077685	39077685	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:39077685delA	ENST00000504108.1	+	2	905	c.622delA	c.(622-624)aaafs	p.K209fs	KLHL5_ENST00000381930.3_Frame_Shift_Del_p.K209fs|KLHL5_ENST00000508137.2_Frame_Shift_Del_p.K22fs|KLHL5_ENST00000261425.3_Frame_Shift_Del_p.K163fs|KLHL5_ENST00000261426.5_Intron|KLHL5_ENST00000359687.2_Frame_Shift_Del_p.K209fs	NM_015990.4	NP_057074.3	Q96PQ7	KLHL5_HUMAN	kelch-like family member 5	209						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.M210fs*5(1)		endometrium(3)|kidney(1)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						GCAAACATTTAAAAAAATGGA	0.363																																					p.K208fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.622delA	4						.						97.0	97.0	97.0					4																	39077685		2203	4300	6503	38754080	SO:0001589	frameshift_variant	51088	exon2			AF272976	CCDS3449.1, CCDS33974.1, CCDS33975.1, CCDS54756.1	4p15.1	2013-01-30	2013-01-30		ENSG00000109790	ENSG00000109790		"""Kelch-like"", ""BTB/POZ domain containing"""	6356	protein-coding gene	gene with protein product		608064	"""kelch (Drosophila)-like 5"", ""kelch-like 5 (Drosophila)"""			11590829, 14672410	Standard	NM_001007075		Approved		uc003gtp.3	Q96PQ7	OTTHUMG00000097819	ENST00000504108.1:c.622delA	4.37:g.39077685delA	ENSP00000423897:p.Lys209fs	Somatic		Capture	Illumina HiSeq	Phase_I	38754080	NM_015990	A8K170|B7WP68|E9PCF4|F8WAE7|G3XA92|Q6Y881|Q86XW0|Q9NUK3|Q9NV27|Q9NVA9|Q9Y2X2	Frame_Shift_Del	DEL	ENST00000504108.1	37	CCDS33974.1																																																																																				0.363	KLHL5-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360604.1		
LIMCH1	22998	broad.mit.edu	37	4	41694392	41694392	+	Nonsense_Mutation	SNP	C	C	T	rs202024828		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:41694392C>T	ENST00000313860.7	+	26	3271	c.3217C>T	c.(3217-3219)Cga>Tga	p.R1073*	LIMCH1_ENST00000512632.1_Nonsense_Mutation_p.R970*|LIMCH1_ENST00000381753.4_Nonsense_Mutation_p.R880*|LIMCH1_ENST00000512946.1_Nonsense_Mutation_p.R1047*|LIMCH1_ENST00000396595.3_Nonsense_Mutation_p.R892*|LIMCH1_ENST00000514096.1_Nonsense_Mutation_p.R887*|LIMCH1_ENST00000509277.1_Nonsense_Mutation_p.R906*|LIMCH1_ENST00000513024.1_Nonsense_Mutation_p.R900*|LIMCH1_ENST00000512820.1_Nonsense_Mutation_p.R1059*|LIMCH1_ENST00000511496.1_Nonsense_Mutation_p.R887*|LIMCH1_ENST00000503057.1_Nonsense_Mutation_p.R1457*|RP11-227F19.5_ENST00000506475.1_RNA|LIMCH1_ENST00000508501.1_Nonsense_Mutation_p.R1046*	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	1073	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)	p.R1073*(1)|p.R1457*(1)		central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						TTGCTACATGCGATCCAGAAG	0.438																																					p.R880X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C2638T	4						.						168.0	146.0	153.0					4																	41694392		2203	4300	6503	41389149	SO:0001587	stop_gained	22998	exon19			AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.3217C>T	4.37:g.41694392C>T	ENSP00000316891:p.Arg1073*	Somatic		Capture	Illumina HiSeq	Phase_I	41389149	NM_001112720	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Nonsense_Mutation	SNP	ENST00000313860.7	37	CCDS33977.1	.	.	.	.	.	.	.	.	.	.	C	39	7.376072	0.98245	.	.	ENSG00000064042	ENST00000513024;ENST00000508501;ENST00000512946;ENST00000313860;ENST00000512632;ENST00000512820;ENST00000503057;ENST00000511496;ENST00000313875;ENST00000514096;ENST00000509277;ENST00000396595;ENST00000381753;ENST00000537405	.	.	.	4.99	4.14	0.48551	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.9159	12.6608	0.56813	0.3004:0.6996:0.0:0.0	.	.	.	.	X	900;1046;1047;1073;970;1059;1457;887;1456;887;906;892;880;399	.	ENSP00000316891:R1073X	R	+	1	2	LIMCH1	41389149	0.998000	0.40836	1.000000	0.80357	0.171000	0.22731	0.580000	0.23803	1.295000	0.44724	0.557000	0.71058	CGA		0.438	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988	
SLC30A9	10463	broad.mit.edu	37	4	42025373	42025373	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:42025373T>C	ENST00000264451.7	+	6	762	c.582T>C	c.(580-582)cgT>cgC	p.R194R		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	194					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R194R(1)		central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AAAAATTGCGTAAGGAAGCAG	0.343																																					p.R194R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T582C	4						.						98.0	103.0	101.0					4																	42025373		2203	4300	6503	41720130	SO:0001819	synonymous_variant	10463	exon6			AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"""Solute carriers"""	1329	protein-coding gene	gene with protein product	"""GRIP1-dependent nuclear receptor coactivator"""	604604	"""chromosome 4 open reading frame 1"""	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.582T>C	4.37:g.42025373T>C		Somatic		Capture	Illumina HiSeq	Phase_I	41720130	NM_006345	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Silent	SNP	ENST00000264451.7	37	CCDS3465.1																																																																																				0.343	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3		
PDGFRA	5156	broad.mit.edu	37	4	55151549	55151549	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:55151549delA	ENST00000257290.5	+	17	2666	c.2335delA	c.(2335-2337)aaafs	p.K779fs	FIP1L1_ENST00000507166.1_Frame_Shift_Del_p.K539fs	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	779	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.N780fs*17(1)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	CTCAGAAGTCAAAAACCTCCT	0.418			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.K779fs	Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"""platelet-derived growth factor, alpha-receptor"""		"""L, M, O"""	.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2335delA	4						.						83.0	84.0	83.0					4																	55151549		2203	4300	6503	54846306	SO:0001589	frameshift_variant	5156	exon17	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.2335delA	4.37:g.55151549delA	ENSP00000257290:p.Lys779fs	Somatic		Capture	Illumina HiSeq	Phase_I	54846306	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Frame_Shift_Del	DEL	ENST00000257290.5	37	CCDS3495.1																																																																																				0.418	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
KIAA1211	57482	broad.mit.edu	37	4	57181632	57181632	+	Frame_Shift_Del	DEL	G	G	-	rs7672073	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:57181632delG	ENST00000504228.1	+	6	2069	c.1964delG	c.(1963-1965)cgcfs	p.R655fs	KIAA1211_ENST00000264229.6_Frame_Shift_Del_p.R655fs|KIAA1211_ENST00000541073.1_Frame_Shift_Del_p.R648fs			Q6ZU35	K1211_HUMAN	KIAA1211	655			R -> P (in dbSNP:rs7672073). {ECO:0000269|PubMed:10574462, ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.4}.					p.R655fs*22(1)		endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					GCTAAGCCCCGCCAGGAGTCT	0.682																																					p.R655fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1964delG	4						.						18.0	23.0	21.0					4																	57181632		1934	4105	6039	56876389	SO:0001589	frameshift_variant	57482	exon8			AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1964delG	4.37:g.57181632delG	ENSP00000423366:p.Arg655fs	Somatic		Capture	Illumina HiSeq	Phase_I	56876389	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Frame_Shift_Del	DEL	ENST00000504228.1	37	CCDS43230.1																																																																																				0.682	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
EPHA5	2044	broad.mit.edu	37	4	66467912	66467912	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:66467912G>T	ENST00000273854.3	-	3	957	c.357C>A	c.(355-357)tcC>tcA	p.S119S	EPHA5_ENST00000354839.4_Silent_p.S119S|EPHA5_ENST00000432638.2_Silent_p.S119S|EPHA5_ENST00000511294.1_Silent_p.S119S	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	119	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)	p.S119S(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						CACCTTCATTGGAGATCCAAC	0.438										TSP Lung(17;0.13)																											p.S119S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C357A	4						.						110.0	115.0	113.0					4																	66467912		2203	4300	6503	66150507	SO:0001819	synonymous_variant	2044	exon3			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3389	protein-coding gene	gene with protein product		600004	"""EphA5"""			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.357C>A	4.37:g.66467912G>T		Somatic		Capture	Illumina HiSeq	Phase_I	66150507	NM_004439	Q7Z3F2	Silent	SNP	ENST00000273854.3	37	CCDS3513.1																																																																																				0.438	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439	
TMPRSS11A	339967	broad.mit.edu	37	4	68810229	68810229	+	Splice_Site	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:68810229T>C	ENST00000334830.7	-	3	1006	c.260A>G	c.(259-261)cAg>cGg	p.Q87R	UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000508048.1_Intron|TMPRSS11A_ENST00000396188.2_Intron			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	87	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.Q87R(1)		breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						GAAGTTTACCTGACTCACCAA	0.338																																					p.Q87R	NSCLC(26;2 894 10941 14480 22546)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A260G	4						.						144.0	149.0	148.0					4																	68810229		2203	4300	6503	68492824	SO:0001630	splice_region_variant	339967	exon3			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.261+1A>G	4.37:g.68810229T>C		Somatic		Capture	Illumina HiSeq	Phase_I	68492824	NM_182606	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Missense_Mutation	SNP	ENST00000334830.7	37	CCDS3519.1	.	.	.	.	.	.	.	.	.	.	T	3.878	-0.026570	0.07589	.	.	ENSG00000187054	ENST00000334830	D	0.88896	-2.44	5.07	-1.92	0.07618	SEA (1);	1.439520	0.04838	U	0.439966	D	0.85022	0.5602	L	0.47716	1.5	0.09310	N	1	P	0.38440	0.631	P	0.45577	0.486	T	0.69774	-0.5054	10	0.08179	T	0.78	.	4.5828	0.12267	0.1654:0.4297:0.0:0.405	.	87	Q6ZMR5	TM11A_HUMAN	R	87	ENSP00000334611:Q87R	ENSP00000334611:Q87R	Q	-	2	0	TMPRSS11A	68492824	0.012000	0.17670	0.001000	0.08648	0.030000	0.12068	-0.043000	0.12043	-0.467000	0.06932	-0.408000	0.06270	CAG		0.338	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606	Missense_Mutation
SULT1B1	27284	broad.mit.edu	37	4	70615504	70615504	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:70615504G>A	ENST00000310613.3	-	4	607	c.310C>T	c.(310-312)Cgg>Tgg	p.R104W		NM_014465.3	NP_055280.2	O43704	ST1B1_HUMAN	sulfotransferase family, cytosolic, 1B, member 1	104					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|cellular biogenic amine metabolic process (GO:0006576)|epithelial cell differentiation (GO:0030855)|flavonoid metabolic process (GO:0009812)|phenol-containing compound metabolic process (GO:0018958)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|thyroid hormone metabolic process (GO:0042403)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|sulfotransferase activity (GO:0008146)	p.R104W(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(14)|prostate(1)|upper_aerodigestive_tract(1)	24						TTCACAATCCGGGGTGATGGA	0.378																																					p.R104W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C310T	4						.						150.0	155.0	153.0					4																	70615504		2203	4300	6503	70650093	SO:0001583	missense	27284	exon4			D89479	CCDS3530.1	4q13.3	2008-02-05			ENSG00000173597	ENSG00000173597		"""Sulfotransferases, cytosolic"""	17845	protein-coding gene	gene with protein product		608436				11688987, 9443824	Standard	NM_014465		Approved	ST1B2	uc003hen.3	O43704	OTTHUMG00000129407	ENST00000310613.3:c.310C>T	4.37:g.70615504G>A	ENSP00000308770:p.Arg104Trp	Somatic		Capture	Illumina HiSeq	Phase_I	70650093	NM_014465	O15497|Q96FI1|Q9UK34	Missense_Mutation	SNP	ENST00000310613.3	37	CCDS3530.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.927387	0.52759	.	.	ENSG00000173597	ENST00000310613;ENST00000510821	D;D	0.87809	-2.3;-2.3	4.69	1.81	0.25067	Sulfotransferase domain (1);	0.000000	0.49305	D	0.000144	D	0.95733	0.8612	H	0.98901	4.365	0.24052	N	0.996047	D	0.89917	1.0	D	0.97110	1.0	D	0.89589	0.3826	10	0.87932	D	0	.	11.82	0.52232	0.0:0.0:0.5442:0.4558	.	104	O43704	ST1B1_HUMAN	W	104	ENSP00000308770:R104W;ENSP00000425464:R104W	ENSP00000308770:R104W	R	-	1	2	SULT1B1	70650093	0.555000	0.26530	0.010000	0.14722	0.054000	0.15201	0.557000	0.23454	0.109000	0.17891	0.460000	0.39030	CGG		0.378	SULT1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251563.2	NM_014465	
ENAM	10117	broad.mit.edu	37	4	71508261	71508261	+	Missense_Mutation	SNP	G	G	A	rs143134915		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:71508261G>A	ENST00000396073.3	+	9	1399	c.1118G>A	c.(1117-1119)cGt>cAt	p.R373H	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	373					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)		p.R373H(2)		haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			CAAGTAGCTCGTCCAGGAAAT	0.443																																					p.R373H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1118A	4						.	G	HIS/ARG	0,4406		0,0,2203	110.0	115.0	113.0		1118	-1.5	0.0	4	dbSNP_134	113	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ENAM	NM_031889.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	373/1143	71508261	1,13005	2203	4300	6503	71727125	SO:0001583	missense	10117	exon9			AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.1118G>A	4.37:g.71508261G>A	ENSP00000379383:p.Arg373His	Somatic		Capture	Illumina HiSeq	Phase_I	71727125	NM_031889	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	.	.	.	.	.	.	.	.	.	.	G	6.130	0.392297	0.11638	0.0	1.16E-4	ENSG00000132464	ENST00000396073	T	0.33216	1.42	5.83	-1.46	0.08800	.	0.946121	0.08814	N	0.889824	T	0.17789	0.0427	L	0.31752	0.955	0.09310	N	1	B	0.21753	0.06	B	0.20384	0.029	T	0.28364	-1.0046	10	0.41790	T	0.15	0.5722	1.9369	0.03339	0.3596:0.1205:0.3964:0.1236	.	373	Q9NRM1	ENAM_HUMAN	H	373	ENSP00000379383:R373H	ENSP00000379383:R373H	R	+	2	0	ENAM	71727125	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.433000	0.06948	-0.336000	0.08438	0.655000	0.94253	CGT		0.443	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889	
ADAMTS3	9508	broad.mit.edu	37	4	73176816	73176816	+	Silent	SNP	C	C	T	rs143790784	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:73176816C>T	ENST00000286657.4	-	14	2040	c.2004G>A	c.(2002-2004)acG>acA	p.T668T		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	668	Cys-rich.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.T668T(3)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AAGAACAGTGCGTTCCATCAT	0.433													C|||	7	0.00139776	0.0	0.0086	5008	,	,		15497	0.0		0.0	False		,,,				2504	0.001				p.T668T	NSCLC(168;1941 2048 2918 13048 43078)											.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.G2004A	4						.	C		1,4405	2.1+/-5.4	0,1,2202	236.0	182.0	200.0		2004	-11.4	0.0	4	dbSNP_134	200	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ADAMTS3	NM_014243.2		0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231		668/1206	73176816	3,13003	2203	4300	6503	73395680	SO:0001819	synonymous_variant	9508	exon14			AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"""ADAM metallopeptidases with thrombospondin type 1 motif"""	219	protein-coding gene	gene with protein product		605011	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"""			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.2004G>A	4.37:g.73176816C>T		Somatic		Capture	Illumina HiSeq	Phase_I	73395680	NM_014243	A1L3U9|Q9BXZ8	Silent	SNP	ENST00000286657.4	37	CCDS3553.1																																																																																				0.433	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2		
SCARB2	950	broad.mit.edu	37	4	77084445	77084445	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:77084445G>A	ENST00000264896.2	-	11	1680	c.1331C>T	c.(1330-1332)gCg>gTg	p.A444V	SCARB2_ENST00000452464.2_Missense_Mutation_p.A301V	NM_005506.3	NP_005497.1	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2	444					cell adhesion (GO:0007155)|protein targeting to lysosome (GO:0006622)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)	p.A444V(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(3)|prostate(2)|skin(1)	22			Lung(101;0.196)			CACACCCAGCGCCATGATGAT	0.458																																					p.A444V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1331T	4						.						236.0	204.0	215.0					4																	77084445		2203	4300	6503	77303469	SO:0001583	missense	950	exon11			D12676	CCDS3577.1, CCDS56335.1	4q21.1	2014-07-11	2002-09-06	2002-09-06	ENSG00000138760	ENSG00000138760			1665	protein-coding gene	gene with protein product		602257	"""CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 2 (lysosomal integral membrane protein II)"""	CD36L2		1374238	Standard	NM_005506		Approved	HLGP85, LIMPII, SR-BII, LIMP-2	uc003hju.2	Q14108	OTTHUMG00000130099	ENST00000264896.2:c.1331C>T	4.37:g.77084445G>A	ENSP00000264896:p.Ala444Val	Somatic		Capture	Illumina HiSeq	Phase_I	77303469	NM_005506	B4DKD8|E7EM68|Q53Y63	Missense_Mutation	SNP	ENST00000264896.2	37	CCDS3577.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.987132	0.74589	.	.	ENSG00000138760	ENST00000264896;ENST00000452464	T;T	0.72394	-0.65;-0.65	5.87	5.87	0.94306	.	0.094437	0.64402	D	0.000001	T	0.76695	0.4023	M	0.64997	1.995	0.39530	D	0.968648	D;P	0.64830	0.994;0.944	P;P	0.56788	0.806;0.689	T	0.76615	-0.2894	10	0.39692	T	0.17	.	11.1097	0.48226	0.0835:0.0:0.9165:0.0	.	301;444	E7EM68;Q14108	.;SCRB2_HUMAN	V	444;301	ENSP00000264896:A444V;ENSP00000399154:A301V	ENSP00000264896:A444V	A	-	2	0	SCARB2	77303469	1.000000	0.71417	0.971000	0.41717	0.503000	0.33858	3.888000	0.56204	2.780000	0.95670	0.655000	0.94253	GCG		0.458	SCARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252403.1	NM_005506	
SHROOM3	57619	broad.mit.edu	37	4	77660525	77660525	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:77660525G>A	ENST00000296043.6	+	5	2152	c.1199G>A	c.(1198-1200)cGg>cAg	p.R400Q		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	400					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)		p.R399Q(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			CACCGTGAGCGGCCCAGCTCC	0.582																																					p.R400Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1199A	4						.						46.0	45.0	45.0					4																	77660525		2203	4300	6503	77879549	SO:0001583	missense	57619	exon5			AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.1199G>A	4.37:g.77660525G>A	ENSP00000296043:p.Arg400Gln	Somatic		Capture	Illumina HiSeq	Phase_I	77879549	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	.	.	.	.	.	.	.	.	.	.	G	29.7	5.029751	0.93518	.	.	ENSG00000138771	ENST00000296043	T	0.48201	0.82	5.63	4.78	0.61160	.	0.086995	0.45126	N	0.000381	T	0.63486	0.2515	M	0.63428	1.95	0.39159	D	0.962367	D;D;D	0.89917	1.0;0.999;0.999	D;P;D	0.63957	0.92;0.806;0.909	T	0.68689	-0.5342	10	0.87932	D	0	-22.7631	14.9499	0.71064	0.0697:0.0:0.9303:0.0	.	224;400;178	B4E244;Q8TF72;B3KY47	.;SHRM3_HUMAN;.	Q	400	ENSP00000296043:R400Q	ENSP00000296043:R400Q	R	+	2	0	SHROOM3	77879549	1.000000	0.71417	0.923000	0.36655	0.936000	0.57629	4.372000	0.59530	2.644000	0.89710	0.563000	0.77884	CGG		0.582	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
FRAS1	80144	broad.mit.edu	37	4	79455696	79455696	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:79455696G>T	ENST00000264895.6	+	71	11459	c.11019G>T	c.(11017-11019)aaG>aaT	p.K3673N		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3669					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.K3673N(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						ATAATGAGAAGGTGTTCCTAA	0.428																																					p.K3673N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G11019T	4						.						155.0	140.0	145.0					4																	79455696		1906	4120	6026	79674720	SO:0001583	missense	80144	exon71			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11019G>T	4.37:g.79455696G>T	ENSP00000264895:p.Lys3673Asn	Somatic		Capture	Illumina HiSeq	Phase_I	79674720	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	37	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.90|15.90	2.968531|2.968531	0.53614|0.53614	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000512123|ENST00000264895	.|T	.|0.63580	.|-0.05	5.05|5.05	3.02|3.02	0.34903|0.34903	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.69504|0.69504	0.3118|0.3118	L|L	0.48362|0.48362	1.52|1.52	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	T|T	0.69079|0.69079	-0.5240|-0.5240	5|10	.|0.54805	.|T	.|0.06	.|.	9.1791|9.1791	0.37129|0.37129	0.279:0.0:0.721:0.0|0.279:0.0:0.721:0.0	.|.	.|3673	.|E9PHH6	.|.	C|N	1902|3673	.|ENSP00000264895:K3673N	.|ENSP00000264895:K3673N	G|K	+|+	1|3	0|2	FRAS1|FRAS1	79674720|79674720	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	1.580000|1.580000	0.36547|0.36547	1.117000|1.117000	0.41842|0.41842	0.591000|0.591000	0.81541|0.81541	GGT|AAG		0.428	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
FRAS1	80144	broad.mit.edu	37	4	79458295	79458295	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:79458295G>T	ENST00000264895.6	+	72	11679	c.11239G>T	c.(11239-11241)Ggg>Tgg	p.G3747W		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3743					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.G3747W(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CTACAATGAAGGGCCCCAGTA	0.433																																					p.G3747W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G11239T	4						.						97.0	93.0	94.0					4																	79458295		1872	4103	5975	79677319	SO:0001583	missense	80144	exon72			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11239G>T	4.37:g.79458295G>T	ENSP00000264895:p.Gly3747Trp	Somatic		Capture	Illumina HiSeq	Phase_I	79677319	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	37	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.9|24.9	4.580299|4.580299	0.86645|0.86645	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000264895|ENST00000512123	T|.	0.72725|.	-0.68|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75961|0.75961	0.3921|0.3921	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.72204|0.72204	-0.4361|-0.4361	10|5	0.87932|.	D|.	0|.	.|.	20.33|20.33	0.98713|0.98713	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	3747|.	E9PHH6|.	.|.	W|M	3747|1975	ENSP00000264895:G3747W|.	ENSP00000264895:G3747W|.	G|R	+|+	1|2	0|0	FRAS1|FRAS1	79677319|79677319	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.718000|0.718000	0.41266|0.41266	9.689000|9.689000	0.98673|0.98673	2.810000|2.810000	0.96702|0.96702	0.585000|0.585000	0.79938|0.79938	GGG|AGG		0.433	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
BMP2K	55589	broad.mit.edu	37	4	79832905	79832905	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:79832905C>A	ENST00000335016.5	+	16	3370	c.3204C>A	c.(3202-3204)ccC>ccA	p.P1068P	PAQR3_ENST00000295462.3_Intron	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	1068					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)	p.P1068P(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						TGTTGGACCCCTTCGGTGCCA	0.532																																					p.P1068P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3204A	4						.						92.0	92.0	92.0					4																	79832905		1971	4161	6132	80051929	SO:0001819	synonymous_variant	55589	exon16			AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.3204C>A	4.37:g.79832905C>A		Somatic		Capture	Illumina HiSeq	Phase_I	80051929	NM_198892	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Silent	SNP	ENST00000335016.5	37	CCDS47083.1	.	.	.	.	.	.	.	.	.	.	C	0.019	-1.458909	0.01062	.	.	ENSG00000138756	ENST00000502613	.	.	.	5.41	-1.32	0.09201	.	.	.	.	.	T	0.42449	0.1203	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27020	-1.0086	4	.	.	.	-11.6557	3.0885	0.06285	0.1092:0.3621:0.1084:0.4203	.	.	.	.	I	761	.	.	L	+	1	0	BMP2K	80051929	0.009000	0.17119	0.982000	0.44146	0.024000	0.10985	-1.235000	0.02928	-0.219000	0.10003	0.484000	0.47621	CTT		0.532	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593	
NUDT9	53343	broad.mit.edu	37	4	88356154	88356154	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:88356154G>A	ENST00000302174.4	+	2	453	c.129G>A	c.(127-129)tgG>tgA	p.W43*	NUDT9_ENST00000473942.1_5'UTR	NM_024047.4	NP_076952.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 9	43					ADP catabolic process (GO:0046032)|IDP catabolic process (GO:0046709)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrial matrix (GO:0005759)	adenosine-diphosphatase activity (GO:0043262)|ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)	p.W43*(1)		endometrium(1)|large_intestine(4)|lung(6)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000937)		CATCTTCTTGGTTTCATCTTA	0.378																																					p.W43X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G129A	4						.						67.0	67.0	67.0					4																	88356154		2203	4300	6503	88575178	SO:0001587	stop_gained	53343	exon2			AY026252	CCDS3620.1, CCDS3621.1	4q22.1	2008-08-29			ENSG00000170502	ENSG00000170502		"""Nudix motif containing"""	8056	protein-coding gene	gene with protein product		606022				11385575, 12427752	Standard	NM_024047		Approved	MGC3037	uc003hqq.3	Q9BW91	OTTHUMG00000130591	ENST00000302174.4:c.129G>A	4.37:g.88356154G>A	ENSP00000303575:p.Trp43*	Somatic		Capture	Illumina HiSeq	Phase_I	88575178	NM_024047	Q8NBN1|Q8NCB9|Q8NG25	Nonsense_Mutation	SNP	ENST00000302174.4	37	CCDS3620.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.120364	0.37436	.	.	ENSG00000170502	ENST00000302174;ENST00000440591	.	.	.	5.05	1.52	0.23074	.	1.104780	0.06645	N	0.761774	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	-0.135	4.7511	0.13061	0.2434:0.0:0.5936:0.163	.	.	.	.	X	43	.	ENSP00000303575:W43X	W	+	3	0	NUDT9	88575178	0.745000	0.28261	0.874000	0.34290	0.551000	0.35334	0.271000	0.18626	0.516000	0.28340	0.467000	0.42956	TGG		0.378	NUDT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253035.2		
DSPP	1834	broad.mit.edu	37	4	88533779	88533779	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:88533779A>G	ENST00000282478.7	+	3	474	c.441A>G	c.(439-441)ggA>ggG	p.G147G	DSPP_ENST00000399271.1_Silent_p.G147G|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	147					biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.G147G(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		ACAATGCTGGAGCCACAAACA	0.428																																					p.G147G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A441G	4						.						120.0	112.0	114.0					4																	88533779		2008	4189	6197	88752803	SO:0001819	synonymous_variant	1834	exon4			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.441A>G	4.37:g.88533779A>G		Somatic		Capture	Illumina HiSeq	Phase_I	88752803	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																				0.428	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
ABCG2	9429	broad.mit.edu	37	4	89013395	89013395	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:89013395delT	ENST00000237612.3	-	16	2504	c.1959delA	c.(1957-1959)aaafs	p.K653fs	ABCG2_ENST00000515655.1_3'UTR	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	653					cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.K653fs*>3(1)		breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	TTTAAGAATATTTTTTAAGAA	0.328																																					p.K653fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1959delA	4						.						37.0	40.0	39.0					4																	89013395		2202	4300	6502	89232419	SO:0001589	frameshift_variant	9429	exon16			AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"""CD molecules"", ""ATP binding cassette transporters / subfamily G"""	74	protein-coding gene	gene with protein product		603756	"""ATP-binding cassette, sub-family G (WHITE), member 2"""			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.1959delA	4.37:g.89013395delT	ENSP00000237612:p.Lys653fs	Somatic		Capture	Illumina HiSeq	Phase_I	89232419	NM_004827	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Frame_Shift_Del	DEL	ENST00000237612.3	37	CCDS3628.1																																																																																				0.328	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827	
CCSER1	401145	broad.mit.edu	37	4	91549203	91549203	+	Silent	SNP	C	C	T	rs559086817		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:91549203C>T	ENST00000509176.1	+	6	2040	c.1752C>T	c.(1750-1752)gaC>gaT	p.D584D	CCSER1_ENST00000432775.2_Silent_p.D584D|CCSER1_ENST00000333691.8_Silent_p.D584D	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	584								p.D586D(1)|p.D584D(1)									TAACAAAGGACGTTGATCAAG	0.418													C|||	1	0.000199681	0.0	0.0	5008	,	,		17511	0.0		0.0	False		,,,				2504	0.001				p.D584D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1752T	4						.						83.0	80.0	81.0					4																	91549203		1872	4117	5989	91768226	SO:0001819	synonymous_variant	401145	exon6				CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"""family with sequence similarity 190, member A"""	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.1752C>T	4.37:g.91549203C>T		Somatic		Capture	Illumina HiSeq	Phase_I	91768226	NM_001145065	Q4W5M0|Q86V57	Silent	SNP	ENST00000509176.1	37	CCDS47099.1																																																																																				0.418	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065	
LARP7	51574	broad.mit.edu	37	4	113570754	113570754	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:113570754delA	ENST00000344442.5	+	9	1484	c.1206delA	c.(1204-1206)ttafs	p.L402fs	MIR302B_ENST00000510655.1_RNA|MIR302A_ENST00000385192.1_RNA|MIR302B_ENST00000509938.1_RNA|LARP7_ENST00000324052.6_Frame_Shift_Del_p.L402fs|MIR302B_ENST00000362188.1_RNA|LARP7_ENST00000509061.1_Frame_Shift_Del_p.L409fs|MIR302C_ENST00000362232.1_RNA|MIR367_ENST00000362299.1_RNA|MIR302D_ENST00000362275.1_RNA|MIR302B_ENST00000505215.1_RNA	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	402					RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T405fs*5(2)		endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		TGGCTTCTTTAAAAAAAACAA	0.333																																					p.L402fs												.	.	2	Deletion - Frameshift(2)	large_intestine(1)|lung(1)	c.1206delA	4						.						46.0	45.0	45.0					4																	113570754		2202	4298	6500	113790203	SO:0001589	frameshift_variant	51574	exon9			AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"""La ribonucleoprotein domain containing"", ""RNA binding motif (RRM) containing"""	24912	protein-coding gene	gene with protein product	"""P-TEFb-interaction protein for 7SK stability"""	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.1206delA	4.37:g.113570754delA	ENSP00000344950:p.Leu402fs	Somatic		Capture	Illumina HiSeq	Phase_I	113790203	NM_016648	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Frame_Shift_Del	DEL	ENST00000344442.5	37	CCDS3701.2																																																																																				0.333	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648	
FBXW7	55294	broad.mit.edu	37	4	153249361	153249361	+	Splice_Site	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:153249361delT	ENST00000281708.4	-	9	2646	c.1417delA	c.(1417-1419)aga>ga	p.R473fs	FBXW7_ENST00000603548.1_Splice_Site_p.R473fs|FBXW7_ENST00000263981.5_Splice_Site_p.R393fs|FBXW7_ENST00000603841.1_Splice_Site_p.R473fs|FBXW7_ENST00000393956.3_Splice_Site_p.R297fs|FBXW7_ENST00000296555.5_Splice_Site_p.R355fs	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	473					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R473fs*25(4)|p.R473fs*4(3)|p.R234fs*25(1)|p.R393fs*25(1)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TTCCCTTACCTTTTTTCATGA	0.418			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																p.R393fs			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	.	.	10	Deletion - Frameshift(6)|Insertion - Frameshift(3)|Unknown(1)	large_intestine(6)|NS(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|endometrium(1)	c.1177delA	4						.						187.0	168.0	175.0					4																	153249361		2203	4300	6503	153468811	SO:0001630	splice_region_variant	55294	exon8			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1418+1A>-	4.37:g.153249361delT		Somatic		Capture	Illumina HiSeq	Phase_I	153468811	NM_018315	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Frame_Shift_Del	DEL	ENST00000281708.4	37	CCDS3777.1																																																																																				0.418	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		Frame_Shift_Del
TMA16	55319	broad.mit.edu	37	4	164428285	164428285	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:164428285delA	ENST00000358572.5	+	2	445	c.104delA	c.(103-105)gaafs	p.E35fs	TMA16_ENST00000513272.1_Frame_Shift_Del_p.E35fs|TMA16_ENST00000508268.1_Frame_Shift_Del_p.E35fs|TMA16_ENST00000513134.1_Frame_Shift_Del_p.E35fs|TMA16_ENST00000511562.1_3'UTR	NM_018352.2	NP_060822.2	Q96EY4	TMA16_HUMAN	translation machinery associated 16 homolog (S. cerevisiae)	35						nucleus (GO:0005634)		p.K37fs*4(1)									CACAAACAAGAAAAAAAGGAA	0.353																																					p.E35fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.104delA	4						.						40.0	34.0	36.0					4																	164428285		1817	4070	5887	164647735	SO:0001589	frameshift_variant	55319	exon2				CCDS43278.1	4q32.3	2012-03-02	2012-03-02	2012-03-02	ENSG00000198498	ENSG00000198498			25638	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 43"""	C4orf43		12477932	Standard	NM_018352		Approved	FLJ11184	uc003iqq.4	Q96EY4	OTTHUMG00000161528	ENST00000358572.5:c.104delA	4.37:g.164428285delA	ENSP00000351380:p.Glu35fs	Somatic		Capture	Illumina HiSeq	Phase_I	164647735	NM_018352	Q0P6E4|Q0P6J1|Q9NUR7	Frame_Shift_Del	DEL	ENST00000358572.5	37	CCDS43278.1																																																																																				0.353	TMA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365208.1	NM_018352	
CFAP97	57587	broad.mit.edu	37	4	186111576	186111576	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr4:186111576A>G	ENST00000458385.2	-	2	894	c.775T>C	c.(775-777)Tca>Cca	p.S259P	KIAA1430_ENST00000296775.6_Missense_Mutation_p.S259P|KIAA1430_ENST00000514798.1_Missense_Mutation_p.S259P	NM_020827.1	NP_065878.1	Q9P2B7	K1430_HUMAN		259								p.S259P(1)		endometrium(3)|kidney(2)|large_intestine(5)|upper_aerodigestive_tract(1)	11		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)		TCTGGAGTTGATAAGGGACTT	0.393																																					p.S259P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T775C	4						.						113.0	98.0	103.0					4																	186111576		1891	4113	6004	186348570	SO:0001583	missense	57587	exon2																														ENST00000458385.2:c.775T>C	4.37:g.186111576A>G	ENSP00000409964:p.Ser259Pro	Somatic		Capture	Illumina HiSeq	Phase_I	186348570	NM_020827	B3KRP7|D3DP60|Q05CU1|Q4W5M4|Q8N6E7|Q9UF45	Missense_Mutation	SNP	ENST00000458385.2	37	CCDS47168.1	.	.	.	.	.	.	.	.	.	.	A	16.04	3.010235	0.54361	.	.	ENSG00000164323	ENST00000458385;ENST00000514798;ENST00000296775	T;T;T	0.61510	0.63;0.1;0.1	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000004	T	0.75221	0.3820	M	0.72894	2.215	0.46222	D	0.99893	D;D	0.89917	1.0;0.999	D;D	0.76575	0.988;0.95	T	0.78321	-0.2249	10	0.87932	D	0	-11.3756	15.9885	0.80179	1.0:0.0:0.0:0.0	.	259;259	Q9P2B7-2;Q9P2B7	.;K1430_HUMAN	P	259	ENSP00000409964:S259P;ENSP00000423312:S259P;ENSP00000296775:S259P	ENSP00000296775:S259P	S	-	1	0	KIAA1430	186348570	1.000000	0.71417	0.789000	0.31954	0.197000	0.23852	7.422000	0.80217	2.234000	0.73211	0.533000	0.62120	TCA		0.393	KIAA1430-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360717.2		
CDH10	1008	broad.mit.edu	37	5	24537692	24537693	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:24537692_24537693insT	ENST00000264463.4	-	3	829_830	c.322_323insA	c.(322-324)acafs	p.T108fs		NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	108	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T108fs*3(1)		NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		AATATCACCTGTTTTTTCATCA	0.401										HNSCC(23;0.051)																											p.T108fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.323_324insA	5						.																																			24573450	SO:0001589	frameshift_variant	1008	exon3			AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"""Cadherins / Major cadherins"""	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.323dupA	5.37:g.24537698_24537698dupT	ENSP00000264463:p.Thr108fs	Somatic		Capture	Illumina HiSeq	Phase_I	24573449	NM_006727	Q9ULB3	Frame_Shift_Ins	INS	ENST00000264463.4	37	CCDS3892.1																																																																																				0.401	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727	
SLCO4C1	353189	broad.mit.edu	37	5	101631746	101631746	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:101631746T>G	ENST00000310954.6	-	1	507	c.221A>C	c.(220-222)aAg>aCg	p.K74T		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1									p.K74T(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		TGACCGGAGCTTCTCTTCGGA	0.572																																					p.K74T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A221C	5						.						90.0	92.0	91.0					5																	101631746		2203	4300	6503	101659645	SO:0001583	missense	353189	exon1			AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"""Solute carriers"""	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.221A>C	5.37:g.101631746T>G	ENSP00000309741:p.Lys74Thr	Somatic		Capture	Illumina HiSeq	Phase_I	101659645	NM_180991		Missense_Mutation	SNP	ENST00000310954.6	37	CCDS34205.1	.	.	.	.	.	.	.	.	.	.	T	4.154	0.026938	0.08054	.	.	ENSG00000173930	ENST00000310954	T	0.39056	1.1	4.11	-8.22	0.01037	.	1.786220	0.03941	N	0.286945	T	0.15003	0.0362	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.12760	-1.0535	10	0.14656	T	0.56	.	0.8946	0.01261	0.1741:0.209:0.2185:0.3984	.	74	Q6ZQN7	SO4C1_HUMAN	T	74	ENSP00000309741:K74T	ENSP00000309741:K74T	K	-	2	0	SLCO4C1	101659645	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.250000	0.01187	-1.519000	0.01775	-0.353000	0.07706	AAG		0.572	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991	
SLCO6A1	133482	broad.mit.edu	37	5	101735297	101735297	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:101735297A>G	ENST00000506729.1	-	10	1947	c.1776T>C	c.(1774-1776)tcT>tcC	p.S592S	SLCO6A1_ENST00000379810.1_Silent_p.S339S|SLCO6A1_ENST00000379807.3_Silent_p.S592S|SLCO6A1_ENST00000513675.1_Silent_p.S339S|SLCO6A1_ENST00000389019.3_Silent_p.S530S			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	592						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.S592S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		CAGAAAAACCAGAAAATATAA	0.323																																					p.S592S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1776C	5						.						91.0	89.0	89.0					5																	101735297		2203	4300	6503	101763196	SO:0001819	synonymous_variant	133482	exon10			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"""Solute carriers"""	23613	protein-coding gene	gene with protein product	"""cancer/testis antigen 48"""	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1776T>C	5.37:g.101735297A>G		Somatic		Capture	Illumina HiSeq	Phase_I	101763196	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Silent	SNP	ENST00000506729.1	37	CCDS34206.1																																																																																				0.323	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	
GIN1	54826	broad.mit.edu	37	5	102423724	102423724	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:102423724G>A	ENST00000399004.2	-	8	1541	c.1447C>T	c.(1447-1449)Cgt>Tgt	p.R483C	GIN1_ENST00000508629.1_3'UTR	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	483					DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)	p.R483C(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		AATAGTTCACGATCCTTGCTT	0.363																																					p.R483C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1447T	5						.						146.0	134.0	138.0					5																	102423724		1856	4095	5951	102451623	SO:0001583	missense	54826	exon8			BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"""gypsy integrase 1"", ""Ty3/Gypsy integrase 1"""		"""zinc finger, H2C2 domain containing"""	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.1447C>T	5.37:g.102423724G>A	ENSP00000381970:p.Arg483Cys	Somatic		Capture	Illumina HiSeq	Phase_I	102451623	NM_017676	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Missense_Mutation	SNP	ENST00000399004.2	37	CCDS43349.1	.	.	.	.	.	.	.	.	.	.	G	9.088	1.000990	0.19121	.	.	ENSG00000145723	ENST00000399004	T	0.19105	2.17	5.64	-0.549	0.11829	.	0.732438	0.11122	U	0.597306	T	0.10981	0.0268	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26985	-1.0087	10	0.87932	D	0	-28.1633	5.4593	0.16607	0.2729:0.2466:0.4805:0.0	.	483	Q9NXP7	GIN1_HUMAN	C	483	ENSP00000381970:R483C	ENSP00000381970:R483C	R	-	1	0	GIN1	102451623	0.005000	0.15991	0.224000	0.23877	0.122000	0.20287	1.025000	0.30090	-0.337000	0.08426	-0.291000	0.09656	CGT		0.363	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676	
ROPN1L	83853	broad.mit.edu	37	5	10461310	10461310	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:10461310G>A	ENST00000503804.1	+	5	953	c.432G>A	c.(430-432)gcG>gcA	p.A144A	ROPN1L_ENST00000274134.4_Silent_p.A144A|ROPN1L_ENST00000510520.1_3'UTR			Q96C74	ROP1L_HUMAN	rhophilin associated tail protein 1-like	144					epithelial cilium movement (GO:0003351)|regulation of protein phosphorylation (GO:0001932)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)		p.A144A(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)	14						TGAACACTGCGCTGAAGCACC	0.557																																					p.A144A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G432A	5						.						83.0	71.0	75.0					5																	10461310		2203	4300	6503	10514310	SO:0001819	synonymous_variant	83853	exon4			AF239723	CCDS3879.1	5p15	2011-01-20	2011-01-20		ENSG00000145491	ENSG00000145491			24060	protein-coding gene	gene with protein product	"""radial spoke head 11 homolog (Chlamydomonas)"""	611756	"""ropporin 1-like"""			11278869	Standard	NM_031916		Approved	ASP, FLJ25776, RSPH11	uc021xwo.1	Q96C74	OTTHUMG00000090507	ENST00000503804.1:c.432G>A	5.37:g.10461310G>A		Somatic		Capture	Illumina HiSeq	Phase_I	10514310	NM_031916	D3DTC9|Q9BZX0	Silent	SNP	ENST00000503804.1	37	CCDS3879.1																																																																																				0.557	ROPN1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367033.1	NM_031916	
GIN1	54826	broad.mit.edu	37	5	102433021	102433021	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:102433021G>A	ENST00000399004.2	-	6	1099	c.1005C>T	c.(1003-1005)ggC>ggT	p.G335G	GIN1_ENST00000508629.1_Intron	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	335					DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)	p.G335G(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		GAATCACCTGGCCCAGTGAAG	0.299																																					p.G335G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1005T	5						.						81.0	76.0	78.0					5																	102433021		1798	4058	5856	102460920	SO:0001819	synonymous_variant	54826	exon6			BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"""gypsy integrase 1"", ""Ty3/Gypsy integrase 1"""		"""zinc finger, H2C2 domain containing"""	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.1005C>T	5.37:g.102433021G>A		Somatic		Capture	Illumina HiSeq	Phase_I	102460920	NM_017676	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Silent	SNP	ENST00000399004.2	37	CCDS43349.1																																																																																				0.299	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676	
DCP2	167227	broad.mit.edu	37	5	112336903	112336903	+	Missense_Mutation	SNP	A	A	C	rs142459154	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:112336903A>C	ENST00000389063.2	+	5	753	c.555A>C	c.(553-555)aaA>aaC	p.K185N	DCP2_ENST00000515408.1_Missense_Mutation_p.K185N|DCP2_ENST00000543319.1_5'UTR	NM_152624.5	NP_689837	Q8IU60	DCP2_HUMAN	decapping mRNA 2	185	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)|RISC complex (GO:0016442)	exoribonuclease activity, producing 5'-phosphomonoesters (GO:0016896)|m7G(5')pppN diphosphatase activity (GO:0050072)|manganese ion binding (GO:0030145)|RNA binding (GO:0003723)	p.K185N(1)		endometrium(3)|large_intestine(6)|lung(1)	10		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		AAGACACAAAATTTAACCCAA	0.333																																					p.K185N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A555C	5						.						75.0	79.0	78.0					5																	112336903		2202	4299	6501	112364802	SO:0001583	missense	167227	exon5			AY135173	CCDS34210.1, CCDS56377.1	5q22	2013-05-02	2013-05-02		ENSG00000172795	ENSG00000172795	3.6.1.62	"""Nudix motif containing"""	24452	protein-coding gene	gene with protein product	"""nudix (nucleoside diphosphate linked moiety X)-type motif 20"", ""M(7)GpppN-mRNA hydrolase"""	609844	"""DCP2 decapping enzyme homolog (S. cerevisiae)"""			12218187, 12417715	Standard	NM_152624		Approved	NUDT20	uc003kqh.3	Q8IU60	OTTHUMG00000162853	ENST00000389063.2:c.555A>C	5.37:g.112336903A>C	ENSP00000373715:p.Lys185Asn	Somatic		Capture	Illumina HiSeq	Phase_I	112364802	NM_152624	C9J778|Q6P2D4|Q7Z5W5|Q8NBG5	Missense_Mutation	SNP	ENST00000389063.2	37	CCDS34210.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.63|18.63	3.664537|3.664537	0.67700|0.67700	.|.	.|.	ENSG00000172795|ENSG00000172795	ENST00000513585|ENST00000515408;ENST00000389063	.|T;T	.|0.08720	.|3.06;3.06	5.71|5.71	3.27|3.27	0.37495|0.37495	.|NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.15739|0.15739	0.0379|0.0379	L|L	0.39085|0.39085	1.19|1.19	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.997;0.998	T|T	0.03148|0.03148	-1.1067|-1.1067	5|10	.|0.29301	.|T	.|0.29	-15.4125|-15.4125	8.5131|8.5131	0.33229|0.33229	0.7875:0.0:0.2125:0.0|0.7875:0.0:0.2125:0.0	.|.	.|185;185	.|Q8IU60-2;Q8IU60	.|.;DCP2_HUMAN	L|N	167|185	.|ENSP00000425770:K185N;ENSP00000373715:K185N	.|ENSP00000373715:K185N	I|K	+|+	1|3	0|2	DCP2|DCP2	112364802|112364802	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	2.529000|2.529000	0.45632|0.45632	0.416000|0.416000	0.25844|0.25844	0.450000|0.450000	0.29827|0.29827	ATT|AAA		0.333	DCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370765.3	NM_152624	
LVRN	206338	broad.mit.edu	37	5	115329444	115329444	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:115329444G>T	ENST00000357872.4	+	6	1391	c.1267G>T	c.(1267-1269)Gga>Tga	p.G423*	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		423						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.G423*(1)									AAAGTGGTTTGGAAACTTGGT	0.294																																					p.G423X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1267T	5						.						76.0	75.0	76.0					5																	115329444		2202	4297	6499	115357343	SO:0001587	stop_gained	206338	exon6																														ENST00000357872.4:c.1267G>T	5.37:g.115329444G>T	ENSP00000350541:p.Gly423*	Somatic		Capture	Illumina HiSeq	Phase_I	115357343	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Nonsense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	G	39	7.792721	0.98492	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	.	.	.	5.35	5.35	0.76521	.	0.000000	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.2158	0.89885	0.0:0.0:1.0:0.0	.	.	.	.	X	423;412	.	ENSP00000350541:G423X	G	+	1	0	AC010282.1	115357343	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.415000	0.90241	2.666000	0.90696	0.650000	0.86243	GGA		0.294	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
SRFBP1	153443	broad.mit.edu	37	5	121354991	121354991	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:121354991C>T	ENST00000339397.4	+	5	379	c.307C>T	c.(307-309)Cta>Tta	p.L103L		NM_152546.2	NP_689759.2			serum response factor binding protein 1									p.L103L(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		AATTGCCAGACTAGCAGTACA	0.313																																					p.L103L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C307T	5						.						95.0	91.0	92.0					5																	121354991		1823	4076	5899	121382890	SO:0001819	synonymous_variant	153443	exon5			AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"""BUD22 homolog (S. cerevisiae)"""	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.307C>T	5.37:g.121354991C>T		Somatic		Capture	Illumina HiSeq	Phase_I	121382890	NM_152546		Silent	SNP	ENST00000339397.4	37	CCDS43354.1																																																																																				0.313	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546	
ZNF474	133923	broad.mit.edu	37	5	121488383	121488383	+	Missense_Mutation	SNP	C	C	A	rs146179557		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:121488383C>A	ENST00000296600.4	+	2	1081	c.698C>A	c.(697-699)aCc>aAc	p.T233N	CTC-441N14.2_ENST00000504829.1_RNA|ZNF474_ENST00000514925.1_Intron|CTC-441N14.1_ENST00000505209.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	233							metal ion binding (GO:0046872)	p.T233N(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		GAATTTGGCACCCTGTCCCTT	0.502																																					p.T233N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C698A	5						.	C	ASN/THR	1,4405	2.1+/-5.4	0,1,2202	95.0	100.0	98.0		698	3.5	1.0	5	dbSNP_134	98	0,8600		0,0,4300	no	missense	ZNF474	NM_207317.1	65	0,1,6502	AA,AC,CC		0.0,0.0227,0.0077	possibly-damaging	233/365	121488383	1,13005	2203	4300	6503	121516282	SO:0001583	missense	133923	exon2			AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"""Zinc fingers, C2H2-type"""	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.698C>A	5.37:g.121488383C>A	ENSP00000296600:p.Thr233Asn	Somatic		Capture	Illumina HiSeq	Phase_I	121516282	NM_207317	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.894356	0.52121	2.27E-4	0.0	ENSG00000164185	ENST00000296600	T	0.45668	0.89	5.43	3.49	0.39957	.	0.281312	0.22562	U	0.058456	T	0.59528	0.2200	M	0.87900	2.915	0.22639	N	0.998909	D	0.54772	0.968	P	0.50314	0.637	T	0.60969	-0.7157	10	0.39692	T	0.17	-13.7366	17.8504	0.88746	0.0:0.703:0.297:0.0	.	233	Q6S9Z5	ZN474_HUMAN	N	233	ENSP00000296600:T233N	ENSP00000296600:T233N	T	+	2	0	ZNF474	121516282	0.710000	0.27896	0.999000	0.59377	0.995000	0.86356	2.332000	0.43903	1.251000	0.43983	0.655000	0.94253	ACC		0.502	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317	
IL3	3562	broad.mit.edu	37	5	131398247	131398247	+	Missense_Mutation	SNP	C	C	T	rs546686029		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:131398247C>T	ENST00000296870.2	+	4	501	c.323C>T	c.(322-324)aCg>aTg	p.T108M		NM_000588.3	NP_000579.2	P08700	IL3_HUMAN	interleukin 3	108					cell-cell signaling (GO:0007267)|embryonic hemopoiesis (GO:0035162)|immune response (GO:0006955)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-3 receptor binding (GO:0005135)	p.T108M(1)		central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)	10		all_cancers(142;7.42e-12)|Lung NSC(810;4.25e-07)|all_lung(232;1.93e-06)|Prostate(281;0.00741)|Breast(839;0.0544)|Lung SC(612;0.122)|Ovarian(839;0.223)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	GBM - Glioblastoma multiforme(465;0.0161)|Lung(113;0.105)	Amlexanox(DB01025)	CCCCTGGCCACGGCCGCACCC	0.587													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19182	0.0		0.0	False		,,,				2504	0.0				p.T108M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C323T	5						.						192.0	190.0	191.0					5																	131398247		2203	4300	6503	131426146	SO:0001583	missense	3562	exon4			M14743	CCDS4149.1	5q23-q31	2014-04-04	2014-04-04		ENSG00000164399	ENSG00000164399		"""Interleukins and interleukin receptors"""	6011	protein-coding gene	gene with protein product	"""multilineage-colony-stimulating factor"", ""hematopoietic growth factor"", ""P-cell stimulating factor"", ""mast-cell growth factor"", ""colony-stimulating factor, multiple"""	147740	"""interleukin 3 (colony-stimulating factor, multiple)"""			3489530	Standard	NM_000588		Approved	IL-3, MULTI-CSF, MCGF, MGC79398, MGC79399	uc003kwe.1	P08700	OTTHUMG00000059640	ENST00000296870.2:c.323C>T	5.37:g.131398247C>T	ENSP00000296870:p.Thr108Met	Somatic		Capture	Illumina HiSeq	Phase_I	131426146	NM_000588	Q6GS87	Missense_Mutation	SNP	ENST00000296870.2	37	CCDS4149.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.692785	0.48202	.	.	ENSG00000164399	ENST00000296870	T	0.38240	1.15	4.38	-1.14	0.09741	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.075470	0.07341	N	0.880801	T	0.28167	0.0695	L	0.39020	1.185	0.09310	N	1	P	0.46457	0.878	B	0.43331	0.416	T	0.23976	-1.0173	10	0.87932	D	0	-0.8959	4.1617	0.10287	0.4945:0.3166:0.0:0.1889	.	108	P08700	IL3_HUMAN	M	108	ENSP00000296870:T108M	ENSP00000296870:T108M	T	+	2	0	IL3	131426146	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.649000	0.01993	-0.215000	0.10063	0.655000	0.94253	ACG		0.587	IL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132639.1	NM_000588	
GDF9	2661	broad.mit.edu	37	5	132200009	132200009	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:132200009G>A	ENST00000378673.2	-	2	1083	c.217C>T	c.(217-219)Cga>Tga	p.R73*	UQCRQ_ENST00000378665.1_5'Flank|UQCRQ_ENST00000378670.3_5'Flank|UQCRQ_ENST00000378667.1_5'Flank|GDF9_ENST00000464378.1_Intron|GDF9_ENST00000296875.2_Nonsense_Mutation_p.R73*			O60383	GDF9_HUMAN	growth differentiation factor 9	73					female gamete generation (GO:0007292)|negative regulation of cell growth (GO:0030308)|oocyte growth (GO:0001555)|positive regulation of cell proliferation (GO:0008284)|regulation of progesterone secretion (GO:2000870)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)	p.R73*(1)		NS(1)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	22		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GACCCACCTCGCCCAACAGAT	0.502																																					p.R73X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C217T	5						.						105.0	112.0	110.0					5																	132200009		2203	4300	6503	132227908	SO:0001587	stop_gained	2661	exon1				CCDS4162.1, CCDS75299.1	5q31.1	2014-01-30			ENSG00000164404	ENSG00000164404		"""Endogenous ligands"""	4224	protein-coding gene	gene with protein product		601918				7760846	Standard	NM_005260		Approved		uc003kxz.1	O60383	OTTHUMG00000059842	ENST00000378673.2:c.217C>T	5.37:g.132200009G>A	ENSP00000367942:p.Arg73*	Somatic		Capture	Illumina HiSeq	Phase_I	132227908	NM_005260	Q4VAW5	Nonsense_Mutation	SNP	ENST00000378673.2	37	CCDS4162.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.540564	0.85917	.	.	ENSG00000164404	ENST00000378673;ENST00000296875	.	.	.	6.02	6.02	0.97574	.	0.866782	0.10567	N	0.659540	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	.	15.9678	0.79987	0.0:0.1721:0.8278:0.0	.	.	.	.	X	73	.	ENSP00000296875:R73X	R	-	1	2	GDF9	132227908	0.004000	0.15560	0.526000	0.27913	0.355000	0.29361	1.321000	0.33678	2.865000	0.98341	0.655000	0.94253	CGA		0.502	GDF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133060.2	NM_005260	
FSTL4	23105	broad.mit.edu	37	5	132535225	132535225	+	Silent	SNP	G	G	A	rs61740558	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:132535225G>A	ENST00000265342.7	-	16	2340	c.2091C>T	c.(2089-2091)gaC>gaT	p.D697D	CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	697						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.D697D(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGAAGCGCCCGTCGGGGGATG	0.607													G|||	110	0.0219649	0.0772	0.0115	5008	,	,		18282	0.0		0.0	False		,,,				2504	0.0				p.D697D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2091T	5						.	G		270,4136	151.8+/-185.6	9,252,1942	49.0	52.0	51.0		2091	-4.1	0.6	5	dbSNP_129	51	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	FSTL4	NM_015082.1		9,258,6236	AA,AG,GG		0.0698,6.128,2.1221		697/843	132535225	276,12730	2203	4300	6503	132563124	SO:0001819	synonymous_variant	23105	exon16			AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.2091C>T	5.37:g.132535225G>A		Somatic		Capture	Illumina HiSeq	Phase_I	132563124	NM_015082	Q8TBU0|Q9UPU1	Silent	SNP	ENST00000265342.7	37	CCDS34238.1																																																																																				0.607	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786	
KDM3B	51780	broad.mit.edu	37	5	137713511	137713511	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:137713511C>T	ENST00000314358.5	+	4	777	c.577C>T	c.(577-579)Cga>Tga	p.R193*		NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	193					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.R193*(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						GATATTCAGCCGAGGTAAGAA	0.413																																					p.R193X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C577T	5						.						114.0	105.0	108.0					5																	137713511		2203	4300	6503	137741410	SO:0001587	stop_gained	51780	exon4			AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"""Chromatin-modifying enzymes / K-demethylases"""	1337	protein-coding gene	gene with protein product		609373	"""chromosome 5 open reading frame 7"", ""jumonji domain containing 1B"""	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.577C>T	5.37:g.137713511C>T	ENSP00000326563:p.Arg193*	Somatic		Capture	Illumina HiSeq	Phase_I	137741410	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Nonsense_Mutation	SNP	ENST00000314358.5	37	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.539949	0.85917	.	.	ENSG00000120733	ENST00000314358	.	.	.	5.62	4.7	0.59300	.	0.193084	0.43416	D	0.000572	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	-6.4805	11.8601	0.52461	0.2636:0.7364:0.0:0.0	.	.	.	.	X	193	.	ENSP00000326563:R193X	R	+	1	2	KDM3B	137741410	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.477000	0.53151	2.822000	0.97130	0.650000	0.86243	CGA		0.413	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604	
ETF1	2107	broad.mit.edu	37	5	137853296	137853296	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:137853296G>A	ENST00000360541.5	-	4	577	c.356C>T	c.(355-357)cCa>cTa	p.P119L	ETF1_ENST00000503014.1_Missense_Mutation_p.P105L|ETF1_ENST00000514005.1_5'UTR|ETF1_ENST00000499810.2_Missense_Mutation_p.P86L	NM_004730.3	NP_004721.1	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1	119					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)|translation termination factor activity (GO:0008079)	p.P119L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CGTATTAATTGGTTTGAAAGG	0.378																																					p.P119L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C356T	5						.						148.0	135.0	139.0					5																	137853296		2203	4300	6503	137881195	SO:0001583	missense	2107	exon4			AF095901	CCDS4207.1, CCDS75313.1, CCDS75314.1	5q31.2	2008-02-05			ENSG00000120705	ENSG00000120705			3477	protein-coding gene	gene with protein product	"""sup45 (yeast omnipotent suppressor 45) homolog-like 1"", ""polypeptide chain release factor 1"""	600285		SUP45L1, ERF1, ERF		1546371, 7990965	Standard	NM_004730		Approved	eRF1, TB3-1, RF1	uc003ldc.5	P62495	OTTHUMG00000129199	ENST00000360541.5:c.356C>T	5.37:g.137853296G>A	ENSP00000353741:p.Pro119Leu	Somatic		Capture	Illumina HiSeq	Phase_I	137881195	NM_004730	B2R6B4|D3DQC1|P46055|Q5M7Z7|Q96CG1	Missense_Mutation	SNP	ENST00000360541.5	37	CCDS4207.1	.	.	.	.	.	.	.	.	.	.	G	31	5.067299	0.93898	.	.	ENSG00000120705	ENST00000499810;ENST00000360541;ENST00000503014;ENST00000507939	.	.	.	5.24	5.24	0.73138	eRF1 domain 1/Pelota-like (1);Peptide Chain Release Factor eRF1/aRF1, N-terminal (2);	0.094675	0.85682	D	0.000000	D	0.89504	0.6734	H	0.96269	3.795	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.79108	0.947;0.992	D	0.92851	0.6297	9	0.87932	D	0	-5.9223	18.4198	0.90586	0.0:0.0:1.0:0.0	.	105;119	B7Z7P8;P62495	.;ERF1_HUMAN	L	86;119;105;86	.	ENSP00000353741:P119L	P	-	2	0	ETF1	137881195	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.819000	0.99357	2.445000	0.82738	0.655000	0.94253	CCA		0.378	ETF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251276.2	NM_004730	
PSD2	84249	broad.mit.edu	37	5	139193892	139193892	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:139193892G>A	ENST00000274710.3	+	4	1164	c.959G>A	c.(958-960)cGt>cAt	p.R320H		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	320	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)	p.R320L(1)|p.R320H(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGCACGCCGTCTCTACCAC	0.652																																					p.R320H												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G959A	5						.						45.0	40.0	42.0					5																	139193892		2203	4300	6503	139174076	SO:0001583	missense	84249	exon4			AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"""Pleckstrin homology (PH) domain containing"""	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.959G>A	5.37:g.139193892G>A	ENSP00000274710:p.Arg320His	Somatic		Capture	Illumina HiSeq	Phase_I	139174076	NM_032289	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	37	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	G	32	5.184388	0.94885	.	.	ENSG00000146005	ENST00000274710	T	0.54675	0.56	4.7	4.7	0.59300	SEC7-like (4);	0.000000	0.85682	D	0.000000	T	0.78947	0.4364	M	0.92923	3.36	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	D	0.84616	0.0681	10	0.56958	D	0.05	.	17.6621	0.88195	0.0:0.0:1.0:0.0	.	320	Q9BQI7	PSD2_HUMAN	H	320	ENSP00000274710:R320H	ENSP00000274710:R320H	R	+	2	0	PSD2	139174076	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	9.358000	0.97109	2.153000	0.67306	0.563000	0.77884	CGT		0.652	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289	
IK	3550	broad.mit.edu	37	5	140038900	140038900	+	Splice_Site	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140038900C>T	ENST00000417647.2	+	13	1316	c.1177C>T	c.(1177-1179)Ccc>Tcc	p.P393S		NM_006083.3	NP_006074.2	Q13123	RED_HUMAN	IK cytokine, down-regulator of HLA II	393					cell-cell signaling (GO:0007267)|immune response (GO:0006955)	extracellular space (GO:0005615)|nucleus (GO:0005634)	identical protein binding (GO:0042802)	p.P393S(1)		large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCTTTCCAGCCCATGGACGT	0.488																																					p.P393S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1177T	5						.						121.0	112.0	115.0					5																	140038900		1998	4188	6186	140019084	SO:0001630	splice_region_variant	3550	exon13			BC051295	CCDS47280.1	5q31.3	2008-08-07			ENSG00000113141	ENSG00000113141			5958	protein-coding gene	gene with protein product		600549				7970704	Standard	NM_006083		Approved		uc003lgq.3	Q13123	OTTHUMG00000163374	ENST00000417647.2:c.1177-1C>T	5.37:g.140038900C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140019084	NM_006083	Q6IPD8	Missense_Mutation	SNP	ENST00000417647.2	37	CCDS47280.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.149749	0.37923	.	.	ENSG00000113141	ENST00000417647	.	.	.	5.35	5.35	0.76521	.	0.490245	0.21167	N	0.079058	T	0.40956	0.1138	N	0.12182	0.205	0.80722	D	1	B	0.11235	0.004	B	0.04013	0.001	T	0.22800	-1.0206	8	.	.	.	.	17.9993	0.89194	0.0:1.0:0.0:0.0	.	393	Q13123	RED_HUMAN	S	393	.	.	P	+	1	0	IK	140019084	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.331000	0.59273	2.663000	0.90544	0.655000	0.94253	CCC		0.488	IK-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372897.1	NM_006083	Missense_Mutation
PCDHA3	56145	broad.mit.edu	37	5	140182686	140182686	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140182686G>A	ENST00000522353.2	+	1	1904	c.1904G>A	c.(1903-1905)cGt>cAt	p.R635H	PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.R635H|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	635	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R635H(2)		NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCACGACCCGTGCCCTGGAC	0.667																																					p.R635H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1904A	5						.						71.0	71.0	71.0					5																	140182686		2203	4299	6502	140162870	SO:0001583	missense	56145	exon1			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1904G>A	5.37:g.140182686G>A	ENSP00000429808:p.Arg635His	Somatic		Capture	Illumina HiSeq	Phase_I	140162870	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	g	19.79	3.893481	0.72639	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.53857	0.6;0.6	4.32	4.32	0.51571	Cadherin (4);Cadherin-like (1);	0.000000	0.34411	U	0.003996	T	0.68723	0.3032	M	0.80028	2.48	0.42256	D	0.991995	D;D	0.71674	0.998;0.996	P;P	0.55303	0.749;0.773	T	0.77075	-0.2722	10	0.87932	D	0	.	17.1531	0.86782	0.0:0.0:1.0:0.0	.	635;635	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	H	635	ENSP00000429808:R635H;ENSP00000434086:R635H	ENSP00000429808:R635H	R	+	2	0	PCDHA3	140162870	1.000000	0.71417	0.999000	0.59377	0.711000	0.40976	9.279000	0.95777	2.117000	0.64856	0.467000	0.42956	CGT		0.667	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
PCDHA8	56140	broad.mit.edu	37	5	140222014	140222014	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140222014G>A	ENST00000531613.1	+	1	1108	c.1108G>A	c.(1108-1110)Gcc>Acc	p.A370T	PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.A370T|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	370	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A370T(2)		NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACTGTCATCGCCCTAATTAG	0.488																																					p.A370T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1108A	5						.						118.0	109.0	112.0					5																	140222014		2203	4297	6500	140202198	SO:0001583	missense	56140	exon1			AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"""Cadherins / Protocadherins : Clustered"""	8674	other	complex locus constituent	"""KIAA0345-like 6"""	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1108G>A	5.37:g.140222014G>A	ENSP00000434655:p.Ala370Thr	Somatic		Capture	Illumina HiSeq	Phase_I	140202198	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.983412	0.93044	.	.	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.01804	4.63;4.63	3.57	2.66	0.31614	Cadherin (3);Cadherin-like (1);	0.000000	0.36482	U	0.002579	T	0.05593	0.0147	L	0.58302	1.8	0.27539	N	0.950869	D;D	0.69078	0.979;0.997	P;P	0.57548	0.823;0.799	T	0.05305	-1.0893	10	0.59425	D	0.04	.	12.1706	0.54157	0.0:0.0:0.8271:0.1728	.	370;370	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	T	370	ENSP00000434655:A370T;ENSP00000367363:A370T	ENSP00000367363:A370T	A	+	1	0	PCDHA8	140202198	1.000000	0.71417	0.426000	0.26672	0.663000	0.39108	3.998000	0.57024	0.581000	0.29539	0.306000	0.20318	GCC		0.488	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
PCDHAC1	56135	broad.mit.edu	37	5	140306930	140306930	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140306930C>T	ENST00000253807.2	+	1	453	c.453C>T	c.(451-453)gaC>gaT	p.D151D	PCDHA10_ENST00000307360.5_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHAC1_ENST00000409700.3_Silent_p.D151D|PCDHA2_ENST00000526136.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA9_ENST00000532602.1_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	151	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.D151D(1)		NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCAAGATGACGACGAGGGAA	0.592																																					p.D151D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C453T	5						.						80.0	82.0	81.0					5																	140306930		2203	4300	6503	140287114	SO:0001819	synonymous_variant	56135	exon1			AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"""Cadherins / Protocadherins : Clustered"""	8676	other	complex locus constituent	"""PCDH-ALPHA-C1"""	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.453C>T	5.37:g.140306930C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140287114	NM_031882	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	37	CCDS4241.1																																																																																				0.592	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898	
PCDHB2	56133	broad.mit.edu	37	5	140474794	140474794	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140474794A>G	ENST00000194155.4	+	1	568	c.420A>G	c.(418-420)atA>atG	p.I140M		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	140	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.I140M(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACAAAGAAATACTTTTGAAAA	0.403																																					p.I140M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A420G	5						.						29.0	32.0	31.0					5																	140474794		2201	4299	6500	140454978	SO:0001583	missense	56133	exon1			AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"""Cadherins / Protocadherins : Clustered"""	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.420A>G	5.37:g.140474794A>G	ENSP00000194155:p.Ile140Met	Somatic		Capture	Illumina HiSeq	Phase_I	140454978	NM_018936	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	37	CCDS4244.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.200471	0.00025	.	.	ENSG00000112852	ENST00000194155	T	0.60299	0.2	4.94	-8.21	0.01041	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.33000	0.0848	L	0.43554	1.36	0.09310	N	1	B	0.15473	0.013	B	0.20184	0.028	T	0.44620	-0.9316	9	0.02654	T	1	.	2.0218	0.03510	0.1381:0.202:0.361:0.2989	.	140	Q9Y5E7	PCDB2_HUMAN	M	140	ENSP00000194155:I140M	ENSP00000194155:I140M	I	+	3	3	PCDHB2	140454978	0.000000	0.05858	0.004000	0.12327	0.000000	0.00434	-5.181000	0.00144	-1.280000	0.02402	-1.182000	0.01712	ATA		0.403	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
PCDHB2	56133	broad.mit.edu	37	5	140476514	140476514	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140476514C>A	ENST00000194155.4	+	1	2288	c.2140C>A	c.(2140-2142)Cgg>Agg	p.R714R		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	714					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R714R(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGTGGCGGTGCGGCTGTGCAG	0.697																																					p.R714R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2140A	5						.						28.0	32.0	31.0					5																	140476514		2058	3985	6043	140456698	SO:0001819	synonymous_variant	56133	exon1			AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"""Cadherins / Protocadherins : Clustered"""	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.2140C>A	5.37:g.140476514C>A		Somatic		Capture	Illumina HiSeq	Phase_I	140456698	NM_018936	Q4KMU1	Silent	SNP	ENST00000194155.4	37	CCDS4244.1																																																																																				0.697	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
PCDHB8	56128	broad.mit.edu	37	5	140558697	140558697	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140558697C>T	ENST00000239444.2	+	1	1327	c.1082C>T	c.(1081-1083)gCg>gTg	p.A361V	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	361	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A361V(1)		NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCTGAGAATGCGCCTGAAACT	0.448																																					p.A361V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1082T	5						.						229.0	298.0	274.0					5																	140558697		2203	4300	6503	140538881	SO:0001583	missense	56128	exon1			AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.1082C>T	5.37:g.140558697C>T	ENSP00000239444:p.Ala361Val	Somatic		Capture	Illumina HiSeq	Phase_I	140538881	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	C	6.054	0.378255	0.11466	.	.	ENSG00000120322	ENST00000239444	T	0.03663	3.85	4.25	2.42	0.29668	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.05823	0.0152	L	0.53249	1.67	0.09310	N	1	B	0.32382	0.368	B	0.35859	0.212	T	0.28427	-1.0044	9	0.66056	D	0.02	.	8.99	0.36017	0.0:0.8118:0.0:0.1882	.	361	Q9UN66	PCDB8_HUMAN	V	361	ENSP00000239444:A361V	ENSP00000239444:A361V	A	+	2	0	PCDHB8	140538881	0.000000	0.05858	0.002000	0.10522	0.021000	0.10359	0.087000	0.14958	0.250000	0.21479	-0.225000	0.12378	GCG		0.448	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
PCDHB11	56125	broad.mit.edu	37	5	140581425	140581425	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140581425C>T	ENST00000354757.3	+	1	2078	c.2078C>T	c.(2077-2079)gCg>gTg	p.A693V	PCDHB11_ENST00000536699.1_Missense_Mutation_p.A328V	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	693					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A693V(1)		NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTGGTGGTGGCGTTGGCCTCG	0.692																																					p.A693V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2078T	5						.						85.0	86.0	85.0					5																	140581425		2203	4295	6498	140561609	SO:0001583	missense	56125	exon1			AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.2078C>T	5.37:g.140581425C>T	ENSP00000346802:p.Ala693Val	Somatic		Capture	Illumina HiSeq	Phase_I	140561609	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	.	.	.	.	.	.	.	.	.	.	c	24.3	4.514543	0.85389	.	.	ENSG00000197479	ENST00000536699;ENST00000354757	T;T	0.25250	1.81;1.81	2.64	2.64	0.31445	.	.	.	.	.	T	0.63498	0.2516	H	0.98559	4.265	0.09310	N	1	D	0.76494	0.999	D	0.66196	0.942	T	0.59005	-0.7535	9	0.87932	D	0	.	10.5162	0.44892	0.0:0.8009:0.1991:0.0	.	693	Q9Y5F2	PCDBB_HUMAN	V	328;693	ENSP00000440344:A328V;ENSP00000346802:A693V	ENSP00000346802:A693V	A	+	2	0	PCDHB11	140561609	0.083000	0.21467	0.009000	0.14445	0.760000	0.43138	3.624000	0.54231	1.481000	0.48307	0.449000	0.29647	GCG		0.692	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
PCDHB12	56124	broad.mit.edu	37	5	140590170	140590170	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140590170C>T	ENST00000239450.2	+	1	1880	c.1691C>T	c.(1690-1692)cCg>cTg	p.P564L	PCDHB12_ENST00000541609.1_Missense_Mutation_p.P227L	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	564					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.P564L(1)|p.P564Q(1)		NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTGCTGTACCCGCTGCAGAAC	0.716																																					p.P564L												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C1691T	5						.						17.0	22.0	21.0					5																	140590170		2187	4270	6457	140570354	SO:0001583	missense	56124	exon1			AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.1691C>T	5.37:g.140590170C>T	ENSP00000239450:p.Pro564Leu	Somatic		Capture	Illumina HiSeq	Phase_I	140570354	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.999788	0.74818	.	.	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.60920	0.15;0.15	3.4	3.4	0.38934	Cadherin-like (1);	.	.	.	.	T	0.81138	0.4760	M	0.93939	3.475	0.51012	D	0.999903	D	0.89917	1.0	D	0.97110	1.0	D	0.87103	0.2180	9	0.87932	D	0	.	14.8086	0.69977	0.0:1.0:0.0:0.0	.	564	Q9Y5F1	PCDBC_HUMAN	L	227;564;184	ENSP00000440199:P227L;ENSP00000239450:P564L	ENSP00000239450:P564L	P	+	2	0	PCDHB12	140570354	0.000000	0.05858	0.993000	0.49108	0.978000	0.69477	0.244000	0.18124	1.626000	0.50381	0.479000	0.44913	CCG		0.716	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
PCDHB14	56122	broad.mit.edu	37	5	140605126	140605126	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140605126C>A	ENST00000239449.4	+	1	2049	c.2049C>A	c.(2047-2049)gcC>gcA	p.A683A	PCDHB14_ENST00000515856.2_Silent_p.A530A	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	683					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A683A(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGCCCAGGCCGACTCCCTCA	0.701																																					p.A683A	Ovarian(141;50 1831 27899 33809 37648)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2049A	5						.						66.0	75.0	72.0					5																	140605126		2184	4278	6462	140585310	SO:0001819	synonymous_variant	56122	exon1			AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.2049C>A	5.37:g.140605126C>A		Somatic		Capture	Illumina HiSeq	Phase_I	140585310	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																				0.701	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
PCDHB15	56121	broad.mit.edu	37	5	140626677	140626677	+	Missense_Mutation	SNP	G	G	A	rs143133095		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140626677G>A	ENST00000231173.3	+	1	1531	c.1531G>A	c.(1531-1533)Ggc>Agc	p.G511S		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	511	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.G511S(1)		NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CACGGACAACGGCCACCTGTT	0.682																																					p.G511S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1531A	5						.						99.0	108.0	105.0					5																	140626677		2203	4300	6503	140606861	SO:0001583	missense	56121	exon1			AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1531G>A	5.37:g.140626677G>A	ENSP00000231173:p.Gly511Ser	Somatic		Capture	Illumina HiSeq	Phase_I	140606861	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.290590	0.59976	.	.	ENSG00000113248	ENST00000231173	D	0.91407	-2.84	4.76	4.76	0.60689	Cadherin (5);Cadherin-like (1);	.	.	.	.	D	0.97701	0.9246	H	0.99600	4.65	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	D	0.99821	1.1047	9	0.87932	D	0	.	17.8023	0.88591	0.0:0.0:1.0:0.0	.	511	Q9Y5E8	PCDBF_HUMAN	S	511	ENSP00000231173:G511S	ENSP00000231173:G511S	G	+	1	0	PCDHB15	140606861	1.000000	0.71417	0.302000	0.25058	0.005000	0.04900	9.562000	0.98145	2.378000	0.81104	0.586000	0.80456	GGC		0.682	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
PCDHGA3	56112	broad.mit.edu	37	5	140725338	140725338	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140725338C>T	ENST00000253812.6	+	1	1738	c.1738C>T	c.(1738-1740)Cgc>Tgc	p.R580C	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	580	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R580C(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGGCGCCTCGCTCCGCAGA	0.672																																					p.R580C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1738T	5						.						87.0	96.0	93.0					5																	140725338		2203	4300	6503	140705522	SO:0001583	missense	56112	exon1			AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1738C>T	5.37:g.140725338C>T	ENSP00000253812:p.Arg580Cys	Somatic		Capture	Illumina HiSeq	Phase_I	140705522	NM_018916	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	16.18	3.049703	0.55218	.	.	ENSG00000254245	ENST00000253812	T	0.59772	0.24	5.27	5.27	0.74061	Cadherin (2);Cadherin-like (1);	0.000000	0.33040	U	0.005342	D	0.82715	0.5097	H	0.96576	3.845	0.36653	D	0.87751	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.988	D	0.89599	0.3833	10	0.87932	D	0	.	12.3353	0.55062	0.0:0.9211:0.0:0.0789	.	580;580	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	C	580	ENSP00000253812:R580C	ENSP00000253812:R580C	R	+	1	0	PCDHGA3	140705522	0.001000	0.12720	1.000000	0.80357	0.767000	0.43475	0.790000	0.26900	2.636000	0.89361	0.558000	0.71614	CGC		0.672	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916	
PCDHGB1	56104	broad.mit.edu	37	5	140731358	140731358	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140731358T>C	ENST00000523390.1	+	1	1531	c.1531T>C	c.(1531-1533)Ttc>Ctc	p.F511L	PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	511	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F511L(2)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGGGTGGTGTTCGCGCAGCG	0.682																																					p.F511L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1531C	5						.						38.0	45.0	43.0					5																	140731358		2012	4184	6196	140711542	SO:0001583	missense	56104	exon1			AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1531T>C	5.37:g.140731358T>C	ENSP00000429273:p.Phe511Leu	Somatic		Capture	Illumina HiSeq	Phase_I	140711542	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	37	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	22.2	4.264094	0.80358	.	.	ENSG00000254221	ENST00000523390	T	0.52057	0.68	5.49	5.49	0.81192	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.55893	0.1949	L	0.32530	0.975	0.24440	N	0.994537	D;P	0.54047	0.964;0.854	P;P	0.59012	0.841;0.85	T	0.52873	-0.8517	9	0.66056	D	0.02	.	15.5567	0.76200	0.0:0.0:0.0:1.0	.	511;511	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	L	511	ENSP00000429273:F511L	ENSP00000429273:F511L	F	+	1	0	PCDHGB1	140711542	0.001000	0.12720	1.000000	0.80357	0.976000	0.68499	1.113000	0.31184	2.212000	0.71576	0.460000	0.39030	TTC		0.682	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922	
PCDHGA6	56109	broad.mit.edu	37	5	140755877	140755877	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140755877G>A	ENST00000517434.1	+	1	2227	c.2227G>A	c.(2227-2229)Gtg>Atg	p.V743M	PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	743					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V743M(1)		breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTTGTGGGCGTGGAAGGGGT	0.612																																					p.V743M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2227A	5						.						75.0	80.0	78.0					5																	140755877		2203	4300	6503	140736061	SO:0001583	missense	56109	exon1			AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"""Cadherins / Protocadherins : Clustered"""	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.2227G>A	5.37:g.140755877G>A	ENSP00000429601:p.Val743Met	Somatic		Capture	Illumina HiSeq	Phase_I	140736061	NM_032086	A6H8K7|B2RN55|Q9Y5D1	Missense_Mutation	SNP	ENST00000517434.1	37	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	7.493	0.651010	0.14516	.	.	ENSG00000253731	ENST00000517434	T	0.50548	0.74	5.15	-0.377	0.12501	.	0.398307	0.14856	N	0.294369	T	0.45115	0.1326	M	0.81497	2.545	0.20638	N	0.99987	B;B	0.30482	0.095;0.281	B;B	0.24394	0.053;0.043	T	0.40997	-0.9533	10	0.51188	T	0.08	.	9.8004	0.40761	0.4966:0.0:0.5034:0.0	.	743;743	Q9Y5G7-2;Q9Y5G7	.;PCDG6_HUMAN	M	743	ENSP00000429601:V743M	ENSP00000429601:V743M	V	+	1	0	PCDHGA6	140736061	0.000000	0.05858	0.756000	0.31282	0.025000	0.11179	-0.171000	0.09883	0.011000	0.14865	-0.812000	0.03155	GTG		0.612	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919	
PCDHGA8	9708	broad.mit.edu	37	5	140774056	140774056	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140774056C>T	ENST00000398604.2	+	1	1676	c.1676C>T	c.(1675-1677)gCg>gTg	p.A559V	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	559	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A559V(1)		endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AATGACAACGCGCCCGAGATC	0.657																																					p.A559V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1676T	5						.						104.0	120.0	114.0					5																	140774056		2203	4300	6503	140754240	SO:0001583	missense	9708	exon1			AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.1676C>T	5.37:g.140774056C>T	ENSP00000381605:p.Ala559Val	Somatic		Capture	Illumina HiSeq	Phase_I	140754240	NM_032088	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	5.018	0.188933	0.09547	.	.	ENSG00000253767	ENST00000398604	T	0.17691	2.26	4.92	-2.06	0.07298	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.30999	U	0.008448	T	0.13415	0.0325	L	0.53617	1.68	0.09310	N	1	B;B	0.27853	0.027;0.191	B;B	0.25759	0.014;0.063	T	0.11179	-1.0598	10	0.44086	T	0.13	.	7.9811	0.30183	0.0:0.6453:0.1:0.2547	.	559;559	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	V	559	ENSP00000381605:A559V	ENSP00000381605:A559V	A	+	2	0	PCDHGA8	140754240	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.434000	0.21494	-0.936000	0.03723	-0.136000	0.14681	GCG		0.657	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
PCDHGA9	56107	broad.mit.edu	37	5	140784200	140784200	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140784200G>T	ENST00000573521.1	+	1	1681	c.1681G>T	c.(1681-1683)Gaa>Taa	p.E561*	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	561	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAATGCCCCAGAAATCCTGTA	0.547																																					p.E561X												.	.	0			c.G1681T	5						.						123.0	136.0	131.0					5																	140784200		2182	4298	6480	140764384	SO:0001587	stop_gained	56107	exon1			AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.1681G>T	5.37:g.140784200G>T	ENSP00000460274:p.Glu561*	Somatic		Capture	Illumina HiSeq	Phase_I	140764384	NM_018921	A2RU65|Q9Y5C9	Nonsense_Mutation	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																				0.547	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
PCDHGB6	56100	broad.mit.edu	37	5	140789679	140789679	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140789679C>T	ENST00000520790.1	+	1	1910	c.1910C>T	c.(1909-1911)gCa>gTa	p.A637V	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	637	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A637V(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GACAGGGACGCAGCCCGCCAG	0.672																																					p.A637V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1910T	5						.						18.0	21.0	20.0					5																	140789679		2073	4194	6267	140769863	SO:0001583	missense	56100	exon1			AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"""Cadherins / Protocadherins : Clustered"""	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.1910C>T	5.37:g.140789679C>T	ENSP00000428603:p.Ala637Val	Somatic		Capture	Illumina HiSeq	Phase_I	140769863	NM_018926	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	37	CCDS54929.1	.	.	.	.	.	.	.	.	.	.	c	12.26	1.884809	0.33255	.	.	ENSG00000253305	ENST00000520790	T	0.51325	0.71	4.99	4.12	0.48240	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.30727	0.0774	N	0.11106	0.095	0.22185	N	0.999303	B;B	0.29671	0.167;0.254	B;B	0.32022	0.119;0.139	T	0.25984	-1.0116	9	0.62326	D	0.03	.	9.8138	0.40840	0.0:0.8429:0.0:0.1571	.	637;637	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	V	637	ENSP00000428603:A637V	ENSP00000428603:A637V	A	+	2	0	PCDHGB6	140769863	0.001000	0.12720	0.918000	0.36340	0.593000	0.36681	1.067000	0.30616	1.094000	0.41399	0.563000	0.77884	GCA		0.672	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926	
PCDHGA12	26025	broad.mit.edu	37	5	140812070	140812070	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:140812070G>A	ENST00000252085.3	+	1	1886	c.1744G>A	c.(1744-1746)Gca>Aca	p.A582T	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	582	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A582T(2)		breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCCCGCTCCGCAGAGCCCGG	0.682																																					p.A582T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1744A	5						.						79.0	92.0	88.0					5																	140812070		2203	4299	6502	140792254	SO:0001583	missense	26025	exon1			AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"""Cadherins / Protocadherins : Clustered"""	8699	other	protocadherin	"""fibroblast cadherin FIB3"""	603059	"""cadherin 21"""	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.1744G>A	5.37:g.140812070G>A	ENSP00000252085:p.Ala582Thr	Somatic		Capture	Illumina HiSeq	Phase_I	140792254	NM_032094	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	37	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	g	15.50	2.853463	0.51270	.	.	ENSG00000253159	ENST00000252085	T	0.55413	0.52	4.89	3.09	0.35607	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.61652	0.2364	M	0.71036	2.16	0.24966	N	0.991691	P;D	0.60160	0.955;0.987	P;P	0.57720	0.538;0.826	T	0.51624	-0.8682	9	0.52906	T	0.07	.	5.0542	0.14524	0.0715:0.1269:0.54:0.2617	.	582;582	O60330-2;O60330	.;PCDGC_HUMAN	T	582	ENSP00000252085:A582T	ENSP00000252085:A582T	A	+	1	0	PCDHGA12	140792254	0.990000	0.36364	0.680000	0.29994	0.945000	0.59286	3.272000	0.51616	0.582000	0.29556	0.556000	0.70494	GCA		0.682	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735	
PCDH1	5097	broad.mit.edu	37	5	141248930	141248930	+	Missense_Mutation	SNP	C	C	T	rs538908747		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:141248930C>T	ENST00000394536.3	-	2	246	c.107G>A	c.(106-108)cGg>cAg	p.R36Q	PCDH1_ENST00000536585.1_Missense_Mutation_p.R14Q|PCDH1_ENST00000456271.1_Missense_Mutation_p.R36Q|PCDH1_ENST00000503492.1_Missense_Mutation_p.R36Q|PCDH1_ENST00000287008.3_Missense_Mutation_p.R36Q	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	36					cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R36Q(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		CAGCAGTAGCCGTTGCCCCCC	0.647																																					p.R36Q	Ovarian(132;1609 1739 4190 14731 45037)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G107A	5						.						19.0	23.0	22.0					5																	141248930		2199	4295	6494	141229114	SO:0001583	missense	5097	exon2			AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"""Cadherins / Protocadherins : Non-clustered"""	8655	protein-coding gene	gene with protein product		603626	"""protocadherin 1 (cadherin-like 1)"""			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000394536.3:c.107G>A	5.37:g.141248930C>T	ENSP00000378043:p.Arg36Gln	Somatic		Capture	Illumina HiSeq	Phase_I	141229114	NM_032420	Q8IUP2	Missense_Mutation	SNP	ENST00000394536.3	37	CCDS43375.1	.	.	.	.	.	.	.	.	.	.	C	10.81	1.455568	0.26161	.	.	ENSG00000156453	ENST00000503492;ENST00000287008;ENST00000394536;ENST00000456271;ENST00000357517;ENST00000536585;ENST00000514773	T;T;T;T;T;T;T	0.55760	0.5;0.56;0.58;0.6;0.54;0.54;1.95	4.0	-5.86	0.02304	.	0.678610	0.12061	N	0.503196	T	0.22166	0.0534	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.13683	-1.0500	10	0.22706	T	0.39	.	5.0537	0.14522	0.2605:0.1958:0.0:0.5437	.	36;36	Q08174;Q08174-2	PCDH1_HUMAN;.	Q	36;36;36;36;47;14;14	ENSP00000424667:R36Q;ENSP00000287008:R36Q;ENSP00000378043:R36Q;ENSP00000403497:R36Q;ENSP00000350122:R47Q;ENSP00000438825:R14Q;ENSP00000424163:R14Q	ENSP00000287008:R36Q	R	-	2	0	PCDH1	141229114	0.606000	0.26949	0.000000	0.03702	0.000000	0.00434	0.878000	0.28126	-1.173000	0.02758	-1.194000	0.01681	CGG		0.647	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420	
PCDH12	51294	broad.mit.edu	37	5	141334773	141334773	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:141334773C>A	ENST00000231484.3	-	1	3854	c.2644G>T	c.(2644-2646)Gtt>Ttt	p.V882F	AC005740.6_ENST00000607378.1_RNA|PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	882					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V882F(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGCCTGCAACCTTCAGAGGC	0.652																																					p.V882F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2644T	5						.						33.0	37.0	35.0					5																	141334773		2203	4300	6503	141314957	SO:0001583	missense	51294	exon1			AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2644G>T	5.37:g.141334773C>A	ENSP00000231484:p.Val882Phe	Somatic		Capture	Illumina HiSeq	Phase_I	141314957	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	C	9.957	1.221647	0.22457	.	.	ENSG00000113555	ENST00000231484	T	0.53640	0.61	4.77	3.89	0.44902	.	1.302160	0.04854	N	0.442886	T	0.42787	0.1218	L	0.44542	1.39	0.22851	N	0.99865	B	0.33379	0.41	B	0.31812	0.136	T	0.35674	-0.9779	10	0.62326	D	0.03	.	8.1991	0.31413	0.0:0.8946:0.0:0.1054	.	882	Q9NPG4	PCD12_HUMAN	F	882	ENSP00000231484:V882F	ENSP00000231484:V882F	V	-	1	0	PCDH12	141314957	0.897000	0.30589	0.516000	0.27786	0.009000	0.06853	0.756000	0.26419	2.653000	0.90120	0.561000	0.74099	GTT		0.652	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
NDFIP1	80762	broad.mit.edu	37	5	141511420	141511420	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:141511420T>C	ENST00000253814.4	+	2	581	c.111T>C	c.(109-111)gaT>gaC	p.D37D	NDFIP1_ENST00000509436.1_3'UTR	NM_030571.3	NP_085048.1	Q9BT67	NFIP1_HUMAN	Nedd4 family interacting protein 1	37					cellular iron ion homeostasis (GO:0006879)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of protein transport (GO:0051224)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transporter activity (GO:0032410)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein ubiquitination (GO:0031398)|regulation of isotype switching to IgG isotypes (GO:0048302)|regulation of lymphocyte differentiation (GO:0045619)|regulation of myeloid leukocyte differentiation (GO:0002761)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cell cortex (GO:0005938)|endosome (GO:0005768)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	signal transducer activity (GO:0004871)	p.D37D(1)		large_intestine(3)|lung(1)|ovary(1)	5		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGCAGGTGATGCTCCTCCAC	0.408																																					p.D37D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T111C	5						.						130.0	138.0	135.0					5																	141511420		2203	4300	6503	141491604	SO:0001819	synonymous_variant	80762	exon2			BC004317	CCDS4273.1	5q31.3	2008-02-05			ENSG00000131507	ENSG00000131507			17592	protein-coding gene	gene with protein product		612050				11042109, 11748237	Standard	NM_030571		Approved	N4WBP5, MGC10924	uc003lmi.4	Q9BT67	OTTHUMG00000129659	ENST00000253814.4:c.111T>C	5.37:g.141511420T>C		Somatic		Capture	Illumina HiSeq	Phase_I	141491604	NM_030571	B2RDB8|D3DQF0|Q658T8|Q8N2E3|Q8N2F9	Silent	SNP	ENST00000253814.4	37	CCDS4273.1																																																																																				0.408	NDFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251859.2	NM_030571	
SPINK5	11005	broad.mit.edu	37	5	147513418	147513418	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:147513418C>T	ENST00000256084.7	+	32	3196	c.3154C>T	c.(3154-3156)Cca>Tca	p.P1052S	SPINK5_ENST00000359874.3_Missense_Mutation_p.P1082S	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	1052					anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P1082S(1)|p.P1052S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGCAGCACCCCAGGAACCAC	0.512																																					p.P1082S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3244T	5						.						76.0	89.0	85.0					5																	147513418		2128	4246	6374	147493611	SO:0001583	missense	11005	exon33			AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.3154C>T	5.37:g.147513418C>T	ENSP00000256084:p.Pro1052Ser	Somatic		Capture	Illumina HiSeq	Phase_I	147493611	NM_001127698	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	C	9.507	1.104716	0.20632	.	.	ENSG00000133710	ENST00000359874;ENST00000256084	T;T	0.40476	1.03;1.09	4.86	1.82	0.25136	.	1.207450	0.06274	N	0.696235	T	0.33147	0.0853	L	0.51422	1.61	0.09310	N	1	P;P	0.47762	0.9;0.651	B;B	0.36567	0.228;0.122	T	0.25641	-1.0126	10	0.35671	T	0.21	-0.0093	6.4487	0.21892	0.0:0.5444:0.3575:0.0981	.	1082;1052	Q9NQ38-3;Q9NQ38	.;ISK5_HUMAN	S	1082;1052	ENSP00000352936:P1082S;ENSP00000256084:P1052S	ENSP00000256084:P1052S	P	+	1	0	SPINK5	147493611	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	0.152000	0.16302	0.702000	0.31825	0.650000	0.86243	CCA		0.512	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
TNIP1	10318	broad.mit.edu	37	5	150407669	150407669	+	IGR	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:150407669C>T	ENST00000389378.2	-	0	3268				GPX3_ENST00000517973.1_3'UTR|GPX3_ENST00000388825.4_Missense_Mutation_p.A220V	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1						defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)	p.A220V(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CGGCAGGCAGCCCTGGGGGTC	0.577																																					p.A220V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C659T	5						.						27.0	35.0	32.0					5																	150407669		2103	4222	6325	150387862	SO:0001628	intergenic_variant	2878	exon5			AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"""virion-associated nuclear-shuttling protein"", ""Nef-associated factor 1 SNP"""	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025			5.37:g.150407669C>T		Somatic		Capture	Illumina HiSeq	Phase_I	150387862	NM_002084	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Missense_Mutation	SNP	ENST00000389378.2	37	CCDS34280.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.336571	0.41398	.	.	ENSG00000211445	ENST00000388825	T	0.03004	4.08	5.03	0.839	0.18907	.	0.817956	0.11038	N	0.606478	T	0.02156	0.0067	N	0.14661	0.345	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.46498	-0.9187	10	0.39692	T	0.17	.	2.4575	0.04533	0.1521:0.5298:0.1478:0.1702	.	220	P22352	GPX3_HUMAN	V	220	ENSP00000373477:A220V	ENSP00000373477:A220V	A	+	2	0	GPX3	150387862	0.063000	0.20901	0.005000	0.12908	0.785000	0.44390	0.261000	0.18442	0.217000	0.20800	0.655000	0.94253	GCC		0.577	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
SLC36A2	153201	broad.mit.edu	37	5	150726884	150726884	+	Silent	SNP	T	T	C	rs145424088		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:150726884T>C	ENST00000335244.4	-	1	267	c.138A>G	c.(136-138)gcA>gcG	p.A46A	SLC36A2_ENST00000521967.1_Silent_p.A46A	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	46					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)	p.A46A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	TCTTCAAGCCTGCTGACTCTG	0.478																																					p.A46A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A138G	5						.						180.0	172.0	175.0					5																	150726884		2203	4300	6503	150707077	SO:0001819	synonymous_variant	153201	exon1			AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"""Solute carriers"""	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.138A>G	5.37:g.150726884T>C		Somatic		Capture	Illumina HiSeq	Phase_I	150707077	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Silent	SNP	ENST00000335244.4	37	CCDS4315.1																																																																																				0.478	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1		
FAT2	2196	broad.mit.edu	37	5	150914046	150914046	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:150914046G>A	ENST00000261800.5	-	12	9363	c.9351C>T	c.(9349-9351)caC>caT	p.H3117H		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3117	Cadherin 28. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.H3117H(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCACAGCACAGTGGCTGGGGA	0.587																																					p.H3117H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9351T	5						.						62.0	55.0	58.0					5																	150914046		2203	4300	6503	150894239	SO:0001819	synonymous_variant	2196	exon12			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.9351C>T	5.37:g.150914046G>A		Somatic		Capture	Illumina HiSeq	Phase_I	150894239	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																				0.587	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
FAT2	2196	broad.mit.edu	37	5	150923781	150923781	+	Missense_Mutation	SNP	G	G	A	rs201714112		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:150923781G>A	ENST00000261800.5	-	9	6919	c.6907C>T	c.(6907-6909)Cgg>Tgg	p.R2303W		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2303	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R2303W(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCACGGTTCCGCCCTGAGTCC	0.507																																					p.R2303W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6907T	5						.	G	TRP/ARG	0,4406		0,0,2203	107.0	106.0	107.0		6907	-1.6	0.9	5		107	3,8597	3.0+/-9.4	0,3,4297	yes	missense	FAT2	NM_001447.2	101	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	2303/4350	150923781	3,13003	2203	4300	6503	150903974	SO:0001583	missense	2196	exon9			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.6907C>T	5.37:g.150923781G>A	ENSP00000261800:p.Arg2303Trp	Somatic		Capture	Illumina HiSeq	Phase_I	150903974	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.307619	0.40795	0.0	3.49E-4	ENSG00000086570	ENST00000261800	T	0.52754	0.65	5.68	-1.58	0.08479	Cadherin (4);Cadherin-like (1);	1.099180	0.06932	N	0.811314	T	0.64327	0.2588	M	0.79475	2.455	0.09310	N	1	D	0.65815	0.995	P	0.54210	0.745	T	0.67860	-0.5561	10	0.66056	D	0.02	.	17.8533	0.88754	0.0:0.0:0.3266:0.6734	.	2303	Q9NYQ8	FAT2_HUMAN	W	2303	ENSP00000261800:R2303W	ENSP00000261800:R2303W	R	-	1	2	FAT2	150903974	0.000000	0.05858	0.869000	0.34112	0.811000	0.45836	0.147000	0.16202	0.008000	0.14787	-0.314000	0.08810	CGG		0.507	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
CNOT8	9337	broad.mit.edu	37	5	154250262	154250262	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:154250262A>T	ENST00000517876.1	+	5	829	c.353A>T	c.(352-354)aAc>aTc	p.N118I	CNOT8_ENST00000524105.1_Intron|CNOT8_ENST00000519404.1_Intron|CNOT8_ENST00000403027.2_Missense_Mutation_p.N118I|CNOT8_ENST00000521583.1_Missense_Mutation_p.N12I|CNOT8_ENST00000521450.1_Missense_Mutation_p.N12I|CNOT8_ENST00000520671.1_Missense_Mutation_p.N12I|CNOT8_ENST00000523698.1_Missense_Mutation_p.N12I|CNOT8_ENST00000285896.6_Missense_Mutation_p.N118I			Q9UFF9	CNOT8_HUMAN	CCR4-NOT transcription complex, subunit 8	118					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|gene silencing by miRNA (GO:0035195)|mRNA metabolic process (GO:0016071)|negative regulation of cell proliferation (GO:0008285)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N118I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CTCCTTGCTAACTCAGGACTA	0.423																																					p.N118I	NSCLC(140;1804 1895 27149 29895 35312)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A353T	5						.						164.0	151.0	155.0					5																	154250262		2203	4300	6503	154230455	SO:0001583	missense	9337	exon4			AF053318	CCDS4329.1, CCDS75361.1	5q31-q33	2008-07-18			ENSG00000155508	ENSG00000155508			9207	protein-coding gene	gene with protein product	"""PGK promoter directed over production"""	603731		POP2		10036195, 10637334	Standard	XM_005268527		Approved	CAF1, hCAF1, CALIF	uc003lvw.3	Q9UFF9	OTTHUMG00000130192	ENST00000517876.1:c.353A>T	5.37:g.154250262A>T	ENSP00000430493:p.Asn118Ile	Somatic		Capture	Illumina HiSeq	Phase_I	154230455	NM_004779	B0AZS3|B2RAR8|B7Z8R1|D3DQI8|O95709|Q7Z521|Q9H6Y1	Missense_Mutation	SNP	ENST00000517876.1	37	CCDS4329.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.694190	0.88735	.	.	ENSG00000155508	ENST00000523698;ENST00000517876;ENST00000520472;ENST00000519211;ENST00000519903;ENST00000521450;ENST00000403027;ENST00000517568;ENST00000285896;ENST00000542339;ENST00000520671;ENST00000521583	T;T;T;T;T;T;T;T;T;T;T	0.50277	1.94;1.94;1.94;1.94;1.94;1.94;1.94;0.75;1.94;1.94;1.94	5.54	5.54	0.83059	Ribonuclease H-like (1);	0.040364	0.85682	D	0.000000	T	0.58623	0.2135	M	0.83012	2.62	0.80722	D	1	P	0.44380	0.834	P	0.49421	0.61	T	0.64179	-0.6468	10	0.56958	D	0.05	-18.6059	8.3321	0.32193	0.8828:0.0:0.1172:0.0	.	118	Q9UFF9	CNOT8_HUMAN	I	12;118;118;118;12;12;118;118;118;95;12;12	ENSP00000428565:N12I;ENSP00000430493:N118I;ENSP00000430215:N118I;ENSP00000429108:N118I;ENSP00000428359:N12I;ENSP00000431034:N12I;ENSP00000384747:N118I;ENSP00000428090:N118I;ENSP00000285896:N118I;ENSP00000428305:N12I;ENSP00000429882:N12I	ENSP00000285896:N118I	N	+	2	0	CNOT8	154230455	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.958000	0.56737	2.102000	0.63906	0.454000	0.30748	AAC		0.423	CNOT8-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377449.1	NM_004779	
SGCD	6444	broad.mit.edu	37	5	155771560	155771560	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:155771560T>C	ENST00000435422.3	+	2	549	c.62T>C	c.(61-63)gTa>gCa	p.V21A	SGCD_ENST00000337851.4_Missense_Mutation_p.V22A|SGCD_ENST00000517913.1_Missense_Mutation_p.V22A|SGCD_ENST00000447401.1_Missense_Mutation_p.V22A	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)	21					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)		p.V22A(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|prostate(1)	24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGGCCACAGGTATACAAGGTG	0.498																																					p.V22A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T65C	5						.						116.0	119.0	118.0					5																	155771560		1957	4158	6115	155704138	SO:0001583	missense	6444	exon3			BX537948	CCDS47325.1, CCDS47326.1, CCDS47327.1	5q33-q34	2014-09-17	2002-08-29						10807	protein-coding gene	gene with protein product		601411	"""sarcoglycan, delta (35kD dystrophin-associated glycoprotein)"""			8776597, 8841194, 10974018	Standard	NM_000337		Approved	DAGD, LGMD2F, CMD1L	uc003lwd.4	Q92629		ENST00000435422.3:c.62T>C	5.37:g.155771560T>C	ENSP00000403003:p.Val21Ala	Somatic		Capture	Illumina HiSeq	Phase_I	155704138	NM_172244	A8K9S9|Q53XA5|Q99644	Missense_Mutation	SNP	ENST00000435422.3	37	CCDS47327.1	.	.	.	.	.	.	.	.	.	.	T	14.16	2.451314	0.43531	.	.	ENSG00000170624	ENST00000517913;ENST00000435422;ENST00000337851;ENST00000447401	D;D;D;D	0.94897	-3.55;-3.55;-3.55;-3.55	5.59	5.59	0.84812	.	0.123766	0.53938	D	0.000050	D	0.93054	0.7789	M	0.61703	1.905	0.46654	D	0.999148	B;B;B	0.30763	0.294;0.25;0.252	B;B;B	0.30943	0.122;0.075;0.107	D	0.91656	0.5338	10	0.40728	T	0.16	-7.6114	15.7811	0.78260	0.0:0.0:0.0:1.0	.	21;22;22	Q92629;Q92629-2;Q92629-3	SGCD_HUMAN;.;.	A	22;21;22;22	ENSP00000429378:V22A;ENSP00000403003:V21A;ENSP00000338343:V22A;ENSP00000408324:V22A	ENSP00000338343:V22A	V	+	2	0	SGCD	155704138	1.000000	0.71417	0.984000	0.44739	0.420000	0.31355	6.035000	0.70940	2.123000	0.65237	0.533000	0.62120	GTA		0.498	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3		
FBXL7	23194	broad.mit.edu	37	5	15616144	15616144	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:15616144G>A	ENST00000504595.1	+	2	571	c.90G>A	c.(88-90)acG>acA	p.T30T	FBXL7_ENST00000510662.1_5'UTR|FBXL7_ENST00000329673.7_Silent_p.T18T	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	30					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.T30T(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						CAGATCACACGCCCACTAAAG	0.468																																					p.T30T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G90A	5						.						88.0	89.0	89.0					5																	15616144		2008	4186	6194	15669144	SO:0001819	synonymous_variant	23194	exon2			AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"""F-boxes / Leucine-rich repeats"""	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.90G>A	5.37:g.15616144G>A		Somatic		Capture	Illumina HiSeq	Phase_I	15669144	NM_012304	B9EGF1|D6RDY7|O94926	Silent	SNP	ENST00000504595.1	37	CCDS54833.1																																																																																				0.468	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304	
FAM71B	153745	broad.mit.edu	37	5	156589814	156589814	+	Missense_Mutation	SNP	C	C	T	rs372740796		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:156589814C>T	ENST00000302938.4	-	2	1557	c.1462G>A	c.(1462-1464)Gta>Ata	p.V488I		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	488						nucleus (GO:0005634)		p.V488I(1)		NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTGCCCCTTACGTTGCTGTAC	0.527																																					p.V488I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1462A	5						.						237.0	227.0	230.0					5																	156589814		2203	4300	6503	156522392	SO:0001583	missense	153745	exon2				CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1462G>A	5.37:g.156589814C>T	ENSP00000305596:p.Val488Ile	Somatic		Capture	Illumina HiSeq	Phase_I	156522392	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	37	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	C	7.111	0.575988	0.13623	.	.	ENSG00000170613	ENST00000302938	T	0.18016	2.24	4.52	-9.05	0.00730	.	4.528010	0.00772	N	0.001202	T	0.10165	0.0249	L	0.36672	1.1	0.09310	N	1	B	0.18166	0.026	B	0.06405	0.002	T	0.14227	-1.0480	10	0.36615	T	0.2	5.9634	1.173	0.01829	0.3449:0.0993:0.1677:0.3881	.	488	Q8TC56	FA71B_HUMAN	I	488	ENSP00000305596:V488I	ENSP00000305596:V488I	V	-	1	0	FAM71B	156522392	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.582000	0.00905	-3.173000	0.00224	-0.169000	0.13324	GTA		0.527	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899	
ADRA1B	147	broad.mit.edu	37	5	159399006	159399006	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:159399006G>A	ENST00000306675.3	+	2	1193	c.1070G>A	c.(1069-1071)cGc>cAc	p.R357H		NM_000679.3	NP_000670.1	P35368	ADA1B_HUMAN	adrenoceptor alpha 1B	357					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|adult heart development (GO:0007512)|behavioral response to cocaine (GO:0048148)|blood vessel remodeling (GO:0001974)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|multicellular organismal development (GO:0007275)|negative regulation of glycogen catabolic process (GO:0045818)|organ growth (GO:0035265)|positive regulation of glycogen catabolic process (GO:0045819)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of the force of heart contraction by epinephrine-norepinephrine (GO:0001997)|regulation of cardiac muscle contraction (GO:0055117)|regulation of vasoconstriction (GO:0019229)|response to amphetamine (GO:0001975)|response to morphine (GO:0043278)|vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure (GO:0001987)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)|protein heterodimerization activity (GO:0046982)	p.R357H(1)		endometrium(3)|large_intestine(6)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acepromazine(DB01614)|Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Dapiprazole(DB00298)|Desipramine(DB01151)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Ziprasidone(DB00246)	GAGTTCAAGCGCGCTTTCGTG	0.697																																					p.R357H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1070A	5						.						24.0	25.0	24.0					5																	159399006		2202	4295	6497	159331584	SO:0001583	missense	147	exon2			L31773	CCDS4347.1	5q33.3	2012-08-08	2012-05-09		ENSG00000170214	ENSG00000170214		"""GPCR / Class A : Adrenoceptors : alpha"""	278	protein-coding gene	gene with protein product		104220	"""adrenergic, alpha-1B-, receptor"""				Standard	XM_005265818		Approved		uc003lxt.1	P35368	OTTHUMG00000130327	ENST00000306675.3:c.1070G>A	5.37:g.159399006G>A	ENSP00000306662:p.Arg357His	Somatic		Capture	Illumina HiSeq	Phase_I	159331584	NM_000679	B0LPE1	Missense_Mutation	SNP	ENST00000306675.3	37	CCDS4347.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.798445	0.70567	.	.	ENSG00000170214	ENST00000306675	T	0.39592	1.07	4.09	3.2	0.36748	.	0.195505	0.45361	D	0.000375	T	0.55305	0.1912	L	0.52573	1.65	0.36691	D	0.879568	D	0.89917	1.0	D	0.69142	0.962	T	0.64309	-0.6438	10	0.72032	D	0.01	.	12.5488	0.56216	0.0:0.1696:0.8304:0.0	.	357	P35368	ADA1B_HUMAN	H	357	ENSP00000306662:R357H	ENSP00000306662:R357H	R	+	2	0	ADRA1B	159331584	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.667000	0.68067	0.822000	0.34565	0.462000	0.41574	CGC		0.697	ADRA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252676.1		
MYO10	4651	broad.mit.edu	37	5	16701082	16701082	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:16701082G>A	ENST00000513610.1	-	25	3876	c.3422C>T	c.(3421-3423)gCg>gTg	p.A1141V	MYO10_ENST00000505695.1_Missense_Mutation_p.A480V|MYO10_ENST00000427430.2_Missense_Mutation_p.A498V|MYO10_ENST00000274203.9_Missense_Mutation_p.A498V|MYO10_ENST00000515803.1_Missense_Mutation_p.A480V|MYO10_ENST00000512061.1_5'Flank	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1141					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.A1141V(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CGAGGACTGCGCCCCCTCAGA	0.607																																					p.A1141V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3422T	5						.						14.0	15.0	15.0					5																	16701082		2059	4149	6208	16754082	SO:0001583	missense	4651	exon25			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.3422C>T	5.37:g.16701082G>A	ENSP00000421280:p.Ala1141Val	Somatic		Capture	Illumina HiSeq	Phase_I	16754082	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.060674	0.36373	.	.	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	D;D;D;D;D	0.87412	-2.17;-2.25;-2.17;-2.25;-2.17	4.84	4.84	0.62591	.	.	.	.	.	T	0.79161	0.4399	N	0.19112	0.55	0.51012	D	0.999909	B;B	0.25312	0.023;0.123	B;B	0.12837	0.007;0.008	T	0.74639	-0.3598	9	0.29301	T	0.29	.	17.9599	0.89082	0.0:0.0:1.0:0.0	.	782;1141	Q69YP8;Q9HD67	.;MYO10_HUMAN	V	1141;480;498;480;498	ENSP00000421280:A1141V;ENSP00000425051:A480V;ENSP00000274203:A498V;ENSP00000421170:A480V;ENSP00000391106:A498V	ENSP00000274203:A498V	A	-	2	0	MYO10	16754082	1.000000	0.71417	0.127000	0.21898	0.080000	0.17528	7.777000	0.85628	2.228000	0.72767	0.462000	0.41574	GCG		0.607	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
MYO10	4651	broad.mit.edu	37	5	16701628	16701628	+	Missense_Mutation	SNP	C	C	T	rs192857675		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:16701628C>T	ENST00000513610.1	-	25	3330	c.2876G>A	c.(2875-2877)cGg>cAg	p.R959Q	MYO10_ENST00000505695.1_Missense_Mutation_p.R298Q|MYO10_ENST00000427430.2_Missense_Mutation_p.R316Q|MYO10_ENST00000274203.9_Missense_Mutation_p.R316Q|MYO10_ENST00000515803.1_Missense_Mutation_p.R298Q|MYO10_ENST00000512061.1_5'Flank	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	959					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.R959Q(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CGACAGGGACCGCTCGATATT	0.612													C|||	1	0.000199681	0.0	0.0	5008	,	,		18885	0.001		0.0	False		,,,				2504	0.0				p.R959Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2876A	5						.						36.0	41.0	40.0					5																	16701628		2133	4245	6378	16754628	SO:0001583	missense	4651	exon25			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.2876G>A	5.37:g.16701628C>T	ENSP00000421280:p.Arg959Gln	Somatic		Capture	Illumina HiSeq	Phase_I	16754628	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	13.99	2.402433	0.42613	.	.	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	T;T;T;T;T	0.41400	1.0;1.96;1.96;1.96;1.96	5.0	5.0	0.66597	.	.	.	.	.	T	0.21427	0.0516	N	0.17082	0.46	0.34277	D	0.681714	P;B	0.39250	0.665;0.154	B;B	0.21360	0.034;0.007	T	0.32455	-0.9906	9	0.22109	T	0.4	.	13.3179	0.60417	0.1579:0.842:0.0:0.0	.	600;959	Q69YP8;Q9HD67	.;MYO10_HUMAN	Q	959;298;316;298;316	ENSP00000421280:R959Q;ENSP00000425051:R298Q;ENSP00000274203:R316Q;ENSP00000421170:R298Q;ENSP00000391106:R316Q	ENSP00000274203:R316Q	R	-	2	0	MYO10	16754628	1.000000	0.71417	1.000000	0.80357	0.268000	0.26511	3.090000	0.50191	2.312000	0.78011	0.563000	0.77884	CGG		0.612	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
FABP6	2172	broad.mit.edu	37	5	159640768	159640768	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:159640768G>A	ENST00000393980.4	+	3	223	c.77G>A	c.(76-78)tGc>tAc	p.C26Y	FABP6_ENST00000393982.1_Missense_Mutation_p.C26Y	NM_001130958.1	NP_001124430.1	P51161	FABP6_HUMAN	fatty acid binding protein 6, ileal	0					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|negative regulation of cell proliferation (GO:0008285)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.C26Y(1)		breast(1)|kidney(1)|large_intestine(1)|lung(2)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTGTCTGCGTGCACATGGGTG	0.493																																					p.C26Y	Colon(29;562 677 12756 16385 20992)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G77A	5						.						149.0	157.0	155.0					5																	159640768		2064	4233	6297	159573346	SO:0001583	missense	2172	exon3			U19869	CCDS4349.1, CCDS43393.1	5q23-q35	2013-03-01	2008-08-01		ENSG00000170231	ENSG00000170231		"""Fatty acid binding protein family"""	3561	protein-coding gene	gene with protein product	"""illeal lipid-binding protein"", ""ileal bile acid binding protein"", ""gastrotropin"""	600422				7894165, 7619861	Standard	NM_001130958		Approved	I-15P, ILLBP, I-BAP, ILBP3, I-BABP, ILBP, I-BALB	uc003lxx.1	P51161	OTTHUMG00000130329	ENST00000393980.4:c.77G>A	5.37:g.159640768G>A	ENSP00000377549:p.Cys26Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	159573346	NM_001130958	Q07DR7|Q8TBI3|Q9UGI7	Missense_Mutation	SNP	ENST00000393980.4	37	CCDS43393.1	.	.	.	.	.	.	.	.	.	.	G	5.746	0.322117	0.10900	.	.	ENSG00000170231	ENST00000393980;ENST00000393982	T;T	0.14022	2.54;2.54	2.25	-0.638	0.11500	.	.	.	.	.	T	0.09598	0.0236	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.31861	-0.9928	8	0.87932	D	0	.	5.261	0.15573	0.4367:0.0:0.5633:0.0	.	26	P51161-2	.	Y	26	ENSP00000377549:C26Y;ENSP00000377551:C26Y	ENSP00000377549:C26Y	C	+	2	0	FABP6	159573346	0.001000	0.12720	0.000000	0.03702	0.012000	0.07955	0.352000	0.20113	-0.200000	0.10300	0.549000	0.68633	TGC		0.493	FABP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252678.4	NM_001040442	
RARS	5917	broad.mit.edu	37	5	167944830	167944830	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:167944830C>T	ENST00000231572.3	+	14	1690	c.1636C>T	c.(1636-1638)Cgt>Tgt	p.R546C	RARS_ENST00000538719.1_Missense_Mutation_p.R340C	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	546					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.R546C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		GTCTATTGCACGTCTGGCCAA	0.388																																					p.R546C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1636T	5						.						62.0	66.0	64.0					5																	167944830		2203	4300	6503	167877408	SO:0001583	missense	5917	exon14			BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1636C>T	5.37:g.167944830C>T	ENSP00000231572:p.Arg546Cys	Somatic		Capture	Illumina HiSeq	Phase_I	167877408	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Missense_Mutation	SNP	ENST00000231572.3	37	CCDS4367.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.404106	0.62288	.	.	ENSG00000113643	ENST00000231572;ENST00000538719	T;T	0.80738	-1.41;-1.41	5.59	5.59	0.84812	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);DALR anticodon binding (2);	0.000000	0.85682	D	0.000000	D	0.92792	0.7708	H	0.97077	3.935	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94442	0.7659	10	0.87932	D	0	-10.8467	13.1238	0.59342	0.2799:0.7201:0.0:0.0	.	546	P54136	SYRC_HUMAN	C	546;340	ENSP00000231572:R546C;ENSP00000439108:R340C	ENSP00000231572:R546C	R	+	1	0	RARS	167877408	0.996000	0.38824	0.856000	0.33681	0.871000	0.50021	3.404000	0.52623	2.620000	0.88729	0.655000	0.94253	CGT		0.388	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	
SLIT3	6586	broad.mit.edu	37	5	168175368	168175368	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:168175368G>A	ENST00000519560.1	-	20	2628	c.2209C>T	c.(2209-2211)Cga>Tga	p.R737*	SLIT3_ENST00000404867.3_Nonsense_Mutation_p.R737*|SLIT3_ENST00000332966.8_Nonsense_Mutation_p.R737*	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	737	LRRNT 4.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.R737*(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTGCTGCATCGCACCACTGTC	0.642																																					p.R737X	Ovarian(29;311 847 10864 17279 24903)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2209T	5						.						70.0	69.0	70.0					5																	168175368		2203	4300	6503	168107946	SO:0001587	stop_gained	6586	exon20			AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.2209C>T	5.37:g.168175368G>A	ENSP00000430333:p.Arg737*	Somatic		Capture	Illumina HiSeq	Phase_I	168107946	NM_003062	A6H8U9|J3KNP3|O95804|Q9UFH5	Nonsense_Mutation	SNP	ENST00000519560.1	37	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	g	41	8.747823	0.98939	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	.	.	.	5.3	4.43	0.53597	.	0.167150	0.53938	D	0.000050	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3695	0.74551	0.0:0.0:0.8595:0.1405	.	.	.	.	X	737	.	ENSP00000332164:R737X	R	-	1	2	SLIT3	168107946	1.000000	0.71417	0.969000	0.41365	0.901000	0.52897	5.395000	0.66291	1.214000	0.43395	0.550000	0.68814	CGA		0.642	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
DOCK2	1794	broad.mit.edu	37	5	169468131	169468131	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:169468131C>T	ENST00000256935.8	+	37	3818	c.3738C>T	c.(3736-3738)ctC>ctT	p.L1246L	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Silent_p.L738L|DOCK2_ENST00000540750.1_Silent_p.L307L	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1246	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.L1246L(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGCTCCTTCTCCACACCTGGC	0.478																																					p.L1246L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3738T	5						.						119.0	98.0	105.0					5																	169468131		2203	4300	6503	169400709	SO:0001819	synonymous_variant	1794	exon37			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.3738C>T	5.37:g.169468131C>T		Somatic		Capture	Illumina HiSeq	Phase_I	169400709	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																				0.478	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
STK10	6793	broad.mit.edu	37	5	171523521	171523521	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:171523521T>G	ENST00000176763.5	-	8	1257	c.914A>C	c.(913-915)gAg>gCg	p.E305A	STK10_ENST00000517775.1_5'Flank	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	305					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)	p.E305A(1)		breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AGCCACCAGCTCCCGCAGAGC	0.622																																					p.E305A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A914C	5						.						111.0	107.0	109.0					5																	171523521		2203	4300	6503	171456126	SO:0001583	missense	6793	exon8			AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.914A>C	5.37:g.171523521T>G	ENSP00000176763:p.Glu305Ala	Somatic		Capture	Illumina HiSeq	Phase_I	171456126	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	37	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	T	18.74	3.688007	0.68271	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.69040	-0.37	4.96	4.96	0.65561	Protein kinase-like domain (1);	0.185725	0.46145	D	0.000307	T	0.70081	0.3183	M	0.73217	2.22	0.58432	D	0.999998	P	0.42010	0.768	P	0.45195	0.473	T	0.74746	-0.3561	10	0.72032	D	0.01	.	12.646	0.56735	0.0:0.0:0.0:1.0	.	305	O94804	STK10_HUMAN	A	305	ENSP00000176763:E305A	ENSP00000176763:E305A	E	-	2	0	STK10	171456126	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.012000	0.88631	1.881000	0.54492	0.397000	0.26171	GAG		0.622	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990	
SH3PXD2B	285590	broad.mit.edu	37	5	171766488	171766488	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:171766488G>A	ENST00000311601.5	-	13	1791	c.1621C>T	c.(1621-1623)Cgg>Tgg	p.R541W	SH3PXD2B_ENST00000519643.1_Intron	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	541					adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)	p.R541W(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGCCGCTCCCGCTCCCGCTCC	0.652																																					p.R541W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1621T	5						.						40.0	45.0	43.0					5																	171766488		2203	4300	6503	171699093	SO:0001583	missense	285590	exon13			AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"""KIAA1295"""	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.1621C>T	5.37:g.171766488G>A	ENSP00000309714:p.Arg541Trp	Somatic		Capture	Illumina HiSeq	Phase_I	171699093	NM_001017995	B6F0V2|Q9P2Q1	Missense_Mutation	SNP	ENST00000311601.5	37	CCDS34291.1	.	.	.	.	.	.	.	.	.	.	G	7.301	0.612983	0.14066	.	.	ENSG00000174705	ENST00000311601	T	0.62498	0.02	0.0465	0.0465	0.14256	.	0.342040	0.29814	N	0.011121	T	0.42449	0.1203	N	0.08118	0	0.30846	N	0.735106	D	0.69078	0.997	P	0.50490	0.642	T	0.49688	-0.8913	8	.	.	.	-27.0803	.	.	.	.	541	A1X283	SPD2B_HUMAN	W	541	ENSP00000309714:R541W	.	R	-	1	2	SH3PXD2B	171699093	0.959000	0.32827	0.982000	0.44146	0.305000	0.27757	0.470000	0.22084	0.132000	0.18615	0.134000	0.15878	CGG		0.652	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963	
CREBRF	153222	broad.mit.edu	37	5	172517726	172517726	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:172517726G>A	ENST00000296953.2	+	4	863	c.544G>A	c.(544-546)Gct>Act	p.A182T	CREBRF_ENST00000540014.1_Missense_Mutation_p.A182T|CREBRF_ENST00000520420.1_Missense_Mutation_p.A182T|CREBRF_ENST00000522692.1_Missense_Mutation_p.A182T	NM_153607.2	NP_705835.2	Q8IUR6	CRERF_HUMAN	CREB3 regulatory factor	182					negative regulation of endoplasmic reticulum unfolded protein response (GO:1900102)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular transport (GO:0032388)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein transport (GO:0051222)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A182T(1)									AAGCAGAGCAGCTGCTCCTGT	0.443																																					p.A182T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G544A	5						.						52.0	50.0	50.0					5																	172517726		2203	4300	6503	172450332	SO:0001583	missense	153222	exon4			AY139008	CCDS34293.1, CCDS54948.1	5q35.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164463	ENSG00000164463			24050	protein-coding gene	gene with protein product	"""luman/CREB3 recruitment factor"""		"""chromosome 5 open reading frame 41"""	C5orf41		18391022	Standard	NM_153607		Approved	LRF	uc003mch.3	Q8IUR6	OTTHUMG00000163322	ENST00000296953.2:c.544G>A	5.37:g.172517726G>A	ENSP00000296953:p.Ala182Thr	Somatic		Capture	Illumina HiSeq	Phase_I	172450332	NM_001168393	B3DFH2|B3KW49|D3DQM2|F5GXN3|Q5HYG4|Q5HYK0|Q86YR3|Q8IZG1	Missense_Mutation	SNP	ENST00000296953.2	37	CCDS34293.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.511522	0.44660	.	.	ENSG00000164463	ENST00000522692;ENST00000296953;ENST00000540014;ENST00000520420;ENST00000538538;ENST00000393776	T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51	5.83	5.83	0.93111	.	0.192223	0.52532	D	0.000068	T	0.50956	0.1646	N	0.08118	0	0.50813	D	0.999899	B;B	0.19331	0.017;0.035	B;B	0.14023	0.007;0.01	T	0.48163	-0.9059	10	0.36615	T	0.2	.	13.3334	0.60503	0.072:0.0:0.928:0.0	.	182;182	Q8IUR6;Q8IUR6-2	CE041_HUMAN;.	T	182	ENSP00000431107:A182T;ENSP00000296953:A182T;ENSP00000440075:A182T;ENSP00000428290:A182T	ENSP00000296953:A182T	A	+	1	0	C5orf41	172450332	0.995000	0.38212	0.998000	0.56505	0.996000	0.88848	2.528000	0.45624	2.758000	0.94735	0.655000	0.94253	GCT		0.443	CREBRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372667.1	NM_153607	
STC2	8614	broad.mit.edu	37	5	172755119	172755119	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:172755119G>A	ENST00000265087.4	-	1	1387	c.78C>T	c.(76-78)gaC>gaT	p.D26D		NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	26					cellular calcium ion homeostasis (GO:0006874)|cellular response to hypoxia (GO:0071456)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|regulation of hormone biosynthetic process (GO:0046885)|regulation of store-operated calcium entry (GO:2001256)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)	p.D26D(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGTTGGTGGCGTCGGTCCCCC	0.642																																					p.D26D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C78T	5						.						99.0	103.0	102.0					5																	172755119		2203	4300	6503	172687725	SO:0001819	synonymous_variant	8614	exon1			AB012664	CCDS4388.1	5q35.2	2004-05-17			ENSG00000113739	ENSG00000113739			11374	protein-coding gene	gene with protein product		603665				9723890, 9753616	Standard	NM_003714		Approved	STC-2	uc003mco.1	O76061	OTTHUMG00000130542	ENST00000265087.4:c.78C>T	5.37:g.172755119G>A		Somatic		Capture	Illumina HiSeq	Phase_I	172687725	NM_003714		Silent	SNP	ENST00000265087.4	37	CCDS4388.1																																																																																				0.642	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252965.1	NM_003714	
SLC34A1	6569	broad.mit.edu	37	5	176813455	176813455	+	Silent	SNP	C	C	T	rs200188041		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:176813455C>T	ENST00000324417.5	+	5	511	c.420C>T	c.(418-420)aaC>aaT	p.N140N	SLC34A1_ENST00000512593.1_Silent_p.N140N	NM_003052.4	NP_003043.3	Q06495	NPT2A_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 1	140					arsenate ion transmembrane transport (GO:1901684)|bone remodeling (GO:0046849)|cellular response to metal ion (GO:0071248)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to staurosporine (GO:0072734)|dentinogenesis (GO:0097187)|gentamycin metabolic process (GO:1901128)|glycoprotein metabolic process (GO:0009100)|indole metabolic process (GO:0042431)|ion transport (GO:0006811)|kidney development (GO:0001822)|ossification (GO:0001503)|phosphate ion homeostasis (GO:0055062)|phosphate ion transport (GO:0006817)|positive regulation of membrane potential (GO:0045838)|positive regulation of phosphate transmembrane transport (GO:2000187)|positive regulation of sodium-dependent phosphate transport (GO:2000120)|protein homooligomerization (GO:0051260)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to lead ion (GO:0010288)|response to magnesium ion (GO:0032026)|response to mercury ion (GO:0046689)|response to potassium ion (GO:0035864)|response to thyroid hormone (GO:0097066)|response to vitamin A (GO:0033189)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|tricarboxylic acid metabolic process (GO:0072350)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|membrane-bounded vesicle (GO:0031988)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)	p.N140N(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCAAGGATAACGCCATCCTGT	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		20318	0.0		0.001	False		,,,				2504	0.0				p.N140N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C420T	5						.						79.0	69.0	73.0					5																	176813455		2203	4300	6503	176746061	SO:0001819	synonymous_variant	6569	exon5			L13258	CCDS4418.1, CCDS54953.1	5q35.3	2013-07-17	2013-07-17		ENSG00000131183	ENSG00000131183		"""Solute carriers"""	11019	protein-coding gene	gene with protein product	"""sodium/phosphate co-transporter"", ""solute carrier family 17 (sodium phosphate), member 2"", ""Na+-phosphate cotransporter type II"""	182309	"""solute carrier family 34 (sodium phosphate), member 1"""	NPT2, SLC17A2		8327470, 8693007	Standard	NM_003052		Approved	NAPI-3, NPTIIa, SLC11	uc003mgk.4	Q06495	OTTHUMG00000130857	ENST00000324417.5:c.420C>T	5.37:g.176813455C>T		Somatic		Capture	Illumina HiSeq	Phase_I	176746061	NM_001167579	B4DPE3	Silent	SNP	ENST00000324417.5	37	CCDS4418.1																																																																																				0.637	SLC34A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253431.1	NM_003052	
TMED9	54732	broad.mit.edu	37	5	177021203	177021203	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:177021203G>A	ENST00000332598.6	+	4	532	c.475G>A	c.(475-477)Gac>Aac	p.D159N		NM_017510.4	NP_059980.2	Q9BVK6	TMED9_HUMAN	transmembrane emp24 protein transport domain containing 9	159	Required for interaction with STX17.				COPI coating of Golgi vesicle (GO:0048205)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network transport vesicle (GO:0030140)	syntaxin binding (GO:0019905)	p.D159N(1)		endometrium(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(2)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGCTGCTAAAGACAAGTTGAG	0.507																																					p.D159N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G475A	5						.						115.0	100.0	105.0					5																	177021203		2203	4300	6503	176953809	SO:0001583	missense	54732	exon4			AF441399	CCDS4428.1	5q35.3	2008-02-05			ENSG00000184840	ENSG00000184840			24878	protein-coding gene	gene with protein product						12477932	Standard	NM_017510		Approved	HSGP25L2G	uc003mhx.3	Q9BVK6	OTTHUMG00000130859	ENST00000332598.6:c.475G>A	5.37:g.177021203G>A	ENSP00000330945:p.Asp159Asn	Somatic		Capture	Illumina HiSeq	Phase_I	176953809	NM_017510	Q14437|Q8WZ61	Missense_Mutation	SNP	ENST00000332598.6	37	CCDS4428.1	.	.	.	.	.	.	.	.	.	.	G	35	5.560576	0.96527	.	.	ENSG00000184840	ENST00000332598	T	0.17854	2.25	5.81	5.81	0.92471	GOLD (1);	0.000000	0.85682	D	0.000000	T	0.34454	0.0898	M	0.80847	2.515	0.80722	D	1	B	0.26845	0.161	B	0.39152	0.292	T	0.10870	-1.0611	10	0.59425	D	0.04	-38.9104	17.5764	0.87950	0.0:0.0:1.0:0.0	.	159	Q9BVK6	TMED9_HUMAN	N	159	ENSP00000330945:D159N	ENSP00000330945:D159N	D	+	1	0	TMED9	176953809	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.404000	0.97306	2.746000	0.94184	0.655000	0.94253	GAC		0.507	TMED9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253433.1	NM_017510	
RMND5B	64777	broad.mit.edu	37	5	177575020	177575020	+	Missense_Mutation	SNP	G	G	A	rs200559247	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:177575020G>A	ENST00000515098.1	+	12	1520	c.1169G>A	c.(1168-1170)cGc>cAc	p.R390H	RMND5B_ENST00000542098.1_Missense_Mutation_p.R377H|RMND5B_ENST00000313386.4_Missense_Mutation_p.R390H			Q96G75	RMD5B_HUMAN	required for meiotic nuclear division 5 homolog B (S. cerevisiae)	390								p.R390H(1)		endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	17	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GATGGGAAACGCATCATATTC	0.532													G|||	4	0.000798722	0.0	0.0	5008	,	,		20361	0.004		0.0	False		,,,				2504	0.0				p.R390H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1169A	5						.						86.0	81.0	83.0					5																	177575020		2203	4300	6503	177507626	SO:0001583	missense	64777	exon11			BC009911	CCDS4431.1, CCDS75382.1	5q35.3	2012-07-20			ENSG00000145916	ENSG00000145916			26181	protein-coding gene	gene with protein product	"""GID complex subunit 2 homolog B"""					12975309	Standard	NM_022762		Approved	FLJ22318, GID2, GID2B	uc003mim.3	Q96G75	OTTHUMG00000130897	ENST00000515098.1:c.1169G>A	5.37:g.177575020G>A	ENSP00000420875:p.Arg390His	Somatic		Capture	Illumina HiSeq	Phase_I	177507626	NM_022762	Q1HE27|Q6UVY7|Q9H6F6	Missense_Mutation	SNP	ENST00000515098.1	37	CCDS4431.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.981874	0.53827	.	.	ENSG00000145916	ENST00000313386;ENST00000515098;ENST00000542098	.	.	.	5.51	5.51	0.81932	.	0.063089	0.64402	D	0.000002	T	0.62036	0.2395	M	0.61703	1.905	0.47547	D	0.999451	D;D;B	0.64830	0.989;0.994;0.221	B;P;B	0.50617	0.443;0.646;0.023	T	0.65928	-0.6049	9	0.66056	D	0.02	-23.0526	10.3737	0.44068	0.0887:0.0:0.9113:0.0	.	377;377;390	B3KSG5;F5H6G4;Q96G75	.;.;RMD5B_HUMAN	H	390;390;377	.	ENSP00000320623:R390H	R	+	2	0	RMND5B	177507626	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	4.490000	0.60319	2.595000	0.87683	0.563000	0.77884	CGC		0.532	RMND5B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373542.1	NM_022762	
GRM6	2916	broad.mit.edu	37	5	178413731	178413731	+	Silent	SNP	G	G	A	rs150342590		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:178413731G>A	ENST00000517717.1	-	9	1562	c.1524C>T	c.(1522-1524)ggC>ggT	p.G508G	RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Silent_p.G508G			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	508					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)	p.G508G(1)		NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		CGTGGGGGTCGCCAGACCACT	0.697													G|||	1	0.000199681	0.0	0.0014	5008	,	,		15902	0.0		0.0	False		,,,				2504	0.0				p.G508G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1524T	5						.	G		0,4406		0,0,2203	29.0	32.0	31.0		1524	-4.6	0.0	5	dbSNP_134	31	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous	GRM6	NM_000843.3		0,4,6498	AA,AG,GG		0.0465,0.0,0.0308		508/878	178413731	4,13000	2203	4299	6502	178346337	SO:0001819	synonymous_variant	2916	exon8			U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1524C>T	5.37:g.178413731G>A		Somatic		Capture	Illumina HiSeq	Phase_I	178346337	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																				0.697	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
MAML1	9794	broad.mit.edu	37	5	179198183	179198183	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:179198183A>G	ENST00000292599.3	+	4	2270	c.2007A>G	c.(2005-2007)ccA>ccG	p.P669P	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)									p.P706P(1)|p.P669P(1)		central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGACCCGCCCACCACCCCAGT	0.517																																					p.P669P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A2007G	5						.						89.0	84.0	86.0					5																	179198183		2203	4300	6503	179130789	SO:0001819	synonymous_variant	9794	exon4			D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.2007A>G	5.37:g.179198183A>G		Somatic		Capture	Illumina HiSeq	Phase_I	179130789	NM_014757		Silent	SNP	ENST00000292599.3	37	CCDS34315.1																																																																																				0.517	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757	
SDHA	6389	broad.mit.edu	37	5	235329	235329	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:235329C>T	ENST00000264932.6	+	9	1250	c.1135C>T	c.(1135-1137)Cgc>Tgc	p.R379C	SDHA_ENST00000510361.1_Missense_Mutation_p.R331C|SDHA_ENST00000504309.1_Missense_Mutation_p.R379C	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	379					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)	p.R379C(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	GCTGGCCACGCGCCTGCCTGG	0.592									Familial Paragangliomas																												p.R379C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1135T	5						.						61.0	55.0	57.0					5																	235329		2203	4300	6503	288329	SO:0001583	missense	6389	exon9	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"""Mitochondrial respiratory chain complex / Complex II"""	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.1135C>T	5.37:g.235329C>T	ENSP00000264932:p.Arg379Cys	Somatic		Capture	Illumina HiSeq	Phase_I	288329	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	.	.	.	.	.	.	.	.	.	.	N	18.04	3.535666	0.64972	.	.	ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361	T;T;T	0.71698	-0.59;-0.59;-0.59	5.12	5.12	0.69794	Fumarate reductase/succinate dehydrogenase flavoprotein, N-terminal (1);	0.000000	0.85682	U	0.000000	D	0.91858	0.7423	H	0.99777	4.77	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.993;0.993	D;D;D;P;P	0.91635	0.997;0.999;0.992;0.789;0.789	D	0.95455	0.8538	10	0.87932	D	0	.	16.4201	0.83755	0.0:1.0:0.0:0.0	.	331;379;379;379;385	E9PBJ5;B4DYN5;D6RFM5;P31040;Q59GW8	.;.;.;DHSA_HUMAN;.	C	379;234;379;331	ENSP00000264932:R379C;ENSP00000426514:R379C;ENSP00000427703:R331C	ENSP00000264932:R379C	R	+	1	0	SDHA	288329	1.000000	0.71417	0.777000	0.31699	0.438000	0.31896	5.481000	0.66826	2.541000	0.85698	0.557000	0.71058	CGC		0.592	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
ADAMTS16	170690	broad.mit.edu	37	5	5182410	5182410	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:5182410G>A	ENST00000274181.7	+	4	893	c.755G>A	c.(754-756)cGc>cAc	p.R252H	ADAMTS16_ENST00000511368.1_Missense_Mutation_p.R252H	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	252					branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						TGTGGAAGACGCAAGAAATGT	0.478																																					p.R252H												.	.	0			c.G755A	5						.						74.0	78.0	77.0					5																	5182410		2094	4249	6343	5235410	SO:0001583	missense	170690	exon4			AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17108	protein-coding gene	gene with protein product		607510	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"""			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.755G>A	5.37:g.5182410G>A	ENSP00000274181:p.Arg252His	None		Capture	Illumina HiSeq	Phase_I	5235410	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	37	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	G	34	5.365343	0.95900	.	.	ENSG00000145536	ENST00000274181;ENST00000511368;ENST00000536857	T;T	0.64438	0.02;-0.1	5.47	5.47	0.80525	.	0.067771	0.64402	D	0.000014	T	0.80701	0.4673	M	0.81341	2.54	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.996;0.991	T	0.81226	-0.1029	10	0.48119	T	0.1	.	18.1389	0.89631	0.0:0.0:1.0:0.0	.	252;252;252	Q8TE57;Q8TE57-2;Q2XQZ0	ATS16_HUMAN;.;.	H	252	ENSP00000274181:R252H;ENSP00000421631:R252H	ENSP00000274181:R252H	R	+	2	0	ADAMTS16	5235410	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.768000	0.74980	2.567000	0.86603	0.650000	0.86243	CGC		0.478	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	
ICE1	23379	broad.mit.edu	37	5	5466529	5466529	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:5466529C>T	ENST00000296564.7	+	14	6197	c.5975C>T	c.(5974-5976)gCc>gTc	p.A1992V		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1992					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)	p.A1992V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						TACATTCACGCCCTCTGCAGG	0.403																																					p.A1992V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5975T	5						.						136.0	123.0	127.0					5																	5466529		1847	4088	5935	5519529	SO:0001583	missense	23379	exon14																														ENST00000296564.7:c.5975C>T	5.37:g.5466529C>T	ENSP00000296564:p.Ala1992Val	Somatic		Capture	Illumina HiSeq	Phase_I	5519529	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178581	0.94846	.	.	ENSG00000164151	ENST00000296564	T	0.34072	1.38	5.81	5.81	0.92471	.	.	.	.	.	T	0.58566	0.2131	L	0.59436	1.845	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.58612	-0.7606	9	0.87932	D	0	-10.8571	17.5828	0.87973	0.0:1.0:0.0:0.0	.	1992	Q9Y2F5	K0947_HUMAN	V	1992	ENSP00000296564:A1992V	ENSP00000296564:A1992V	A	+	2	0	KIAA0947	5519529	1.000000	0.71417	0.569000	0.28460	0.980000	0.70556	6.880000	0.75578	2.752000	0.94435	0.557000	0.71058	GCC		0.403	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
PRDM9	56979	broad.mit.edu	37	5	23526956	23526956	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:23526956C>T	ENST00000296682.3	+	11	1941	c.1759C>T	c.(1759-1761)Cgg>Tgg	p.R587W		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	587					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.R587R(1)|p.R587W(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGAGTGTGGGCGGGGCTTTAG	0.607										HNSCC(3;0.000094)																											p.R587W												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.C1759T	5						.						45.0	51.0	49.0					5																	23526956		2174	4277	6451	23562713	SO:0001583	missense	56979	exon11			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1759C>T	5.37:g.23526956C>T	ENSP00000296682:p.Arg587Trp	Somatic		Capture	Illumina HiSeq	Phase_I	23562713	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.761742	0.31228	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	T	0.19806	2.12	2.31	2.31	0.28768	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19087	0.0458	L	0.51914	1.62	0.27726	N	0.944952	B	0.34399	0.452	B	0.34779	0.189	T	0.17868	-1.0355	9	0.87932	D	0	-0.8007	6.3198	0.21211	0.295:0.7049:0.0:0.0	.	587	Q9NQV7	PRDM9_HUMAN	W	587;353	ENSP00000296682:R587W	ENSP00000253473:R353W	R	+	1	2	PRDM9	23562713	0.003000	0.15002	0.991000	0.47740	0.651000	0.38670	1.685000	0.37659	1.575000	0.49775	0.400000	0.26472	CGG		0.607	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
DROSHA	29102	broad.mit.edu	37	5	31526538	31526538	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:31526538A>G	ENST00000511367.2	-	4	746	c.502T>C	c.(502-504)Tac>Cac	p.Y168H	DROSHA_ENST00000344624.3_Missense_Mutation_p.Y168H|DROSHA_ENST00000513349.1_Missense_Mutation_p.Y168H|DROSHA_ENST00000442743.1_Missense_Mutation_p.Y168H|DROSHA_ENST00000504361.1_5'Flank	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	168	Pro-rich.			YQYPPGYSH -> RERERTSLE (in Ref. 4; CAB45133). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)	p.Y168H(1)		breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						CCCGGAGGGTACTGATAATTA	0.542																																					p.Y168H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T502C	5						.						43.0	43.0	43.0					5																	31526538		1872	4103	5975	31562295	SO:0001583	missense	29102	exon4			AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.502T>C	5.37:g.31526538A>G	ENSP00000425979:p.Tyr168His	Somatic		Capture	Illumina HiSeq	Phase_I	31562295	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.507311	0.44558	.	.	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188;ENST00000507438	T;T;T;T;T	0.52983	1.21;1.21;0.8;0.8;0.64	5.12	5.12	0.69794	.	0.067872	0.64402	D	0.000009	T	0.53174	0.1780	L	0.27053	0.805	0.49389	D	0.999783	P;D;D	0.65815	0.772;0.995;0.995	P;D;D	0.70487	0.556;0.969;0.969	T	0.47262	-0.9131	10	0.20519	T	0.43	-5.3047	14.9429	0.71009	1.0:0.0:0.0:0.0	.	168;168;168	Q9NRR4-2;E7EMP9;Q9NRR4	.;.;RNC_HUMAN	H	168;168;168;168;161;161;168	ENSP00000425979:Y168H;ENSP00000339845:Y168H;ENSP00000409335:Y168H;ENSP00000424161:Y168H;ENSP00000430921:Y168H	ENSP00000265075:Y161H	Y	-	1	0	DROSHA	31562295	1.000000	0.71417	0.998000	0.56505	0.576000	0.36127	7.746000	0.85057	1.918000	0.55548	0.533000	0.62120	TAC		0.542	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
C5orf22	55322	broad.mit.edu	37	5	31535912	31535912	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:31535912A>G	ENST00000325366.9	+	3	416	c.289A>G	c.(289-291)Ata>Gta	p.I97V	C5orf22_ENST00000355907.3_5'UTR	NM_018356.2	NP_060826.2	Q49AR2	CE022_HUMAN	chromosome 5 open reading frame 22	97								p.I97V(1)		kidney(3)|large_intestine(2)|lung(10)|ovary(2)|skin(1)	18						TTCACATGTAATATGGTTTCA	0.373																																					p.I97V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A289G	5						.						109.0	99.0	102.0					5																	31535912		2203	4300	6503	31571669	SO:0001583	missense	55322	exon3			AK002055	CCDS3895.1	5p13.3	2012-02-22			ENSG00000082213	ENSG00000082213			25639	protein-coding gene	gene with protein product							Standard	NM_018356		Approved	FLJ11193	uc003jhj.4	Q49AR2	OTTHUMG00000131067	ENST00000325366.9:c.289A>G	5.37:g.31535912A>G	ENSP00000326879:p.Ile97Val	Somatic		Capture	Illumina HiSeq	Phase_I	31571669	NM_018356	Q8ND28|Q8WU61|Q9NUR1	Missense_Mutation	SNP	ENST00000325366.9	37	CCDS3895.1	.	.	.	.	.	.	.	.	.	.	A	0.091	-1.167675	0.01660	.	.	ENSG00000082213	ENST00000325366;ENST00000507818	T;T	0.38560	1.13;1.13	6.03	-6.35	0.01975	.	0.603497	0.19744	N	0.107053	T	0.14917	0.0360	N	0.05592	-0.015	0.22648	N	0.998893	B	0.06786	0.001	B	0.06405	0.002	T	0.24905	-1.0147	10	0.08179	T	0.78	-0.4266	10.0024	0.41938	0.4207:0.1742:0.4051:0.0	.	97	Q49AR2	CE022_HUMAN	V	97;128	ENSP00000326879:I97V;ENSP00000430860:I128V	ENSP00000326879:I97V	I	+	1	0	C5orf22	31571669	0.002000	0.14202	0.000000	0.03702	0.473000	0.32948	0.187000	0.16998	-2.011000	0.00952	-1.937000	0.00501	ATA		0.373	C5orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253726.2	NM_018356	
PDZD2	23037	broad.mit.edu	37	5	32010498	32010498	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:32010498G>A	ENST00000438447.1	+	6	1705	c.1317G>A	c.(1315-1317)tcG>tcA	p.S439S	PDZD2_ENST00000282493.3_Silent_p.S439S			O15018	PDZD2_HUMAN	PDZ domain containing 2	439					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.S439S(1)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						TGACCAGCTCGGTAGAAGATG	0.512																																					p.S439S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1317A	5						.						97.0	95.0	96.0					5																	32010498		2203	4300	6503	32046255	SO:0001819	synonymous_variant	23037	exon5			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.1317G>A	5.37:g.32010498G>A		Somatic		Capture	Illumina HiSeq	Phase_I	32046255	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																				0.512	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
ADAMTS12	81792	broad.mit.edu	37	5	33649706	33649706	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:33649706C>T	ENST00000504830.1	-	8	1622	c.1287G>A	c.(1285-1287)ccG>ccA	p.P429P	ADAMTS12_ENST00000352040.3_Silent_p.P429P|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	429	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.P429P(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						ACCATGTCAGCGGAGTGGGAT	0.542										HNSCC(64;0.19)																											p.P429P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1287A	5						.						164.0	137.0	146.0					5																	33649706		2203	4300	6503	33685463	SO:0001819	synonymous_variant	81792	exon8			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.1287G>A	5.37:g.33649706C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33685463	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	CCDS34140.1																																																																																				0.542	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
ADAMTS12	81792	broad.mit.edu	37	5	33891873	33891873	+	Missense_Mutation	SNP	G	G	T	rs148311380	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:33891873G>T	ENST00000504830.1	-	1	424	c.89C>A	c.(88-90)cCt>cAt	p.P30H	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.P30H|ADAMTS12_ENST00000515401.1_Missense_Mutation_p.P30H	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	30					cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.P30H(2)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GCCTGGCTGAGGCTGTCTCCC	0.507										HNSCC(64;0.19)																											p.P30H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C89A	5						.	G	HIS/PRO	0,4406		0,0,2203	112.0	121.0	118.0		89	4.7	0.2	5	dbSNP_134	118	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ADAMTS12	NM_030955.2	77	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	benign	30/1595	33891873	1,13005	2203	4300	6503	33927630	SO:0001583	missense	81792	exon1			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.89C>A	5.37:g.33891873G>T	ENSP00000422554:p.Pro30His	Somatic		Capture	Illumina HiSeq	Phase_I	33927630	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.211257	0.39102	0.0	1.16E-4	ENSG00000151388	ENST00000504830;ENST00000352040;ENST00000515401	T;T;T	0.59638	0.25;0.25;3.07	5.61	4.74	0.60224	.	0.734607	0.12697	N	0.446622	T	0.49012	0.1532	N	0.19112	0.55	0.09310	N	1	D;D;D	0.58268	0.982;0.97;0.97	P;P;B	0.50378	0.639;0.62;0.436	T	0.38866	-0.9641	10	0.87932	D	0	.	6.2207	0.20679	0.1635:0.1541:0.6824:0.0	.	30;30;30	P58397-3;D6REX0;P58397	.;.;ATS12_HUMAN	H	30	ENSP00000422554:P30H;ENSP00000344847:P30H;ENSP00000421638:P30H	ENSP00000344847:P30H	P	-	2	0	ADAMTS12	33927630	0.958000	0.32768	0.171000	0.22900	0.441000	0.31987	3.365000	0.52335	1.361000	0.45981	0.585000	0.79938	CCT		0.507	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
AMACR	23600	broad.mit.edu	37	5	33997585	33997585	+	Intron	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:33997585C>T	ENST00000335606.6	-	4	828				AMACR_ENST00000441713.2_Intron|AMACR_ENST00000382085.3_Intron|AMACR_ENST00000426255.2_Missense_Mutation_p.A260T|AMACR_ENST00000512079.1_Intron|AMACR_ENST00000382068.3_Missense_Mutation_p.S206N|AMACR_ENST00000502637.1_Intron|RP11-1084J3.4_ENST00000382079.3_Intron|AMACR_ENST00000514195.1_Intron|AMACR_ENST00000382072.2_Intron	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase						bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)			endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						CACGATACTGCTTCCTGTTGT	0.498											OREG0016555	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A260T												.	.	0			c.G778A	5						.						97.0	82.0	87.0					5																	33997585		1568	3582	5150	34033342	SO:0001627	intron_variant	23600	exon5			AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.739+1160G>A	5.37:g.33997585C>T		Somatic	844	Capture	Illumina HiSeq	Phase_I	34033342	NM_001167596	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	37	CCDS3902.1																																																																																				0.498	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324	
CAPSL	133690	broad.mit.edu	37	5	35910614	35910614	+	Nonsense_Mutation	SNP	G	G	A	rs202156612	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:35910614G>A	ENST00000397367.2	-	3	295	c.169C>T	c.(169-171)Cga>Tga	p.R57*	CAPSL_ENST00000397366.1_Nonsense_Mutation_p.R57*|CAPSL_ENST00000514524.1_Nonsense_Mutation_p.R57*	NM_144647.3	NP_653248.3	Q8WWF8	CAPSL_HUMAN	calcyphosine-like	57	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)	p.R57*(1)		central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(10)|skin(1)|urinary_tract(1)	19	all_lung(31;0.000268)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.167)|Colorectal(62;0.202)			TCAAGGGTTCGATTATTATCG	0.308																																					p.R57X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C169T	5						.						56.0	58.0	57.0					5																	35910614		2201	4300	6501	35946371	SO:0001587	stop_gained	133690	exon3			BC017586	CCDS3912.2	5p13.2	2013-01-10			ENSG00000152611	ENSG00000152611		"""EF-hand domain containing"""	28375	protein-coding gene	gene with protein product						12477932	Standard	NM_001042625		Approved	MGC26610	uc003jju.1	Q8WWF8	OTTHUMG00000131109	ENST00000397367.2:c.169C>T	5.37:g.35910614G>A	ENSP00000380524:p.Arg57*	Somatic		Capture	Illumina HiSeq	Phase_I	35946371	NM_144647		Nonsense_Mutation	SNP	ENST00000397367.2	37	CCDS3912.2	.	.	.	.	.	.	.	.	.	.	G	15.62	2.887612	0.52014	.	.	ENSG00000152611	ENST00000397367;ENST00000397366;ENST00000513623;ENST00000514524	.	.	.	5.26	0.895	0.19247	.	0.111607	0.56097	D	0.000024	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-8.7212	14.2359	0.65927	0.0:0.0:0.3558:0.6442	.	.	.	.	X	57	.	ENSP00000380523:R57X	R	-	1	2	CAPSL	35946371	1.000000	0.71417	1.000000	0.80357	0.490000	0.33462	2.352000	0.44080	0.568000	0.29311	0.407000	0.27541	CGA		0.308	CAPSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253772.2	NM_144647	
NIPBL	25836	broad.mit.edu	37	5	36985410	36985410	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:36985410C>T	ENST00000282516.8	+	10	2627	c.2128C>T	c.(2128-2130)Cgg>Tgg	p.R710W	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Missense_Mutation_p.R710W	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	710					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.R710W(2)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			GGGTGAAAGCCGGCCTGAGAC	0.448																																					p.R710W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2128T	5						.						56.0	57.0	57.0					5																	36985410		2203	4300	6503	37021167	SO:0001583	missense	25836	exon10			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.2128C>T	5.37:g.36985410C>T	ENSP00000282516:p.Arg710Trp	Somatic		Capture	Illumina HiSeq	Phase_I	37021167	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.631334	0.46944	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.95035	-3.59;-3.58	5.98	4.14	0.48551	.	0.190124	0.36409	N	0.002602	D	0.93631	0.7966	N	0.24115	0.695	0.35546	D	0.80343	D;D	0.69078	0.994;0.997	P;P	0.59761	0.734;0.863	D	0.96452	0.9335	10	0.87932	D	0	.	14.5062	0.67755	0.4816:0.5184:0.0:0.0	.	710;710	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	W	710	ENSP00000282516:R710W;ENSP00000406266:R710W	ENSP00000282516:R710W	R	+	1	2	NIPBL	37021167	0.996000	0.38824	1.000000	0.80357	0.977000	0.68977	0.801000	0.27055	1.525000	0.49052	-0.175000	0.13238	CGG		0.448	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
WDR70	55100	broad.mit.edu	37	5	37605239	37605239	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:37605239delA	ENST00000265107.4	+	10	1147	c.991delA	c.(991-993)aaafs	p.K332fs	WDR70_ENST00000504564.1_Frame_Shift_Del_p.K332fs|WDR70_ENST00000510699.1_3'UTR	NM_018034.2	NP_060504.1	Q9NW82	WDR70_HUMAN	WD repeat domain 70	332							enzyme binding (GO:0019899)	p.V333fs*15(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GATGCAAGGCAAAAAAGTCAT	0.423																																					p.K331fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.991delA	5						.						95.0	83.0	87.0					5																	37605239		2203	4300	6503	37640996	SO:0001589	frameshift_variant	55100	exon10			BC009648	CCDS34147.1	5p13.2	2013-01-09			ENSG00000082068	ENSG00000082068		"""WD repeat domain containing"""	25495	protein-coding gene	gene with protein product						12477932	Standard	NM_018034		Approved	FLJ10233	uc003jkv.3	Q9NW82	OTTHUMG00000162263	ENST00000265107.4:c.991delA	5.37:g.37605239delA	ENSP00000265107:p.Lys332fs	Somatic		Capture	Illumina HiSeq	Phase_I	37640996	NM_018034	Q9H053	Frame_Shift_Del	DEL	ENST00000265107.4	37	CCDS34147.1																																																																																				0.423	WDR70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368294.1	NM_018034	
LIFR	3977	broad.mit.edu	37	5	38496539	38496539	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:38496539T>C	ENST00000263409.4	-	13	1992	c.1830A>G	c.(1828-1830)aaA>aaG	p.K610K	LIFR_ENST00000453190.2_Silent_p.K610K|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	610	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)	p.K610K(2)		NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					CCACAGAATTTTTAGCCACTA	0.413			T	PLAG1	salivary adenoma																																p.K610K	Melanoma(13;4 730 6426 9861 34751)		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A1830G	5						.						217.0	190.0	199.0					5																	38496539		2203	4300	6503	38532296	SO:0001819	synonymous_variant	3977	exon13			X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.1830A>G	5.37:g.38496539T>C		Somatic		Capture	Illumina HiSeq	Phase_I	38532296	NM_001127671	Q6LCD9	Silent	SNP	ENST00000263409.4	37	CCDS3927.1																																																																																				0.413	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
PRKAA1	5562	broad.mit.edu	37	5	40771830	40771830	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:40771830C>T	ENST00000397128.2	-	4	507	c.499G>A	c.(499-501)Gct>Act	p.A167T	PRKAA1_ENST00000354209.3_Missense_Mutation_p.A182T|PRKAA1_ENST00000296800.4_Missense_Mutation_p.A158T	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	167	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to glucose starvation (GO:0042149)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|cold acclimation (GO:0009631)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|fatty acid oxidation (GO:0019395)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of glucosylceramide biosynthetic process (GO:0046318)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of gene expression (GO:0010628)|positive regulation of glycolytic process (GO:0045821)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of transcription, DNA-templated (GO:0006355)|regulation of vesicle-mediated transport (GO:0060627)|response to activity (GO:0014823)|response to caffeine (GO:0031000)|response to camptothecin (GO:1901563)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	AMP-activated protein kinase complex (GO:0031588)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|tau-protein kinase activity (GO:0050321)	p.A182T(1)		breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	CCAAAATCAGCTATCTTTGCA	0.343																																					p.A167T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G499A	5						.						113.0	110.0	111.0					5																	40771830		1930	4174	6104	40807587	SO:0001583	missense	5562	exon4				CCDS3932.2, CCDS3933.2	5p13.1	2012-10-03			ENSG00000132356	ENSG00000132356			9376	protein-coding gene	gene with protein product	"""AMPK, alpha, 1"""	602739				8557660	Standard	XM_006714481		Approved	AMPKa1	uc003jmb.3	Q13131	OTTHUMG00000162269	ENST00000397128.2:c.499G>A	5.37:g.40771830C>T	ENSP00000380317:p.Ala167Thr	Somatic		Capture	Illumina HiSeq	Phase_I	40807587	NM_006251	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Missense_Mutation	SNP	ENST00000397128.2	37	CCDS3932.2	.	.	.	.	.	.	.	.	.	.	C	24.3	4.517553	0.85495	.	.	ENSG00000132356	ENST00000397128;ENST00000354209;ENST00000296800	T;T;T	0.26223	1.75;1.75;1.75	6.08	6.08	0.98989	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.36608	0.0973	N	0.16066	0.365	0.80722	D	1	D;D	0.61697	0.989;0.99	D;D	0.64687	0.927;0.928	T	0.28554	-1.0040	10	0.87932	D	0	-17.9211	20.6721	0.99693	0.0:1.0:0.0:0.0	.	167;182	Q13131;Q13131-2	AAPK1_HUMAN;.	T	167;182;158	ENSP00000380317:A167T;ENSP00000346148:A182T;ENSP00000296800:A158T	ENSP00000296800:A158T	A	-	1	0	AC008810.1	40807587	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.477000	0.81069	2.894000	0.99253	0.591000	0.81541	GCT		0.343	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251	
C6	729	broad.mit.edu	37	5	41199977	41199977	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:41199977C>A	ENST00000263413.3	-	4	602	c.338G>T	c.(337-339)gGg>gTg	p.G113V	C6_ENST00000337836.5_Missense_Mutation_p.G113V	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	113	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)		p.G113V(1)		central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TGGCTGTCCCCCAAACTGACT	0.448																																					p.G113V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G338T	5						.						86.0	81.0	83.0					5																	41199977		2203	4300	6503	41235734	SO:0001583	missense	729	exon4			J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.338G>T	5.37:g.41199977C>A	ENSP00000263413:p.Gly113Val	Somatic		Capture	Illumina HiSeq	Phase_I	41235734	NM_000065		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.845391	0.91197	.	.	ENSG00000039537	ENST00000337836;ENST00000263413;ENST00000417809	T;T;T	0.23147	1.92;1.92;1.92	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.67116	0.2859	H	0.96208	3.785	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77005	-0.2748	10	0.87932	D	0	-20.1462	19.3087	0.94175	0.0:1.0:0.0:0.0	.	113	P13671	CO6_HUMAN	V	113	ENSP00000338861:G113V;ENSP00000263413:G113V;ENSP00000396565:G113V	ENSP00000263413:G113V	G	-	2	0	C6	41235734	0.998000	0.40836	1.000000	0.80357	0.973000	0.67179	1.847000	0.39299	2.857000	0.98124	0.650000	0.86243	GGG		0.448	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1		
ISL1	3670	broad.mit.edu	37	5	50683335	50683335	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:50683335T>A	ENST00000230658.7	+	3	815	c.230T>A	c.(229-231)aTc>aAc	p.I77N	ISL1_ENST00000511384.1_Missense_Mutation_p.I77N|ISL1_ENST00000505475.2_3'UTR	NM_002202.2	NP_002193.2	P61371	ISL1_HUMAN	ISL LIM homeobox 1	77					atrial septum morphogenesis (GO:0060413)|axon regeneration (GO:0031103)|cardiac cell fate determination (GO:0060913)|cardiac muscle cell myoblast differentiation (GO:0060379)|cardiac right ventricle morphogenesis (GO:0003215)|cellular response to glucocorticoid stimulus (GO:0071385)|endocardial cushion morphogenesis (GO:0003203)|innervation (GO:0060384)|mesenchymal cell differentiation (GO:0048762)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of protein homodimerization activity (GO:0090074)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate specification (GO:0048665)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|pancreas development (GO:0031016)|peripheral nervous system neuron axonogenesis (GO:0048936)|pharyngeal system development (GO:0060037)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of granulocyte colony-stimulating factor production (GO:0071657)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage colony-stimulating factor production (GO:1901258)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|retinal ganglion cell axon guidance (GO:0031290)|secondary heart field specification (GO:0003139)|sensory system development (GO:0048880)|spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron differentiation (GO:0021522)|trigeminal nerve development (GO:0021559)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|zinc ion binding (GO:0008270)	p.I77N(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(11)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		Lung NSC(810;0.000845)|Breast(144;0.0411)				TTGTACGGGATCAAATGCGCC	0.627																																					p.I77N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T230A	5						.						30.0	32.0	32.0					5																	50683335		2021	4170	6191	50719092	SO:0001583	missense	3670	exon3			BC031213	CCDS43314.1	5q11.2	2012-03-09	2007-07-13		ENSG00000016082	ENSG00000016082		"""Homeoboxes / LIM class"""	6132	protein-coding gene	gene with protein product		600366	"""ISL1 transcription factor, LIM/homeodomain, (islet-1)"""			7912209	Standard	NM_002202		Approved	Isl-1, ISLET1	uc003jor.3	P61371	OTTHUMG00000162281	ENST00000230658.7:c.230T>A	5.37:g.50683335T>A	ENSP00000230658:p.Ile77Asn	Somatic		Capture	Illumina HiSeq	Phase_I	50719092	NM_002202	P20663|P47894	Missense_Mutation	SNP	ENST00000230658.7	37	CCDS43314.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.13|16.13	3.035559|3.035559	0.54896|0.54896	.|.	.|.	ENSG00000016082|ENSG00000016082	ENST00000505475|ENST00000230658;ENST00000503187;ENST00000511384	.|D;D	.|0.86769	.|-2.17;-2.17	5.58|5.58	4.37|4.37	0.52481|0.52481	.|Zinc finger, LIM-type (2);	.|0.175183	.|0.49305	.|N	.|0.000158	T|T	0.77831|0.77831	0.4189|0.4189	N|N	0.19112|0.19112	0.55|0.55	0.52501|0.52501	D|D	0.999957|0.999957	.|B	.|0.24618	.|0.107	.|B	.|0.17433	.|0.018	T|T	0.73353|0.73353	-0.4009|-0.4009	6|10	0.87932|0.66056	D|D	0|0.02	.|.	11.4134|11.4134	0.49939|0.49939	0.1357:0.0:0.0:0.8643|0.1357:0.0:0.0:0.8643	.|.	.|77	.|P61371	.|ISL1_HUMAN	E|N	23|77	.|ENSP00000230658:I77N;ENSP00000422676:I77N	ENSP00000421737:D23E|ENSP00000230658:I77N	D|I	+|+	3|2	2|0	ISL1|ISL1	50719092|50719092	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.930000|7.930000	0.87610|0.87610	0.897000|0.897000	0.36392|0.36392	0.454000|0.454000	0.30748|0.30748	GAT|ATC		0.627	ISL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368413.3	NM_002202	
ITGA2	3673	broad.mit.edu	37	5	52361727	52361727	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:52361727C>T	ENST00000296585.5	+	15	2006	c.1863C>T	c.(1861-1863)tcC>tcT	p.S621S		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	621					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)	p.S621S(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				TTGGGAGGTCCTTGGATGGCT	0.463																																					p.S621S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1863T	5						.						136.0	128.0	131.0					5																	52361727		2203	4300	6503	52397484	SO:0001819	synonymous_variant	3673	exon15				CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.1863C>T	5.37:g.52361727C>T		Somatic		Capture	Illumina HiSeq	Phase_I	52397484	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																				0.463	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
ARL15	54622	broad.mit.edu	37	5	53409077	53409077	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:53409077T>C	ENST00000504924.1	-	4	510	c.417A>G	c.(415-417)atA>atG	p.I139M	ARL15_ENST00000502271.1_De_novo_Start_InFrame|ARL15_ENST00000510591.2_5'UTR|ARL15_ENST00000507646.2_Missense_Mutation_p.I139M	NM_019087.2	NP_061960.1	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15	139					small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	GTP binding (GO:0005525)	p.I127M(1)|p.I139M(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6		Lung NSC(810;0.000779)				GATTGGCCAATATTAAAAAGG	0.433																																					p.I139M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A417G	5						.						78.0	81.0	80.0					5																	53409077		1959	4160	6119	53444834	SO:0001583	missense	54622	exon4			BC026093	CCDS54850.1	5p15.2	2014-05-09	2005-11-03	2005-11-03		ENSG00000185305		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	25945	protein-coding gene	gene with protein product			"""ADP-ribosylation factor related protein 2"""	ARFRP2		12477932	Standard	NM_019087		Approved	FLJ20051	uc003jpg.1	Q9NXU5		ENST00000504924.1:c.417A>G	5.37:g.53409077T>C	ENSP00000433427:p.Ile139Met	Somatic		Capture	Illumina HiSeq	Phase_I	53444834	NM_019087	Q6IAD0	Missense_Mutation	SNP	ENST00000504924.1	37	CCDS54850.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.893861	0.72639	.	.	ENSG00000185305	ENST00000504924;ENST00000507646	T;T	0.73469	-0.75;-0.52	5.9	4.72	0.59763	.	0.000000	0.85682	D	0.000000	D	0.84138	0.5406	M	0.74647	2.275	0.48571	D	0.999671	D	0.62365	0.991	D	0.64877	0.93	D	0.85549	0.1220	10	0.87932	D	0	-18.7939	13.2618	0.60108	0.0:0.0:0.1325:0.8675	.	139	Q9NXU5	ARL15_HUMAN	M	139	ENSP00000433427:I139M;ENSP00000432680:I139M	ENSP00000433427:I139M	I	-	3	3	ARL15	53444834	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.658000	0.46733	1.027000	0.39758	0.460000	0.39030	ATA		0.433	ARL15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368432.2	NM_019087	
SNX18	112574	broad.mit.edu	37	5	53814994	53814994	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:53814994C>T	ENST00000326277.3	+	1	1402	c.1212C>T	c.(1210-1212)ggC>ggT	p.G404G	SNX18_ENST00000381410.4_Silent_p.G404G|SNX18_ENST00000343017.6_Silent_p.G404G	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	404					cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.G404G(2)		endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				AGATGGTGGGCGCCAACTTCT	0.612																																					p.G404G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1212T	5						.						61.0	70.0	67.0					5																	53814994		2203	4300	6503	53850751	SO:0001819	synonymous_variant	112574	exon1			AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"""Sorting nexins"""	19245	protein-coding gene	gene with protein product			"""sorting nexin associated golgi protein 1"""	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.1212C>T	5.37:g.53814994C>T		Somatic		Capture	Illumina HiSeq	Phase_I	53850751	NM_001145427	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Silent	SNP	ENST00000326277.3	37	CCDS3962.1																																																																																				0.612	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2		
IL31RA	133396	broad.mit.edu	37	5	55202043	55202043	+	Silent	SNP	G	G	A	rs547992094		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:55202043G>A	ENST00000447346.2	+	9	1244	c.1179G>A	c.(1177-1179)ccG>ccA	p.P393P	IL31RA_ENST00000396834.1_Silent_p.P374P|IL31RA_ENST00000297015.3_Silent_p.P251P|IL31RA_ENST00000354961.4_Silent_p.P374P|IL31RA_ENST00000359040.5_Silent_p.P393P|IL31RA_ENST00000396836.2_Silent_p.P393P|IL31RA_ENST00000490985.1_Silent_p.P251P	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	361	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)	p.P393P(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				AATGGTTTCCGGATGTGGACT	0.557													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19411	0.0		0.0	False		,,,				2504	0.0				p.P393P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1179A	5						.						170.0	153.0	159.0					5																	55202043		2203	4300	6503	55237800	SO:0001819	synonymous_variant	133396	exon9			AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.1179G>A	5.37:g.55202043G>A		Somatic		Capture	Illumina HiSeq	Phase_I	55237800	NM_139017	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Silent	SNP	ENST00000447346.2	37	CCDS3970.2																																																																																				0.557	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
ANKRD55	79722	broad.mit.edu	37	5	55479366	55479366	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:55479366A>G	ENST00000341048.4	-	3	305	c.154T>C	c.(154-156)Tct>Cct	p.S52P	ANKRD55_ENST00000504958.2_Missense_Mutation_p.S52P|ANKRD55_ENST00000513241.2_Missense_Mutation_p.S23P	NM_024669.2	NP_078945.2	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55	52								p.S52P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(1)	34		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				TCTAGGATAGAAGGGTCTTCC	0.433																																					p.S52P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T154C	5						.						138.0	116.0	123.0					5																	55479366		2203	4300	6503	55515123	SO:0001583	missense	79722	exon3			AK021857	CCDS34161.1	5q11.2	2013-01-10			ENSG00000164512	ENSG00000164512		"""Ankyrin repeat domain containing"""	25681	protein-coding gene	gene with protein product		615189					Standard	XM_005248599		Approved	FLJ11795	uc003jqu.3	Q3KP44	OTTHUMG00000162305	ENST00000341048.4:c.154T>C	5.37:g.55479366A>G	ENSP00000342295:p.Ser52Pro	Somatic		Capture	Illumina HiSeq	Phase_I	55515123	NM_024669	B3KVT8|Q3KP45|Q9HAD3	Missense_Mutation	SNP	ENST00000341048.4	37	CCDS34161.1	.	.	.	.	.	.	.	.	.	.	A	18.41	3.617098	0.66672	.	.	ENSG00000164512	ENST00000507283;ENST00000341048;ENST00000504958;ENST00000513241;ENST00000519586	T;T;T	0.65916	-0.18;-0.18;-0.18	5.11	2.61	0.31194	.	0.139052	0.49305	D	0.000155	T	0.62122	0.2402	L	0.41124	1.26	0.43394	D	0.995518	P	0.40332	0.713	P	0.50405	0.64	T	0.57814	-0.7746	10	0.42905	T	0.14	.	11.5911	0.50945	0.7159:0.2841:0.0:0.0	.	52	B3KVT8	.	P	52;52;52;23;52	ENSP00000342295:S52P;ENSP00000424230:S52P;ENSP00000423507:S23P	ENSP00000342295:S52P	S	-	1	0	ANKRD55	55515123	1.000000	0.71417	0.991000	0.47740	0.974000	0.67602	5.578000	0.67450	0.242000	0.21303	-0.461000	0.05368	TCT		0.433	ANKRD55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368510.4	NM_024669	
MIER3	166968	broad.mit.edu	37	5	56219767	56219767	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:56219767delT	ENST00000381199.3	-	11	1037	c.1027delA	c.(1027-1029)agafs	p.R343fs	MIER3_ENST00000381226.3_Frame_Shift_Del_p.R348fs|SETD9_ENST00000541720.1_Intron|MIER3_ENST00000381213.3_Frame_Shift_Del_p.R342fs|MIER3_ENST00000409421.1_Frame_Shift_Del_p.R280fs			Q7Z3K6	MIER3_HUMAN	mesoderm induction early response 1, family member 3	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R342fs*15(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(2)|urinary_tract(1)	19		Lung NSC(810;4.65e-05)|Prostate(74;0.0253)|Breast(144;0.0503)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;1.24e-37)		TGGTTATATCTTTTTTTCCCA	0.368																																					p.R342fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1024delA	5						.						144.0	141.0	142.0					5																	56219767		2203	4300	6503	56255524	SO:0001589	frameshift_variant	166968	exon11			BX537798	CCDS3973.2, CCDS75248.1	5q11.2	2009-03-19			ENSG00000155545	ENSG00000155545			26678	protein-coding gene	gene with protein product						12477932	Standard	XM_005248448		Approved	FLJ35954, DKFZp686L09111, DKFZp781I1119	uc003jra.1	Q7Z3K6	OTTHUMG00000059589	ENST00000381199.3:c.1027delA	5.37:g.56219767delT	ENSP00000370596:p.Arg343fs	Somatic		Capture	Illumina HiSeq	Phase_I	56255524	NM_152622	B4DRI9|B8ZZQ0|Q5CZI0|Q68CS3|Q6MZS7|Q86YG8|Q8NA13	Frame_Shift_Del	DEL	ENST00000381199.3	37																																																																																					0.368	MIER3-004	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000132523.2	NM_152622	
PDE4D	5144	broad.mit.edu	37	5	58271593	58271593	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:58271593G>A	ENST00000340635.6	-	14	2079	c.1904C>T	c.(1903-1905)aCg>aTg	p.T635M	PDE4D_ENST00000502484.2_Missense_Mutation_p.T574M|PDE4D_ENST00000507116.1_Missense_Mutation_p.T571M|PDE4D_ENST00000317118.8_Missense_Mutation_p.T344M|PDE4D_ENST00000405755.2_Missense_Mutation_p.T513M|PDE4D_ENST00000360047.5_Missense_Mutation_p.T499M|PDE4D_ENST00000503258.1_Missense_Mutation_p.T505M|PDE4D_ENST00000358923.6_Missense_Mutation_p.T333M|PDE4D_ENST00000546160.1_Missense_Mutation_p.T574M	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	635					adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)	p.T499M(1)|p.T571M(1)|p.T635M(1)|p.T513M(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	TATCCGGTCCGTCCACTGGCG	0.507																																					p.T411M												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.C1232T	5						.						94.0	99.0	97.0					5																	58271593		2190	4296	6486	58307350	SO:0001583	missense	5144	exon9				CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"""Phosphodiesterases"""	8783	protein-coding gene	gene with protein product	"""phosphodiesterase E3 dunce homolog (Drosophila)"""	600129	"""phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"""	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.1904C>T	5.37:g.58271593G>A	ENSP00000345502:p.Thr635Met	Somatic		Capture	Illumina HiSeq	Phase_I	58307350	NM_001197222	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Missense_Mutation	SNP	ENST00000340635.6	37	CCDS47213.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.448142	0.84101	.	.	ENSG00000113448	ENST00000340635;ENST00000356665;ENST00000360047;ENST00000507116;ENST00000358923;ENST00000317118;ENST00000503258;ENST00000405755;ENST00000502484;ENST00000546160;ENST00000505453	D;D;D;D;D;D;D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65;-1.65;-1.65;-1.65;-1.65;-1.65;-1.65	4.4	4.4	0.53042	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	D	0.90424	0.7002	M	0.70595	2.14	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;0.998;0.999	D	0.91733	0.5398	10	0.87932	D	0	.	17.5214	0.87787	0.0:0.0:1.0:0.0	.	574;635;571;498;513;505;410;344	Q08499-11;Q08499;Q08499-6;Q08499-2;Q08499-9;Q08499-10;Q08499-4;Q08499-8	.;PDE4D_HUMAN;.;.;.;.;.;.	M	635;504;499;571;333;344;505;513;574;574;333	ENSP00000345502:T635M;ENSP00000353152:T499M;ENSP00000424852:T571M;ENSP00000351800:T333M;ENSP00000321739:T344M;ENSP00000425605:T505M;ENSP00000384806:T513M;ENSP00000423094:T574M;ENSP00000442734:T574M;ENSP00000421013:T333M	ENSP00000321739:T344M	T	-	2	0	PDE4D	58307350	1.000000	0.71417	0.992000	0.48379	0.889000	0.51656	9.592000	0.98245	2.427000	0.82271	0.655000	0.94253	ACG		0.507	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3		
CWC27	10283	broad.mit.edu	37	5	64100103	64100103	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:64100103T>C	ENST00000381070.3	+	10	1045	c.828T>C	c.(826-828)gaT>gaC	p.D276D	CWC27_ENST00000508024.1_Silent_p.D276D	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	276					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.D276D(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(5)|prostate(1)	21						TTGATGGTGATGAAAAGAACC	0.373																																					p.D276D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T828C	5						.						88.0	91.0	90.0					5																	64100103		2203	4300	6503	64135859	SO:0001819	synonymous_variant	10283	exon10			AF039692	CCDS3982.2, CCDS75252.1	5q12.3	2010-01-26	2010-01-26	2010-01-26	ENSG00000153015	ENSG00000153015			10664	protein-coding gene	gene with protein product			"""serologically defined colon cancer antigen 10"""	SDCCAG10		9610721, 19941820	Standard	XM_005248399		Approved	NY-CO-10	uc003jtn.1	Q6UX04	OTTHUMG00000074069	ENST00000381070.3:c.828T>C	5.37:g.64100103T>C		Somatic		Capture	Illumina HiSeq	Phase_I	64135859	NM_005869	O60529|O60530|Q96EM3	Silent	SNP	ENST00000381070.3	37	CCDS3982.2																																																																																				0.373	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869	
PPWD1	23398	broad.mit.edu	37	5	64883155	64883155	+	Missense_Mutation	SNP	G	G	A	rs139664723		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:64883155G>A	ENST00000261308.5	+	11	1945	c.1873G>A	c.(1873-1875)Gtc>Atc	p.V625I	PPWD1_ENST00000535264.1_Missense_Mutation_p.V595I|PPWD1_ENST00000538977.1_Missense_Mutation_p.V469I	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	625	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.V625I(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		GATCTCCAACGTCAAAGTCAA	0.358																																					p.V625I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1873A	5						.						119.0	115.0	116.0					5																	64883155		2203	4300	6503	64918911	SO:0001583	missense	23398	exon11			AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"""WD repeat domain containing"""	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.1873G>A	5.37:g.64883155G>A	ENSP00000261308:p.Val625Ile	Somatic		Capture	Illumina HiSeq	Phase_I	64918911	NM_015342	B4DWR9|Q15002|Q7KZ89	Missense_Mutation	SNP	ENST00000261308.5	37	CCDS3985.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.528887	0.44969	.	.	ENSG00000113593	ENST00000261308;ENST00000535264;ENST00000538977	T;T;T	0.47528	0.84;0.84;0.84	5.74	4.87	0.63330	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.489229	0.22386	N	0.060743	T	0.40119	0.1104	L	0.48174	1.505	0.31854	N	0.62189	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.001	T	0.47355	-0.9124	10	0.48119	T	0.1	.	9.5629	0.39380	0.0711:0.0:0.7876:0.1413	.	595;625	F5H7P7;Q96BP3	.;PPWD1_HUMAN	I	625;595;469	ENSP00000261308:V625I;ENSP00000442371:V595I;ENSP00000444496:V469I	ENSP00000261308:V625I	V	+	1	0	PPWD1	64918911	1.000000	0.71417	0.941000	0.38009	0.963000	0.63663	4.605000	0.61119	1.440000	0.47531	0.557000	0.71058	GTC		0.358	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342	
MAST4	375449	broad.mit.edu	37	5	66460957	66460957	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:66460957G>A	ENST00000403625.2	+	29	6245	c.5950G>A	c.(5950-5952)Gag>Aag	p.E1984K	MAST4_ENST00000404260.3_Missense_Mutation_p.E1987K|MAST4_ENST00000405643.1_Missense_Mutation_p.E1805K|MAST4_ENST00000403666.1_Missense_Mutation_p.E1795K|MAST4_ENST00000261569.7_Missense_Mutation_p.E1790K	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1987						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.E1987K(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AGCCAGAAGCGAGCGCTCTGC	0.597																																					p.E1795K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5383A	5						.						19.0	23.0	22.0					5																	66460957		1934	4139	6073	66496713	SO:0001583	missense	375449	exon28			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.5950G>A	5.37:g.66460957G>A	ENSP00000385727:p.Glu1984Lys	Somatic		Capture	Illumina HiSeq	Phase_I	66496713	NM_015183	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.52|15.52	2.859143|2.859143	0.51376|0.51376	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569|ENST00000443808	T;T;T;T;T|.	0.69685|.	-0.41;-0.41;-0.42;-0.42;-0.39|.	4.99|4.99	3.15|3.15	0.36227|0.36227	.|.	0.116255|.	0.38605|.	N|.	0.001626|.	T|T	0.35393|0.35393	0.0930|0.0930	L|L	0.34521|0.34521	1.04|1.04	0.26405|0.26405	N|N	0.976355|0.976355	P;P|.	0.39624|.	0.553;0.681|.	B;B|.	0.26614|.	0.032;0.071|.	T|T	0.19877|0.19877	-1.0292|-1.0292	10|5	0.45353|.	T|.	0.12|.	-25.0513|-25.0513	9.4401|9.4401	0.38664|0.38664	0.0778:0.142:0.7802:0.0|0.0778:0.142:0.7802:0.0	.|.	1987;1795|.	O15021;O15021-3|.	MAST4_HUMAN;.|.	K|Q	1987;1984;1795;1805;1805;1790|1040	ENSP00000385048:E1987K;ENSP00000385727:E1984K;ENSP00000384313:E1795K;ENSP00000384099:E1805K;ENSP00000261569:E1790K|.	ENSP00000261569:E1790K|.	E|R	+|+	1|2	0|0	MAST4|MAST4	66496713|66496713	0.992000|0.992000	0.36948|0.36948	0.122000|0.122000	0.21767|0.21767	0.049000|0.049000	0.14656|0.14656	2.179000|2.179000	0.42528|0.42528	1.301000|1.301000	0.44836|0.44836	0.563000|0.563000	0.77884|0.77884	GAG|CGA		0.597	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2		
MAST4	375449	broad.mit.edu	37	5	66462271	66462271	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:66462271C>T	ENST00000403625.2	+	29	7559	c.7264C>T	c.(7264-7266)Ccc>Tcc	p.P2422S	MAST4_ENST00000404260.3_Missense_Mutation_p.P2425S|MAST4_ENST00000405643.1_Missense_Mutation_p.P2243S|MAST4_ENST00000403666.1_Missense_Mutation_p.P2233S|MAST4_ENST00000261569.7_Missense_Mutation_p.P2228S	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2425						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.P2425S(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AGGGAAAGGGCCCGGTCCCCA	0.667											OREG0016638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P2233S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6697T	5						.						14.0	19.0	17.0					5																	66462271		1923	4124	6047	66498027	SO:0001583	missense	375449	exon28			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.7264C>T	5.37:g.66462271C>T	ENSP00000385727:p.Pro2422Ser	Somatic	1092	Capture	Illumina HiSeq	Phase_I	66498027	NM_015183	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.014|0.014	-1.571630|-1.571630	0.00895|0.00895	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000443808|ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569	.|T;T;T;T;T	.|0.64260	.|-0.07;-0.07;-0.09;-0.08;-0.06	4.67|4.67	2.83|2.83	0.33086|0.33086	.|.	.|0.889371	.|0.09438	.|N	.|0.802192	T|T	0.43765|0.43765	0.1262|0.1262	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.20075|0.20075	-1.0286|-1.0286	5|10	.|0.05833	.|T	.|0.94	0.8372|0.8372	10.4052|10.4052	0.44252|0.44252	0.1339:0.79:0.0:0.076|0.1339:0.79:0.0:0.076	.|.	.|2425;2233	.|O15021;O15021-3	.|MAST4_HUMAN;.	V|S	1478|2425;2422;2233;2243;2243;2228	.|ENSP00000385048:P2425S;ENSP00000385727:P2422S;ENSP00000384313:P2233S;ENSP00000384099:P2243S;ENSP00000261569:P2228S	.|ENSP00000261569:P2228S	A|P	+|+	2|1	0|0	MAST4|MAST4	66498027|66498027	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.071000|0.071000	0.16799|0.16799	0.323000|0.323000	0.19593|0.19593	0.186000|0.186000	0.20125|0.20125	-1.598000|-1.598000	0.00824|0.00824	GCC|CCC		0.667	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2		
CD180	4064	broad.mit.edu	37	5	66478788	66478788	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:66478788G>A	ENST00000256447.4	-	3	2040	c.1883C>T	c.(1882-1884)aCa>aTa	p.T628I	CTD-2306M10.1_ENST00000602471.1_lincRNA	NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	628					B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T628I(1)		cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		GCCTATGGCTGTAATCCCACA	0.418																																					p.T628I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1883T	5						.						107.0	107.0	107.0					5																	66478788		2203	4300	6503	66514544	SO:0001583	missense	4064	exon3			D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"""CD molecules"""	6726	protein-coding gene	gene with protein product		602226	"""lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD"", ""CD180 antigen"""	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.1883C>T	5.37:g.66478788G>A	ENSP00000256447:p.Thr628Ile	Somatic		Capture	Illumina HiSeq	Phase_I	66514544	NM_005582	B2R7Z7|Q32MM5	Missense_Mutation	SNP	ENST00000256447.4	37	CCDS3992.1	.	.	.	.	.	.	.	.	.	.	G	9.790	1.177607	0.21787	.	.	ENSG00000134061	ENST00000256447	T	0.38240	1.15	5.7	5.7	0.88788	.	0.385935	0.22265	N	0.062346	T	0.45175	0.1329	L	0.50333	1.59	0.09310	N	1	D	0.53619	0.961	P	0.50405	0.64	T	0.36187	-0.9758	10	0.37606	T	0.19	.	17.6046	0.88034	0.0:0.0:1.0:0.0	.	628	Q99467	CD180_HUMAN	I	628	ENSP00000256447:T628I	ENSP00000256447:T628I	T	-	2	0	CD180	66514544	0.523000	0.26274	0.153000	0.22517	0.156000	0.22039	3.207000	0.51106	2.687000	0.91594	0.563000	0.77884	ACA		0.418	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582	
MAP1B	4131	broad.mit.edu	37	5	71482444	71482444	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:71482444C>T	ENST00000296755.7	+	4	671	c.373C>T	c.(373-375)Cgc>Tgc	p.R125C		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	125					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.R125C(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ATTTCAGGTGCGCTTAATGAT	0.547																																					p.R125C	Melanoma(17;367 822 11631 31730 47712)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C373T	5						.						127.0	123.0	124.0					5																	71482444		2203	4300	6503	71518200	SO:0001583	missense	4131	exon4			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.373C>T	5.37:g.71482444C>T	ENSP00000296755:p.Arg125Cys	Somatic		Capture	Illumina HiSeq	Phase_I	71518200	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.534547	0.85812	.	.	ENSG00000131711	ENST00000296755;ENST00000511641	T;T	0.07114	3.22;3.22	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000003	T	0.33585	0.0868	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.02477	-1.1153	10	0.87932	D	0	-12.4949	19.8968	0.96969	0.0:1.0:0.0:0.0	.	125	P46821	MAP1B_HUMAN	C	125	ENSP00000296755:R125C;ENSP00000423444:R125C	ENSP00000296755:R125C	R	+	1	0	MAP1B	71518200	1.000000	0.71417	1.000000	0.80357	0.468000	0.32798	7.705000	0.84606	2.691000	0.91804	0.655000	0.94253	CGC		0.547	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
MAP1B	4131	broad.mit.edu	37	5	71493385	71493385	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:71493385G>T	ENST00000296755.7	+	5	4501	c.4203G>T	c.(4201-4203)ccG>ccT	p.P1401P		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1401					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.P1401P(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		TACGCAGCCCGCCCCTCATTG	0.478																																					p.P1401P	Melanoma(17;367 822 11631 31730 47712)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4203T	5						.						47.0	49.0	48.0					5																	71493385		2203	4300	6503	71529141	SO:0001819	synonymous_variant	4131	exon5			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.4203G>T	5.37:g.71493385G>T		Somatic		Capture	Illumina HiSeq	Phase_I	71529141	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																				0.478	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
MRPS27	23107	broad.mit.edu	37	5	71528329	71528329	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:71528329T>C	ENST00000261413.5	-	7	571	c.532A>G	c.(532-534)Acc>Gcc	p.T178A	MRPS27_ENST00000515404.1_Missense_Mutation_p.T122A|MRPS27_ENST00000513900.1_Missense_Mutation_p.T192A|MRPS27_ENST00000522562.1_5'UTR|MRPS27_ENST00000457646.4_Missense_Mutation_p.T122A	NM_015084.2	NP_055899.2	Q92552	RT27_HUMAN	mitochondrial ribosomal protein S27	178						mitochondrion (GO:0005739)|ribosome (GO:0005840)		p.T178A(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-53)		AGAAGTTGGGTGGAAGGCACT	0.383																																					p.T178A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A532G	5						.						95.0	92.0	93.0					5																	71528329		2203	4300	6503	71564085	SO:0001583	missense	23107	exon7			D87453	CCDS4013.1, CCDS68890.1, CCDS75257.1	5q13.2	2012-09-13			ENSG00000113048	ENSG00000113048		"""Mitochondrial ribosomal proteins / small subunits"""	14512	protein-coding gene	gene with protein product		611989					Standard	NM_015084		Approved	KIAA0264	uc003kbz.4	Q92552	OTTHUMG00000100951	ENST00000261413.5:c.532A>G	5.37:g.71528329T>C	ENSP00000261413:p.Thr178Ala	Somatic		Capture	Illumina HiSeq	Phase_I	71564085	NM_015084	B4DRT2|Q6P1S1	Missense_Mutation	SNP	ENST00000261413.5	37	CCDS4013.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.846719	0.71603	.	.	ENSG00000113048	ENST00000261413;ENST00000457646;ENST00000513900;ENST00000508863;ENST00000515404	T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.69708	0.3141	M	0.76328	2.33	0.80722	D	1	D;D;D	0.89917	1.0;0.973;1.0	D;P;D	0.87578	0.998;0.813;0.998	T	0.71994	-0.4424	10	0.59425	D	0.04	-2.4941	16.6154	0.84909	0.0:0.0:0.0:1.0	.	192;122;178	B4DRT2;D6RJC7;Q92552	.;.;RT27_HUMAN	A	178;122;192;122;122	ENSP00000261413:T178A;ENSP00000428120:T122A;ENSP00000426941:T192A;ENSP00000426176:T122A;ENSP00000427237:T122A	ENSP00000261413:T178A	T	-	1	0	MRPS27	71564085	1.000000	0.71417	1.000000	0.80357	0.272000	0.26649	6.982000	0.76173	2.315000	0.78130	0.533000	0.62120	ACC		0.383	MRPS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218560.2	NM_015084	
PTCD2	79810	broad.mit.edu	37	5	71654067	71654067	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:71654067C>T	ENST00000380639.5	+	10	996	c.980C>T	c.(979-981)gCc>gTc	p.A327V	CTC-365E16.1_ENST00000606310.1_lincRNA|PTCD2_ENST00000460837.2_3'UTR|PTCD2_ENST00000536805.1_Missense_Mutation_p.A155V|PTCD2_ENST00000503868.1_Missense_Mutation_p.A218V	NM_024754.3	NP_079030.3	Q8WV60	PTCD2_HUMAN	pentatricopeptide repeat domain 2	327					kidney development (GO:0001822)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|muscle fiber development (GO:0048747)|regulation of mRNA processing (GO:0050684)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)	p.A327V(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(1)|skin(1)	11		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.73e-53)		GATGTGCCTGCCCTTGTGGCC	0.468																																					p.A327V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C980T	5						.						87.0	76.0	80.0					5																	71654067		2203	4300	6503	71689823	SO:0001583	missense	79810	exon10			BC018720	CCDS4014.2, CCDS68891.1, CCDS68892.1, CCDS75258.1	5q13.2	2008-02-05			ENSG00000049883	ENSG00000049883			25734	protein-coding gene	gene with protein product		615484				12477932	Standard	XM_005248601		Approved	FLJ12598	uc003kcb.3	Q8WV60	OTTHUMG00000100953	ENST00000380639.5:c.980C>T	5.37:g.71654067C>T	ENSP00000370013:p.Ala327Val	Somatic		Capture	Illumina HiSeq	Phase_I	71689823	NM_024754	B7Z5D0|B7Z8L7|E9PFV7|Q6IA65|Q9H9R0	Missense_Mutation	SNP	ENST00000380639.5	37	CCDS4014.2	.	.	.	.	.	.	.	.	.	.	C	11.06	1.528945	0.27387	.	.	ENSG00000049883	ENST00000380639;ENST00000503868;ENST00000510676;ENST00000536805	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	5.4	1.45	0.22620	.	0.801037	0.11577	N	0.550146	T	0.32615	0.0835	L	0.41710	1.295	0.09310	N	1	B;B;B	0.24721	0.11;0.01;0.005	B;B;B	0.20767	0.031;0.01;0.008	T	0.22277	-1.0221	10	0.30854	T	0.27	.	3.4948	0.07650	0.3047:0.4644:0.1477:0.0832	.	218;155;327	E9PFV7;B7Z8L7;Q8WV60	.;.;PTCD2_HUMAN	V	327;218;156;155	ENSP00000370013:A327V;ENSP00000427349:A218V;ENSP00000426295:A156V;ENSP00000444772:A155V	ENSP00000308948:A327V	A	+	2	0	PTCD2	71689823	0.000000	0.05858	0.003000	0.11579	0.846000	0.48090	-0.165000	0.09968	-0.024000	0.13941	0.561000	0.74099	GCC		0.468	PTCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218562.6	NM_024754	
TMEM171	134285	broad.mit.edu	37	5	72419375	72419375	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:72419375C>T	ENST00000454765.2	+	2	648	c.175C>T	c.(175-177)Ctc>Ttc	p.L59F	TMEM171_ENST00000287773.5_Missense_Mutation_p.L59F			Q8WVE6	TM171_HUMAN	transmembrane protein 171	59						integral component of membrane (GO:0016021)		p.L59F(1)		endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|stomach(1)	15		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;1.87e-54)|Lung(70;0.115)		CCCCATGGTGCTCAAGGTGGC	0.627																																					p.L59F	NSCLC(112;638 2280 27369 30736)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C175T	5						.						72.0	70.0	71.0					5																	72419375		2203	4300	6503	72455131	SO:0001583	missense	134285	exon2			BC018083	CCDS4017.1, CCDS54869.1	5q13.2	2008-02-05			ENSG00000157111	ENSG00000157111			27031	protein-coding gene	gene with protein product						12477932	Standard	NM_173490		Approved	PRP2	uc003kcm.2	Q8WVE6	OTTHUMG00000131269	ENST00000454765.2:c.175C>T	5.37:g.72419375C>T	ENSP00000415030:p.Leu59Phe	Somatic		Capture	Illumina HiSeq	Phase_I	72455131	NM_173490	Q8N0S1|Q8TDT7	Missense_Mutation	SNP	ENST00000454765.2	37	CCDS4017.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.358399	0.41801	.	.	ENSG00000157111	ENST00000454765;ENST00000287773	T;T	0.38077	1.16;1.16	5.2	5.2	0.72013	.	0.110783	0.39759	N	0.001274	T	0.33206	0.0855	N	0.24115	0.695	0.38365	D	0.944718	P;P	0.45634	0.863;0.863	P;P	0.48873	0.593;0.593	T	0.19418	-1.0306	10	0.46703	T	0.11	-14.8784	12.131	0.53942	0.0:0.9213:0.0:0.0787	.	59;59	Q8WVE6-2;Q8WVE6	.;TM171_HUMAN	F	59	ENSP00000415030:L59F;ENSP00000287773:L59F	ENSP00000287773:L59F	L	+	1	0	TMEM171	72455131	1.000000	0.71417	1.000000	0.80357	0.102000	0.19082	3.712000	0.54875	2.431000	0.82371	0.462000	0.41574	CTC		0.627	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490	
ENC1	8507	broad.mit.edu	37	5	73930775	73930775	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:73930775G>A	ENST00000302351.4	-	2	2666	c.1536C>T	c.(1534-1536)aaC>aaT	p.N512N	ENC1_ENST00000510316.1_Silent_p.N439N|ENC1_ENST00000509284.1_5'Flank|ENC1_ENST00000537006.1_Silent_p.N512N	NM_003633.3	NP_003624.1	O14682	ENC1_HUMAN	ectodermal-neural cortex 1 (with BTB domain)	512				YTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQWTKVGDV TAKRMSCHAVASGNKLYVVGGYFGIQRCKTLDCYDPTLDVW NSITTVPYSLIPTAFVSTWKHLPS -> IHSQASCPGGTQD FLLWGVIQNFSACFCL (in Ref. 1; AAC39532). {ECO:0000305}.	multicellular organismal development (GO:0007275)|negative regulation of translation (GO:0017148)|nervous system development (GO:0007399)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.N512N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	20		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		AAGTCTCACTGTTGAATTTAT	0.512																																					p.N512N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1536T	5						.						86.0	89.0	88.0					5																	73930775		2203	4300	6503	73966531	SO:0001819	synonymous_variant	8507	exon2			AF059611	CCDS4021.1, CCDS58958.1	5q13	2013-01-30	2013-01-30		ENSG00000171617	ENSG00000171617		"""Kelch-like"", ""BTB/POZ domain containing"""	3345	protein-coding gene	gene with protein product	"""kelch-like family member 37"""	605173	"""ectodermal-neural cortex 1 (with BTB-like domain)"""	NRPB		9305847, 9566959	Standard	NM_003633		Approved	PIG10, ENC-1, TP53I10, KLHL37	uc003kdc.5	O14682	OTTHUMG00000102059	ENST00000302351.4:c.1536C>T	5.37:g.73930775G>A		Somatic		Capture	Illumina HiSeq	Phase_I	73966531	NM_003633	B4DHJ1|E9PFU0|O75464|Q9UPG9	Silent	SNP	ENST00000302351.4	37	CCDS4021.1																																																																																				0.512	ENC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219862.2	NM_003633	
COL4A3BP	10087	broad.mit.edu	37	5	74675210	74675210	+	Silent	SNP	G	G	A	rs565479126		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:74675210G>A	ENST00000405807.4	-	17	2257	c.1836C>T	c.(1834-1836)taC>taT	p.Y612Y	COL4A3BP_ENST00000508692.1_Intron|COL4A3BP_ENST00000380494.5_Silent_p.Y740Y|COL4A3BP_ENST00000261415.7_Silent_p.Y586Y	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	612	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)	p.Y612Y(1)		breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		TTTCTTGGACGTAAGAAGTAA	0.363													G|||	1	0.000199681	0.0	0.0	5008	,	,		17572	0.001		0.0	False		,,,				2504	0.0				p.Y740Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2220T	5						.						48.0	50.0	50.0					5																	74675210		2203	4300	6503	74710966	SO:0001819	synonymous_variant	10087	exon18			AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"""StAR-related lipid transfer (START) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2205	protein-coding gene	gene with protein product	"""ceramide transporter"", ""StAR-related lipid transfer (START) domain containing 11"""	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.1836C>T	5.37:g.74675210G>A		Somatic		Capture	Illumina HiSeq	Phase_I	74710966	NM_001130105	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	Silent	SNP	ENST00000405807.4	37	CCDS4028.1	.	.	.	.	.	.	.	.	.	.	G	8.559	0.877373	0.17395	.	.	ENSG00000113163	ENST00000508809	.	.	.	5.68	-2.28	0.06826	.	.	.	.	.	T	0.64057	0.2564	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62798	-0.6778	4	.	.	.	-12.7213	13.9821	0.64310	0.6902:0.0:0.3098:0.0	.	.	.	.	C	114	.	.	R	-	1	0	COL4A3BP	74710966	0.016000	0.18221	0.989000	0.46669	0.996000	0.88848	-0.766000	0.04725	-0.296000	0.08947	0.591000	0.81541	CGT		0.363	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713	
COL4A3BP	10087	broad.mit.edu	37	5	74721304	74721304	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:74721304C>A	ENST00000405807.4	-	5	898	c.477G>T	c.(475-477)gaG>gaT	p.E159D	COL4A3BP_ENST00000380494.5_Missense_Mutation_p.E287D|COL4A3BP_ENST00000261415.7_Missense_Mutation_p.E159D	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	159					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)	p.E159D(1)		breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		CAGCCAACTTCTCACGTAAAC	0.388																																					p.E287D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G861T	5						.						131.0	120.0	124.0					5																	74721304		2203	4300	6503	74757060	SO:0001583	missense	10087	exon6			AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"""StAR-related lipid transfer (START) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2205	protein-coding gene	gene with protein product	"""ceramide transporter"", ""StAR-related lipid transfer (START) domain containing 11"""	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.477G>T	5.37:g.74721304C>A	ENSP00000383996:p.Glu159Asp	Somatic		Capture	Illumina HiSeq	Phase_I	74757060	NM_001130105	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	Missense_Mutation	SNP	ENST00000405807.4	37	CCDS4028.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.905962	0.52333	.	.	ENSG00000113163	ENST00000405807;ENST00000380494;ENST00000261415	T;T;T	0.36520	1.3;1.25;1.32	5.75	1.89	0.25635	.	0.000000	0.85682	D	0.000000	T	0.39306	0.1073	M	0.68952	2.095	0.48395	D	0.999641	B;P;P	0.51653	0.376;0.947;0.649	B;P;B	0.47299	0.113;0.543;0.433	T	0.19321	-1.0309	10	0.44086	T	0.13	-1.4652	9.5065	0.39051	0.0:0.7072:0.0:0.2928	.	159;287;159	Q9Y5P4;Q9Y5P4-3;Q9Y5P4-2	C43BP_HUMAN;.;.	D	159;287;159	ENSP00000383996:E159D;ENSP00000369862:E287D;ENSP00000261415:E159D	ENSP00000261415:E159D	E	-	3	2	COL4A3BP	74757060	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.019000	0.30014	0.329000	0.23460	0.579000	0.79373	GAG		0.388	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713	
SV2C	22987	broad.mit.edu	37	5	75427856	75427856	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:75427856A>G	ENST00000502798.2	+	2	723	c.281A>G	c.(280-282)cAg>cGg	p.Q94R	SV2C_ENST00000322285.7_Missense_Mutation_p.Q94R	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	94					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)	p.Q94R(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		GGGGAGTATCAGGGCATCCCC	0.547																																					p.Q94R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A281G	5						.						76.0	81.0	79.0					5																	75427856		2123	4259	6382	75463612	SO:0001583	missense	22987	exon2			AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.281A>G	5.37:g.75427856A>G	ENSP00000423541:p.Gln94Arg	Somatic		Capture	Illumina HiSeq	Phase_I	75463612	NM_014979	Q496K1|Q9UPU8	Missense_Mutation	SNP	ENST00000502798.2	37	CCDS43331.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.665086	0.88251	.	.	ENSG00000122012	ENST00000502798;ENST00000322285	T;T	0.31510	1.49;1.49	5.76	5.76	0.90799	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.58032	0.2094	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.63014	-0.6731	10	0.87932	D	0	-18.4431	16.075	0.80962	1.0:0.0:0.0:0.0	.	94	Q496J9	SV2C_HUMAN	R	94	ENSP00000423541:Q94R;ENSP00000316983:Q94R	ENSP00000316983:Q94R	Q	+	2	0	SV2C	75463612	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	9.339000	0.96797	2.195000	0.70347	0.533000	0.62120	CAG		0.547	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4		
F2RL2	2151	broad.mit.edu	37	5	75913946	75913946	+	Missense_Mutation	SNP	C	C	T	rs150312521		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:75913946C>T	ENST00000296641.4	-	2	789	c.586G>A	c.(586-588)Gtc>Atc	p.V196I	IQGAP2_ENST00000396234.3_Intron|IQGAP2_ENST00000379730.3_Intron|IQGAP2_ENST00000274364.6_Intron|IQGAP2_ENST00000502745.1_Intron|F2RL2_ENST00000504899.1_Missense_Mutation_p.V174I	NM_004101.3	NP_004092.1	O00254	PAR3_HUMAN	coagulation factor II (thrombin) receptor-like 2	196					blood coagulation (GO:0007596)|metabolic process (GO:0008152)|platelet activation (GO:0030168)|response to wounding (GO:0009611)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|thrombin receptor activity (GO:0015057)	p.V196I(2)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(3)	32		all_lung(232;0.000462)|Lung NSC(167;0.00124)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)		AAAGGATGGACGATGGCCAGG	0.527																																					p.V196I												.	.	2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.G586A	5						.	C	ILE/VAL,	2,4404	4.2+/-10.8	0,2,2201	78.0	64.0	69.0		586,	3.3	0.1	5	dbSNP_134	69	0,8600		0,0,4300	no	missense,intron	F2RL2,IQGAP2	NM_004101.2,NM_006633.2	29,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,	196/375,	75913946	2,13004	2203	4300	6503	75949702	SO:0001583	missense	2151	exon2			U92971	CCDS4031.1, CCDS58959.1	5q13	2012-08-08			ENSG00000164220	ENSG00000164220		"""GPCR / Class A : Protease activated receptors"""	3539	protein-coding gene	gene with protein product	"""proteinase-activated receptor-3"""	601919				9087410, 9722561	Standard	NM_004101		Approved	PAR3	uc003kem.4	O00254	OTTHUMG00000102119	ENST00000296641.4:c.586G>A	5.37:g.75913946C>T	ENSP00000296641:p.Val196Ile	Somatic		Capture	Illumina HiSeq	Phase_I	75949702	NM_004101	B2R754|B4DQ13|Q52M68|Q7Z3W3	Missense_Mutation	SNP	ENST00000296641.4	37	CCDS4031.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	15.09	2.731011	0.48939	4.54E-4	0.0	ENSG00000164220	ENST00000296641;ENST00000504899	T;T	0.39592	1.07;1.07	5.09	3.31	0.37934	GPCR, rhodopsin-like superfamily (1);	0.130030	0.51477	N	0.000096	T	0.45597	0.1350	M	0.80508	2.5	0.39565	D	0.969198	B	0.31859	0.343	B	0.32393	0.145	T	0.50242	-0.8851	10	0.72032	D	0.01	-13.2681	11.2754	0.49163	0.0:0.8522:0.0:0.1478	.	196	O00254	PAR3_HUMAN	I	196;174	ENSP00000296641:V196I;ENSP00000426703:V174I	ENSP00000296641:V196I	V	-	1	0	F2RL2	75949702	0.998000	0.40836	0.116000	0.21606	0.695000	0.40330	3.763000	0.55257	0.554000	0.29061	0.563000	0.77884	GTC		0.527	F2RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219958.3		
ARSB	411	broad.mit.edu	37	5	78076321	78076321	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:78076321G>A	ENST00000264914.4	-	8	2037	c.1501C>T	c.(1501-1503)Cgc>Tgc	p.R501C		NM_000046.3	NP_000037.2	P15848	ARSB_HUMAN	arylsulfatase B	501					autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|lysosomal transport (GO:0007041)|lysosome organization (GO:0007040)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|rough endoplasmic reticulum (GO:0005791)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)	p.R501C(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		AACTGTAGGCGGGACAGGAGC	0.542																																					p.R501C	Melanoma(169;563 1968 25780 26156 52266)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1501T	5						.						109.0	91.0	97.0					5																	78076321		2203	4300	6503	78112077	SO:0001583	missense	411	exon8			M32373	CCDS4043.1, CCDS43334.1	5q14.1	2013-02-14			ENSG00000113273	ENSG00000113273	3.1.6.1	"""Arylsulfatase family"""	714	protein-coding gene	gene with protein product		611542				2303452	Standard	NM_000046		Approved		uc003kfq.3	P15848	OTTHUMG00000108129	ENST00000264914.4:c.1501C>T	5.37:g.78076321G>A	ENSP00000264914:p.Arg501Cys	Somatic		Capture	Illumina HiSeq	Phase_I	78112077	NM_000046	B2RC20|Q8N322|Q9UDI9	Missense_Mutation	SNP	ENST00000264914.4	37	CCDS4043.1	.	.	.	.	.	.	.	.	.	.	G	17.52	3.409185	0.62399	.	.	ENSG00000113273	ENST00000264914	D	0.94650	-3.48	5.58	3.77	0.43336	Alkaline-phosphatase-like, core domain (1);	0.376195	0.28241	N	0.016073	D	0.97198	0.9084	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.96513	0.9380	10	0.72032	D	0.01	.	9.6974	0.40165	0.0728:0.0:0.7863:0.1409	.	501	P15848	ARSB_HUMAN	C	501	ENSP00000264914:R501C	ENSP00000264914:R501C	R	-	1	0	ARSB	78112077	1.000000	0.71417	0.388000	0.26195	0.614000	0.37383	4.100000	0.57762	0.683000	0.31428	0.555000	0.69702	CGC		0.542	ARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226932.2	NM_000046	
BHMT	635	broad.mit.edu	37	5	78416233	78416233	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:78416233G>A	ENST00000274353.5	+	4	453	c.346G>A	c.(346-348)Gct>Act	p.A116T	BHMT_ENST00000524080.1_Intron|DMGDH_ENST00000520388.1_5'UTR	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	116	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				amino-acid betaine catabolic process (GO:0006579)|amino-acid betaine metabolic process (GO:0006577)|cellular nitrogen compound metabolic process (GO:0034641)|L-methionine salvage (GO:0071267)|protein methylation (GO:0006479)|regulation of homocysteine metabolic process (GO:0050666)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	betaine-homocysteine S-methyltransferase activity (GO:0047150)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)	p.A116T(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)	29		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	TGAAGGAGATGCTTTGGTAGC	0.433																																					p.A116T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G346A	5						.						64.0	60.0	62.0					5																	78416233		2203	4300	6503	78451989	SO:0001583	missense	635	exon4			BC012616	CCDS4046.1	5q14.1	2012-09-20	2010-04-28		ENSG00000145692	ENSG00000145692	2.1.1.5		1047	protein-coding gene	gene with protein product	"""betaine homocysteine methyltransferase"""	602888				8798461, 9281325	Standard	NM_001713		Approved	BHMT1	uc003kfu.4	Q93088	OTTHUMG00000108157	ENST00000274353.5:c.346G>A	5.37:g.78416233G>A	ENSP00000274353:p.Ala116Thr	Somatic		Capture	Illumina HiSeq	Phase_I	78451989	NM_001713	Q9UNI9	Missense_Mutation	SNP	ENST00000274353.5	37	CCDS4046.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.616581	0.87359	.	.	ENSG00000145692	ENST00000274353	T	0.12361	2.69	5.22	4.36	0.52297	Homocysteine S-methyltransferase (4);	0.000000	0.85682	D	0.000000	T	0.31263	0.0791	M	0.71206	2.165	0.80722	D	1	D	0.63880	0.993	P	0.60236	0.871	T	0.03807	-1.1002	10	0.33940	T	0.23	-16.6596	14.1634	0.65461	0.0727:0.0:0.9273:0.0	.	116	Q93088	BHMT1_HUMAN	T	116	ENSP00000274353:A116T	ENSP00000274353:A116T	A	+	1	0	BHMT	78451989	1.000000	0.71417	0.796000	0.32109	0.906000	0.53458	7.583000	0.82559	1.346000	0.45694	0.557000	0.71058	GCT		0.433	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713	
HOMER1	9456	broad.mit.edu	37	5	78697868	78697868	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:78697868T>C	ENST00000334082.6	-	6	1980	c.538A>G	c.(538-540)Agc>Ggc	p.S180G	HOMER1_ENST00000508576.1_Intron|HOMER1_ENST00000282260.6_Intron|HOMER1_ENST00000535690.1_Missense_Mutation_p.S6G	NM_004272.3	NP_004263.1	Q86YM7	HOME1_HUMAN	homer homolog 1 (Drosophila)	180					behavioral response to cocaine (GO:0048148)|chemical homeostasis within a tissue (GO:0048875)|circadian rhythm (GO:0007623)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of signal transduction (GO:0009967)|protein localization to synapse (GO:0035418)|regulation of calcium ion import (GO:0090279)|regulation of cation channel activity (GO:2001257)|regulation of store-operated calcium entry (GO:2001256)|response to calcium ion (GO:0051592)|response to nicotine (GO:0035094)|skeletal muscle contraction (GO:0003009)|skeletal muscle fiber development (GO:0048741)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell junction (GO:0030054)|costamere (GO:0043034)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|signaling adaptor activity (GO:0035591)	p.S180G(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|skin(1)	14		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)		CAATGTTTGCTGATTGCTGAA	0.413																																					p.S180G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A538G	5						.						60.0	55.0	56.0					5																	78697868		1860	4105	5965	78733624	SO:0001583	missense	9456	exon6			BC015502	CCDS43335.1, CCDS64188.1, CCDS64189.1	5q14.2	2008-02-05			ENSG00000152413	ENSG00000152413			17512	protein-coding gene	gene with protein product		604798				9808459, 9808458	Standard	NM_004272		Approved	Ves-1, SYN47, HOMER-1B	uc003kfy.4	Q86YM7	OTTHUMG00000134278	ENST00000334082.6:c.538A>G	5.37:g.78697868T>C	ENSP00000334382:p.Ser180Gly	Somatic		Capture	Illumina HiSeq	Phase_I	78733624	NM_004272	B2R688|O96003|Q86YM5	Missense_Mutation	SNP	ENST00000334082.6	37	CCDS43335.1	.	.	.	.	.	.	.	.	.	.	T	13.92	2.382266	0.42207	.	.	ENSG00000152413	ENST00000334082;ENST00000535690	T;T	0.23552	2.22;1.9	5.46	5.46	0.80206	.	0.172299	0.64402	D	0.000004	T	0.10337	0.0253	N	0.01352	-0.895	0.46149	D	0.998893	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.22977	-1.0201	10	0.19147	T	0.46	-0.3572	15.817	0.78612	0.0:0.0:0.0:1.0	.	6;180	Q86YM6;Q86YM7	.;HOME1_HUMAN	G	180;6	ENSP00000334382:S180G;ENSP00000441587:S6G	ENSP00000334382:S180G	S	-	1	0	HOMER1	78733624	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.749000	0.62155	2.193000	0.70182	0.533000	0.62120	AGC		0.413	HOMER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258856.1	NM_004272	
MSH3	4437	broad.mit.edu	37	5	79966084	79966084	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:79966084G>A	ENST00000265081.6	+	4	828	c.748G>A	c.(748-750)Gtg>Atg	p.V250M		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	250	Interaction with EXO1.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)	p.V241M(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		AGTTTTGTGTGTGGAATGTGG	0.373								Mismatch excision repair (MMR)																													p.V250M	Melanoma(88;1010 1399 13793 26548 36275)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G748A	5						.						141.0	145.0	144.0					5																	79966084		2203	4300	6503	80001840	SO:0001583	missense	4437	exon4			U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.748G>A	5.37:g.79966084G>A	ENSP00000265081:p.Val250Met	Somatic		Capture	Illumina HiSeq	Phase_I	80001840	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.075352	0.76415	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.89617	-2.54	5.67	4.62	0.57501	DNA mismatch repair protein MutS, N-terminal (2);DNA mismatch repair protein MutS-like, N-terminal (1);	0.214427	0.37623	N	0.002011	D	0.92548	0.7633	L	0.57130	1.785	0.42926	D	0.994301	D	0.65815	0.995	D	0.72625	0.978	D	0.91790	0.5443	9	.	.	.	-16.6505	15.2335	0.73411	0.0799:0.0:0.9201:0.0	.	250	P20585	MSH3_HUMAN	M	250;241	ENSP00000265081:V250M	.	V	+	1	0	MSH3	80001840	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.366000	0.79548	2.666000	0.90696	0.655000	0.94253	GTG		0.373	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
RASGRF2	5924	broad.mit.edu	37	5	80256722	80256722	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:80256722G>A	ENST00000265080.4	+	1	232	c.165G>A	c.(163-165)gaG>gaA	p.E55E	CTC-459I6.1_ENST00000505694.1_RNA	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	55	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E55E(1)		biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		TCTACTTCGAGGGCGAGCAGA	0.692																																					p.E55E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G165A	5						.						27.0	29.0	28.0					5																	80256722		2203	4300	6503	80292478	SO:0001819	synonymous_variant	5924	exon1			AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.165G>A	5.37:g.80256722G>A		Somatic		Capture	Illumina HiSeq	Phase_I	80292478	NM_006909	B9EG89|Q9UK56	Silent	SNP	ENST00000265080.4	37	CCDS4052.1																																																																																				0.692	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909	
RPS23	6228	broad.mit.edu	37	5	81573578	81573578	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:81573578C>T	ENST00000296674.8	-	2	351	c.98G>A	c.(97-99)gGc>gAc	p.G33D	RPS23_ENST00000510019.1_Missense_Mutation_p.G33D|RPS23_ENST00000511844.1_Missense_Mutation_p.G33D|RPS23_ENST00000512493.1_Missense_Mutation_p.G33D|RPS23_ENST00000507980.1_Missense_Mutation_p.G33D|RPS23_ENST00000510210.1_Missense_Mutation_p.G33D|ATP6AP1L_ENST00000380167.4_5'Flank|RPS23_ENST00000503605.1_5'UTR	NM_001025.4	NP_001016.1	P62266	RS23_HUMAN	ribosomal protein S23	33					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)|nucleolus (GO:0005730)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.G33D(1)		prostate(1)	1		Lung NSC(167;0.0025)|all_lung(232;0.00278)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-42)|Epithelial(54;8.38e-37)|all cancers(79;1.42e-31)		TAGGGCTGTGCCCAAATGAGC	0.458																																					p.G33D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G98A	5						.						122.0	121.0	121.0					5																	81573578		1908	4129	6037	81609334	SO:0001583	missense	6228	exon2			AB007158	CCDS47241.1	5q14.2	2013-05-09			ENSG00000186468	ENSG00000186468		"""S ribosomal proteins"""	10410	protein-coding gene	gene with protein product		603683				9582194	Standard	NM_001025		Approved	S23	uc003khu.3	P62266	OTTHUMG00000162557	ENST00000296674.8:c.98G>A	5.37:g.81573578C>T	ENSP00000296674:p.Gly33Asp	Somatic		Capture	Illumina HiSeq	Phase_I	81609334	NM_001025	P39028|Q6IB08	Missense_Mutation	SNP	ENST00000296674.8	37	CCDS47241.1	.	.	.	.	.	.	.	.	.	.	C	35	5.456381	0.96223	.	.	ENSG00000186468	ENST00000296674;ENST00000510210;ENST00000512493;ENST00000510019;ENST00000507980;ENST00000511844	.	.	.	5.45	5.45	0.79879	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	D	0.84401	0.5464	M	0.93062	3.375	0.80722	D	1	P	0.46142	0.873	P	0.55923	0.787	D	0.87596	0.2494	9	0.66056	D	0.02	.	18.8735	0.92325	0.0:1.0:0.0:0.0	.	33	P62266	RS23_HUMAN	D	33	.	ENSP00000296674:G33D	G	-	2	0	RPS23	81609334	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.676000	0.84012	2.550000	0.86006	0.655000	0.94253	GGC		0.458	RPS23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369546.2	NM_001025	
XRCC4	7518	broad.mit.edu	37	5	82648982	82648982	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:82648982A>G	ENST00000511817.1	+	8	1012	c.932A>G	c.(931-933)aAg>aGg	p.K311R	XRCC4_ENST00000338635.6_Missense_Mutation_p.K311R|XRCC4_ENST00000396027.4_Missense_Mutation_p.K309R|XRCC4_ENST00000282268.3_Missense_Mutation_p.K309R			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	311					cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)	p.K309R(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		ACGTCTAAAAAGGAGCACATC	0.333								Non-homologous end-joining																													p.K311R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A932G	5						.						116.0	126.0	123.0					5																	82648982		2203	4299	6502	82684738	SO:0001583	missense	7518	exon8			AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"""X-ray repair, complementing defective, repair in Chinese hamster"", ""DNA repair protein XRCC4"""	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.932A>G	5.37:g.82648982A>G	ENSP00000421491:p.Lys311Arg	Somatic		Capture	Illumina HiSeq	Phase_I	82684738	NM_022406	A8K3X4|Q9BS72|Q9UP94	Missense_Mutation	SNP	ENST00000511817.1	37	CCDS4059.1	.	.	.	.	.	.	.	.	.	.	A	14.07	2.425058	0.43020	.	.	ENSG00000152422	ENST00000282268;ENST00000338635;ENST00000396027;ENST00000511817;ENST00000514538	T;T;T;T	0.12774	2.65;2.65;2.65;2.65	5.76	4.53	0.55603	.	0.274096	0.33235	N	0.005127	T	0.22475	0.0542	L	0.50333	1.59	0.09310	N	1	P;P	0.52170	0.925;0.951	P;P	0.56398	0.621;0.797	T	0.03728	-1.1009	10	0.40728	T	0.16	-27.2518	9.2492	0.37545	0.818:0.182:0.0:0.0	.	309;311	Q13426-2;Q13426	.;XRCC4_HUMAN	R	309;311;309;311;36	ENSP00000282268:K309R;ENSP00000342011:K311R;ENSP00000379344:K309R;ENSP00000421491:K311R	ENSP00000282268:K309R	K	+	2	0	XRCC4	82684738	0.689000	0.27690	0.879000	0.34478	0.429000	0.31625	2.110000	0.41873	2.196000	0.70406	0.533000	0.62120	AAG		0.333	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550	
GPR98	84059	broad.mit.edu	37	5	89923559	89923559	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:89923559A>G	ENST00000405460.2	+	7	1300	c.1204A>G	c.(1204-1206)Agg>Ggg	p.R402G		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	402	Calx-beta 4. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.R402G(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TTTGTTTGAAAGGACAGTTAT	0.303																																					p.R402G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1204G	5						.						42.0	41.0	41.0					5																	89923559		1816	4069	5885	89959315	SO:0001583	missense	84059	exon7			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.1204A>G	5.37:g.89923559A>G	ENSP00000384582:p.Arg402Gly	Somatic		Capture	Illumina HiSeq	Phase_I	89959315	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	13.80	2.346657	0.41599	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.28069	1.63	5.85	4.74	0.60224	.	0.258293	0.45606	D	0.000351	T	0.30510	0.0767	M	0.62723	1.935	0.80722	D	1	B	0.26258	0.145	B	0.23419	0.046	T	0.09400	-1.0676	10	0.40728	T	0.16	.	11.0431	0.47842	0.6149:0.3851:0.0:0.0	.	402	Q8WXG9	GPR98_HUMAN	G	402	ENSP00000384582:R402G	ENSP00000296619:R402G	R	+	1	2	GPR98	89959315	1.000000	0.71417	0.971000	0.41717	0.639000	0.38242	5.173000	0.65010	2.238000	0.73509	0.477000	0.44152	AGG		0.303	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
NR2F1	7025	broad.mit.edu	37	5	92923702	92923702	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:92923702C>T	ENST00000327111.3	+	2	2230	c.543C>T	c.(541-543)ggC>ggT	p.G181G	NR2F1-AS1_ENST00000513055.1_RNA	NM_005654.4	NP_005645.1	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	181					cerebral cortex regionalization (GO:0021796)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|retinoic acid-responsive element binding (GO:0044323)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.G181G(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(6)|lung(2)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	21		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)		CCCTCAACGGCCACTGCTACC	0.607																																					p.G181G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C543T	5						.						70.0	69.0	69.0					5																	92923702		2203	4300	6503	92949458	SO:0001819	synonymous_variant	7025	exon2			BC004154	CCDS4068.1	5q14	2013-01-16			ENSG00000175745	ENSG00000175745		"""Nuclear hormone receptors"""	7975	protein-coding gene	gene with protein product		132890		ERBAL3, TFCOUP1		8530078	Standard	NM_005654		Approved	EAR-3, COUP-TFI, TCFCOUP1, SVP44	uc003kkj.3	P10589	OTTHUMG00000119079	ENST00000327111.3:c.543C>T	5.37:g.92923702C>T		Somatic		Capture	Illumina HiSeq	Phase_I	92949458	NM_005654		Silent	SNP	ENST00000327111.3	37	CCDS4068.1																																																																																				0.607	NR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239293.2	NM_005654	
NR2F1	7025	broad.mit.edu	37	5	92923832	92923832	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:92923832C>T	ENST00000327111.3	+	2	2360	c.673C>T	c.(673-675)Cgc>Tgc	p.R225C	NR2F1-AS1_ENST00000513055.1_RNA	NM_005654.4	NP_005645.1	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	225					cerebral cortex regionalization (GO:0021796)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|retinoic acid-responsive element binding (GO:0044323)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.R225C(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(6)|lung(2)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	21		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)		GCTGGCCGCGCGCCTGCTCTT	0.657																																					p.R225C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C673T	5						.						75.0	74.0	74.0					5																	92923832		2203	4300	6503	92949588	SO:0001583	missense	7025	exon2			BC004154	CCDS4068.1	5q14	2013-01-16			ENSG00000175745	ENSG00000175745		"""Nuclear hormone receptors"""	7975	protein-coding gene	gene with protein product		132890		ERBAL3, TFCOUP1		8530078	Standard	NM_005654		Approved	EAR-3, COUP-TFI, TCFCOUP1, SVP44	uc003kkj.3	P10589	OTTHUMG00000119079	ENST00000327111.3:c.673C>T	5.37:g.92923832C>T	ENSP00000325819:p.Arg225Cys	Somatic		Capture	Illumina HiSeq	Phase_I	92949588	NM_005654		Missense_Mutation	SNP	ENST00000327111.3	37	CCDS4068.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.608322	0.87258	.	.	ENSG00000175745	ENST00000327111	D	0.97256	-4.31	4.47	4.47	0.54385	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.98880	0.9621	H	0.94925	3.6	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99671	1.0996	10	0.87932	D	0	.	17.3064	0.87196	0.0:1.0:0.0:0.0	.	225	P10589	COT1_HUMAN	C	225	ENSP00000325819:R225C	ENSP00000325819:R225C	R	+	1	0	NR2F1	92949588	0.999000	0.42202	1.000000	0.80357	0.578000	0.36192	2.466000	0.45084	2.292000	0.77174	0.407000	0.27541	CGC		0.657	NR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239293.2	NM_005654	
CHD1	1105	broad.mit.edu	37	5	98206409	98206409	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:98206409delT	ENST00000284049.3	-	28	4109	c.3960delA	c.(3958-3960)aaafs	p.K1320fs	CHD1_ENST00000511067.1_5'UTR	NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1320					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)	p.E1321fs*22(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	AAAGAGCTTCTTTTTTTGCAA	0.383																																					p.K1320fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3960delA	5						.						127.0	129.0	129.0					5																	98206409		2203	4300	6503	98234309	SO:0001589	frameshift_variant	1105	exon28			AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.3960delA	5.37:g.98206409delT	ENSP00000284049:p.Lys1320fs	Somatic		Capture	Illumina HiSeq	Phase_I	98234309	NM_001270	Q17RZ3	Frame_Shift_Del	DEL	ENST00000284049.3	37	CCDS34204.1																																																																																				0.383	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
SLCO6A1	133482	broad.mit.edu	37	5	101748695	101748695	+	Splice_Site	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:101748695delT	ENST00000506729.1	-	9	1796	c.1625delA	c.(1624-1626)aag>ag	p.K542fs	SLCO6A1_ENST00000379810.1_Splice_Site_p.K289fs|SLCO6A1_ENST00000379807.3_Splice_Site_p.K542fs|SLCO6A1_ENST00000513675.1_Splice_Site_p.K289fs|SLCO6A1_ENST00000389019.3_Splice_Site_p.K480fs			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	542	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.K542fs*13(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		aataatTACCTTTTTTTGGTT	0.234																																					p.K542fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1625delA	5						.			22,4044		6,10,2017	10.0	10.0	10.0			3.3	0.8	5		9	39,8049		3,33,4008	no	frameshift-near-splice	SLCO6A1	NM_173488.3		9,43,6025	A1A1,A1R,RR		0.4822,0.5411,0.5019			101748695	61,12093	2105	4221	6326	101776594	SO:0001630	splice_region_variant	133482	exon9			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"""Solute carriers"""	23613	protein-coding gene	gene with protein product	"""cancer/testis antigen 48"""	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1626+1A>-	5.37:g.101748695delT		Somatic		Capture	Illumina HiSeq	Phase_I	101776594	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Frame_Shift_Del	DEL	ENST00000506729.1	37	CCDS34206.1																																																																																				0.234	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	Frame_Shift_Del
FSTL4	23105	broad.mit.edu	37	5	132534817	132534817	+	Frame_Shift_Del	DEL	C	C	-	rs140495211		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:132534817delC	ENST00000265342.7	-	16	2748	c.2499delG	c.(2497-2499)gggfs	p.G833fs	CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	833						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.T834fs*>9(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCACTGTGGTCCCCCCCTTTA	0.582																																					p.G833fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2499delG	5						.						59.0	57.0	58.0					5																	132534817		2203	4300	6503	132562716	SO:0001589	frameshift_variant	23105	exon16			AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.2499delG	5.37:g.132534817delC	ENSP00000265342:p.Gly833fs	Somatic		Capture	Illumina HiSeq	Phase_I	132562716	NM_015082	Q8TBU0|Q9UPU1	Frame_Shift_Del	DEL	ENST00000265342.7	37	CCDS34238.1																																																																																				0.582	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786	
CNOT6	57472	broad.mit.edu	37	5	179992865	179992865	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr5:179992865C>T	ENST00000393356.1	+	9	1029	c.605C>T	c.(604-606)gCg>gTg	p.A202V	CNOT6_ENST00000261951.4_Missense_Mutation_p.A202V			Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6	202	Nuclease domain. {ECO:0000250}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|gene silencing by miRNA (GO:0035195)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of ligand-dependent nuclear receptor transcription coactivator activity (GO:2000327)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	exoribonuclease activity (GO:0004532)|metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)|RNA binding (GO:0003723)	p.A202V(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|skin(1)	23	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		GATAAATATGCGACCCGGCAG	0.383																																					p.A202V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C605T	5						.						134.0	127.0	129.0					5																	179992865		2203	4300	6503	179925471	SO:0001583	missense	57472	exon7			AB033020	CCDS4455.1	5q35.3	2014-06-17			ENSG00000113300	ENSG00000113300			14099	protein-coding gene	gene with protein product		608951				11889047	Standard	XM_005265953		Approved	CCR4, KIAA1194, Ccr4a	uc003mlx.3	Q9ULM6	OTTHUMG00000130935	ENST00000393356.1:c.605C>T	5.37:g.179992865C>T	ENSP00000377024:p.Ala202Val	Somatic		Capture	Illumina HiSeq	Phase_I	179925471	NM_015455	A7MD46|D3DWR0	Missense_Mutation	SNP	ENST00000393356.1	37	CCDS4455.1	.	.	.	.	.	.	.	.	.	.	C	36	5.897278	0.97081	.	.	ENSG00000113300	ENST00000261951;ENST00000393356;ENST00000504343	T;T;T	0.30981	1.51;1.51;1.51	6.02	6.02	0.97574	Endonuclease/exonuclease/phosphatase (2);	0.000000	0.85682	D	0.000000	T	0.59487	0.2197	M	0.77616	2.38	0.80722	D	1	D;D	0.76494	0.994;0.999	P;D	0.70716	0.79;0.97	T	0.55805	-0.8083	9	.	.	.	-7.6475	20.5407	0.99260	0.0:1.0:0.0:0.0	.	106;202	D6R9H6;Q9ULM6	.;CNOT6_HUMAN	V	202;202;106	ENSP00000261951:A202V;ENSP00000377024:A202V;ENSP00000422087:A106V	.	A	+	2	0	CNOT6	179925471	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.865000	0.98341	0.655000	0.94253	GCG		0.383	CNOT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253532.1	NM_015455	
RBM24	221662	broad.mit.edu	37	6	17292208	17292209	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:17292208_17292209insT	ENST00000379052.5	+	4	805_806	c.569_570insT	c.(568-573)gctgggfs	p.G191fs	RBM24_ENST00000425446.2_Frame_Shift_Ins_p.G133fs|RBM24_ENST00000318204.5_Frame_Shift_Ins_p.G146fs|RBM24_ENST00000508508.1_3'UTR	NM_001143942.1	NP_001137414.1	Q9BX46	RBM24_HUMAN	RNA binding motif protein 24	191	Ala-rich.				cell differentiation (GO:0030154)|regulation of mRNA stability (GO:0043488)|regulation of myotube differentiation (GO:0010830)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)	p.G146fs*>47(1)		endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)	13	Breast(50;0.0615)|Ovarian(93;0.0733)	all_hematologic(90;0.062)	all cancers(50;0.131)|Epithelial(50;0.15)			TATGTTACTGCTGGGGGCTATG	0.644																																					p.A190fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.569_570insT	6						.																																			17400188	SO:0001589	frameshift_variant	221662	exon4			BC040928	CCDS4538.1, CCDS47378.1, CCDS47379.1	6p22.3	2013-02-12	2004-04-23	2004-04-23	ENSG00000112183	ENSG00000112183		"""RNA binding motif (RRM) containing"""	21539	protein-coding gene	gene with protein product			"""RNA-binding region (RNP1, RRM) containing 6"""	RNPC6			Standard	NM_153020		Approved	FLJ30829, dJ259A10.1	uc003nbz.4	Q9BX46	OTTHUMG00000014306	ENST00000379052.5:c.570dupT	6.37:g.17292209_17292209dupT	ENSP00000368341:p.Gly191fs	Somatic		Capture	Illumina HiSeq	Phase_I	17400187	NM_001143942	E9PAY4|Q6QDA4|Q8N9D3|Q96NI3	Frame_Shift_Ins	INS	ENST00000379052.5	37	CCDS47378.1																																																																																				0.644	RBM24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039946.2	NM_153020	
BVES	11149	broad.mit.edu	37	6	105573388	105573388	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:105573388T>C	ENST00000314641.5	-	4	633	c.417A>G	c.(415-417)ccA>ccG	p.P139P	BVES_ENST00000336775.5_Silent_p.P139P|BVES_ENST00000446408.2_Silent_p.P139P	NM_001199563.1	NP_001186492.1	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance	139					epithelial cell-cell adhesion (GO:0090136)|hematopoietic progenitor cell differentiation (GO:0002244)|muscle organ development (GO:0007517)|positive regulation of locomotion (GO:0040017)|positive regulation of receptor recycling (GO:0001921)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|regulation of Rac GTPase activity (GO:0032314)|sinoatrial node cell development (GO:0060931)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cAMP binding (GO:0030552)|structural molecule activity (GO:0005198)	p.P139P(1)		NS(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|urinary_tract(1)	21		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)				TGAACAAATCTGGAGGCACAC	0.443																																					p.P139P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A417G	6						.						151.0	146.0	147.0					6																	105573388		2203	4300	6503	105680081	SO:0001819	synonymous_variant	11149	exon4			AF124512	CCDS5051.1	6q21	2008-11-25			ENSG00000112276	ENSG00000112276			1152	protein-coding gene	gene with protein product	"""popeye domain containing 1"""	604577				10441744, 10882522	Standard	NM_147147		Approved	HBVES, POP1, POPDC1	uc003pqx.3	Q8NE79	OTTHUMG00000015291	ENST00000314641.5:c.417A>G	6.37:g.105573388T>C		Somatic		Capture	Illumina HiSeq	Phase_I	105680081	NM_007073	A8K1R4|E1P5D8|Q5T550|Q5T551|Q8IWC6|Q9HBV0|Q9UNG6	Silent	SNP	ENST00000314641.5	37	CCDS5051.1																																																																																				0.443	BVES-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406075.1	NM_147147	
TMEM14B	81853	broad.mit.edu	37	6	10756713	10756713	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:10756713G>A	ENST00000379542.5	+	6	474	c.307G>A	c.(307-309)Gcc>Acc	p.A103T	TMEM14B_ENST00000481240.1_Intron|TMEM14B_ENST00000473276.1_Missense_Mutation_p.R43H|RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron|TMEM14B_ENST00000379530.3_Missense_Mutation_p.A69T|TMEM14B_ENST00000491103.1_3'UTR|TMEM14B_ENST00000467317.1_Intron	NM_030969.3	NP_112231.3	Q9NUH8	TM14B_HUMAN	transmembrane protein 14B	103						integral component of membrane (GO:0016021)		p.A103T(1)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(2)|skin(2)	11	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)				GCTGATGGCCGCCAAAGTTGG	0.383																																					p.A69T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G205A	6						.						153.0	132.0	139.0					6																	10756713		2203	4300	6503	10864699	SO:0001583	missense	81853	exon5			AL024498	CCDS4515.1, CCDS47372.1, CCDS75395.1, CCDS75396.1, CCDS75397.1	6p25.1-p23	2008-08-12			ENSG00000137210	ENSG00000137210			21384	protein-coding gene	gene with protein product							Standard	NM_030969		Approved	MGC1223	uc003mzk.4	Q9NUH8	OTTHUMG00000014246	ENST00000379542.5:c.307G>A	6.37:g.10756713G>A	ENSP00000368858:p.Ala103Thr	Somatic		Capture	Illumina HiSeq	Phase_I	10864699	NM_001127711	Q5THN7|Q5THN8|Q96IX7|Q9BVN8	Missense_Mutation	SNP	ENST00000379542.5	37	CCDS4515.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.26|16.26	3.072831|3.072831	0.55646|0.55646	.|.	.|.	ENSG00000137210|ENSG00000137210	ENST00000472062;ENST00000379542;ENST00000379530|ENST00000473276	T;T|T	0.44083|0.58797	0.93;0.93|0.31	3.75|3.75	3.75|3.75	0.43078|0.43078	.|.	0.225856|.	0.44902|.	D|.	0.000409|.	T|T	0.60274|0.60274	0.2256|0.2256	M|M	0.64567|0.64567	1.98|1.98	0.80722|0.80722	D|D	1|1	P;B|.	0.40398|.	0.716;0.104|.	B;B|.	0.28385|.	0.089;0.073|.	T|T	0.65409|0.65409	-0.6175|-0.6175	10|7	0.42905|0.87932	T|D	0.14|0	.|.	13.4411|13.4411	0.61114|0.61114	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	69;103|.	Q5THN7;Q9NUH8|.	.;TM14B_HUMAN|.	T|H	103;103;69|43	ENSP00000368858:A103T;ENSP00000368845:A69T|ENSP00000420580:R43H	ENSP00000368845:A69T|ENSP00000420580:R43H	A|R	+|+	1|2	0|0	TMEM14B|TMEM14B	10864699|10864699	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.901000|0.901000	0.52897|0.52897	1.641000|1.641000	0.37197|0.37197	2.414000|2.414000	0.81942|0.81942	0.650000|0.650000	0.86243|0.86243	GCC|CGC		0.383	TMEM14B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039836.1	NM_030969	
SYCP2L	221711	broad.mit.edu	37	6	10907866	10907866	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:10907866T>A	ENST00000283141.6	+	10	1064	c.768T>A	c.(766-768)gaT>gaA	p.D256E	RP11-637O19.3_ENST00000480294.1_3'UTR|SYCP2L_ENST00000543878.1_Missense_Mutation_p.D97E	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	256						nucleus (GO:0005634)		p.D256E(1)		breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			GGTTTGATGATGAAGTCATTG	0.373																																					p.D256E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T768A	6						.						127.0	123.0	124.0					6																	10907866		1844	4100	5944	11015852	SO:0001583	missense	221711	exon10			AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 177"""	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.768T>A	6.37:g.10907866T>A	ENSP00000283141:p.Asp256Glu	Somatic		Capture	Illumina HiSeq	Phase_I	11015852	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Missense_Mutation	SNP	ENST00000283141.6	37	CCDS43423.1	.	.	.	.	.	.	.	.	.	.	T	14.29	2.491056	0.44249	.	.	ENSG00000153157	ENST00000543878;ENST00000283141	T;T	0.48201	0.82;2.11	5.48	1.8	0.24995	.	0.071697	0.56097	D	0.000023	T	0.50531	0.1621	M	0.74258	2.255	0.80722	D	1	D;D	0.69078	0.99;0.997	P;D	0.68353	0.896;0.957	T	0.50783	-0.8787	10	0.44086	T	0.13	.	8.9852	0.35990	0.0:0.2146:0.0:0.7854	.	97;256	B4DFB8;Q5T4T6	.;SYC2L_HUMAN	E	97;256	ENSP00000440676:D97E;ENSP00000283141:D256E	ENSP00000283141:D256E	D	+	3	2	SYCP2L	11015852	0.991000	0.36638	0.119000	0.21687	0.233000	0.25261	1.031000	0.30165	0.071000	0.16664	0.533000	0.62120	GAT		0.373	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299	
AIM1	202	broad.mit.edu	37	6	106992708	106992708	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:106992708G>A	ENST00000369066.3	+	11	4475	c.3988G>A	c.(3988-3990)Gga>Aga	p.G1330R	AIM1_ENST00000535438.1_Missense_Mutation_p.G149R|AIM1_ENST00000487681.1_3'UTR	NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.G1330R(1)		breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		AAAAAACTTTGGATCCAAAGG	0.328																																					p.G1330R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3988A	6						.						111.0	113.0	112.0					6																	106992708		2203	4300	6503	107099401	SO:0001583	missense	202	exon11			U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.3988G>A	6.37:g.106992708G>A	ENSP00000358062:p.Gly1330Arg	Somatic		Capture	Illumina HiSeq	Phase_I	107099401	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.946061	0.73672	.	.	ENSG00000112297	ENST00000369066;ENST00000457437;ENST00000535438	T;T;T	0.75367	-0.93;-0.93;-0.93	5.6	5.6	0.85130	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.872013	0.10559	N	0.660469	T	0.79118	0.4392	L	0.35487	1.065	0.40512	D	0.980745	D;D	0.76494	0.996;0.999	D;D	0.77557	0.98;0.99	T	0.79298	-0.1861	10	0.87932	D	0	.	19.2152	0.93774	0.0:0.0:1.0:0.0	.	149;1330	B4DU04;Q9Y4K1	.;AIM1_HUMAN	R	1330;149;149	ENSP00000358062:G1330R;ENSP00000391419:G149R;ENSP00000439183:G149R	ENSP00000358062:G1330R	G	+	1	0	AIM1	107099401	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.464000	0.45067	2.632000	0.89209	0.561000	0.74099	GGA		0.328	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
WASF1	8936	broad.mit.edu	37	6	110426673	110426673	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:110426673T>C	ENST00000392589.1	-	8	1486	c.650A>G	c.(649-651)gAt>gGt	p.D217G	WASF1_ENST00000359451.2_Missense_Mutation_p.D217G|WASF1_ENST00000392586.1_Missense_Mutation_p.D217G|WASF1_ENST00000392588.1_Missense_Mutation_p.D217G|WASF1_ENST00000392587.2_Missense_Mutation_p.D217G	NM_003931.2	NP_003922.1	Q92558	WASF1_HUMAN	WAS protein family, member 1	217					actin filament polymerization (GO:0030041)|cellular component movement (GO:0006928)|lamellipodium morphogenesis (GO:0072673)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|Rac protein signal transduction (GO:0016601)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|lamellipodium (GO:0030027)|mitochondrial outer membrane (GO:0005741)|SCAR complex (GO:0031209)|synapse (GO:0045202)	protein complex binding (GO:0032403)	p.D217G(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)		GAGATTAGCATCATCTTCAGC	0.418																																					p.D217G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A650G	6						.						82.0	76.0	78.0					6																	110426673		2203	4300	6503	110533366	SO:0001583	missense	8936	exon7			D87459	CCDS5080.1	6q21	2010-08-20			ENSG00000112290	ENSG00000112290		"""A-kinase anchor proteins"""	12732	protein-coding gene	gene with protein product		605035				9843499, 9889097	Standard	XM_005267204		Approved	WAVE1, SCAR1, KIAA0269, WAVE	uc003pty.1	Q92558	OTTHUMG00000015357	ENST00000392589.1:c.650A>G	6.37:g.110426673T>C	ENSP00000376368:p.Asp217Gly	Somatic		Capture	Illumina HiSeq	Phase_I	110533366	NM_001024934	E1P5F2|Q5SZK7	Missense_Mutation	SNP	ENST00000392589.1	37	CCDS5080.1	.	.	.	.	.	.	.	.	.	.	T	15.24	2.775052	0.49786	.	.	ENSG00000112290	ENST00000392586;ENST00000392587;ENST00000392589;ENST00000392588;ENST00000359451	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	5.37	5.37	0.77165	.	0.301292	0.35838	N	0.002955	T	0.15305	0.0369	L	0.27053	0.805	0.43195	D	0.995038	P	0.37466	0.596	B	0.26864	0.074	T	0.04386	-1.0955	10	0.36615	T	0.2	.	15.4258	0.75048	0.0:0.0:0.0:1.0	.	217	Q92558	WASF1_HUMAN	G	217	ENSP00000376365:D217G;ENSP00000376366:D217G;ENSP00000376368:D217G;ENSP00000376367:D217G;ENSP00000352425:D217G	ENSP00000352425:D217G	D	-	2	0	WASF1	110533366	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.287000	0.59001	2.042000	0.60477	0.477000	0.44152	GAT		0.418	WASF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041784.3	NM_003931	
REV3L	5980	broad.mit.edu	37	6	111696913	111696913	+	Missense_Mutation	SNP	C	C	T	rs148134079		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:111696913C>T	ENST00000358835.3	-	14	3099	c.2645G>A	c.(2644-2646)cGt>cAt	p.R882H	REV3L_ENST00000368802.3_Missense_Mutation_p.R882H|REV3L_ENST00000368805.1_Missense_Mutation_p.R882H|REV3L_ENST00000435970.1_Missense_Mutation_p.R804H			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	882					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.R804H(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		AAAAGCTCCACGAGTGGTTTT	0.353								DNA polymerases (catalytic subunits)					c|||	1	0.000199681	0.0008	0.0	5008	,	,		17172	0.0		0.0	False		,,,				2504	0.0				p.R882H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2645A	6						.	T	HIS/ARG	1,4389		0,1,2194	62.0	67.0	66.0		2645	0.3	0.1	6	dbSNP_134	66	0,8594		0,0,4297	yes	missense	REV3L	NM_002912.3	29	0,1,6491	TT,TC,CC		0.0,0.0228,0.0077	benign	882/3131	111696913	1,12983	2195	4297	6492	111803606	SO:0001583	missense	5980	exon13			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.2645G>A	6.37:g.111696913C>T	ENSP00000351697:p.Arg882His	Somatic		Capture	Illumina HiSeq	Phase_I	111803606	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	c	0.004	-2.330834	0.00227	2.28E-4	0.0	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01464	4.95;4.95;4.95;4.86	5.47	0.334	0.15948	Ribonuclease H-like (1);	2.491440	0.01099	N	0.005331	T	0.00412	0.0013	N	0.21448	0.665	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46884	-0.9159	10	0.13470	T	0.59	-5.5323	2.0832	0.03640	0.1393:0.2781:0.1214:0.4611	.	882	O60673	DPOLZ_HUMAN	H	882;882;882;804	ENSP00000357792:R882H;ENSP00000357795:R882H;ENSP00000351697:R882H;ENSP00000402003:R804H	ENSP00000351697:R882H	R	-	2	0	REV3L	111803606	0.000000	0.05858	0.129000	0.21949	0.118000	0.20060	-0.172000	0.09868	0.030000	0.15379	-0.119000	0.15052	CGT		0.353	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
TSPYL4	23270	broad.mit.edu	37	6	116574466	116574466	+	Nonsense_Mutation	SNP	G	G	A	rs61736142		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:116574466G>A	ENST00000420283.1	-	1	795	c.706C>T	c.(706-708)Cga>Tga	p.R236*	DSE_ENST00000540275.1_5'Flank|RP3-486I3.7_ENST00000448740.2_lincRNA	NM_021648.4	NP_067680.3	Q9UJ04	TSYL4_HUMAN	TSPY-like 4	236					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)		p.R236*(1)		endometrium(2)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(2)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.045)|OV - Ovarian serous cystadenocarcinoma(136;0.0666)|GBM - Glioblastoma multiforme(226;0.095)|Epithelial(106;0.125)		TGGAGCCTTCGCATGCGGCCA	0.527																																					p.R236X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C706T	6						.						34.0	34.0	34.0					6																	116574466		2013	4175	6188	116681159	SO:0001587	stop_gained	23270	exon1				CCDS5106.1	6q22.1	2010-05-12			ENSG00000187189	ENSG00000187189			21559	protein-coding gene	gene with protein product							Standard	NM_021648		Approved	dJ486I3.2, KIAA0721	uc003pwn.3	Q9UJ04	OTTHUMG00000015429	ENST00000420283.1:c.706C>T	6.37:g.116574466G>A	ENSP00000410943:p.Arg236*	Somatic		Capture	Illumina HiSeq	Phase_I	116681159	NM_021648	B4DYQ2|O94828|Q96GW8	Nonsense_Mutation	SNP	ENST00000420283.1	37	CCDS5106.1	.	.	.	.	.	.	.	.	.	.	G	36	5.676237	0.96764	.	.	ENSG00000187189	ENST00000420283	.	.	.	3.98	2.09	0.27110	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.636	10.5651	0.45167	0.0:0.0:0.647:0.353	.	.	.	.	X	236	.	ENSP00000410943:R236X	R	-	1	2	TSPYL4	116681159	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	0.975000	0.29449	0.576000	0.29452	0.462000	0.41574	CGA		0.527	TSPYL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041934.2		
DSE	29940	broad.mit.edu	37	6	116757959	116757959	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:116757959C>T	ENST00000331677.3	+	7	2772	c.2328C>T	c.(2326-2328)cgC>cgT	p.R776R	DSE_ENST00000537543.1_Silent_p.R795R|DSE_ENST00000359564.2_Silent_p.R776R|DSE_ENST00000452085.3_Silent_p.R776R			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	776					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)	p.R776R(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		CTGCTGAACGCCTGCTGAGAT	0.463																																					p.R776R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2328T	6						.						76.0	79.0	78.0					6																	116757959		2203	4300	6503	116864652	SO:0001819	synonymous_variant	29940	exon6			AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"""squamous cell carcinoma antigen recognized by T cells 2"""	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.2328C>T	6.37:g.116757959C>T		Somatic		Capture	Illumina HiSeq	Phase_I	116864652	NM_001080976	Q5R3K6	Silent	SNP	ENST00000331677.3	37	CCDS5107.1																																																																																				0.463	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
GPRC6A	222545	broad.mit.edu	37	6	117127676	117127676	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:117127676T>C	ENST00000310357.3	-	3	1213	c.1192A>G	c.(1192-1194)Atg>Gtg	p.M398V	GPRC6A_ENST00000368549.3_Missense_Mutation_p.M398V|GPRC6A_ENST00000530250.1_Intron	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	398					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.M398V(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TCATTTCTCATGACGAAGTTC	0.438																																					p.M398V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1192G	6						.						122.0	109.0	114.0					6																	117127676		2203	4299	6502	117234369	SO:0001583	missense	222545	exon3			AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.1192A>G	6.37:g.117127676T>C	ENSP00000309493:p.Met398Val	Somatic		Capture	Illumina HiSeq	Phase_I	117234369	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	37	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.879524	0.00537	.	.	ENSG00000173612	ENST00000310357;ENST00000368549	D;D	0.90004	-2.42;-2.6	5.48	-3.53	0.04667	Extracellular ligand-binding receptor (1);	0.688419	0.12675	N	0.448476	T	0.52273	0.1724	N	0.08118	0	0.09310	N	0.999998	B;B	0.13145	0.005;0.007	B;B	0.15484	0.001;0.013	T	0.51663	-0.8677	10	0.29301	T	0.29	.	5.3625	0.16095	0.3655:0.0:0.1985:0.436	.	398;398	Q5T6X5-3;Q5T6X5	.;GPC6A_HUMAN	V	398	ENSP00000309493:M398V;ENSP00000357537:M398V	ENSP00000309493:M398V	M	-	1	0	GPRC6A	117234369	0.129000	0.22400	0.037000	0.18230	0.016000	0.09150	0.463000	0.21972	-0.485000	0.06754	-1.116000	0.02052	ATG		0.438	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
ROS1	6098	broad.mit.edu	37	6	117609675	117609675	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:117609675A>G	ENST00000368508.3	-	43	7222	c.7024T>C	c.(7024-7026)Tat>Cat	p.Y2342H	ROS1_ENST00000368507.3_Missense_Mutation_p.Y2336H	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2342					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.Y2342H(2)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CCATCTCCATATCCACTGTGA	0.423			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																p.Y2342H			Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T7024C	6						.						106.0	98.0	101.0					6																	117609675		2203	4300	6503	117716368	SO:0001583	missense	6098	exon43			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.7024T>C	6.37:g.117609675A>G	ENSP00000357494:p.Tyr2342His	Somatic		Capture	Illumina HiSeq	Phase_I	117716368	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	A	2.125	-0.400559	0.04865	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.70164	-0.45;-0.46	4.18	-1.52	0.08637	.	1.093500	0.07155	N	0.849687	T	0.15565	0.0375	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.06661	-1.0814	10	0.09590	T	0.72	.	0.455	0.00507	0.4191:0.1827:0.2207:0.1775	.	2342	P08922	ROS1_HUMAN	H	2342;2336	ENSP00000357494:Y2342H;ENSP00000357493:Y2336H	ENSP00000357493:Y2336H	Y	-	1	0	ROS1	117716368	0.003000	0.15002	0.059000	0.19551	0.589000	0.36550	0.432000	0.21461	-0.077000	0.12752	0.460000	0.39030	TAT		0.423	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
NUS1	116150	broad.mit.edu	37	6	118015231	118015231	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:118015231G>A	ENST00000368494.3	+	3	748	c.579G>A	c.(577-579)ccG>ccA	p.P193P		NM_138459.3	NP_612468.1	Q96E22	NGBR_HUMAN	nuclear undecaprenyl pyrophosphate synthase 1 homolog (S. cerevisiae)	193					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|intracellular cholesterol transport (GO:0032367)|protein glycosylation (GO:0006486)|sterol homeostasis (GO:0055092)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)	p.P193P(2)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|prostate(2)	8		all_cancers(87;0.0395)|all_epithelial(87;0.0301)		GBM - Glioblastoma multiforme(226;0.02)|OV - Ovarian serous cystadenocarcinoma(136;0.115)|all cancers(137;0.146)		TGCTGTCTCCGGAAGATGGAA	0.393																																					p.P193P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G579A	6						.						83.0	87.0	86.0					6																	118015231		2203	4299	6502	118121924	SO:0001819	synonymous_variant	116150	exon3			BC013026	CCDS5118.1	6q22.1	2012-12-13	2006-11-24	2006-11-24	ENSG00000153989	ENSG00000153989			21042	protein-coding gene	gene with protein product	"""Nogo-B receptor"", ""transport and golgi organization 14 homolog (Drosophila)"""	610463	"""chromosome 6 open reading frame 68"""	C6orf68			Standard	NM_138459		Approved	MGC7199, NgBR, TANGO14	uc003pxw.3	Q96E22	OTTHUMG00000015458	ENST00000368494.3:c.579G>A	6.37:g.118015231G>A		Somatic		Capture	Illumina HiSeq	Phase_I	118121924	NM_138459	B2RWQ4|O00251	Silent	SNP	ENST00000368494.3	37	CCDS5118.1																																																																																				0.393	NUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041989.1	NM_138459	
HSF2	3298	broad.mit.edu	37	6	122741280	122741280	+	Splice_Site	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:122741280G>A	ENST00000368455.4	+	7	786	c.594G>A	c.(592-594)agG>agA	p.R198R	HSF2_ENST00000452194.1_Splice_Site_p.R198R	NM_004506.3	NP_004497.1	Q03933	HSF2_HUMAN	heat shock transcription factor 2	198					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to stress (GO:0006950)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.R198R(1)		large_intestine(4)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(136;0.00371)|all cancers(137;0.0299)|GBM - Glioblastoma multiforme(226;0.0586)		TGGTTTTCAGGCCTCTACTTC	0.358																																					p.R198R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G594A	6						.						102.0	97.0	99.0					6																	122741280		2203	4299	6502	122782979	SO:0001630	splice_region_variant	3298	exon7			M65217	CCDS5124.1, CCDS47470.1	6q22	2008-08-29			ENSG00000025156	ENSG00000025156			5225	protein-coding gene	gene with protein product		140581				1871106	Standard	NM_004506		Approved		uc003pyu.2	Q03933	OTTHUMG00000016216	ENST00000368455.4:c.594-1G>A	6.37:g.122741280G>A		Somatic		Capture	Illumina HiSeq	Phase_I	122782979	NM_004506	B4DGJ4|Q0VAH9|Q2M1K4|Q9H445	Silent	SNP	ENST00000368455.4	37	CCDS5124.1																																																																																				0.358	HSF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043520.1	NM_004506	Silent
SIRT5	23408	broad.mit.edu	37	6	13597207	13597207	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:13597207T>C	ENST00000606117.1	+	7	872	c.576T>C	c.(574-576)ccT>ccC	p.P192P	SIRT5_ENST00000359782.3_Intron|SIRT5_ENST00000397350.2_Silent_p.P84P|SIRT5_ENST00000379262.4_Silent_p.P192P	NM_012241.4	NP_036373.1			sirtuin 5									p.P192P(2)		breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	11	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.176)			CTCCAGAACCTGGAACTCAAG	0.348																																					p.P192P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T576C	6						.						55.0	57.0	57.0					6																	13597207		2203	4300	6503	13705186	SO:0001819	synonymous_variant	23408	exon7			AF083110	CCDS4526.1, CCDS4527.1, CCDS54966.1, CCDS56398.1	6p23	2010-08-05	2010-06-25		ENSG00000124523	ENSG00000124523			14933	protein-coding gene	gene with protein product		604483	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 5"", ""sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae)"""			10381378	Standard	NM_012241		Approved		uc003nay.3	Q9NXA8	OTTHUMG00000014278	ENST00000606117.1:c.576T>C	6.37:g.13597207T>C		Somatic		Capture	Illumina HiSeq	Phase_I	13705186	NM_012241		Silent	SNP	ENST00000606117.1	37	CCDS4526.1																																																																																				0.348	SIRT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039908.2		
TAAR1	134864	broad.mit.edu	37	6	132966995	132966995	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:132966995G>A	ENST00000275216.1	-	1	147	c.148C>T	c.(148-150)Cac>Tac	p.H50Y		NM_138327.1	NP_612200.1	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	50					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)	p.H50Y(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)	18	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00616)|GBM - Glioblastoma multiforme(226;0.0154)	Amphetamine(DB00182)|Dextroamphetamine(DB01576)|Methamphetamine(DB01577)|Propylhexedrine(DB06714)	TGTTTGAAGTGTGATATAGAA	0.433																																					p.H50Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C148T	6						.						147.0	144.0	145.0					6																	132966995		2203	4300	6503	133008688	SO:0001583	missense	134864	exon1			AY180374	CCDS5158.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146399	ENSG00000146399		"""GPCR / Class A : Trace amine associated receptors"""	17734	protein-coding gene	gene with protein product		609333	"""trace amine receptor 1"""	TRAR1		11459929, 15718104	Standard	NM_138327		Approved	TAR1, TA1	uc003qdm.1	Q96RJ0	OTTHUMG00000015583	ENST00000275216.1:c.148C>T	6.37:g.132966995G>A	ENSP00000275216:p.His50Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	133008688	NM_138327	Q2M1W5|Q3MIH8|Q5VUQ1	Missense_Mutation	SNP	ENST00000275216.1	37	CCDS5158.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.771237	0.49680	.	.	ENSG00000146399	ENST00000275216	T	0.36699	1.24	5.82	5.82	0.92795	GPCR, rhodopsin-like superfamily (1);	0.054174	0.64402	D	0.000001	T	0.24967	0.0606	L	0.46670	1.46	0.44454	D	0.997383	B	0.17667	0.023	B	0.20577	0.03	T	0.02437	-1.1159	10	0.39692	T	0.17	-9.5512	20.1041	0.97884	0.0:0.0:1.0:0.0	.	50	Q96RJ0	TAAR1_HUMAN	Y	50	ENSP00000275216:H50Y	ENSP00000275216:H50Y	H	-	1	0	TAAR1	133008688	1.000000	0.71417	0.981000	0.43875	0.701000	0.40568	3.257000	0.51500	2.755000	0.94549	0.555000	0.69702	CAC		0.433	TAAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042259.1	NM_138327	
ECT2L	345930	broad.mit.edu	37	6	139164330	139164330	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:139164330T>C	ENST00000423192.1	+	5	718	c.557T>C	c.(556-558)cTg>cCg	p.L186P	ECT2L_ENST00000367682.2_Missense_Mutation_p.L186P|ECT2L_ENST00000541398.1_Missense_Mutation_p.L117P			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	186							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.L186P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						GAAAAGTGCCTGAGGAAAAGA	0.403			"""N, Splice, Mis"""		ETP ALL																																p.L186P			Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T557C	6						.						115.0	115.0	115.0					6																	139164330		1858	4093	5951	139206023	SO:0001583	missense	345930	exon6				CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"""Rho guanine nucleotide exchange factors"", ""F-boxes /  ""other"""""	21118	protein-coding gene	gene with protein product	"""lung specific F-box and DH domain containing protein"", ""F-box protein 49"""		"""chromosome 6 open reading frame 91"", ""epithelial cell transforming sequence 2 oncogene-like"""	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.557T>C	6.37:g.139164330T>C	ENSP00000387388:p.Leu186Pro	Somatic		Capture	Illumina HiSeq	Phase_I	139206023	NM_001077706	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	37	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	T	13.41	2.229499	0.39399	.	.	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	T;T;T	0.77489	-0.02;-0.02;-1.1	5.72	5.72	0.89469	.	423.176000	0.01740	U	0.029332	T	0.80314	0.4600	L	0.32530	0.975	0.49798	D	0.999826	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	T	0.64854	-0.6309	10	0.40728	T	0.16	-3.2501	13.523	0.61578	0.0:0.0:0.0:1.0	.	117;186	F5H7S9;Q008S8	.;ECT2L_HUMAN	P	186;186;117	ENSP00000387388:L186P;ENSP00000356655:L186P;ENSP00000442307:L117P	ENSP00000356655:L186P	L	+	2	0	ECT2L	139206023	0.835000	0.29415	0.508000	0.27688	0.020000	0.10135	6.128000	0.71650	2.187000	0.69744	0.482000	0.46254	CTG		0.403	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706	
GPR126	57211	broad.mit.edu	37	6	142741124	142741124	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:142741124C>T	ENST00000230173.6	+	22	3678	c.3202C>T	c.(3202-3204)Cgc>Tgc	p.R1068C	GPR126_ENST00000367609.3_Missense_Mutation_p.R1068C|GPR126_ENST00000296932.8_Missense_Mutation_p.R1040C|GPR126_ENST00000367608.2_Missense_Mutation_p.R1040C	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	1068					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R1068C(1)|p.R1039C(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		AAGGAACCTGCGCAGTGTGGT	0.483																																					p.R1040C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3118T	6						.						283.0	281.0	282.0					6																	142741124		1964	4150	6114	142782817	SO:0001583	missense	57211	exon21			AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"""-"", ""GPCR / Class B : Orphans"""	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.3202C>T	6.37:g.142741124C>T	ENSP00000230173:p.Arg1068Cys	Somatic		Capture	Illumina HiSeq	Phase_I	142782817	NM_001032394	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	37	CCDS47490.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789793	0.70337	.	.	ENSG00000112414	ENST00000230173;ENST00000367608;ENST00000296932;ENST00000367609	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.55	5.55	0.83447	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000002	T	0.72342	0.3448	H	0.94462	3.54	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.80699	-0.1266	10	0.87932	D	0	.	19.5048	0.95111	0.0:1.0:0.0:0.0	.	128;1040;1068;1040;1068	B4DSK4;Q86SQ4-4;Q86SQ4-3;Q86SQ4-2;Q86SQ4	.;.;.;.;GP126_HUMAN	C	1068;1040;1040;1068	ENSP00000230173:R1068C;ENSP00000356580:R1040C;ENSP00000296932:R1040C;ENSP00000356581:R1068C	ENSP00000230173:R1068C	R	+	1	0	GPR126	142782817	1.000000	0.71417	1.000000	0.80357	0.497000	0.33675	5.687000	0.68219	2.600000	0.87896	0.650000	0.86243	CGC		0.483	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2		
UTRN	7402	broad.mit.edu	37	6	144612996	144612996	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:144612996C>A	ENST00000367545.3	+	1	32	c.32C>A	c.(31-33)cCt>cAt	p.P11H		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	11	Actin-binding.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.P11H(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GAAGCCAGTCCTGACAATGGG	0.393																																					p.P11H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C32A	6						.						102.0	88.0	93.0					6																	144612996		2203	4300	6503	144654689	SO:0001583	missense	7402	exon1			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.32C>A	6.37:g.144612996C>A	ENSP00000356515:p.Pro11His	Somatic		Capture	Illumina HiSeq	Phase_I	144654689	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	C	4.774	0.143945	0.09134	.	.	ENSG00000152818	ENST00000433557;ENST00000367529;ENST00000367545	T	0.60171	0.21	5.71	4.84	0.62591	.	0.685714	0.12720	N	0.444757	T	0.31420	0.0796	N	0.19112	0.55	0.34086	D	0.660123	P	0.46327	0.876	B	0.43360	0.417	T	0.13282	-1.0515	10	0.45353	T	0.12	.	12.7626	0.57374	0.0:0.8353:0.1647:0.0	.	11	P46939	UTRO_HUMAN	H	11	ENSP00000356515:P11H	ENSP00000356499:P11H	P	+	2	0	UTRN	144654689	0.244000	0.23889	0.104000	0.21259	0.483000	0.33249	3.903000	0.56318	1.414000	0.47017	0.655000	0.94253	CCT		0.393	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
LRP11	84918	broad.mit.edu	37	6	150164137	150164137	+	Missense_Mutation	SNP	C	C	T	rs374603588		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:150164137C>T	ENST00000239367.2	-	3	900	c.895G>A	c.(895-897)Gca>Aca	p.A299T	LRP11_ENST00000546019.1_Missense_Mutation_p.A44T|LRP11_ENST00000367368.2_Missense_Mutation_p.A299T	NM_032832.5	NP_116221.3	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein 11	299	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.					integral component of membrane (GO:0016021)		p.A299T(3)		cervix(1)|kidney(5)|large_intestine(1)|lung(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		GAGTAGGCTGCGCGAAGCACT	0.592													C|||	1	0.000199681	0.0	0.0	5008	,	,		20612	0.0		0.0	False		,,,				2504	0.001				p.A299T												.	.	3	Substitution - Missense(3)	kidney(2)|large_intestine(1)	c.G895A	6						.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	123.0	96.0	105.0		895	-3.8	0.0	6		105	0,8600		0,0,4300	no	missense	LRP11	NM_032832.5	58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	299/501	150164137	1,13005	2203	4300	6503	150205830	SO:0001583	missense	84918	exon3			AK027641	CCDS5220.1	6q24.3	2013-02-27			ENSG00000120256	ENSG00000120256		"""Low density lipoprotein receptors"""	16936	protein-coding gene	gene with protein product							Standard	NM_032832		Approved	bA350J20.3, MANSC3	uc003qng.2	Q86VZ4	OTTHUMG00000015801	ENST00000239367.2:c.895G>A	6.37:g.150164137C>T	ENSP00000239367:p.Ala299Thr	Somatic		Capture	Illumina HiSeq	Phase_I	150205830	NM_032832	Q5VYC0|Q96SN6	Missense_Mutation	SNP	ENST00000239367.2	37	CCDS5220.1	.	.	.	.	.	.	.	.	.	.	C	7.925	0.739482	0.15642	2.27E-4	0.0	ENSG00000120256	ENST00000239367;ENST00000546019;ENST00000367368	T;D;T	0.96365	3.6;-3.99;2.88	5.05	-3.75	0.04372	PKD/Chitinase domain (1);PKD domain (1);	1.227860	0.05358	N	0.533188	T	0.82006	0.4943	N	0.25890	0.77	0.09310	N	1	B;B	0.16802	0.019;0.003	B;B	0.08055	0.003;0.002	T	0.76315	-0.3004	10	0.18276	T	0.48	3.0488	6.5669	0.22517	0.0:0.4301:0.1412:0.4286	.	299;299	Q5VYB9;Q86VZ4	.;LRP11_HUMAN	T	299;44;299	ENSP00000239367:A299T;ENSP00000440196:A44T;ENSP00000356338:A299T	ENSP00000239367:A299T	A	-	1	0	LRP11	150205830	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.641000	0.05434	-0.987000	0.03494	-0.982000	0.02568	GCA		0.592	LRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042664.1	NM_032832	
AKAP12	9590	broad.mit.edu	37	6	151672759	151672759	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:151672759A>G	ENST00000253332.1	+	3	3422	c.3233A>G	c.(3232-3234)gAa>gGa	p.E1078G	AKAP12_ENST00000402676.2_Missense_Mutation_p.E1078G|AKAP12_ENST00000354675.6_Missense_Mutation_p.E980G|AKAP12_ENST00000359755.5_Missense_Mutation_p.E973G			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1078					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)	p.E1078G(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GAAAGACCAGAAGAGCAGGCT	0.527																																					p.E1078G	Melanoma(141;1616 1805 10049 24534 51979)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3233G	6						.						53.0	56.0	55.0					6																	151672759		2203	4300	6503	151714452	SO:0001583	missense	9590	exon4			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"""A-kinase anchor proteins"""	370	protein-coding gene	gene with protein product	"""gravin"", ""Src-Suppressed C Kinase Substrate"""	604698	"""A kinase (PRKA) anchor protein (gravin) 12"""			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.3233A>G	6.37:g.151672759A>G	ENSP00000253332:p.Glu1078Gly	Somatic		Capture	Illumina HiSeq	Phase_I	151714452	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	A	15.92	2.975706	0.53720	.	.	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.09817	2.94;2.94;2.96;2.96	5.26	1.4	0.22301	.	0.182670	0.26753	N	0.022677	T	0.02342	0.0072	L	0.29908	0.895	0.09310	N	1	B;B;B	0.21225	0.053;0.053;0.031	B;B;B	0.23419	0.046;0.046;0.021	T	0.41610	-0.9499	10	0.49607	T	0.09	.	5.6608	0.17668	0.6963:0.1431:0.1606:0.0	.	973;980;1078	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	G	1078;1078;980;973	ENSP00000384537:E1078G;ENSP00000253332:E1078G;ENSP00000346702:E980G;ENSP00000352794:E973G	ENSP00000253332:E1078G	E	+	2	0	AKAP12	151714452	0.076000	0.21285	0.003000	0.11579	0.019000	0.09904	1.023000	0.30065	0.301000	0.22738	0.374000	0.22700	GAA		0.527	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
SYNE1	23345	broad.mit.edu	37	6	152702271	152702271	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:152702271C>T	ENST00000367255.5	-	56	9480	c.8879G>A	c.(8878-8880)gGc>gAc	p.G2960D	SYNE1_ENST00000423061.1_Missense_Mutation_p.G2967D|SYNE1-AS1_ENST00000412161.1_RNA|SYNE1_ENST00000448038.1_Missense_Mutation_p.G2967D|SYNE1_ENST00000265368.4_Missense_Mutation_p.G2960D|SYNE1_ENST00000341594.5_Missense_Mutation_p.G2999D	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2960					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.G2960D(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGCCACTTGGCCTGAGAATTC	0.557										HNSCC(10;0.0054)																											p.G2967D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G8900A	6						.						100.0	93.0	95.0					6																	152702271		2203	4300	6503	152743964	SO:0001583	missense	23345	exon56			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.8879G>A	6.37:g.152702271C>T	ENSP00000356224:p.Gly2960Asp	Somatic		Capture	Illumina HiSeq	Phase_I	152743964	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.88|12.88	2.070556|2.070556	0.36566|0.36566	.|.	.|.	ENSG00000131018|ENSG00000131018	ENST00000454018|ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	.|T;T;T;T;T	.|0.52057	.|0.77;0.82;0.68;0.81;0.92	6.01|6.01	1.92|1.92	0.25849|0.25849	.|.	.|0.418696	.|0.22284	.|N	.|0.062096	T|T	0.11665|0.11665	0.0284|0.0284	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B	.|0.31910	.|0.047;0.072;0.346;0.072;0.191	.|B;B;B;B;B	.|0.26969	.|0.036;0.034;0.052;0.034;0.075	T|T	0.08432|0.08432	-1.0722|-1.0722	5|10	.|0.12103	.|T	.|0.63	.|.	9.5585|9.5585	0.39355|0.39355	0.0933:0.1969:0.637:0.0728|0.0933:0.1969:0.637:0.0728	.|.	.|2943;2960;77;2960;2967	.|B3W695;Q8NF91;B7ZBC4;E7EQI5;Q8NF91-4	.|.;SYNE1_HUMAN;.;.;.	T|D	77|2960;2967;2960;2967;2999	.|ENSP00000356224:G2960D;ENSP00000396024:G2967D;ENSP00000265368:G2960D;ENSP00000390975:G2967D;ENSP00000341887:G2999D	.|ENSP00000265368:G2960D	A|G	-|-	1|2	0|0	SYNE1|SYNE1	152743964|152743964	0.398000|0.398000	0.25279|0.25279	0.968000|0.968000	0.41197|0.41197	0.658000|0.658000	0.38924|0.38924	0.274000|0.274000	0.18680|0.18680	0.348000|0.348000	0.23949|0.23949	0.650000|0.650000	0.86243|0.86243	GCC|GGC		0.557	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
TIAM2	26230	broad.mit.edu	37	6	155469457	155469457	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:155469457A>G	ENST00000461783.3	+	9	3290	c.2017A>G	c.(2017-2019)Ata>Gta	p.I673V	TIAM2_ENST00000528391.2_5'Flank|TIAM2_ENST00000456877.2_5'Flank|TIAM2_ENST00000318981.5_Missense_Mutation_p.I673V|TIAM2_ENST00000360366.4_Missense_Mutation_p.I673V|TIAM2_ENST00000529824.2_Missense_Mutation_p.I673V|TIAM2_ENST00000367174.2_Missense_Mutation_p.I25V|TIAM2_ENST00000456144.1_Missense_Mutation_p.I673V			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	673					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.I673V(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		CAGGAAAGCCATAGAGAACCA	0.473																																					p.I673V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2017G	6						.						85.0	77.0	80.0					6																	155469457		2203	4300	6503	155511149	SO:0001583	missense	26230	exon6				CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.2017A>G	6.37:g.155469457A>G	ENSP00000437188:p.Ile673Val	Somatic		Capture	Illumina HiSeq	Phase_I	155511149	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	A	18.43	3.622099	0.66787	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824	T;T;T;T;T;T;T	0.11930	3.17;3.08;3.14;3.17;2.73;3.2;3.14	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.10937	0.0267	M	0.73217	2.22	0.49389	D	0.99978	B;B;B	0.34161	0.439;0.439;0.312	B;B;B	0.32864	0.154;0.154;0.074	T	0.01720	-1.1288	10	0.87932	D	0	.	15.3722	0.74573	1.0:0.0:0.0:0.0	.	673;673;673	Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;TIAM2_HUMAN	V	673;919;673;673;673;25;673;673	ENSP00000437188:I673V;ENSP00000434901:I673V;ENSP00000407746:I673V;ENSP00000327315:I673V;ENSP00000356142:I25V;ENSP00000353528:I673V;ENSP00000433348:I673V	ENSP00000327315:I673V	I	+	1	0	TIAM2	155511149	1.000000	0.71417	0.993000	0.49108	0.977000	0.68977	8.962000	0.93254	2.027000	0.59764	0.460000	0.39030	ATA		0.473	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
TULP4	56995	broad.mit.edu	37	6	158923537	158923537	+	Missense_Mutation	SNP	G	G	A	rs201183348		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:158923537G>A	ENST00000367097.3	+	13	4199	c.2842G>A	c.(2842-2844)Gtc>Atc	p.V948I	TULP4_ENST00000367094.2_Intron	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	948					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V948I(1)		endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		CCGCCTGACCGTCCCTCGCTA	0.682													G|||	1	0.000199681	0.0	0.0	5008	,	,		11886	0.001		0.0	False		,,,				2504	0.0				p.V948I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2842A	6						.						54.0	54.0	54.0					6																	158923537		2203	4300	6503	158843525	SO:0001583	missense	56995	exon13				CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.2842G>A	6.37:g.158923537G>A	ENSP00000356064:p.Val948Ile	Somatic		Capture	Illumina HiSeq	Phase_I	158843525	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	CCDS34561.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.485841	0.26686	.	.	ENSG00000130338	ENST00000367097	T	0.64438	-0.1	4.49	1.16	0.20824	.	0.275449	0.35646	N	0.003069	T	0.34629	0.0904	L	0.58101	1.795	0.21064	N	0.999799	B	0.06786	0.001	B	0.04013	0.001	T	0.41161	-0.9524	10	0.56958	D	0.05	-5.9682	8.9406	0.35727	0.284:0.0:0.716:0.0	.	948	Q9NRJ4	TULP4_HUMAN	I	948	ENSP00000356064:V948I	ENSP00000356064:V948I	V	+	1	0	TULP4	158843525	0.987000	0.35691	0.131000	0.22000	0.994000	0.84299	3.268000	0.51585	-0.016000	0.14127	-0.258000	0.10820	GTC		0.682	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
TMEM181	57583	broad.mit.edu	37	6	158994458	158994458	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:158994458G>A	ENST00000367090.3	+	2	437	c.426G>A	c.(424-426)gcG>gcA	p.A142A		NM_020823.1	NP_065874.1	Q9P2C4	TM181_HUMAN	transmembrane protein 181	142					pathogenesis (GO:0009405)	integral component of membrane (GO:0016021)	toxic substance binding (GO:0015643)	p.A142A(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)	22		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)		CCAGGCTGGCGCCCATGCGGC	0.617																																					p.A142A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G426A	6						.						48.0	51.0	50.0					6																	158994458		2128	4214	6342	158914446	SO:0001819	synonymous_variant	57583	exon2			AB037844	CCDS43520.1	6q25.3	2012-08-10	2006-10-19	2006-10-19	ENSG00000146433	ENSG00000146433			20958	protein-coding gene	gene with protein product		613209	"""G protein-coupled receptor 178"", ""KIAA1423"""	KIAA1423, GPR178		16452613	Standard	NM_020823		Approved		uc003qrm.4	Q9P2C4	OTTHUMG00000015913	ENST00000367090.3:c.426G>A	6.37:g.158994458G>A		Somatic		Capture	Illumina HiSeq	Phase_I	158914446	NM_020823	Q5VTU1	Silent	SNP	ENST00000367090.3	37	CCDS43520.1																																																																																				0.617	TMEM181-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042873.1	NM_020823	
PNLDC1	154197	broad.mit.edu	37	6	160221822	160221822	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:160221822C>T	ENST00000610273.1	+	2	233	c.62C>T	c.(61-63)aCg>aTg	p.T21M	PNLDC1_ENST00000392167.3_Missense_Mutation_p.T32M|PNLDC1_ENST00000609334.1_3'UTR	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1	21						integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.T21M(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		ATAGAGTTCACGGGCCTTCGT	0.547																																					p.T21M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C62T	6						.						161.0	157.0	158.0					6																	160221822		2203	4300	6503	160141812	SO:0001583	missense	154197	exon2			AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.62C>T	6.37:g.160221822C>T	ENSP00000476448:p.Thr21Met	Somatic		Capture	Illumina HiSeq	Phase_I	160141812	NM_173516	Q5TAP7|Q8N7X5	Missense_Mutation	SNP	ENST00000610273.1	37	CCDS5271.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.226914	0.58668	.	.	ENSG00000146453	ENST00000275275;ENST00000392167	T;T	0.26223	1.75;1.75	5.0	1.81	0.25067	Ribonuclease H-like (1);	0.109282	0.40385	N	0.001104	T	0.36166	0.0957	M	0.83312	2.635	0.09310	N	0.999997	D;D	0.89917	0.999;1.0	P;D	0.75484	0.88;0.986	T	0.04373	-1.0956	10	0.87932	D	0	.	9.2438	0.37513	0.2889:0.5713:0.1398:0.0	.	32;21	Q8NA58-2;Q8NA58	.;PNDC1_HUMAN	M	21;32	ENSP00000275275:T21M;ENSP00000376007:T32M	ENSP00000275275:T21M	T	+	2	0	PNLDC1	160141812	0.913000	0.31002	0.347000	0.25668	0.783000	0.44284	2.020000	0.41010	1.106000	0.41623	0.650000	0.86243	ACG		0.547	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516	
PNLDC1	154197	broad.mit.edu	37	6	160239603	160239603	+	Missense_Mutation	SNP	G	G	A	rs202013209		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:160239603G>A	ENST00000610273.1	+	16	1312	c.1141G>A	c.(1141-1143)Gag>Aag	p.E381K	PNLDC1_ENST00000392167.3_Missense_Mutation_p.E392K	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1	381						integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.E381K(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CCCCGTGCCCGAGTCATCCTT	0.552													g|||	1	0.000199681	0.0	0.0	5008	,	,		18359	0.001		0.0	False		,,,				2504	0.0				p.E381K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1141A	6						.	A	LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	82.0	75.0	77.0		1141	3.6	0.0	6		77	0,8600		0,0,4300	yes	missense	PNLDC1	NM_173516.1	56	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	381/521	160239603	2,13004	2203	4300	6503	160159593	SO:0001583	missense	154197	exon16			AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.1141G>A	6.37:g.160239603G>A	ENSP00000476448:p.Glu381Lys	Somatic		Capture	Illumina HiSeq	Phase_I	160159593	NM_173516	Q5TAP7|Q8N7X5	Missense_Mutation	SNP	ENST00000610273.1	37	CCDS5271.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	g	7.499	0.652209	0.14580	4.54E-4	0.0	ENSG00000146453	ENST00000275275;ENST00000392167	.	.	.	5.36	3.6	0.41247	.	0.536026	0.19466	N	0.113570	T	0.11793	0.0287	N	0.24115	0.695	0.09310	N	1	D;D	0.62365	0.991;0.968	P;B	0.49561	0.615;0.248	T	0.07888	-1.0749	9	0.10111	T	0.7	.	9.1308	0.36843	0.2367:0.0:0.7633:0.0	.	392;381	Q8NA58-2;Q8NA58	.;PNDC1_HUMAN	K	381;392	.	ENSP00000275275:E381K	E	+	1	0	PNLDC1	160159593	0.297000	0.24408	0.009000	0.14445	0.049000	0.14656	1.598000	0.36740	0.764000	0.33197	-0.215000	0.12644	GAG		0.552	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516	
IGF2R	3482	broad.mit.edu	37	6	160496999	160496999	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:160496999G>A	ENST00000356956.1	+	36	5435	c.5287G>A	c.(5287-5289)Gcg>Acg	p.A1763T		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1763					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)	p.A1763T(1)		breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	CTCGCTCATCGCGTTTCACTG	0.458																																					p.A1763T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5287A	6						.						181.0	164.0	170.0					6																	160496999		2203	4300	6503	160416989	SO:0001583	missense	3482	exon36			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.5287G>A	6.37:g.160496999G>A	ENSP00000349437:p.Ala1763Thr	Somatic		Capture	Illumina HiSeq	Phase_I	160416989	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	8.082	0.772692	0.16051	.	.	ENSG00000197081	ENST00000356956	T	0.10099	2.91	5.31	-5.64	0.02466	Mannose-6-phosphate receptor, binding (1);	1.138800	0.06318	N	0.703930	T	0.00754	0.0025	N	0.03608	-0.345	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.43972	-0.9358	10	0.05351	T	0.99	-7.6509	5.5481	0.17076	0.5295:0.089:0.291:0.0905	.	1763	P11717	MPRI_HUMAN	T	1763	ENSP00000349437:A1763T	ENSP00000349437:A1763T	A	+	1	0	IGF2R	160416989	0.000000	0.05858	0.006000	0.13384	0.586000	0.36452	-0.411000	0.07142	-1.116000	0.02969	0.655000	0.94253	GCG		0.458	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
IGF2R	3482	broad.mit.edu	37	6	160517475	160517475	+	Silent	SNP	C	C	T	rs141757600	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:160517475C>T	ENST00000356956.1	+	45	6808	c.6660C>T	c.(6658-6660)ggC>ggT	p.G2220G	RP11-288H12.3_ENST00000569097.1_RNA	NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	2220					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)	p.G2220G(1)		breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TGACAGACGGCGATCTCGATG	0.488													C|||	2	0.000399361	0.0015	0.0	5008	,	,		22166	0.0		0.0	False		,,,				2504	0.0				p.G2220G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C6660T	6						.	C		8,4398	14.3+/-33.2	0,8,2195	273.0	192.0	219.0		6660	-9.8	0.3	6	dbSNP_134	219	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	IGF2R	NM_000876.2		0,10,6493	TT,TC,CC		0.0233,0.1816,0.0769		2220/2492	160517475	10,12996	2203	4300	6503	160437465	SO:0001819	synonymous_variant	3482	exon45			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.6660C>T	6.37:g.160517475C>T		Somatic		Capture	Illumina HiSeq	Phase_I	160437465	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																				0.488	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
MYLIP	29116	broad.mit.edu	37	6	16144086	16144086	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:16144086A>G	ENST00000356840.3	+	5	1017	c.819A>G	c.(817-819)gcA>gcG	p.A273A	MYLIP_ENST00000349606.4_Silent_p.A92A|MIR4639_ENST00000584938.1_RNA	NM_013262.3	NP_037394.2	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting protein	273	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|cholesterol homeostasis (GO:0042632)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|nervous system development (GO:0007399)|positive regulation of protein catabolic process (GO:0045732)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	cytoskeletal protein binding (GO:0008092)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A273A(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			AGACGCACGCATTCTACAGGC	0.527																																					p.A273A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A819G	6						.						123.0	117.0	119.0					6																	16144086		2203	4300	6503	16252065	SO:0001819	synonymous_variant	29116	exon5			AF187016	CCDS4536.1	6p23-p22.3	2011-11-17			ENSG00000007944	ENSG00000007944			21155	protein-coding gene	gene with protein product	"""E3 ubiquitin ligase-inducible degrader of the low density lipoprotein receptor"""	610082				10593918, 11162443, 19688294	Standard	NM_013262		Approved	MIR, IDOL	uc003nbq.3	Q8WY64	OTTHUMG00000016405	ENST00000356840.3:c.819A>G	6.37:g.16144086A>G		Somatic		Capture	Illumina HiSeq	Phase_I	16252065	NM_013262	Q5TIA4|Q9BU73|Q9NRL9|Q9UHE7	Silent	SNP	ENST00000356840.3	37	CCDS4536.1																																																																																				0.527	MYLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043864.1	NM_013262	
SLC22A3	6581	broad.mit.edu	37	6	160829922	160829922	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:160829922C>T	ENST00000275300.2	+	4	978	c.826C>T	c.(826-828)Ctg>Ttg	p.L276L	SLC22A3_ENST00000392145.1_Silent_p.L276L	NM_021977.3	NP_068812.1	O75751	S22A3_HUMAN	solute carrier family 22 (organic cation transporter), member 3	276					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|histamine uptake (GO:0051615)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|regulation of appetite (GO:0032098)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine transmembrane transporter activity (GO:0005329)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|toxin transporter activity (GO:0019534)	p.L276L(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)	Adefovir Dipivoxil(DB00718)|Amphetamine(DB00182)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Colchicine(DB01394)|Desipramine(DB01151)|Dopamine(DB00988)|Estradiol(DB00783)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imipramine(DB00458)|Irinotecan(DB00762)|Lamivudine(DB00709)|Melphalan(DB01042)|Metformin(DB00331)|Methamphetamine(DB01577)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Phenoxybenzamine(DB00925)|Prazosin(DB00457)|Procainamide(DB01035)|Progesterone(DB00396)|Testosterone(DB00624)|Vincristine(DB00541)	AGCCATCACGCTGCCCAGCTT	0.408																																					p.L276L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C826T	6						.						127.0	121.0	123.0					6																	160829922		2203	4300	6503	160749912	SO:0001819	synonymous_variant	6581	exon4			AF078749	CCDS5277.1	6q25.3	2013-07-18	2013-07-18		ENSG00000146477	ENSG00000146477		"""Solute carriers"""	10967	protein-coding gene	gene with protein product		604842	"""solute carrier family 22 (extraneuronal monoamine transporter), member 3"""			9632645, 9933568	Standard	NM_021977		Approved	OCT3, EMT	uc003qti.4	O75751	OTTHUMG00000015953	ENST00000275300.2:c.826C>T	6.37:g.160829922C>T		Somatic		Capture	Illumina HiSeq	Phase_I	160749912	NM_021977	Q5SYN6|Q9UP02	Silent	SNP	ENST00000275300.2	37	CCDS5277.1																																																																																				0.408	SLC22A3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042953.1	NM_021977	
T	6862	broad.mit.edu	37	6	166572040	166572040	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:166572040G>A	ENST00000296946.2	-	9	1539	c.1071C>T	c.(1069-1071)gcC>gcT	p.A357A	T_ENST00000366871.3_Silent_p.A299A	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	357					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|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 transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A357A(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		CCGGGGTGACGGCGCCGTTGC	0.672									Chordoma, Familial Clustering of																												p.A357A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1071T	6						.						14.0	18.0	16.0					6																	166572040		2195	4292	6487	166492030	SO:0001819	synonymous_variant	6862	exon9	Familial Cancer Database		AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"""T-boxes"""	11515	protein-coding gene	gene with protein product		601397	"""T brachyury (mouse) homolog"""			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.1071C>T	6.37:g.166572040G>A		Somatic		Capture	Illumina HiSeq	Phase_I	166492030	NM_003181	E7ERD6|Q4KMP4	Silent	SNP	ENST00000296946.2	37	CCDS5290.1																																																																																				0.672	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	
T	6862	broad.mit.edu	37	6	166576059	166576059	+	Silent	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:166576059A>C	ENST00000296946.2	-	7	1248	c.780T>G	c.(778-780)ccT>ccG	p.P260P	T_ENST00000366871.3_Intron	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	260					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|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 transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P260P(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		ACTGAGGATGAGGATTTGCAG	0.597									Chordoma, Familial Clustering of																												p.P260P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T780G	6						.						108.0	108.0	108.0					6																	166576059		2203	4300	6503	166496049	SO:0001819	synonymous_variant	6862	exon7	Familial Cancer Database		AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"""T-boxes"""	11515	protein-coding gene	gene with protein product		601397	"""T brachyury (mouse) homolog"""			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.780T>G	6.37:g.166576059A>C		Somatic		Capture	Illumina HiSeq	Phase_I	166496049	NM_003181	E7ERD6|Q4KMP4	Silent	SNP	ENST00000296946.2	37	CCDS5290.1																																																																																				0.597	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	
UNC93A	54346	broad.mit.edu	37	6	167721286	167721286	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:167721286C>A	ENST00000230256.3	+	7	1171	c.996C>A	c.(994-996)tcC>tcA	p.S332S	UNC93A_ENST00000366829.2_Silent_p.S290S	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	332						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S332S(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CCCACGTGTCCTGCATGATTG	0.637																																					p.S290S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C870A	6						.						146.0	111.0	123.0					6																	167721286		2203	4300	6503	167641276	SO:0001819	synonymous_variant	54346	exon6			AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"""unc93 (C.elegans) homolog A"""			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.996C>A	6.37:g.167721286C>A		Somatic		Capture	Illumina HiSeq	Phase_I	167641276	NM_001143947	B3KRP5|Q4QQJ4|Q5JZD6	Silent	SNP	ENST00000230256.3	37	CCDS5300.1																																																																																				0.637	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974	
SLC22A23	63027	broad.mit.edu	37	6	3283988	3283989	+	Intron	DEL	AG	AG	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	AG	AG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:3283988_3283989delAG	ENST00000406686.3	-	9	1703				SLC22A23_ENST00000490273.1_Intron|SLC22A23_ENST00000436008.2_Intron|PSMG4_ENST00000451246.2_Intron|SLC22A23_ENST00000380302.4_Intron	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23						ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				AGCCAGAGACAGAGCTGACGCT	0.609																																					.												.	.	0			.	6						.																																			3228988	SO:0001627	intron_variant	63027	.			AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266		"""Solute carriers"""	21106	protein-coding gene	gene with protein product		611697	"""chromosome 6 open reading frame 85"""	C6orf85		17714910	Standard	NM_015482		Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000406686.3:c.1703+96CT>-	6.37:g.3283990_3283991delAG		Somatic		Capture	Illumina HiSeq	Phase_I	3228987	.	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Frame_Shift_Del	DEL	ENST00000406686.3	37	CCDS47363.1																																																																																				0.609	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945	
FAM217A	222826	broad.mit.edu	37	6	4077639	4077639	+	Silent	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:4077639T>G	ENST00000274673.3	-	2	413	c.10A>C	c.(10-12)Aga>Cga	p.R4R	FAM217A_ENST00000380188.2_Intron|C6orf201_ENST00000380175.4_5'Flank|C6orf201_ENST00000333388.5_5'Flank|snoU13_ENST00000516859.1_RNA	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	4								p.R4R(1)									TTCTCATTTCTTCTCCCCATT	0.453																																					p.R4R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A10C	6						.						277.0	215.0	236.0					6																	4077639		2203	4300	6503	4022638	SO:0001819	synonymous_variant	222826	exon2			BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 146"""	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.10A>C	6.37:g.4077639T>G		Somatic		Capture	Illumina HiSeq	Phase_I	4022638	NM_173563	Q5JYK1	Silent	SNP	ENST00000274673.3	37	CCDS4489.1																																																																																				0.453	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563	
SSR1	6745	broad.mit.edu	37	6	7301590	7301590	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:7301590C>T	ENST00000244763.4	-	4	582	c.496G>A	c.(496-498)Gga>Aga	p.G166R	SSR1_ENST00000397511.2_Missense_Mutation_p.G166R|SSR1_ENST00000488834.1_5'UTR|SSR1_ENST00000462112.1_Missense_Mutation_p.G166R|RP11-69L16.4_ENST00000379928.4_RNA|SSR1_ENST00000474597.1_Missense_Mutation_p.G166R|SSR1_ENST00000479365.1_Missense_Mutation_p.G166R|SSR1_ENST00000489567.1_Missense_Mutation_p.G98R|SSR1_ENST00000534851.1_Missense_Mutation_p.G139R	NM_003144.3	NP_003135.2	P43307	SSRA_HUMAN	signal sequence receptor, alpha	166					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|positive regulation of cell proliferation (GO:0008284)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.G166R(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(1)	9	Ovarian(93;0.0398)					AATGGTCGTCCGCCCATGGGC	0.443																																					p.G166R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G496A	6						.						68.0	70.0	69.0					6																	7301590		2203	4300	6503	7246589	SO:0001583	missense	6745	exon4				CCDS4499.1	6p24.3	2010-11-24	2008-08-26		ENSG00000124783	ENSG00000124783			11323	protein-coding gene	gene with protein product	"""translocon-associated protein alpha"""	600868					Standard	NM_001292008		Approved	TRAPA	uc003mxf.4	P43307	OTTHUMG00000014202	ENST00000244763.4:c.496G>A	6.37:g.7301590C>T	ENSP00000244763:p.Gly166Arg	Somatic		Capture	Illumina HiSeq	Phase_I	7246589	NM_003144	A8K685|Q53GX2|Q53H19|Q5TAM3|Q6IB43|Q8NBH9|Q96IA2|Q9TNQ8|Q9UN49	Missense_Mutation	SNP	ENST00000244763.4	37	CCDS4499.1	.	.	.	.	.	.	.	.	.	.	C	32	5.155483	0.94686	.	.	ENSG00000124783	ENST00000474597;ENST00000244763;ENST00000397511;ENST00000534851;ENST00000489567;ENST00000479365;ENST00000479485;ENST00000462112	T;T;T;T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53;-0.53;-0.53;-0.53	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.86058	0.5842	M	0.89840	3.065	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.995;0.998	D	0.87814	0.2633	10	0.66056	D	0.02	.	18.8387	0.92172	0.0:1.0:0.0:0.0	.	166;98;166	C9J5W0;C9JBX5;P43307	.;.;SSRA_HUMAN	R	166;166;166;139;98;166;3;166	ENSP00000418617:G166R;ENSP00000244763:G166R;ENSP00000380647:G166R;ENSP00000443020:G139R;ENSP00000420730:G98R;ENSP00000417911:G166R;ENSP00000419953:G3R;ENSP00000417290:G166R	ENSP00000244763:G166R	G	-	1	0	SSR1	7246589	1.000000	0.71417	0.159000	0.22649	0.966000	0.64601	7.640000	0.83355	2.688000	0.91661	0.655000	0.94253	GGA		0.443	SSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039775.2		
DSP	1832	broad.mit.edu	37	6	7568069	7568069	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:7568069T>C	ENST00000379802.3	+	10	1537	c.1196T>C	c.(1195-1197)aTc>aCc	p.I399T	DSP_ENST00000418664.2_Missense_Mutation_p.I399T	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	399	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.I399T(1)		biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		CAGGACTCCATCAGGAAGAAG	0.517																																					p.I399T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1196C	6						.						74.0	65.0	68.0					6																	7568069		2203	4300	6503	7513068	SO:0001583	missense	1832	exon10			J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.1196T>C	6.37:g.7568069T>C	ENSP00000369129:p.Ile399Thr	Somatic		Capture	Illumina HiSeq	Phase_I	7513068	NM_001008844	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.774099	0.90108	.	.	ENSG00000096696	ENST00000379802;ENST00000418664;ENST00000397483	D;D	0.95518	-3.73;-3.73	5.45	5.45	0.79879	.	0.000000	0.64402	D	0.000008	D	0.94925	0.8359	M	0.72353	2.195	0.58432	D	0.999999	B;P	0.45672	0.286;0.864	B;P	0.47744	0.197;0.556	D	0.95672	0.8724	10	0.87932	D	0	.	15.8	0.78447	0.0:0.0:0.0:1.0	.	446;399	Q4LE79;P15924	.;DESP_HUMAN	T	399;399;204	ENSP00000369129:I399T;ENSP00000396591:I399T	ENSP00000369129:I399T	I	+	2	0	DSP	7513068	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.231000	0.72307	2.185000	0.69588	0.482000	0.46254	ATC		0.517	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
BMP6	654	broad.mit.edu	37	6	7880428	7880428	+	Splice_Site	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:7880428T>C	ENST00000283147.6	+	7	1553	c.1394T>C	c.(1393-1395)gTt>gCt	p.V465A		NM_001718.4	NP_001709.1	P22004	BMP6_HUMAN	bone morphogenetic protein 6	465					BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular response to mechanical stimulus (GO:0071260)|endochondral ossification (GO:0001958)|eye development (GO:0001654)|growth (GO:0040007)|immune response (GO:0006955)|inflammatory response (GO:0006954)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|osteoblast differentiation (GO:0001649)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of bone mineralization (GO:0030501)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to activity (GO:0014823)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to retinoic acid (GO:0032526)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|type B pancreatic cell development (GO:0003323)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)|protein heterodimerization activity (GO:0046982)	p.V465A(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	23	Ovarian(93;0.0721)					TTGGAACAGGTTCACCTTATG	0.468																																					p.V465A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1394C	6						.						181.0	189.0	187.0					6																	7880428		2203	4300	6503	7825427	SO:0001630	splice_region_variant	654	exon7			AF083030	CCDS4503.1	6p24-p23	2014-01-30	2003-10-06		ENSG00000153162	ENSG00000153162		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1073	protein-coding gene	gene with protein product		112266	"""vegetal related growth factor (TGFB-related)"""	VGR		1427904, 1453478	Standard	NM_001718		Approved	VGR1	uc003mxu.4	P22004	OTTHUMG00000014217	ENST00000283147.6:c.1393-1T>C	6.37:g.7880428T>C		Somatic		Capture	Illumina HiSeq	Phase_I	7825427	NM_001718	Q5TCP3	Missense_Mutation	SNP	ENST00000283147.6	37	CCDS4503.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.974773	0.92919	.	.	ENSG00000153162	ENST00000537240;ENST00000283147;ENST00000540959	D	0.84944	-1.92	5.64	5.64	0.86602	Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.91019	0.7175	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92406	0.5933	10	0.87932	D	0	.	15.8612	0.79021	0.0:0.0:0.0:1.0	.	465	P22004	BMP6_HUMAN	A	387;465;428	ENSP00000283147:V465A	ENSP00000283147:V465A	V	+	2	0	BMP6	7825427	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.726000	0.84824	2.145000	0.66743	0.528000	0.53228	GTT		0.468	BMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039794.1	NM_001718	Missense_Mutation
RBM24	221662	broad.mit.edu	37	6	17292125	17292125	+	Silent	SNP	A	A	T	rs539936955	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:17292125A>T	ENST00000379052.5	+	4	722	c.486A>T	c.(484-486)gcA>gcT	p.A162A	RBM24_ENST00000425446.2_Silent_p.A104A|RBM24_ENST00000318204.5_Silent_p.A117A|RBM24_ENST00000508508.1_3'UTR	NM_001143942.1	NP_001137414.1	Q9BX46	RBM24_HUMAN	RNA binding motif protein 24	162	Ala-rich.				cell differentiation (GO:0030154)|regulation of mRNA stability (GO:0043488)|regulation of myotube differentiation (GO:0010830)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)	p.A117A(1)		endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)	13	Breast(50;0.0615)|Ovarian(93;0.0733)	all_hematologic(90;0.062)	all cancers(50;0.131)|Epithelial(50;0.15)			AATACTCAGCAgctgctgctg	0.602																																					p.A117A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A351T	6						.						29.0	37.0	34.0					6																	17292125		2188	4299	6487	17400104	SO:0001819	synonymous_variant	221662	exon3			BC040928	CCDS4538.1, CCDS47378.1, CCDS47379.1	6p22.3	2013-02-12	2004-04-23	2004-04-23	ENSG00000112183	ENSG00000112183		"""RNA binding motif (RRM) containing"""	21539	protein-coding gene	gene with protein product			"""RNA-binding region (RNP1, RRM) containing 6"""	RNPC6			Standard	NM_153020		Approved	FLJ30829, dJ259A10.1	uc003nbz.4	Q9BX46	OTTHUMG00000014306	ENST00000379052.5:c.486A>T	6.37:g.17292125A>T		Somatic		Capture	Illumina HiSeq	Phase_I	17400104	NM_153020	E9PAY4|Q6QDA4|Q8N9D3|Q96NI3	Silent	SNP	ENST00000379052.5	37	CCDS47378.1	.	.	.	.	.	.	.	.	.	.	A	12.34	1.908279	0.33721	.	.	ENSG00000112183	ENST00000503965	.	.	.	5.71	-11.4	0.00090	.	.	.	.	.	T	0.11879	0.0289	.	.	.	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.57768	-0.7754	6	.	.	.	-2.8548	6.4643	0.21973	0.0736:0.4823:0.2031:0.241	.	61;76	B7Z6B4;B7Z6B7	.;.	L	127	.	.	Q	+	2	0	RBM24	17400104	0.000000	0.05858	0.001000	0.08648	0.609000	0.37215	-4.581000	0.00213	-5.632000	0.00011	-0.435000	0.05868	CAG		0.602	RBM24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039946.2	NM_153020	
CDKAL1	54901	broad.mit.edu	37	6	20739812	20739812	+	Missense_Mutation	SNP	G	G	A	rs149431105		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:20739812G>A	ENST00000378610.1	+	4	444	c.434G>A	c.(433-435)cGc>cAc	p.R145H	CDKAL1_ENST00000274695.4_Missense_Mutation_p.R145H|CDKAL1_ENST00000378624.4_Missense_Mutation_p.R75H			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	145	MTTase N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00780}.				maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)	p.R145H(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			GCCCAGCCTCGCCAGGACTAC	0.428													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18809	0.0		0.0	False		,,,				2504	0.0				p.R145H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G434A	6						.						68.0	66.0	66.0					6																	20739812		2203	4300	6503	20847791	SO:0001583	missense	54901	exon6			AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.434G>A	6.37:g.20739812G>A	ENSP00000367873:p.Arg145His	Somatic		Capture	Illumina HiSeq	Phase_I	20847791	NM_017774	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Missense_Mutation	SNP	ENST00000378610.1	37	CCDS4546.1	.	.	.	.	.	.	.	.	.	.	.	16.89	3.247695	0.59103	.	.	ENSG00000145996	ENST00000274695;ENST00000378624;ENST00000378610	T;T;T	0.47528	0.84;0.85;0.84	4.77	4.77	0.60923	Methylthiotransferase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.33644	0.0870	L	0.51914	1.62	0.46376	D	0.999019	P;P	0.43314	0.803;0.766	B;B	0.40285	0.325;0.142	T	0.29427	-1.0012	10	0.48119	T	0.1	.	16.602	0.84818	0.0:0.0:1.0:0.0	.	75;145	Q5VV42-2;Q5VV42	.;CDKAL_HUMAN	H	145;75;145	ENSP00000274695:R145H;ENSP00000367889:R75H;ENSP00000367873:R145H	ENSP00000274695:R145H	R	+	2	0	CDKAL1	20847791	1.000000	0.71417	0.959000	0.39883	0.809000	0.45718	6.888000	0.75622	2.192000	0.70111	0.557000	0.71058	CGC		0.428	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774	
DCDC2	51473	broad.mit.edu	37	6	24174969	24174969	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:24174969C>T	ENST00000378454.3	-	10	1721	c.1420G>A	c.(1420-1422)Gcc>Acc	p.A474T	DCDC2_ENST00000378450.3_Missense_Mutation_p.A227T	NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	474					cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)			p.A474T(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				TAAGCCACGGCAGCATAGTCC	0.368																																					p.A474T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1420A	6						.						172.0	143.0	153.0					6																	24174969		2203	4300	6503	24282948	SO:0001583	missense	51473	exon11			AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.1420G>A	6.37:g.24174969C>T	ENSP00000367715:p.Ala474Thr	Somatic		Capture	Illumina HiSeq	Phase_I	24282948	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Missense_Mutation	SNP	ENST00000378454.3	37	CCDS4550.1	.	.	.	.	.	.	.	.	.	.	C	12.45	1.942018	0.34283	.	.	ENSG00000146038	ENST00000378454;ENST00000378450	T;T	0.52295	1.92;0.67	5.67	3.9	0.45041	.	0.579894	0.15172	N	0.276565	T	0.13243	0.0321	N	0.19112	0.55	0.09310	N	1	B;P	0.41848	0.016;0.763	B;B	0.33392	0.016;0.163	T	0.03008	-1.1083	10	0.72032	D	0.01	-1.7176	8.9157	0.35581	0.0:0.8293:0.0:0.1707	.	474;227	Q9UHG0;Q9UHG0-2	DCDC2_HUMAN;.	T	474;227	ENSP00000367715:A474T;ENSP00000367711:A227T	ENSP00000367711:A227T	A	-	1	0	DCDC2	24282948	0.169000	0.23002	0.005000	0.12908	0.145000	0.21501	1.722000	0.38042	0.760000	0.33108	0.655000	0.94253	GCC		0.368	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356	
LRRC16A	55604	broad.mit.edu	37	6	25466140	25466140	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:25466140G>A	ENST00000329474.6	+	9	1022	c.654G>A	c.(652-654)caG>caA	p.Q218Q	LRRC16A_ENST00000377969.3_Silent_p.Q57Q	NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	218					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)	p.Q218Q(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						AATATAATCAGTGGTTCACAA	0.383																																					p.Q218Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G654A	6						.						185.0	175.0	179.0					6																	25466140		1866	4100	5966	25574119	SO:0001819	synonymous_variant	55604	exon9			AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"""capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"""	609593	"""leucine rich repeat containing 16"""	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.654G>A	6.37:g.25466140G>A		Somatic		Capture	Illumina HiSeq	Phase_I	25574119	NM_017640	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Silent	SNP	ENST00000329474.6	37	CCDS54973.1																																																																																				0.383	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
HIST1H1B	3009	broad.mit.edu	37	6	27834672	27834672	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:27834672T>C	ENST00000331442.3	-	1	687	c.636A>G	c.(634-636)aaA>aaG	p.K212K		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	212					chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)	p.K212K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						CAGCTTTAGGTTTTGCTGCTT	0.547																																					p.K212K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A636G	6						.						63.0	58.0	60.0					6																	27834672		2203	4300	6503	27942651	SO:0001819	synonymous_variant	3009	exon1			AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"""Histones / Replication-dependent"""	4719	protein-coding gene	gene with protein product		142711	"""H1 histone family, member 5"", ""histone 1, H1b"""	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.636A>G	6.37:g.27834672T>C		Somatic		Capture	Illumina HiSeq	Phase_I	27942651	NM_005322	Q14529|Q3MJ42	Silent	SNP	ENST00000331442.3	37	CCDS4635.1																																																																																				0.547	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322	
HIST1H2BO	8348	broad.mit.edu	37	6	27861436	27861436	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:27861436T>G	ENST00000303806.4	+	1	234	c.196T>G	c.(196-198)Ttc>Gtc	p.F66V	HIST1H2AM_ENST00000359611.2_5'Flank|HIST1H3J_ENST00000359303.2_5'Flank|HIST1H3J_ENST00000479986.1_5'Flank	NM_003527.4	NP_003518.2	P23527	H2B1O_HUMAN	histone cluster 1, H2bo	66					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.F66V(1)									CATGAACTCCTTCGTCAATGA	0.567																																					p.F66V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T196G	6						.						151.0	136.0	141.0					6																	27861436		2203	4300	6503	27969415	SO:0001583	missense	8348	exon1			X57138	CCDS4640.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000196331			"""Histones / Replication-dependent"""	4758	protein-coding gene	gene with protein product		602808	"""H2B histone family, member N"", ""histone 1, H2bo"""	H2BFN		1768865, 12408966	Standard	NM_003527		Approved	H2B/n, H2B.2	uc003nkc.1	P23527	OTTHUMG00000014493	ENST00000303806.4:c.196T>G	6.37:g.27861436T>G	ENSP00000303408:p.Phe66Val	Somatic		Capture	Illumina HiSeq	Phase_I	27969415	NM_003527	Q3KPI7|Q8TCV6	Missense_Mutation	SNP	ENST00000303806.4	37	CCDS4640.1	.	.	.	.	.	.	.	.	.	.	T	18.07	3.542250	0.65198	.	.	ENSG00000196331	ENST00000303806	T	0.26957	1.7	3.51	3.51	0.40186	Histone-fold (2);Histone core (1);	.	.	.	.	T	0.50650	0.1628	M	0.93150	3.385	0.38303	D	0.943024	D	0.89917	1.0	D	0.76071	0.987	T	0.64618	-0.6365	9	0.87932	D	0	.	11.9008	0.52682	0.0:0.0:0.0:1.0	.	66	P23527	H2B1O_HUMAN	V	66	ENSP00000303408:F66V	ENSP00000303408:F66V	F	+	1	0	HIST1H2BO	27969415	1.000000	0.71417	0.995000	0.50966	0.519000	0.34347	4.653000	0.61462	1.842000	0.53543	0.454000	0.30748	TTC		0.567	HIST1H2BO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040161.1	NM_003527	
Unknown	0	broad.mit.edu	37	6	28244320	28244320	+	IGR	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:28244320C>A								NKAPL (15584 upstream) : PGBD1 (4993 downstream)																							CAGAGGAGTTCACACCTCGTC	0.453																																					p.S161X												.	.	0			c.C482A	6						.						75.0	76.0	76.0					6																	28244320		2047	4232	6279	28352299	SO:0001628	intergenic_variant	7741	exon4																															6.37:g.28244320C>A		Somatic		Capture	Illumina HiSeq	Phase_I	28352299	NM_152736		Nonsense_Mutation	SNP		37																																																																																				0	0.453								
OR2H1	26716	broad.mit.edu	37	6	29429798	29429798	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:29429798G>T	ENST00000377136.1	+	4	717	c.252G>T	c.(250-252)tgG>tgT	p.W84C	OR2H1_ENST00000442615.1_Missense_Mutation_p.W84C|OR2H1_ENST00000396792.2_Missense_Mutation_p.W84C|OR2H1_ENST00000473369.1_3'UTR|OR2H1_ENST00000377132.1_Missense_Mutation_p.W84C|OR2H1_ENST00000377133.1_Missense_Mutation_p.W84C			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	84						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.W84C(1)		large_intestine(5)|lung(12)	17						TCAACCTCTGGGGCCCAAAGA	0.547																																					p.W84C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G252T	6						.						95.0	96.0	96.0					6																	29429798		1511	2709	4220	29537777	SO:0001583	missense	26716	exon3			AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"""GPCR / Class A : Olfactory receptors"""	8252	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily H, member 8"""	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.252G>T	6.37:g.29429798G>T	ENSP00000366340:p.Trp84Cys	Somatic		Capture	Illumina HiSeq	Phase_I	29537777	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.571520	0.28003	.	.	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.01838	4.61;4.61;4.61;4.61;4.61	2.92	2.02	0.26589	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37906	N	0.001883	T	0.01870	0.0059	L	0.46157	1.445	0.20489	N	0.999897	D	0.89917	1.0	D	0.69142	0.962	T	0.47560	-0.9108	10	0.30854	T	0.27	.	2.4544	0.04526	0.1105:0.3556:0.3515:0.1824	.	84	Q9GZK4	OR2H1_HUMAN	C	84	ENSP00000366340:W84C;ENSP00000366337:W84C;ENSP00000393254:W84C;ENSP00000366336:W84C;ENSP00000380010:W84C	ENSP00000366336:W84C	W	+	3	0	OR2H1	29537777	0.000000	0.05858	0.992000	0.48379	0.978000	0.69477	-2.106000	0.01338	0.769000	0.33313	0.603000	0.83216	TGG		0.547	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
ZFP57	346171	broad.mit.edu	37	6	29644682	29644682	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:29644682G>T	ENST00000488757.1	-	1	249	c.99C>A	c.(97-99)tgC>tgA	p.C33*	ZFP57_ENST00000376883.1_Nonsense_Mutation_p.C13*|ZFP57_ENST00000376881.3_Nonsense_Mutation_p.C13*	NM_001109809.2	NP_001103279.2	Q9NU63	ZFP57_HUMAN	ZFP57 zinc finger protein	0	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				DNA methylation involved in embryo development (GO:0043045)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peripheral nervous system development (GO:0007422)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	nuclear heterochromatin (GO:0005720)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C13*(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(16)|ovary(4)|skin(4)|urinary_tract(5)	44						CCTCCCTCCAGCAATCTCTCT	0.557																																					p.C33X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C99A	6						.						154.0	145.0	148.0					6																	29644682		1957	4141	6098	29752661	SO:0001587	stop_gained	346171	exon1			AL050328	CCDS43436.1, CCDS43436.2	6p22.1	2013-01-08	2012-11-27	2005-07-20	ENSG00000204644	ENSG00000204644		"""Zinc fingers, C2H2-type"", ""-"""	18791	protein-coding gene	gene with protein product		612192	"""chromosome 6 open reading frame 40"", ""zinc finger protein 57 homolog (mouse)"""	C6orf40			Standard	NM_001109809		Approved	ZNF698, bA145L22, bA145L22.2	uc011dlw.2	Q9NU63	OTTHUMG00000031158	ENST00000488757.1:c.99C>A	6.37:g.29644682G>T	ENSP00000418259:p.Cys33*	Somatic		Capture	Illumina HiSeq	Phase_I	29752661	NM_001109809	B0S894|B0V254|B2RXJ7|Q5SSB1	Nonsense_Mutation	SNP	ENST00000488757.1	37	CCDS43436.2	.	.	.	.	.	.	.	.	.	.	G	37	6.388967	0.97529	.	.	ENSG00000204644	ENST00000488757;ENST00000376881;ENST00000376883	.	.	.	4.42	2.62	0.31277	.	0.941296	0.08841	N	0.885897	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.6901	7.3534	0.26704	0.1968:0.0:0.8032:0.0	.	.	.	.	X	33;13;13	.	ENSP00000366078:C13X	C	-	3	2	ZFP57	29752661	0.390000	0.25213	0.011000	0.14972	0.058000	0.15608	2.958000	0.49145	0.791000	0.33826	0.655000	0.94253	TGC		0.557	ZFP57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355773.1	XM_294093	
TRIM31	11074	broad.mit.edu	37	6	30071565	30071565	+	Splice_Site	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:30071565G>A	ENST00000376734.3	-	9	1151	c.1026C>T	c.(1024-1026)ggC>ggT	p.G342G	TRIM31_ENST00000540829.1_Splice_Site_p.G342G|TRIM31_ENST00000485864.1_5'Flank|TRIM31-AS1_ENST00000440874.1_RNA	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	342					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.G342G(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						TAGTTCTGCCGCCTTTGCGGG	0.562																																					p.G342G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1026T	6						.						99.0	110.0	106.0					6																	30071565		1509	2709	4218	30179544	SO:0001630	splice_region_variant	11074	exon9			AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.1025-1C>T	6.37:g.30071565G>A		Somatic		Capture	Illumina HiSeq	Phase_I	30179544	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																				0.562	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		Silent
HLA-E	3133	broad.mit.edu	37	6	30458151	30458151	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:30458151G>A	ENST00000376630.4	+	3	534	c.469G>A	c.(469-471)Gtg>Atg	p.V157M		NM_005516.5	NP_005507.3	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	157	Alpha-2.				antigen processing and presentation of endogenous peptide antigen via MHC class Ib (GO:0002476)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protection from natural killer cell mediated cytotoxicity (GO:0042270)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)	p.V157M(1)		breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)|ovary(3)|skin(1)|urinary_tract(1)	18						CTGGACCGCGGTGGACACGGC	0.617																																					p.V157M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G469A	6						.						75.0	75.0	75.0					6																	30458151		1509	2709	4218	30566130	SO:0001583	missense	3133	exon3			M20022	CCDS34379.1	6p21.3	2013-01-11			ENSG00000204592	ENSG00000204592		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4962	protein-coding gene	gene with protein product		143010				3131426	Standard	NM_005516		Approved		uc003nqg.3	P13747	OTTHUMG00000031155	ENST00000376630.4:c.469G>A	6.37:g.30458151G>A	ENSP00000365817:p.Val157Met	Somatic		Capture	Illumina HiSeq	Phase_I	30566130	NM_005516	Q30169|Q9BT83|Q9GIY7|Q9GIY8	Missense_Mutation	SNP	ENST00000376630.4	37	CCDS34379.1	.	.	.	.	.	.	.	.	.	.	.	12.39	1.922792	0.33908	.	.	ENSG00000204592	ENST00000376630	T	0.00011	9.36	1.67	0.693	0.18056	.	0.225856	0.21217	U	0.078212	T	0.00012	0.0000	N	0.20574	0.59	0.09310	N	1	B;B	0.30114	0.269;0.114	B;B	0.22152	0.038;0.022	T	0.10823	-1.0613	10	0.87932	D	0	.	4.5217	0.11962	0.2201:0.0:0.7799:0.0	.	198;157	E7ENN9;Q6DU44	.;.	M	157	ENSP00000365817:V157M	ENSP00000365817:V157M	V	+	1	0	HLA-E	30566130	0.000000	0.05858	0.156000	0.22583	0.338000	0.28826	0.350000	0.20079	0.214000	0.20742	0.462000	0.41574	GTG		0.617	HLA-E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076282.2	NM_005516	
DHX16	8449	broad.mit.edu	37	6	30638665	30638665	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:30638665G>A	ENST00000376442.3	-	3	706	c.511C>T	c.(511-513)Cgc>Tgc	p.R171C		NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	171					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.R171C(1)		kidney(2)|ovary(2)	4						TCCTGAAGGCGTTCACGCTCT	0.557																																					p.R171C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C511T	6						.						164.0	116.0	133.0					6																	30638665		1511	2709	4220	30746644	SO:0001583	missense	8449	exon3			AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"""DEAH-boxes"""	2739	protein-coding gene	gene with protein product		603405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"""	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.511C>T	6.37:g.30638665G>A	ENSP00000365625:p.Arg171Cys	Somatic		Capture	Illumina HiSeq	Phase_I	30746644	NM_003587	O60322|Q5JP45|Q969X7|Q96QC1	Missense_Mutation	SNP	ENST00000376442.3	37	CCDS4685.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.146083	0.57044	.	.	ENSG00000204560	ENST00000376442;ENST00000415603	T;T	0.57436	0.4;0.4	4.62	3.7	0.42460	.	0.000000	0.85682	D	0.000000	T	0.69851	0.3157	M	0.88640	2.97	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.75020	0.973;0.985	T	0.75977	-0.3127	10	0.87932	D	0	.	13.0619	0.59012	0.0:0.0:0.8389:0.1611	.	111;171	B4DZ28;O60231	.;DHX16_HUMAN	C	171;111	ENSP00000365625:R171C;ENSP00000399101:R111C	ENSP00000365625:R171C	R	-	1	0	DHX16	30746644	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.049000	0.57397	2.399000	0.81585	0.460000	0.39030	CGC		0.557	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587	
PPP1R18	170954	broad.mit.edu	37	6	30653428	30653428	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:30653428C>T	ENST00000274853.3	-	1	2244	c.368G>A	c.(367-369)aGa>aAa	p.R123K	NRM_ENST00000470733.1_5'Flank|PPP1R18_ENST00000488324.1_Intron|PPP1R18_ENST00000399199.3_Missense_Mutation_p.R123K	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	123						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R123K(1)									AGGGCTGGGTCTCCGCTCCCG	0.612																																					p.R123K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G368A	6						.						88.0	99.0	96.0					6																	30653428		1175	2516	3691	30761407	SO:0001583	missense	170954	exon2			AK097089	CCDS43444.1	6p21.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000146112	ENSG00000146112		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29413	protein-coding gene	gene with protein product	"""protein phosphatase 1 F-actin cytoskeleton targeting subunit"""	610990	"""KIAA1949"""	KIAA1949		11853319	Standard	NM_001134870		Approved	phostensin	uc003nra.3	Q6NYC8	OTTHUMG00000031237	ENST00000274853.3:c.368G>A	6.37:g.30653428C>T	ENSP00000274853:p.Arg123Lys	Somatic		Capture	Illumina HiSeq	Phase_I	30761407	NM_001134870	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Missense_Mutation	SNP	ENST00000274853.3	37	CCDS43444.1	.	.	.	.	.	.	.	.	.	.	C	17.32	3.359248	0.61403	.	.	ENSG00000146112	ENST00000274853;ENST00000399199;ENST00000376424	T;T	0.26660	1.72;1.72	5.05	1.3	0.21679	.	0.255070	0.28156	N	0.016391	T	0.04770	0.0129	L	0.27053	0.805	0.31205	N	0.699318	B	0.15473	0.013	B	0.11329	0.006	T	0.29397	-1.0013	10	0.44086	T	0.13	-3.6793	2.2752	0.04101	0.1349:0.5028:0.1313:0.2309	.	123	Q6NYC8	PPR18_HUMAN	K	123	ENSP00000274853:R123K;ENSP00000382150:R123K	ENSP00000274853:R123K	R	-	2	0	KIAA1949	30761407	0.900000	0.30661	0.163000	0.22734	0.853000	0.48598	0.396000	0.20867	0.049000	0.15920	0.655000	0.94253	AGA		0.612	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471	
DDR1	780	broad.mit.edu	37	6	30864547	30864547	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:30864547delC	ENST00000324771.8	+	15	2322	c.1774delC	c.(1774-1776)cccfs	p.P593fs	DDR1_ENST00000376569.3_Frame_Shift_Del_p.P556fs|DDR1_ENST00000508312.1_Frame_Shift_Del_p.P574fs|DDR1_ENST00000361741.4_Frame_Shift_Del_p.P260fs|DDR1_ENST00000376567.2_Frame_Shift_Del_p.P556fs|DDR1_ENST00000376570.4_Frame_Shift_Del_p.P556fs|DDR1_ENST00000454612.2_Frame_Shift_Del_p.P556fs|DDR1_ENST00000513240.1_Frame_Shift_Del_p.P593fs|DDR1_ENST00000452441.1_Frame_Shift_Del_p.P593fs|DDR1_ENST00000376575.3_Frame_Shift_Del_p.P593fs|DDR1_ENST00000418800.2_Frame_Shift_Del_p.P556fs|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000376568.3_Frame_Shift_Del_p.P593fs			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	593	Gly/Pro-rich.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.P593fs*60(2)|p.G594fs*35(2)|p.G556fs*35(1)|p.P555fs*60(1)		central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	GCCTGCACTGCCCCCAGGGGC	0.642																																					p.P592fs												.	.	6	Deletion - Frameshift(3)|Insertion - Frameshift(3)	large_intestine(3)|lung(3)	c.1774delC	6						.						50.0	57.0	55.0					6																	30864547		2203	4300	6503	30972526	SO:0001589	frameshift_variant	780	exon14			X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1774delC	6.37:g.30864547delC	ENSP00000318217:p.Pro593fs	Somatic		Capture	Illumina HiSeq	Phase_I	30972526	NM_013993	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Frame_Shift_Del	DEL	ENST00000324771.8	37	CCDS34385.1																																																																																				0.642	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
DDR1	780	broad.mit.edu	37	6	30865941	30865941	+	Missense_Mutation	SNP	C	C	T	rs368543890		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:30865941C>T	ENST00000324771.8	+	18	2856	c.2308C>T	c.(2308-2310)Cgg>Tgg	p.R770W	DDR1_ENST00000376569.3_Missense_Mutation_p.R733W|DDR1_ENST00000508312.1_Missense_Mutation_p.R751W|DDR1_ENST00000361741.4_Intron|DDR1_ENST00000376567.2_Missense_Mutation_p.R733W|DDR1_ENST00000376570.4_Missense_Mutation_p.R733W|DDR1_ENST00000454612.2_Missense_Mutation_p.R733W|DDR1_ENST00000513240.1_Missense_Mutation_p.R776W|DDR1_ENST00000452441.1_Missense_Mutation_p.R770W|DDR1_ENST00000376575.3_Missense_Mutation_p.R776W|DDR1_ENST00000418800.2_Missense_Mutation_p.R733W|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000376568.3_Missense_Mutation_p.R770W			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	770	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R732W(1)|p.R776W(1)|p.R770W(1)		central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	CCTGGCCACGCGGAACTGCCT	0.572																																					p.R770W												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.C2308T	6						.	C	,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	74.0	72.0	73.0		,1870,2251,2197,2308,2326	2.8	0.6	6		73	1,8599	1.2+/-3.3	0,1,4299	no	utr-3,missense,missense,missense,missense,missense	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	,101,101,101,101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	,624/768,751/895,733/877,770/914,776/920	30865941	1,13005	2203	4300	6503	30973920	SO:0001583	missense	780	exon17			X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.2308C>T	6.37:g.30865941C>T	ENSP00000318217:p.Arg770Trp	Somatic		Capture	Illumina HiSeq	Phase_I	30973920	NM_013993	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	37	CCDS34385.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.040234	0.75732	0.0	1.16E-4	ENSG00000204580	ENST00000324771;ENST00000418800;ENST00000454612;ENST00000376569;ENST00000376575;ENST00000376570;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000376567;ENST00000513240	D;D;D;D;D;D;D;D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32;-2.32	4.96	2.84	0.33178	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92394	0.7586	H	0.94886	3.595	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;1.0;1.0	D	0.91147	0.4950	10	0.87932	D	0	.	6.1985	0.20563	0.3271:0.5491:0.0:0.1238	.	751;234;776;770	B7Z2K0;A2ABL4;Q08345-5;Q08345	.;.;.;DDR1_HUMAN	W	770;733;733;733;776;733;770;770;751;733;776	ENSP00000318217:R770W;ENSP00000407699:R733W;ENSP00000406091:R733W;ENSP00000365753:R733W;ENSP00000365759:R776W;ENSP00000365754:R733W;ENSP00000365752:R770W;ENSP00000405039:R770W;ENSP00000422442:R751W;ENSP00000365751:R733W;ENSP00000427552:R776W	ENSP00000318217:R770W	R	+	1	2	DDR1	30973920	0.977000	0.34250	0.560000	0.28344	0.969000	0.65631	2.557000	0.45871	0.501000	0.28013	0.563000	0.77884	CGG		0.572	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
HLA-C	3107	broad.mit.edu	37	6	31238109	31238109	+	Missense_Mutation	SNP	C	C	A	rs185215782		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:31238109C>A	ENST00000376228.5	-	4	787	c.773G>T	c.(772-774)aGg>aTg	p.R258M	HLA-C_ENST00000383329.3_Missense_Mutation_p.R258M	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	258	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)	p.R258M(2)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TCCTGCTGGCCTGGTCTCCAC	0.617																																					p.R258M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G773T	6						.						57.0	47.0	50.0					6																	31238109		2203	4300	6503	31346088	SO:0001583	missense	3107	exon4			M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.773G>T	6.37:g.31238109C>A	ENSP00000365402:p.Arg258Met	Somatic		Capture	Illumina HiSeq	Phase_I	31346088	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|.	3.440|3.440	-0.114319|-0.114319	0.06881|0.06881	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.14640	.|2.49;2.49	2.67|2.67	2.67|2.67	0.31697|0.31697	.|Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	.|0.156108	.|0.27891	.|U	.|0.017422	.|T	.|0.22166	.|0.0534	M|M	0.77103|0.77103	2.36|2.36	0.24268|0.24268	N|N	0.995252|0.995252	.|D;D;D;D	.|0.89917	.|0.999;0.999;0.999;1.0	.|D;D;D;D	.|0.91635	.|0.999;0.999;0.999;0.999	.|T	.|0.00832	.|-1.1548	.|10	.|0.87932	.|D	.|0	.|.	9.019|9.019	0.36188|0.36188	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|258;258;258;258	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	.|M	-1|258;258;258;295	.|ENSP00000365402:R258M;ENSP00000372819:R258M	.|ENSP00000365402:R258M	.|R	-|-	.|2	.|0	HLA-C|HLA-C	31346088|31346088	0.718000|0.718000	0.27976|0.27976	0.993000|0.993000	0.49108|0.49108	0.046000|0.046000	0.14306|0.14306	0.917000|0.917000	0.28665|0.28665	1.821000|1.821000	0.53095|0.53095	0.298000|0.298000	0.19748|0.19748	.|AGG		0.617	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
LTB	4050	broad.mit.edu	37	6	31549626	31549626	+	Missense_Mutation	SNP	G	G	A	rs567302751		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:31549626G>A	ENST00000429299.2	-	2	180	c.173C>T	c.(172-174)aCg>aTg	p.T58M	LTB_ENST00000483972.1_Intron|LTB_ENST00000446745.2_Intron	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	58					cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.T58M(1)		haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GGGGTCGGCCGTCTCCGTTAC	0.637																																					p.T58M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C173T	6						.						83.0	92.0	89.0					6																	31549626		1509	2709	4218	31657605	SO:0001583	missense	4050	exon2			L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"""Tumor necrosis factor (ligand) superfamily"""	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.173C>T	6.37:g.31549626G>A	ENSP00000410481:p.Thr58Met	Somatic		Capture	Illumina HiSeq	Phase_I	31657605	NM_002341	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.801952	0.50315	.	.	ENSG00000227507	ENST00000429299	T	0.20881	2.04	5.45	1.61	0.23674	.	1.166430	0.06123	N	0.669160	T	0.06188	0.0160	L	0.51422	1.61	0.09310	N	0.999998	B	0.28208	0.203	B	0.20184	0.028	T	0.38329	-0.9666	10	0.33940	T	0.23	-4.0148	3.9155	0.09220	0.2954:0.1801:0.5245:0.0	.	58	Q06643	TNFC_HUMAN	M	58	ENSP00000410481:T58M	ENSP00000410481:T58M	T	-	2	0	LTB	31657605	0.001000	0.12720	0.000000	0.03702	0.011000	0.07611	0.741000	0.26202	0.250000	0.21479	0.655000	0.94253	ACG		0.637	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3		
ABHD16A	7920	broad.mit.edu	37	6	31669864	31669864	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:31669864C>T	ENST00000395952.3	-	2	338	c.176G>A	c.(175-177)aGc>aAc	p.S59N	ABHD16A_ENST00000375842.4_5'UTR|ABHD16A_ENST00000440843.2_Intron|MIR4646_ENST00000580775.1_RNA|XXbac-BPG32J3.20_ENST00000461287.1_3'UTR|ABHD16A_ENST00000538874.1_5'UTR	NM_021160.2	NP_066983.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	59						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)	p.S59N(1)		endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						TGCCAGGATGCTGTCAGCATG	0.552																																					p.S59N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G176A	6						.						167.0	113.0	132.0					6																	31669864		1511	2709	4220	31777843	SO:0001583	missense	7920	exon2			AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427		"""Abhydrolase domain containing"""	13921	protein-coding gene	gene with protein product		142620	"""HLA-B associated transcript 5"""	BAT5		2911734, 2813433	Standard	NM_021160		Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000395952.3:c.176G>A	6.37:g.31669864C>T	ENSP00000379282:p.Ser59Asn	Somatic		Capture	Illumina HiSeq	Phase_I	31777843	NM_021160	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	Missense_Mutation	SNP	ENST00000395952.3	37	CCDS4713.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.385128	0.61956	.	.	ENSG00000204427	ENST00000395952	.	.	.	5.66	5.66	0.87406	.	0.082268	0.85682	D	0.000000	T	0.34948	0.0915	L	0.41236	1.265	0.80722	D	1	P	0.46987	0.888	B	0.42163	0.378	T	0.16571	-1.0398	9	0.39692	T	0.17	-9.3868	15.2318	0.73395	0.0:1.0:0.0:0.0	.	59	O95870	ABHGA_HUMAN	N	59	.	ENSP00000379282:S59N	S	-	2	0	ABHD16A	31777843	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.818000	0.55678	2.668000	0.90789	0.561000	0.74099	AGC		0.552	ABHD16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076342.4		
LY6G6C	80740	broad.mit.edu	37	6	31691164	31691164	+	5'Flank	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:31691164G>A	ENST00000375819.2	-	0	0				C6orf25_ENST00000375810.4_Missense_Mutation_p.A2T|LY6G6C_ENST00000495859.1_5'Flank|C6orf25_ENST00000375809.3_Missense_Mutation_p.A2T|C6orf25_ENST00000375805.2_Missense_Mutation_p.A2T|C6orf25_ENST00000480039.1_Missense_Mutation_p.A2T	NM_025261.2	NP_079537.1	O95867	LY66C_HUMAN	lymphocyte antigen 6 complex, locus G6C							anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.A2T(1)		NS(1)|large_intestine(1)|lung(1)|skin(1)	4						CCTAACCATGGCTGTGTTTCT	0.642																																					p.A2T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4A	6						.						34.0	29.0	31.0					6																	31691164		1511	2708	4219	31799143	SO:0001631	upstream_gene_variant	80739	exon1				CCDS4714.1	6p21	2008-08-29	2002-07-29	2002-08-01	ENSG00000204421	ENSG00000204421			13936	protein-coding gene	gene with protein product		610435	"""chromosome 6 open reading frame 24"""	C6orf24		10384126, 12079290	Standard	NM_025261		Approved	G6c, NG24	uc003nwh.3	O95867	OTTHUMG00000031251		6.37:g.31691164G>A	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	31799143	NM_138272	Q5SRS8|Q8IY94	Missense_Mutation	SNP	ENST00000375819.2	37	CCDS4714.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.435739	0.62955	.	.	ENSG00000204420	ENST00000480039;ENST00000375810;ENST00000375805;ENST00000375809;ENST00000375804;ENST00000375814;ENST00000375806	T;T;T;T	0.55588	0.53;0.51;0.51;0.54	4.35	1.47	0.22746	.	0.493499	0.17140	N	0.185497	T	0.14960	0.0361	N	0.19112	0.55	0.28253	N	0.925187	B;B;B;B;B;B	0.22909	0.019;0.019;0.077;0.077;0.077;0.077	B;B;B;B;B;B	0.20767	0.017;0.011;0.017;0.031;0.017;0.031	T	0.12528	-1.0544	10	0.87932	D	0	-1.9254	4.6027	0.12361	0.2083:0.1825:0.6092:0.0	.	2;2;2;2;2;2	O95866-3;O95866-5;O95866;O95866-4;O95866-7;B0V023	.;.;G6B_HUMAN;.;.;.	T	2	ENSP00000419306:A2T;ENSP00000364968:A2T;ENSP00000364967:A2T;ENSP00000364964:A2T	ENSP00000364962:A2T	A	+	1	0	C6orf25	31799143	0.966000	0.33281	0.996000	0.52242	0.526000	0.34562	1.141000	0.31528	0.452000	0.26830	0.585000	0.79938	GCT		0.642	LY6G6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076530.2		
TAP2	6891	broad.mit.edu	37	6	32798084	32798084	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:32798084delT	ENST00000452392.2	-	9	1768	c.1595delA	c.(1594-1596)aagfs	p.K532fs	TAP2_ENST00000485701.1_5'Flank|TAP2_ENST00000374897.2_Frame_Shift_Del_p.K532fs|TAP2_ENST00000374899.4_Frame_Shift_Del_p.K532fs			Q9UDX4	S14L3_HUMAN	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.K532fs*29(2)								Vitamin E(DB00163)	TGAGATGGGCTTTTCATCCAG	0.597																																					p.K532fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1595delA	6						.						140.0	130.0	134.0					6																	32798084		1511	2708	4219	32906062	SO:0001589	frameshift_variant	6891	exon9			M74447	CCDS4755.1	6p21.3	2014-09-17			ENSG00000204267	ENSG00000204267		"""ATP binding cassette transporters / subfamily B"""	44	protein-coding gene	gene with protein product		170261		ABCB3		1529427, 1946428, 16395595	Standard	NM_001290043		Approved	PSF2, RING11, D6S217E	uc003ocd.3	Q03519	OTTHUMG00000031068	ENST00000452392.2:c.1595delA	6.37:g.32798084delT	ENSP00000391806:p.Lys532fs	Somatic		Capture	Illumina HiSeq	Phase_I	32906062	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Frame_Shift_Del	DEL	ENST00000452392.2	37																																																																																					0.597	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544	
PSMB8	5696	broad.mit.edu	37	6	32805788	32805788	+	IGR	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:32805788delG	ENST00000374882.3	-	0	1124				TAP2_ENST00000374897.2_Frame_Shift_Del_p.L75fs|TAP2_ENST00000374899.4_Frame_Shift_Del_p.L75fs|TAP2_ENST00000452392.2_Frame_Shift_Del_p.L75fs	NM_148919.3	NP_683720.2	P28062	PSB8_HUMAN	proteasome (prosome, macropain) subunit, beta type, 8						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)	p.L75fs*1(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	11					Carfilzomib(DB08889)	GAGACAGTCAGGGGGGTGGCC	0.692																																					p.L75X	NSCLC(48;53 1172 10859 13624 22883)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.223delC	6						.						41.0	46.0	44.0					6																	32805788		1508	2707	4215	32913766	SO:0001628	intergenic_variant	6891	exon2				CCDS4756.1, CCDS4757.1	6p21.3	2013-03-27	2013-03-27		ENSG00000204264	ENSG00000204264		"""Proteasome (prosome, macropain) subunits"""	9545	protein-coding gene	gene with protein product		177046	"""proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7)"", ""large multifunctional peptidase 7"""	LMP7		1529427, 10329130	Standard	XM_005275000		Approved	RING10, D6S216E, PSMB5i, beta5i	uc003oce.3	P28062	OTTHUMG00000031285		6.37:g.32805788delG		Somatic		Capture	Illumina HiSeq	Phase_I	32913766	NM_018833	B0UZC0|Q29824|Q5JNW6|Q5QNR8|Q96J48	Frame_Shift_Del	DEL	ENST00000374882.3	37	CCDS4757.1																																																																																				0.692	PSMB8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076617.3	NM_148919	
PSMB9	5698	broad.mit.edu	37	6	32825852	32825852	+	Nonsense_Mutation	SNP	C	C	T	rs367733308		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:32825852C>T	ENST00000374859.2	+	4	400	c.331C>T	c.(331-333)Cga>Tga	p.R111*	PSMB9_ENST00000395330.1_Nonsense_Mutation_p.R88*|PSMB9_ENST00000453265.2_Nonsense_Mutation_p.R67*	NM_002800.4	NP_002791.1	P28065	PSB9_HUMAN	proteasome (prosome, macropain) subunit, beta type, 9	111					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)	p.R111*(1)		large_intestine(4)|lung(4)|skin(1)	9					Carfilzomib(DB08889)	CTATAAATATCGAGAGGACTT	0.473																																					p.R111X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C331T	6						.						122.0	125.0	124.0					6																	32825852		1511	2709	4220	32933830	SO:0001587	stop_gained	5698	exon4				CCDS4759.1	6p21.3	2013-03-27	2013-03-27		ENSG00000240065	ENSG00000240065		"""Proteasome (prosome, macropain) subunits"""	9546	protein-coding gene	gene with protein product		177045	"""proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional protease 2)"", ""large multifunctional peptidase 2"""	LMP2		1922385, 1529427	Standard	NM_002800		Approved	RING12, beta1i, PSMB6i	uc003sga.3	P28065	OTTHUMG00000031287	ENST00000374859.2:c.331C>T	6.37:g.32825852C>T	ENSP00000363993:p.Arg111*	Somatic		Capture	Illumina HiSeq	Phase_I	32933830	NM_002800	B0V0T1|Q16523|Q5JNW4	Nonsense_Mutation	SNP	ENST00000374859.2	37	CCDS4759.1	.	.	.	.	.	.	.	.	.	.	C	32	5.190091	0.94923	.	.	ENSG00000240065	ENST00000395330;ENST00000414474;ENST00000374859;ENST00000453265;ENST00000395333	.	.	.	5.04	4.16	0.48862	.	0.130400	0.51477	D	0.000092	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-30.6133	10.4464	0.44497	0.3551:0.6449:0.0:0.0	.	.	.	.	X	88;88;111;67;67	.	ENSP00000363993:R111X	R	+	1	2	PSMB9	32933830	0.131000	0.22433	0.653000	0.29593	0.677000	0.39632	2.063000	0.41423	1.329000	0.45376	0.643000	0.83706	CGA		0.473	PSMB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076624.5	NM_002800	
BAK1	578	broad.mit.edu	37	6	33541593	33541593	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:33541593A>T	ENST00000374467.3	-	6	871	c.623T>A	c.(622-624)tTc>tAc	p.F208Y	BAK1_ENST00000442998.2_3'UTR|BAK1_ENST00000360661.5_Missense_Mutation_p.F208Y	NM_001188.3	NP_001179.1	Q16611	BAK_HUMAN	BCL2-antagonist/killer 1	208					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|apoptotic process involved in patterning of blood vessels (GO:1902262)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|B cell negative selection (GO:0002352)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fibroblast apoptotic process (GO:0044346)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|limb morphogenesis (GO:0035108)|mitochondrial fusion (GO:0008053)|myeloid cell homeostasis (GO:0002262)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of gene expression (GO:0010629)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|post-embryonic camera-type eye morphogenesis (GO:0048597)|regulation of cell cycle (GO:0051726)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|release of cytochrome c from mitochondria (GO:0001836)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to fungus (GO:0009620)|response to gamma radiation (GO:0010332)|response to hydrogen peroxide (GO:0042542)|response to mycotoxin (GO:0010046)|response to organic cyclic compound (GO:0014070)|response to UV-C (GO:0010225)|thymocyte apoptotic process (GO:0070242)|vagina development (GO:0060068)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|pore complex (GO:0046930)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.F208Y(1)		large_intestine(1)|lung(1)|ovary(1)|skin(1)	4						TGATTTGAAGAATCTTCGTAC	0.567																																					p.F208Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T623A	6						.						50.0	49.0	49.0					6																	33541593		2203	4299	6502	33649571	SO:0001583	missense	578	exon6			U23765	CCDS4781.1	6p21.31	2014-03-07			ENSG00000030110	ENSG00000030110			949	protein-coding gene	gene with protein product		600516		CDN1		7715730, 7715731	Standard	NM_001188		Approved	BCL2L7, BAK	uc003oes.3	Q16611	OTTHUMG00000014530	ENST00000374467.3:c.623T>A	6.37:g.33541593A>T	ENSP00000363591:p.Phe208Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	33649571	NM_001188	C0H5Y7|Q6I9T6|Q92533	Missense_Mutation	SNP	ENST00000374467.3	37	CCDS4781.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.851782	0.51270	.	.	ENSG00000030110	ENST00000374460;ENST00000374467;ENST00000360661	T;T	0.12569	2.67;2.67	4.5	1.94	0.25998	.	0.282367	0.30658	N	0.009145	T	0.03608	0.0103	L	0.29908	0.895	0.80722	D	1	B	0.12013	0.005	B	0.08055	0.003	T	0.24835	-1.0149	10	0.72032	D	0.01	-5.1949	7.7492	0.28888	0.6655:0.0:0.0:0.3345	.	208	Q16611	BAK_HUMAN	Y	188;208;208	ENSP00000363591:F208Y;ENSP00000353878:F208Y	ENSP00000353878:F208Y	F	-	2	0	BAK1	33649571	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	3.384000	0.52478	0.214000	0.20742	0.477000	0.44152	TTC		0.567	BAK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040202.1	NM_001188	
GRM4	2914	broad.mit.edu	37	6	33995987	33995987	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:33995987C>T	ENST00000538487.2	-	10	3042	c.2599G>A	c.(2599-2601)Gcc>Acc	p.A867T	GRM4_ENST00000455714.2_Missense_Mutation_p.A727T|GRM4_ENST00000535756.1_Missense_Mutation_p.A734T|GRM4_ENST00000374177.3_Missense_Mutation_p.A751T|GRM4_ENST00000374181.4_Missense_Mutation_p.A867T|GRM4_ENST00000544773.2_Missense_Mutation_p.A698T|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000609222.1_Missense_Mutation_p.A734T	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	867					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.A867T(2)|p.A751T(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GACATGGTGGCCGCCGTAACG	0.597																																					p.A867T												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G2599A	6						.						81.0	70.0	74.0					6																	33995987		2203	4300	6503	34103965	SO:0001583	missense	2914	exon9			U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.2599G>A	6.37:g.33995987C>T	ENSP00000440556:p.Ala867Thr	Somatic		Capture	Illumina HiSeq	Phase_I	34103965	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Missense_Mutation	SNP	ENST00000538487.2	37	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737926	0.69304	.	.	ENSG00000124493	ENST00000374181;ENST00000374177;ENST00000545715;ENST00000535756;ENST00000544773;ENST00000538487;ENST00000455714	D;D;D;D;D;D;D	0.88509	-2.37;-2.39;-2.13;-2.17;-2.2;-2.37;-2.21	4.28	4.28	0.50868	.	0.226096	0.35349	N	0.003271	D	0.90177	0.6930	M	0.70595	2.14	0.58432	D	0.999994	P;P;B;B;P	0.45594	0.726;0.862;0.026;0.004;0.852	B;P;B;B;P	0.52109	0.25;0.69;0.028;0.008;0.58	D	0.91025	0.4860	10	0.54805	T	0.06	.	16.8937	0.86094	0.0:1.0:0.0:0.0	.	820;698;727;867;734	B7ZLU9;B7Z1T9;F5GXM5;Q14833;B3KVL9	.;.;.;GRM4_HUMAN;.	T	867;751;559;734;698;867;727	ENSP00000363296:A867T;ENSP00000363292:A751T;ENSP00000445533:A559T;ENSP00000437925:A734T;ENSP00000437730:A698T;ENSP00000440556:A867T;ENSP00000398456:A727T	ENSP00000363292:A751T	A	-	1	0	GRM4	34103965	1.000000	0.71417	0.970000	0.41538	0.583000	0.36354	5.864000	0.69575	2.218000	0.71995	0.478000	0.44815	GCC		0.597	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2		
GRM4	2914	broad.mit.edu	37	6	34003799	34003799	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:34003799delG	ENST00000538487.2	-	9	2531	c.2088delC	c.(2086-2088)cccfs	p.P696fs	GRM4_ENST00000455714.2_Frame_Shift_Del_p.P556fs|GRM4_ENST00000535756.1_Frame_Shift_Del_p.P563fs|GRM4_ENST00000374177.3_Frame_Shift_Del_p.P580fs|GRM4_ENST00000374181.4_Frame_Shift_Del_p.P696fs|GRM4_ENST00000544773.2_Frame_Shift_Del_p.P527fs|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000609222.1_Frame_Shift_Del_p.P563fs	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	696					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.A697fs*126(2)|p.A581fs*126(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GCTGTGAGGCGGGGCTGATGA	0.617																																					p.P696fs												.	.	3	Deletion - Frameshift(3)	large_intestine(3)	c.2088delC	6						.						110.0	121.0	117.0					6																	34003799		2203	4300	6503	34111777	SO:0001589	frameshift_variant	2914	exon8			U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.2088delC	6.37:g.34003799delG	ENSP00000440556:p.Pro696fs	Somatic		Capture	Illumina HiSeq	Phase_I	34111777	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Frame_Shift_Del	DEL	ENST00000538487.2	37	CCDS4787.1																																																																																				0.617	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2		
PACSIN1	29993	broad.mit.edu	37	6	34499407	34499407	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:34499407C>T	ENST00000538621.1	+	9	1313	c.1068C>T	c.(1066-1068)taC>taT	p.Y356Y	PACSIN1_ENST00000374043.2_Silent_p.Y314Y|PACSIN1_ENST00000244458.2_Silent_p.Y356Y	NM_001199583.2	NP_001186512.1	Q9BY11	PACN1_HUMAN	protein kinase C and casein kinase substrate in neurons 1	356					actin filament organization (GO:0007015)|establishment of protein localization to plasma membrane (GO:0090002)|membrane tubulation (GO:0097320)|neuron projection morphogenesis (GO:0048812)|positive regulation of dendrite development (GO:1900006)|protein localization to membrane (GO:0072657)|synaptic vesicle endocytosis (GO:0048488)	axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|synapse (GO:0045202)	phospholipid binding (GO:0005543)	p.Y356Y(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)	13						GCCAGCCCTACGCCACCGAGT	0.642																																					p.Y356Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1068T	6						.						84.0	86.0	86.0					6																	34499407		2203	4300	6503	34607385	SO:0001819	synonymous_variant	29993	exon9			AB037800	CCDS4793.1	6p21.3	2008-02-05			ENSG00000124507	ENSG00000124507			8570	protein-coding gene	gene with protein product	"""syndapin I"""	606512				11179684	Standard	NM_020804		Approved	SDPI	uc003ojp.4	Q9BY11	OTTHUMG00000014547	ENST00000538621.1:c.1068C>T	6.37:g.34499407C>T		Somatic		Capture	Illumina HiSeq	Phase_I	34607385	NM_020804	Q9P2G8	Silent	SNP	ENST00000538621.1	37	CCDS4793.1																																																																																				0.642	PACSIN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040236.1		
SPDEF	25803	broad.mit.edu	37	6	34512065	34512065	+	Silent	SNP	G	G	A	rs2233638		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:34512065G>A	ENST00000374037.3	-	2	582	c.168C>T	c.(166-168)tcC>tcT	p.S56S	SPDEF_ENST00000544425.1_Silent_p.S56S	NM_012391.2	NP_036523.1	O95238	SPDEF_HUMAN	SAM pointed domain containing ETS transcription factor	56					cell differentiation (GO:0030154)|intestinal epithelial cell development (GO:0060576)|lung goblet cell differentiation (GO:0060480)|multicellular organismal development (GO:0007275)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell fate commitment (GO:0010455)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.S56S(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)	15						GGTAGAAGGCGGACAGGCCCT	0.677																																					p.S56S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C168T	6						.						38.0	42.0	41.0					6																	34512065		2203	4300	6503	34620043	SO:0001819	synonymous_variant	25803	exon2			AF071538	CCDS4794.1, CCDS59013.1	6p21.3	2013-08-07	2013-08-07		ENSG00000124664	ENSG00000124664			17257	protein-coding gene	gene with protein product		608144	"""SAM pointed domain containing ets transcription factor"""			10625666, 6857767	Standard	NM_012391		Approved	PDEF, bA375E1.3	uc003ojq.2	O95238	OTTHUMG00000014548	ENST00000374037.3:c.168C>T	6.37:g.34512065G>A		Somatic		Capture	Illumina HiSeq	Phase_I	34620043	NM_012391	B4DWH8|F5H778	Silent	SNP	ENST00000374037.3	37	CCDS4794.1																																																																																				0.677	SPDEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040246.1	NM_012391	
UHRF1BP1	54887	broad.mit.edu	37	6	34826767	34826767	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:34826767T>C	ENST00000192788.5	+	14	2805	c.2634T>C	c.(2632-2634)gcT>gcC	p.A878A	UHRF1BP1_ENST00000452449.2_Silent_p.A878A	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	878							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)	p.A878A(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						TTCCCAGTGCTGAAGTGGCTC	0.527																																					p.A878A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2634C	6						.						73.0	74.0	73.0					6																	34826767		2089	4233	6322	34934745	SO:0001819	synonymous_variant	54887	exon14			AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.2634T>C	6.37:g.34826767T>C		Somatic		Capture	Illumina HiSeq	Phase_I	34934745	NM_017754	Q9NXE0	Silent	SNP	ENST00000192788.5	37	CCDS43455.1																																																																																				0.527	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
TMEM217	221468	broad.mit.edu	37	6	37186635	37186635	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:37186635T>A	ENST00000336655.2	-	2	211	c.172A>T	c.(172-174)Aac>Tac	p.N58Y	TMEM217_ENST00000356757.2_Missense_Mutation_p.N58Y|TMEM217_ENST00000497775.1_Intron	NM_145316.3	NP_660359.2	Q8N7C4	TM217_HUMAN	transmembrane protein 217	58						integral component of membrane (GO:0016021)		p.N58D(1)|p.N58Y(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(1)	9						ATGATGAAGTTATTTATGATG	0.448																																					p.N58Y												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A172T	6						.						282.0	264.0	270.0					6																	37186635		2203	4300	6503	37294613	SO:0001583	missense	221468	exon2				CCDS4831.1, CCDS69102.1	6p21.31-p21.2	2008-10-20	2008-07-07	2008-07-07	ENSG00000172738	ENSG00000172738			21238	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 128"""	C6orf128			Standard	NM_001162900		Approved	dJ355M6.2	uc010jws.3	Q8N7C4	OTTHUMG00000014618	ENST00000336655.2:c.172A>T	6.37:g.37186635T>A	ENSP00000338164:p.Asn58Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	37294613	NM_145316	Q8TC54	Missense_Mutation	SNP	ENST00000336655.2	37	CCDS4831.1	.	.	.	.	.	.	.	.	.	.	T	7.677	0.688156	0.14973	.	.	ENSG00000172738	ENST00000356757;ENST00000336655	.	.	.	4.23	-8.46	0.00942	.	.	.	.	.	T	0.02571	0.0078	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.33752	-0.9856	8	0.27082	T	0.32	5.8042	3.0377	0.06128	0.1548:0.4314:0.1277:0.2861	.	58;58	Q8N7C4-2;Q8N7C4	.;TM217_HUMAN	Y	58	.	ENSP00000338164:N58Y	N	-	1	0	TMEM217	37294613	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.872000	0.00720	-1.765000	0.01303	-1.024000	0.02432	AAC		0.448	TMEM217-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357542.1	NM_145316	
CMTR1	23070	broad.mit.edu	37	6	37441313	37441313	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:37441313G>A	ENST00000373451.4	+	17	1921	c.1757G>A	c.(1756-1758)cGc>cAc	p.R586H		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	586					7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)	p.R586H(1)									GAGAAGATCCGCCCTGTGTTT	0.557																																					p.R586H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1757A	6						.						147.0	127.0	134.0					6																	37441313		2203	4300	6503	37549291	SO:0001583	missense	23070	exon17			BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"""G patch domain containing"""	21077	protein-coding gene	gene with protein product			"""KIAA0082"", ""FtsJ methyltransferase domain containing 2"""	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.1757G>A	6.37:g.37441313G>A	ENSP00000362550:p.Arg586His	Somatic		Capture	Illumina HiSeq	Phase_I	37549291	NM_015050	A8K949|Q14670|Q96FJ9	Missense_Mutation	SNP	ENST00000373451.4	37	CCDS4835.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.210705	0.58343	.	.	ENSG00000137200	ENST00000373451	.	.	.	6.17	6.17	0.99709	.	0.142988	0.64402	D	0.000004	T	0.36054	0.0953	L	0.57536	1.79	0.49687	D	0.999814	B	0.30851	0.297	B	0.17433	0.018	T	0.16482	-1.0401	9	0.20046	T	0.44	-17.9645	14.2995	0.66336	0.0:0.0:0.8515:0.1485	.	586	Q8N1G2	MTR1_HUMAN	H	586	.	ENSP00000362550:R586H	R	+	2	0	FTSJD2	37549291	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.593000	0.61034	2.941000	0.99782	0.655000	0.94253	CGC		0.557	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050	
DNAH8	1769	broad.mit.edu	37	6	38840790	38840790	+	Missense_Mutation	SNP	G	G	A	rs149449115	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:38840790G>A	ENST00000359357.3	+	49	6949	c.6695G>A	c.(6694-6696)cGc>cAc	p.R2232H	DNAH8_ENST00000441566.1_Missense_Mutation_p.R2196H|DNAH8_ENST00000449981.2_Missense_Mutation_p.R2449H			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2232	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R2232H(3)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						AATGGAGATCGCATTCCCATG	0.443																																					p.R2232H												.	.	3	Substitution - Missense(3)	large_intestine(2)|upper_aerodigestive_tract(1)	c.G6695A	6						.						110.0	112.0	111.0					6																	38840790		2203	4300	6503	38948768	SO:0001583	missense	1769	exon49			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.6695G>A	6.37:g.38840790G>A	ENSP00000352312:p.Arg2232His	Somatic		Capture	Illumina HiSeq	Phase_I	38948768	NM_001371	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	G	36	5.600693	0.96614	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	D;D;D	0.89270	-2.49;-2.49;-2.49	5.9	5.9	0.94986	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.000000	0.85682	D	0.000000	D	0.97278	0.9110	H	0.98901	4.365	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98231	1.0483	10	0.87932	D	0	.	20.2822	0.98520	0.0:0.0:1.0:0.0	.	2232	Q96JB1	DYH8_HUMAN	H	2437;2437;2232;2196	ENSP00000333363:R2437H;ENSP00000352312:R2232H;ENSP00000402294:R2196H	ENSP00000333363:R2437H	R	+	2	0	DNAH8	38948768	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.869000	0.99810	2.806000	0.96561	0.655000	0.94253	CGC		0.443	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
KIF6	221458	broad.mit.edu	37	6	39311555	39311555	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:39311555G>A	ENST00000287152.7	-	22	2452	c.2358C>T	c.(2356-2358)acC>acT	p.T786T	KIF6_ENST00000229913.5_Silent_p.T237T|KIF6_ENST00000373215.3_Silent_p.T769T|KIF6_ENST00000373216.3_Silent_p.T769T|KIF6_ENST00000373213.4_Silent_p.T625T|KIF6_ENST00000394362.1_Silent_p.T220T|KIF6_ENST00000541946.1_Silent_p.T237T|KIF6_ENST00000538893.1_Silent_p.T730T	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	786					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.T786T(2)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						GGCTGTCTCCGGTGAGAGGGA	0.532																																					p.T786T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2358T	6						.						159.0	113.0	128.0					6																	39311555		2203	4300	6503	39419533	SO:0001819	synonymous_variant	221458	exon22			AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"""Kinesins"""	21202	protein-coding gene	gene with protein product		613919	"""chromosome 6 open reading frame 102"""	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.2358C>T	6.37:g.39311555G>A		Somatic		Capture	Illumina HiSeq	Phase_I	39419533	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Silent	SNP	ENST00000287152.7	37	CCDS4844.1	.	.	.	.	.	.	.	.	.	.	G	7.465	0.645550	0.14451	.	.	ENSG00000164627	ENST00000458470	.	.	.	4.91	-7.21	0.01490	.	.	.	.	.	T	0.25457	0.0619	.	.	.	0.51233	D	0.999914	.	.	.	.	.	.	T	0.40627	-0.9553	4	.	.	.	.	4.427	0.11507	0.5298:0.1001:0.2692:0.1009	.	.	.	.	L	661	.	.	P	-	2	0	KIF6	39419533	0.004000	0.15560	0.711000	0.30485	0.710000	0.40934	-2.216000	0.01221	-1.674000	0.01461	0.462000	0.41574	CCG		0.532	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027	
KIF6	221458	broad.mit.edu	37	6	39398906	39398906	+	Missense_Mutation	SNP	C	C	A	rs201410117	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:39398906C>A	ENST00000287152.7	-	14	1771	c.1677G>T	c.(1675-1677)caG>caT	p.Q559H	KIF6_ENST00000229913.5_Missense_Mutation_p.Q10H|KIF6_ENST00000373215.3_Missense_Mutation_p.Q559H|KIF6_ENST00000373216.3_Missense_Mutation_p.Q559H|KIF6_ENST00000373213.4_Missense_Mutation_p.Q398H|KIF6_ENST00000394362.1_Missense_Mutation_p.Q10H|KIF6_ENST00000541946.1_Missense_Mutation_p.Q10H|KIF6_ENST00000538893.1_Missense_Mutation_p.Q503H	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	559				CQEAFEIFKRDHADSVTIDDNKQILKQ -> NATILSSLTG PGLQHFGEKIQFAPQEN (in Ref. 4; CAD89950). {ECO:0000305}.	ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.Q559H(2)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						CAAAAGCCTCCTGGCATCCTA	0.458																																					p.Q559H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1677T	6						.						136.0	114.0	121.0					6																	39398906		2203	4300	6503	39506884	SO:0001583	missense	221458	exon14			AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"""Kinesins"""	21202	protein-coding gene	gene with protein product		613919	"""chromosome 6 open reading frame 102"""	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.1677G>T	6.37:g.39398906C>A	ENSP00000287152:p.Gln559His	Somatic		Capture	Illumina HiSeq	Phase_I	39506884	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	37	CCDS4844.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.37|18.37	3.609818|3.609818	0.66558|0.66558	.|.	.|.	ENSG00000164627|ENSG00000164627	ENST00000287152;ENST00000394362;ENST00000373216;ENST00000373213;ENST00000229913;ENST00000373215;ENST00000538893;ENST00000541946;ENST00000540362|ENST00000458470	T;T;T;T;T;T;T;T|.	0.73152|.	0.97;1.24;0.97;0.97;1.18;-0.72;0.97;1.14|.	5.84|5.84	4.01|4.01	0.46588|0.46588	.|.	.|.	.|.	.|.	.|.	T|T	0.48786|0.48786	0.1519|0.1519	M|M	0.65975|0.65975	2.015|2.015	0.39168|0.39168	D|D	0.962537|0.962537	D;P;P;D|.	0.76494|.	0.999;0.794;0.903;0.998|.	D;B;B;D|.	0.73380|.	0.98;0.21;0.288;0.956|.	T|T	0.53528|0.53528	-0.8426|-0.8426	9|5	0.72032|.	D|.	0.01|.	.|.	6.1908|6.1908	0.20524|0.20524	0.0:0.6593:0.0:0.3407|0.0:0.6593:0.0:0.3407	.|.	559;503;559;559|.	E7EUN7;F6VGH2;Q6ZMV9-3;Q6ZMV9|.	.;.;.;KIF6_HUMAN|.	H|M	559;10;559;398;10;559;503;10;10|451	ENSP00000287152:Q559H;ENSP00000377889:Q10H;ENSP00000362312:Q559H;ENSP00000362309:Q398H;ENSP00000229913:Q10H;ENSP00000362311:Q559H;ENSP00000441435:Q503H;ENSP00000439064:Q10H|.	ENSP00000229913:Q10H|.	Q|R	-|-	3|2	2|0	KIF6|KIF6	39506884|39506884	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.953000|0.953000	0.61014|0.61014	1.583000|1.583000	0.36579|0.36579	1.404000|1.404000	0.46819|0.46819	0.655000|0.655000	0.94253|0.94253	CAG|AGG		0.458	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027	
DAAM2	23500	broad.mit.edu	37	6	39869691	39869691	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:39869691G>C	ENST00000398904.2	+	25	3267	c.3085G>C	c.(3085-3087)Gcc>Ccc	p.A1029P	DAAM2_ENST00000538976.1_Missense_Mutation_p.A1028P|RP11-61I13.3_ENST00000437947.1_RNA|DAAM2_ENST00000274867.4_Missense_Mutation_p.A1029P			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	1029	DAD. {ECO:0000255|PROSITE- ProRule:PRU00577}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)			p.A1028P(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					CCTGGTGTCGGCCCTGCGCTC	0.657																																					p.A1028P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3082C	6						.						37.0	46.0	43.0					6																	39869691		2113	4223	6336	39977669	SO:0001583	missense	23500	exon25			AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.3085G>C	6.37:g.39869691G>C	ENSP00000381876:p.Ala1029Pro	Somatic		Capture	Illumina HiSeq	Phase_I	39977669	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.565715	0.86439	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	D;D;D	0.81579	-1.51;-1.51;-1.51	5.63	5.63	0.86233	Actin-binding FH2/DRF autoregulatory (1);Diaphanous autoregulatory (1);	0.000000	0.85682	D	0.000000	D	0.88314	0.6403	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.991	D	0.88843	0.3314	10	0.87932	D	0	.	19.2792	0.94046	0.0:0.0:1.0:0.0	.	1028;1029	G5EA45;Q86T65	.;DAAM2_HUMAN	P	1029;1029;1028	ENSP00000274867:A1029P;ENSP00000381876:A1029P;ENSP00000437808:A1028P	ENSP00000274867:A1029P	A	+	1	0	DAAM2	39977669	1.000000	0.71417	0.681000	0.30009	0.358000	0.29455	9.794000	0.99096	2.651000	0.90000	0.650000	0.86243	GCC		0.657	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
TRERF1	55809	broad.mit.edu	37	6	42204058	42204058	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:42204058G>A	ENST00000372922.4	-	16	3513	c.2951C>T	c.(2950-2952)cCg>cTg	p.P984L	TRERF1_ENST00000541110.1_Missense_Mutation_p.P1004L|TRERF1_ENST00000340840.2_Missense_Mutation_p.P901L|TRERF1_ENST00000372917.4_Missense_Mutation_p.P901L|TRERF1_ENST00000354325.2_Missense_Mutation_p.P901L	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	984	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.P984L(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CGGGGACTTCGGCACCTCACT	0.587																																					p.P984L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2951T	6						.						97.0	97.0	97.0					6																	42204058		2203	4299	6502	42312036	SO:0001583	missense	55809	exon16			AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.2951C>T	6.37:g.42204058G>A	ENSP00000362013:p.Pro984Leu	Somatic		Capture	Illumina HiSeq	Phase_I	42312036	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.142642	0.57044	.	.	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.12147	2.89;2.71;2.88;2.71;2.72	5.61	2.51	0.30379	.	0.351810	0.24195	N	0.040667	T	0.02848	0.0085	N	0.08118	0	0.26886	N	0.967431	B;B;B;B;D	0.63046	0.001;0.001;0.001;0.001;0.992	B;B;B;B;P	0.45712	0.001;0.0;0.0;0.001;0.491	T	0.32025	-0.9922	10	0.62326	D	0.03	-2.828	7.4468	0.27215	0.0871:0.0:0.3623:0.5505	.	901;1004;984;740;740	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	L	1004;901;984;901;901	ENSP00000439689:P1004L;ENSP00000362008:P901L;ENSP00000362013:P984L;ENSP00000339438:P901L;ENSP00000346285:P901L	ENSP00000339438:P901L	P	-	2	0	TRERF1	42312036	0.037000	0.19845	0.039000	0.18376	0.989000	0.77384	0.909000	0.28558	0.702000	0.31825	0.655000	0.94253	CCG		0.587	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
CUL9	23113	broad.mit.edu	37	6	43160851	43160851	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:43160851C>T	ENST00000252050.4	+	9	2377	c.2293C>T	c.(2293-2295)Cgg>Tgg	p.R765W	CUL9_ENST00000354495.3_Missense_Mutation_p.R655W|CUL9_ENST00000372647.2_Missense_Mutation_p.R765W	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	765					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)	p.R765W(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						GCACGAGTGGCGGCCGCTCTT	0.592																																					p.R765W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2293T	6						.						178.0	159.0	166.0					6																	43160851		2203	4300	6503	43268829	SO:0001583	missense	23113	exon9			AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.2293C>T	6.37:g.43160851C>T	ENSP00000252050:p.Arg765Trp	Somatic		Capture	Illumina HiSeq	Phase_I	43268829	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.723502	0.68959	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.38887	1.11;1.11;1.11	4.99	4.99	0.66335	Armadillo-like helical (1);Armadillo-type fold (1);	0.131761	0.52532	D	0.000067	T	0.42877	0.1222	L	0.29908	0.895	0.52099	D	0.99994	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	T	0.47983	-0.9074	10	0.87932	D	0	-18.1744	13.6746	0.62447	0.0:0.9225:0.0:0.0775	.	765;765	E9PEZ1;Q8IWT3	.;CUL9_HUMAN	W	765;655;765	ENSP00000252050:R765W;ENSP00000346490:R655W;ENSP00000361730:R765W	ENSP00000252050:R765W	R	+	1	2	CUL9	43268829	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	4.447000	0.60020	2.312000	0.78011	0.297000	0.19635	CGG		0.592	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
CUL9	23113	broad.mit.edu	37	6	43167758	43167758	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:43167758T>C	ENST00000252050.4	+	14	3332	c.3248T>C	c.(3247-3249)aTc>aCc	p.I1083T	CUL9_ENST00000354495.3_Missense_Mutation_p.I973T|CUL9_ENST00000372647.2_Missense_Mutation_p.I1083T	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1083					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)	p.I1083T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						GCAAAAGAGATCCTCTCCAAA	0.557																																					p.I1083T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3248C	6						.						118.0	92.0	101.0					6																	43167758		2203	4300	6503	43275736	SO:0001583	missense	23113	exon14			AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.3248T>C	6.37:g.43167758T>C	ENSP00000252050:p.Ile1083Thr	Somatic		Capture	Illumina HiSeq	Phase_I	43275736	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.050284	0.36181	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.71934	-0.61;-0.61;-0.5	5.37	2.32	0.28847	Armadillo-like helical (1);Armadillo-type fold (1);	0.407010	0.29172	N	0.012934	T	0.22126	0.0533	N	0.02011	-0.69	0.22601	N	0.998941	B;B;B	0.11235	0.004;0.0;0.0	B;B;B	0.14023	0.01;0.0;0.0	T	0.27706	-1.0066	10	0.44086	T	0.13	-1.8885	11.0241	0.47734	0.0:0.8713:0.0:0.1287	.	973;1083;1083	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	T	1083;973;1083	ENSP00000252050:I1083T;ENSP00000346490:I973T;ENSP00000361730:I1083T	ENSP00000252050:I1083T	I	+	2	0	CUL9	43275736	1.000000	0.71417	0.469000	0.27204	0.933000	0.57130	1.253000	0.32886	0.141000	0.18875	-0.408000	0.06270	ATC		0.557	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
CUL9	23113	broad.mit.edu	37	6	43180994	43180994	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:43180994G>A	ENST00000252050.4	+	27	5404	c.5320G>A	c.(5320-5322)Gtg>Atg	p.V1774M	CUL9_ENST00000354495.3_Missense_Mutation_p.V1664M|CUL9_ENST00000502937.1_3'UTR|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000372647.2_Missense_Mutation_p.V1774M	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1774					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)	p.V1774M(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						TGTGTCCACCGTGCAGATGTG	0.572																																					p.V1774M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5320A	6						.						93.0	86.0	88.0					6																	43180994		2203	4300	6503	43288972	SO:0001583	missense	23113	exon27			AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.5320G>A	6.37:g.43180994G>A	ENSP00000252050:p.Val1774Met	Somatic		Capture	Illumina HiSeq	Phase_I	43288972	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	G	13.79	2.342409	0.41498	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.75821	-0.97;-0.97;-0.97	4.97	1.76	0.24704	Cullin, N-terminal (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Cullin homology (2);	0.147080	0.46758	N	0.000280	T	0.55847	0.1946	L	0.42245	1.32	0.24798	N	0.992716	D;D;D	0.65815	0.995;0.988;0.988	P;P;P	0.53450	0.726;0.657;0.657	T	0.53892	-0.8374	10	0.87932	D	0	-11.7211	2.5552	0.04758	0.0895:0.2273:0.2925:0.3907	.	1664;1774;1774	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	M	1774;1664;1774	ENSP00000252050:V1774M;ENSP00000346490:V1664M;ENSP00000361730:V1774M	ENSP00000252050:V1774M	V	+	1	0	CUL9	43288972	0.970000	0.33590	0.886000	0.34754	0.908000	0.53690	2.009000	0.40903	0.472000	0.27344	-0.181000	0.13052	GTG		0.572	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
TTBK1	84630	broad.mit.edu	37	6	43250796	43250796	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:43250796C>T	ENST00000259750.4	+	14	2401	c.2318C>T	c.(2317-2319)gCa>gTa	p.A773V		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	773	Poly-Ala.				substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A773V(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			gaggaggCTGCAGCGGCAGTT	0.612																																					p.A773V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2318T	6						.						12.0	12.0	12.0					6																	43250796		2196	4289	6485	43358774	SO:0001583	missense	84630	exon14			AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.2318C>T	6.37:g.43250796C>T	ENSP00000259750:p.Ala773Val	Somatic		Capture	Illumina HiSeq	Phase_I	43358774	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	37	CCDS34455.1	.	.	.	.	.	.	.	.	.	.	C	2.326	-0.354448	0.05173	.	.	ENSG00000146216	ENST00000259750	T	0.30981	1.51	4.31	-2.4	0.06583	.	1.048150	0.07691	U	0.938761	T	0.04363	0.0120	N	0.14661	0.345	0.09310	N	0.999996	B	0.18461	0.028	B	0.09377	0.004	T	0.38436	-0.9661	10	0.30854	T	0.27	.	2.4749	0.04573	0.1447:0.4443:0.2453:0.1657	.	773	Q5TCY1	TTBK1_HUMAN	V	773	ENSP00000259750:A773V	ENSP00000259750:A773V	A	+	2	0	TTBK1	43358774	0.021000	0.18746	0.001000	0.08648	0.001000	0.01503	-0.114000	0.10757	-0.053000	0.13289	-0.277000	0.10078	GCA		0.612	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		
TTBK1	84630	broad.mit.edu	37	6	43250927	43250927	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:43250927A>G	ENST00000259750.4	+	14	2532	c.2449A>G	c.(2449-2451)Agg>Ggg	p.R817G		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	817					substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R817G(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			GAAGGAGTCCAGGGGCCGGGC	0.657																																					p.R817G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2449G	6						.						5.0	6.0	6.0					6																	43250927		2121	4194	6315	43358905	SO:0001583	missense	84630	exon14			AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.2449A>G	6.37:g.43250927A>G	ENSP00000259750:p.Arg817Gly	Somatic		Capture	Illumina HiSeq	Phase_I	43358905	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	37	CCDS34455.1	.	.	.	.	.	.	.	.	.	.	A	13.00	2.105675	0.37145	.	.	ENSG00000146216	ENST00000259750	T	0.55930	0.49	4.62	3.41	0.39046	.	0.180315	0.36482	N	0.002566	T	0.19805	0.0476	N	0.22421	0.69	0.80722	D	1	P	0.34522	0.455	B	0.30105	0.111	T	0.07139	-1.0788	10	0.59425	D	0.04	.	10.1919	0.43032	0.832:0.168:0.0:0.0	.	817	Q5TCY1	TTBK1_HUMAN	G	817	ENSP00000259750:R817G	ENSP00000259750:R817G	R	+	1	2	TTBK1	43358905	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	4.574000	0.60900	0.577000	0.29470	0.459000	0.35465	AGG		0.657	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		
POLH	5429	broad.mit.edu	37	6	43581890	43581890	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:43581890G>T	ENST00000372236.4	+	11	2033	c.1738G>T	c.(1738-1740)Ggg>Tgg	p.G580W	POLH_ENST00000535400.1_Missense_Mutation_p.G518W|POLH_ENST00000372226.1_3'UTR	NM_006502.2	NP_006493.1	O75417	DPOLQ_HUMAN	polymerase (DNA directed), eta	0					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.G580W(1)		breast(4)|endometrium(5)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			TGTTTGTGAAGGGGTGTCGAA	0.473								DNA polymerases (catalytic subunits)	Xeroderma Pigmentosum																												p.G580W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1738T	6						.						69.0	73.0	71.0					6																	43581890		2203	4300	6503	43689868	SO:0001583	missense	5429	exon11	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AB024313	CCDS4902.1	6p21	2014-09-17			ENSG00000170734	ENSG00000170734			9181	protein-coding gene	gene with protein product		603968				10385124, 10398605	Standard	NM_006502		Approved	RAD30A, XP-V	uc003ovq.4	Q9Y253	OTTHUMG00000014743	ENST00000372236.4:c.1738G>T	6.37:g.43581890G>T	ENSP00000361310:p.Gly580Trp	Somatic		Capture	Illumina HiSeq	Phase_I	43689868	NM_006502	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000372236.4	37	CCDS4902.1	.	.	.	.	.	.	.	.	.	.	G	7.232	0.599587	0.13939	.	.	ENSG00000170734	ENST00000372236;ENST00000535400	T;T	0.58797	0.42;0.31	5.58	3.78	0.43462	.	1.105560	0.06658	N	0.763985	T	0.24661	0.0598	N	0.14661	0.345	0.22330	N	0.9992	P;P	0.52463	0.953;0.953	B;B	0.43754	0.43;0.315	T	0.17531	-1.0366	10	0.66056	D	0.02	-27.6277	6.6804	0.23117	0.3504:0.0:0.6496:0.0	.	518;580	B4DG64;Q9Y253	.;POLH_HUMAN	W	580;518	ENSP00000361310:G580W;ENSP00000442102:G518W	ENSP00000361310:G580W	G	+	1	0	POLH	43689868	0.283000	0.24277	0.002000	0.10522	0.175000	0.22909	0.679000	0.25291	0.809000	0.34255	0.561000	0.74099	GGG		0.473	POLH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040666.1	NM_006502	
VEGFA	7422	broad.mit.edu	37	6	43749781	43749781	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:43749781C>T	ENST00000523873.1	+	7	672	c.634C>T	c.(634-636)Cgt>Tgt	p.R212C	VEGFA_ENST00000324450.6_Intron|VEGFA_ENST00000372055.4_Missense_Mutation_p.R392C|VEGFA_ENST00000518824.1_Missense_Mutation_p.R171C|VEGFA_ENST00000523950.1_Missense_Mutation_p.R171C|VEGFA_ENST00000372067.3_Missense_Mutation_p.R351C|VEGFA_ENST00000372077.4_Intron|VEGFA_ENST00000425836.2_Missense_Mutation_p.R375C|VEGFA_ENST00000523125.1_Missense_Mutation_p.R171C|VEGFA_ENST00000482630.2_Missense_Mutation_p.R351C|VEGFA_ENST00000230480.6_Missense_Mutation_p.R143C|VEGFA_ENST00000518689.1_Missense_Mutation_p.R189C|VEGFA_ENST00000520948.1_Missense_Mutation_p.R195C|VEGFA_ENST00000417285.2_Missense_Mutation_p.R351C|VEGFA_ENST00000413642.3_Missense_Mutation_p.R369C|VEGFA_ENST00000372064.4_Intron|VEGFA_ENST00000457104.2_Intron			P15692	VEGFA_HUMAN	vascular endothelial growth factor A	212					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|artery morphogenesis (GO:0048844)|basophil chemotaxis (GO:0002575)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|camera-type eye morphogenesis (GO:0048593)|cardiac muscle fiber development (GO:0048739)|cardiac vascular smooth muscle cell development (GO:0060948)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to hypoxia (GO:0071456)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|dopaminergic neuron differentiation (GO:0071542)|endothelial cell chemotaxis (GO:0035767)|epithelial cell differentiation (GO:0030855)|eye photoreceptor cell development (GO:0042462)|growth (GO:0040007)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|induction of positive chemotaxis (GO:0050930)|kidney development (GO:0001822)|lactation (GO:0007595)|lung development (GO:0030324)|lymph vessel morphogenesis (GO:0036303)|macrophage differentiation (GO:0030225)|mammary gland alveolus development (GO:0060749)|mesoderm development (GO:0007498)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|outflow tract morphogenesis (GO:0003151)|ovarian follicle development (GO:0001541)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cellular component movement (GO:0051272)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine autophosphorylation (GO:1900086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein localization to early endosome (GO:1902966)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor internalization (GO:0002092)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of vascular permeability (GO:0043117)|post-embryonic camera-type eye development (GO:0031077)|primitive erythrocyte differentiation (GO:0060319)|regulation of cell shape (GO:0008360)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)|surfactant homeostasis (GO:0043129)|tube formation (GO:0035148)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|VEGF-activated neuropilin signaling pathway (GO:0038190)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|neuropilin binding (GO:0038191)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor agonist activity (GO:0048018)|vascular endothelial growth factor receptor 1 binding (GO:0043183)|vascular endothelial growth factor receptor 2 binding (GO:0043184)|vascular endothelial growth factor receptor binding (GO:0005172)	p.R392C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9	all_cancers(18;5.46e-07)|all_epithelial(2;5.96e-08)|Lung NSC(15;0.000157)|all_lung(25;0.000486)|Hepatocellular(11;0.00309)		all cancers(41;0.000413)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0742)|OV - Ovarian serous cystadenocarcinoma(102;0.196)		Aflibercept(DB08885)|Bevacizumab(DB00112)|Carvedilol(DB01136)|Dalteparin(DB06779)|Gliclazide(DB01120)|Minocycline(DB01017)|Ranibizumab(DB01270)|Vandetanib(DB05294)	CACAGACTCGCGTTGCAAGGC	0.522																																					p.R351C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1051T	6						.						98.0	85.0	90.0					6																	43749781		2203	4300	6503	43857759	SO:0001583	missense	7422	exon6			AB021221	CCDS34457.1, CCDS4907.2, CCDS34458.1, CCDS47432.1, CCDS47433.1, CCDS47434.1, CCDS47435.1, CCDS55007.1, CCDS55008.1, CCDS55009.1, CCDS55010.1, CCDS55011.1, CCDS55012.1, CCDS55013.1, CCDS55014.1, CCDS55015.1, CCDS69125.1	6p12	2008-02-05	2006-10-31	2006-10-31	ENSG00000112715	ENSG00000112715			12680	protein-coding gene	gene with protein product		192240	"""vascular endothelial growth factor"""	VEGF		8786112	Standard	NM_001025366		Approved	VEGF-A, VPF	uc003owh.3	P15692	OTTHUMG00000014745	ENST00000523873.1:c.634C>T	6.37:g.43749781C>T	ENSP00000430479:p.Arg212Cys	Somatic		Capture	Illumina HiSeq	Phase_I	43857759	NM_001025369	B5BU86|H0Y2S8|H0Y407|H0Y414|H0Y462|H0Y8N2|H3BLW7|O60720|O75875|Q074Z4|Q16889|Q5UB46|Q6P0P5|Q96KJ0|Q96L82|Q96NW5|Q9H1W8|Q9H1W9|Q9UH58|Q9UL23	Missense_Mutation	SNP	ENST00000523873.1	37	CCDS55010.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.310971	0.60414	.	.	ENSG00000112715	ENST00000372067;ENST00000417285;ENST00000413642;ENST00000372055;ENST00000482630;ENST00000425836;ENST00000520948;ENST00000523873;ENST00000523950;ENST00000518689;ENST00000523125;ENST00000518824;ENST00000230480;ENST00000520265	.	.	.	5.83	4.88	0.63580	.	0.158958	0.53938	D	0.000043	T	0.61337	0.2339	L	0.34521	1.04	0.58432	D	0.999994	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.975;0.999;0.975;0.998;0.988	T	0.65150	-0.6238	9	0.87932	D	0	-3.7466	16.7965	0.85603	0.1371:0.8628:0.0:0.0	.	171;392;189;375;351	P15692-8;P15692-14;P15692-3;P15692-13;P15692-11	.;.;.;.;.	C	351;351;369;392;351;375;195;212;171;189;171;171;143;91	.	ENSP00000230480:R143C	R	+	1	0	VEGFA	43857759	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	2.683000	0.46943	2.769000	0.95229	0.655000	0.94253	CGT		0.522	VEGFA-021	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374460.1	NM_001025366	
AARS2	57505	broad.mit.edu	37	6	44272837	44272837	+	Silent	SNP	G	G	A	rs372094957		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:44272837G>A	ENST00000244571.4	-	11	1535	c.1533C>T	c.(1531-1533)gaC>gaT	p.D511D	RP11-444E17.6_ENST00000505802.1_Intron|TMEM151B_ENST00000438774.2_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial									p.D511D(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGGGGCTGTCGTCAGTTGGGG	0.607											OREG0017473	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D511D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1533T	6						.	G		1,4405	2.1+/-5.4	0,1,2202	127.0	118.0	121.0		1533	-2.3	0.8	6		121	0,8600		0,0,4300	no	coding-synonymous	AARS2	NM_020745.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		511/986	44272837	1,13005	2203	4300	6503	44380815	SO:0001819	synonymous_variant	57505	exon11			AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	21022	protein-coding gene	gene with protein product	"""alanine tRNA ligase 2, mitochondrial"""	612035	"""alanyl-tRNA synthetase like"", ""alanyl-tRNA synthetase 2, mitochondrial (putative)"""	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.1533C>T	6.37:g.44272837G>A		Somatic	922	Capture	Illumina HiSeq	Phase_I	44380815	NM_020745		Silent	SNP	ENST00000244571.4	37	CCDS34464.1																																																																																				0.607	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745	
ENPP4	22875	broad.mit.edu	37	6	46107332	46107332	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:46107332A>G	ENST00000321037.4	+	2	242	c.12A>G	c.(10-12)ttA>ttG	p.L4L		NM_014936.4	NP_055751.1	Q9Y6X5	ENPP4_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative)	4					blood coagulation (GO:0007596)|positive regulation of blood coagulation (GO:0030194)|purine ribonucleoside catabolic process (GO:0046130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|metal ion binding (GO:0046872)	p.L4L(1)		central_nervous_system(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	18						TGAAGTTATTAGTAATACTTT	0.338																																					p.L4L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A12G	6						.						49.0	50.0	49.0					6																	46107332		2200	4292	6492	46215291	SO:0001819	synonymous_variant	22875	exon2			AB020686	CCDS34468.1	6p12.3	2010-06-24	2010-06-24		ENSG00000001561	ENSG00000001561			3359	protein-coding gene	gene with protein product						11027689	Standard	NM_014936		Approved	NPP4, KIAA0879	uc003oxy.3	Q9Y6X5	OTTHUMG00000014779	ENST00000321037.4:c.12A>G	6.37:g.46107332A>G		Somatic		Capture	Illumina HiSeq	Phase_I	46215291	NM_014936	A8K5G1|Q7L2N1	Silent	SNP	ENST00000321037.4	37	CCDS34468.1																																																																																				0.338	ENPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040777.2		
ENPP5	59084	broad.mit.edu	37	6	46135329	46135329	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:46135329delT	ENST00000371383.2	-	3	931	c.671delA	c.(670-672)aagfs	p.K224fs	ENPP5_ENST00000492313.1_5'Flank|ENPP5_ENST00000230565.3_Frame_Shift_Del_p.K224fs					ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative)									p.K224fs*8(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	12						CAACTTTGCCTTTTTCAGCAT	0.443																																					p.K224fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.671delA	6						.						126.0	111.0	116.0					6																	46135329		2203	4300	6503	46243288	SO:0001589	frameshift_variant	59084	exon2			AL035701	CCDS4915.1	6p21.1-p11.2	2010-06-24	2010-06-24		ENSG00000112796	ENSG00000112796			13717	protein-coding gene	gene with protein product						11027689	Standard	XM_005249259		Approved		uc003oxz.1	Q9UJA9	OTTHUMG00000014781	ENST00000371383.2:c.671delA	6.37:g.46135329delT	ENSP00000360436:p.Lys224fs	Somatic		Capture	Illumina HiSeq	Phase_I	46243288	NM_021572		Frame_Shift_Del	DEL	ENST00000371383.2	37	CCDS4915.1																																																																																				0.443	ENPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040779.2		
CYP39A1	51302	broad.mit.edu	37	6	46518152	46518152	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:46518152A>G	ENST00000275016.2	-	12	1564	c.1361T>C	c.(1360-1362)gTc>gCc	p.V454A		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	454					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)	p.V454D(1)|p.V454A(1)	EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						CGGCTGGGGGACACCCACCAA	0.438																																					p.V454A												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.T1361C	6						.						105.0	109.0	108.0					6																	46518152		2203	4300	6503	46626111	SO:0001583	missense	51302	exon12			AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.1361T>C	6.37:g.46518152A>G	ENSP00000275016:p.Val454Ala	Somatic		Capture	Illumina HiSeq	Phase_I	46626111	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.959675	0.53400	.	.	ENSG00000146233	ENST00000275016	D	0.85556	-2.0	5.82	4.67	0.58626	.	0.250569	0.30519	N	0.009447	T	0.74596	0.3737	L	0.59436	1.845	0.27106	N	0.962506	P;P	0.35684	0.454;0.515	B;B	0.40636	0.334;0.335	T	0.69304	-0.5180	10	0.48119	T	0.1	-1.529	7.7914	0.29123	0.9096:0.0:0.0904:0.0	.	434;454	B7Z786;Q9NYL5	.;CP39A_HUMAN	A	454	ENSP00000275016:V454A	ENSP00000275016:V454A	V	-	2	0	CYP39A1	46626111	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	2.583000	0.46094	2.234000	0.73211	0.533000	0.62120	GTC		0.438	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
TNFRSF21	27242	broad.mit.edu	37	6	47200700	47200700	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:47200700C>T	ENST00000296861.2	-	6	2162	c.1769G>A	c.(1768-1770)cGc>cAc	p.R590H		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	590					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)		p.R590H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			GGGGTCCAGGCGTACCTGCCG	0.532																																					p.R590H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1769A	6						.																																			47308659	SO:0001583	missense	27242	exon6			AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	13469	protein-coding gene	gene with protein product	"""death receptor 6"""	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1769G>A	6.37:g.47200700C>T	ENSP00000296861:p.Arg590His	Somatic		Capture	Illumina HiSeq	Phase_I	47308659	NM_014452	B2RDI9|Q0D2P5|Q96D86	Missense_Mutation	SNP	ENST00000296861.2	37	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.848599	0.91277	.	.	ENSG00000146072	ENST00000296861;ENST00000419206	T	0.70749	-0.51	5.84	5.84	0.93424	.	0.046611	0.85682	D	0.000000	T	0.72301	0.3443	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	T	0.76143	-0.3067	10	0.87932	D	0	.	18.3151	0.90218	0.0:1.0:0.0:0.0	.	590	O75509	TNR21_HUMAN	H	590;279	ENSP00000296861:R590H	ENSP00000296861:R590H	R	-	2	0	TNFRSF21	47308659	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.920000	0.70017	2.765000	0.95021	0.655000	0.94253	CGC		0.532	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452	
CD2AP	23607	broad.mit.edu	37	6	47547185	47547185	+	Missense_Mutation	SNP	A	A	T	rs377756180		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:47547185A>T	ENST00000359314.5	+	9	1424	c.968A>T	c.(967-969)aAt>aTt	p.N323I		NM_012120.2	NP_036252.1	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	323	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				mitotic nuclear division (GO:0007067)|negative regulation of transforming growth factor beta1 production (GO:0032911)|positive regulation of protein localization to nucleus (GO:1900182)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of receptor-mediated endocytosis (GO:0048259)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|substrate-dependent cell migration, cell extension (GO:0006930)|vesicle organization (GO:0016050)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)	p.N323I(1)		kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	20			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			TTTCCAGACAATTTTGCTGTC	0.348																																					p.N323I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A968T	6						.						102.0	106.0	105.0					6																	47547185		2203	4300	6503	47655144	SO:0001583	missense	23607	exon9			AF146277	CCDS34472.1	6p12	2008-02-05			ENSG00000198087	ENSG00000198087			14258	protein-coding gene	gene with protein product		604241				10339567	Standard	NM_012120		Approved	CMS	uc003oyw.3	Q9Y5K6	OTTHUMG00000014799	ENST00000359314.5:c.968A>T	6.37:g.47547185A>T	ENSP00000352264:p.Asn323Ile	Somatic		Capture	Illumina HiSeq	Phase_I	47655144	NM_012120	A6NL34|Q5VYA3|Q9UG97	Missense_Mutation	SNP	ENST00000359314.5	37	CCDS34472.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.204930	0.79127	.	.	ENSG00000198087	ENST00000359314	T	0.38240	1.15	5.47	4.31	0.51392	Src homology-3 domain (4);	0.043402	0.85682	D	0.000000	T	0.67487	0.2898	H	0.98701	4.305	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79040	-0.1966	10	0.87932	D	0	-21.557	11.1065	0.48205	0.9278:0.0:0.0722:0.0	.	323	Q9Y5K6	CD2AP_HUMAN	I	323	ENSP00000352264:N323I	ENSP00000352264:N323I	N	+	2	0	CD2AP	47655144	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.897000	0.87356	0.925000	0.37094	0.477000	0.44152	AAT		0.348	CD2AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040817.2		
TFAP2D	83741	broad.mit.edu	37	6	50686861	50686861	+	Missense_Mutation	SNP	G	G	T	rs372669669		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:50686861G>T	ENST00000008391.3	+	3	824	c.596G>T	c.(595-597)aGa>aTa	p.R199I	TFAP2D_ENST00000492804.1_3'UTR	NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)									p.R199I(1)		NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					GTGATAAGAAGAGGTAAGTAA	0.383																																					p.R199I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G596T	6						.	G	ILE/ARG	0,4406		0,0,2203	122.0	112.0	115.0		596	5.0	1.0	6		115	1,8599	1.2+/-3.3	0,1,4299	no	missense	TFAP2D	NM_172238.3	97	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	possibly-damaging	199/453	50686861	1,13005	2203	4300	6503	50794820	SO:0001583	missense	83741	exon3			AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"""transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"""	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.596G>T	6.37:g.50686861G>T	ENSP00000008391:p.Arg199Ile	Somatic		Capture	Illumina HiSeq	Phase_I	50794820	NM_172238		Missense_Mutation	SNP	ENST00000008391.3	37	CCDS4933.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.938814	0.73557	0.0	1.16E-4	ENSG00000008197	ENST00000008391	D	0.97256	-4.31	5.87	5.0	0.66597	.	0.000000	0.85682	D	0.000000	D	0.88284	0.6395	N	0.08118	0	0.80722	D	1	P	0.38745	0.645	B	0.32533	0.147	D	0.90613	0.4553	10	0.87932	D	0	-6.2348	16.3504	0.83202	0.0:0.0:0.8669:0.1331	.	199	Q7Z6R9	AP2D_HUMAN	I	199	ENSP00000008391:R199I	ENSP00000008391:R199I	R	+	2	0	TFAP2D	50794820	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.553000	0.98118	1.469000	0.48083	0.655000	0.94253	AGA		0.383	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238	
BMP5	653	broad.mit.edu	37	6	55739445	55739445	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:55739445T>C	ENST00000370830.3	-	1	917	c.219A>G	c.(217-219)caA>caG	p.Q73Q	BMP5_ENST00000446683.2_Silent_p.Q73Q	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	73					cartilage development (GO:0051216)|growth (GO:0040007)|male genitalia development (GO:0030539)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of steroid biosynthetic process (GO:0010894)|ossification (GO:0001503)|pattern specification process (GO:0007389)|positive regulation of dendrite development (GO:1900006)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)|type B pancreatic cell development (GO:0003323)	extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)	p.Q73Q(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	45	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			CAGAGGACGCTTGTTTTCCAG	0.463																																					p.Q73Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A219G	6						.						192.0	175.0	181.0					6																	55739445		2203	4300	6503	55847404	SO:0001819	synonymous_variant	653	exon1				CCDS4958.1	6p12.1	2014-01-30			ENSG00000112175	ENSG00000112175		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1072	protein-coding gene	gene with protein product		112265				1427904, 11580864	Standard	NM_021073		Approved		uc003pcq.3	P22003	OTTHUMG00000014903	ENST00000370830.3:c.219A>G	6.37:g.55739445T>C		Somatic		Capture	Illumina HiSeq	Phase_I	55847404	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Silent	SNP	ENST00000370830.3	37	CCDS4958.1																																																																																				0.463	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1		
DST	667	broad.mit.edu	37	6	56417112	56417112	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:56417112C>T	ENST00000361203.3	-	57	15852	c.15845G>A	c.(15844-15846)cGc>cAc	p.R5282H	DST_ENST00000312431.6_3'UTR|DST_ENST00000244364.6_Missense_Mutation_p.R2870H|DST_ENST00000370769.4_Missense_Mutation_p.R5284H|DST_ENST00000446842.2_Missense_Mutation_p.R4958H|DST_ENST00000370754.5_Missense_Mutation_p.R5462H|DST_ENST00000421834.2_Missense_Mutation_p.R3196H|DST_ENST00000370788.2_Missense_Mutation_p.R3196H			Q03001	DYST_HUMAN	dystonin	5282					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.R5284H(1)|p.R2870H(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTCTTCAAGGCGCTTAATTGT	0.443																																					p.R2870H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G8609A	6						.						82.0	78.0	79.0					6																	56417112		1847	4095	5942	56525071	SO:0001583	missense	667	exon42			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.15845G>A	6.37:g.56417112C>T	ENSP00000354508:p.Arg5282His	Somatic		Capture	Illumina HiSeq	Phase_I	56525071	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	C	11.38	1.621919	0.28889	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72	6.17	5.3	0.74995	.	0.149973	0.27397	N	0.019560	T	0.53077	0.1774	L	0.52126	1.63	0.27802	N	0.942446	D;P;P;D;P	0.89917	1.0;0.766;0.602;0.976;0.913	D;B;B;P;B	0.76071	0.987;0.206;0.091;0.807;0.3	T	0.58440	-0.7636	9	0.49607	T	0.09	.	14.6875	0.69059	0.0:0.9302:0.0:0.0698	.	3196;5284;5462;5282;2870	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	H	2870;5462;5284;3196;4958;3196;5282	ENSP00000244364:R2870H;ENSP00000359790:R5462H;ENSP00000359805:R5284H;ENSP00000400883:R3196H;ENSP00000393645:R4958H;ENSP00000359824:R3196H;ENSP00000354508:R5282H	ENSP00000244364:R2870H	R	-	2	0	DST	56525071	0.993000	0.37304	0.026000	0.17262	0.965000	0.64279	3.613000	0.54152	1.598000	0.50083	0.655000	0.94253	CGC		0.443	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
DST	667	broad.mit.edu	37	6	56506872	56506872	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:56506872G>A	ENST00000361203.3	-	13	1274	c.1267C>T	c.(1267-1269)Cag>Tag	p.Q423*	DST_ENST00000312431.6_Nonsense_Mutation_p.Q423*|DST_ENST00000244364.6_Nonsense_Mutation_p.Q97*|DST_ENST00000370769.4_Nonsense_Mutation_p.Q423*|DST_ENST00000446842.2_Nonsense_Mutation_p.Q97*|DST_ENST00000370754.5_Nonsense_Mutation_p.Q601*|DST_ENST00000518935.1_Nonsense_Mutation_p.Q97*|DST_ENST00000421834.2_Nonsense_Mutation_p.Q423*|DST_ENST00000370765.6_Nonsense_Mutation_p.Q97*|DST_ENST00000370788.2_Nonsense_Mutation_p.Q423*			Q03001	DYST_HUMAN	dystonin	423					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.Q97*(3)|p.Q423*(1)|p.Q601*(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTCTGAAACTGCACTCCTGAT	0.308																																					p.Q97X												.	.	5	Substitution - Nonsense(5)	large_intestine(5)	c.C289T	6						.						86.0	81.0	83.0					6																	56506872		2203	4299	6502	56614831	SO:0001587	stop_gained	667	exon3			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.1267C>T	6.37:g.56506872G>A	ENSP00000354508:p.Gln423*	Somatic		Capture	Illumina HiSeq	Phase_I	56614831	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Nonsense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	G	22.7	4.326626	0.81690	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935;ENST00000449297	.	.	.	5.3	5.3	0.74995	.	0.000000	0.45606	D	0.000358	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.1447	0.93459	0.0:0.0:1.0:0.0	.	.	.	.	X	97;601;423;423;97;423;423;423;97;463;97;97;601	.	ENSP00000244364:Q97X	Q	-	1	0	DST	56614831	1.000000	0.71417	0.982000	0.44146	0.994000	0.84299	9.082000	0.94059	2.753000	0.94483	0.585000	0.79938	CAG		0.308	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
LMBRD1	55788	broad.mit.edu	37	6	70409009	70409009	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:70409009G>T	ENST00000370577.3	-	13	1493	c.1264C>A	c.(1264-1266)Ctt>Att	p.L422I	LMBRD1_ENST00000370570.1_Missense_Mutation_p.L349I	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	422					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)	p.L422I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						CTAGTGTGAAGGACAATAAGC	0.348																																					p.L422I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1264A	6						.						116.0	119.0	118.0					6																	70409009		2203	4300	6503	70465730	SO:0001583	missense	55788	exon13			AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"""chromosome 6 open reading frame 209"""	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.1264C>A	6.37:g.70409009G>T	ENSP00000359609:p.Leu422Ile	Somatic		Capture	Illumina HiSeq	Phase_I	70465730	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Missense_Mutation	SNP	ENST00000370577.3	37	CCDS4969.1	.	.	.	.	.	.	.	.	.	.	G	19.42	3.823468	0.71143	.	.	ENSG00000168216	ENST00000370577;ENST00000370570	T;T	0.20463	2.07;2.07	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.39358	0.1075	M	0.86178	2.8	0.80722	D	1	D	0.67145	0.996	P	0.57283	0.817	T	0.30446	-0.9978	10	0.41790	T	0.15	-14.4506	19.4477	0.94854	0.0:0.0:1.0:0.0	.	422	Q9NUN5	LMBD1_HUMAN	I	422;349	ENSP00000359609:L422I;ENSP00000359602:L349I	ENSP00000359602:L349I	L	-	1	0	LMBRD1	70465730	1.000000	0.71417	1.000000	0.80357	0.390000	0.30446	7.818000	0.86416	2.591000	0.87537	0.591000	0.81541	CTT		0.348	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368	
COL19A1	1310	broad.mit.edu	37	6	70639515	70639515	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:70639515A>C	ENST00000322773.4	+	6	691	c.589A>C	c.(589-591)Act>Cct	p.T197P		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	197	Laminin G-like.				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)	p.T197P(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						GAGGAGGCAGACTGATGAAAA	0.433																																					p.T197P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A589C	6						.						112.0	106.0	108.0					6																	70639515		2203	4300	6503	70696236	SO:0001583	missense	1310	exon6				CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.589A>C	6.37:g.70639515A>C	ENSP00000316030:p.Thr197Pro	Somatic		Capture	Illumina HiSeq	Phase_I	70696236	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	37	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	A	8.656	0.899330	0.17686	.	.	ENSG00000082293	ENST00000322773	T	0.02216	4.39	5.64	5.64	0.86602	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.130223	0.50627	D	0.000117	T	0.04137	0.0115	L	0.59436	1.845	0.80722	D	1	D	0.57899	0.981	P	0.55055	0.767	T	0.44360	-0.9333	10	0.54805	T	0.06	.	15.8534	0.78952	1.0:0.0:0.0:0.0	.	197	Q14993	COJA1_HUMAN	P	197	ENSP00000316030:T197P	ENSP00000316030:T197P	T	+	1	0	COL19A1	70696236	1.000000	0.71417	0.038000	0.18304	0.031000	0.12232	8.726000	0.91474	2.131000	0.65755	0.533000	0.62120	ACT		0.433	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		
COL19A1	1310	broad.mit.edu	37	6	70646766	70646766	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:70646766G>T	ENST00000322773.4	+	8	939	c.837G>T	c.(835-837)caG>caT	p.Q279H		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	279				Q -> L (in Ref. 1; BAA07368). {ECO:0000305}.	cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)	p.Q279H(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						CAGCAAAGCAGGAACTTAAAG	0.443																																					p.Q279H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G837T	6						.						166.0	155.0	159.0					6																	70646766		2203	4300	6503	70703487	SO:0001583	missense	1310	exon8				CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.837G>T	6.37:g.70646766G>T	ENSP00000316030:p.Gln279His	Somatic		Capture	Illumina HiSeq	Phase_I	70703487	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	37	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	G	3.951	-0.012203	0.07727	.	.	ENSG00000082293	ENST00000322773	D	0.91945	-2.94	5.63	2.89	0.33648	.	0.071575	0.56097	D	0.000035	D	0.87815	0.6272	L	0.59436	1.845	0.80722	D	1	D	0.56521	0.976	P	0.51016	0.656	D	0.85362	0.1108	10	0.45353	T	0.12	.	7.8964	0.29708	0.3745:0.0:0.6255:0.0	.	279	Q14993	COJA1_HUMAN	H	279	ENSP00000316030:Q279H	ENSP00000316030:Q279H	Q	+	3	2	COL19A1	70703487	0.965000	0.33210	0.997000	0.53966	0.099000	0.18886	-0.077000	0.11394	0.417000	0.25871	0.655000	0.94253	CAG		0.443	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		
KCNQ5	56479	broad.mit.edu	37	6	73904967	73904967	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:73904967G>A	ENST00000370398.1	+	14	2738	c.2629G>A	c.(2629-2631)Ggt>Agt	p.G877S	KCNQ5_ENST00000414165.2_Missense_Mutation_p.G767S|KCNQ5_ENST00000355194.4_Missense_Mutation_p.G877S|KCNQ5_ENST00000355635.3_Missense_Mutation_p.G878S|KCNQ5_ENST00000342056.2_Missense_Mutation_p.G896S|KCNQ5_ENST00000403813.2_Missense_Mutation_p.G868S|KCNQ5_ENST00000402622.2_Missense_Mutation_p.G887S	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	877					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)	p.G877S(1)		breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	TGAAGAGGTGGGTCCCGAAGA	0.498																																					p.G896S	GBM(142;1375 1859 14391 23261 44706)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2686A	6						.						84.0	89.0	87.0					6																	73904967		2203	4300	6503	73961688	SO:0001583	missense	56479	exon15			AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.2629G>A	6.37:g.73904967G>A	ENSP00000359425:p.Gly877Ser	Somatic		Capture	Illumina HiSeq	Phase_I	73961688	NM_001160133	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	37	CCDS4976.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.886586	0.51908	.	.	ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000402622;ENST00000355635;ENST00000403813;ENST00000414165	D;D;D;D;D;D;D	0.99287	-5.5;-5.5;-5.5;-5.5;-5.5;-5.53;-5.69	5.9	5.02	0.67125	.	0.429941	0.24818	N	0.035356	D	0.97142	0.9066	N	0.19112	0.55	0.24216	N	0.995457	D;P;B;B;P	0.60575	0.988;0.571;0.296;0.187;0.455	P;B;B;B;B	0.57911	0.829;0.124;0.041;0.04;0.081	D	0.94148	0.7403	10	0.17369	T	0.5	.	14.6134	0.68531	0.0:0.0:0.854:0.146	.	767;887;896;868;877	F5GZV0;Q9NR82-3;A6PVT6;Q9NR82-2;Q9NR82	.;.;.;.;KCNQ5_HUMAN	S	896;896;877;877;887;878;868;767	ENSP00000345055:G896S;ENSP00000347326:G877S;ENSP00000359425:G877S;ENSP00000385501:G887S;ENSP00000347853:G878S;ENSP00000384453:G868S;ENSP00000409861:G767S	ENSP00000345055:G896S	G	+	1	0	KCNQ5	73961688	1.000000	0.71417	0.989000	0.46669	0.981000	0.71138	3.670000	0.54569	1.461000	0.47929	0.650000	0.86243	GGT		0.498	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842	
CD109	135228	broad.mit.edu	37	6	74533227	74533227	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:74533227C>T	ENST00000287097.5	+	33	4320	c.4208C>T	c.(4207-4209)tCc>tTc	p.S1403F	CD109_ENST00000437994.2_Missense_Mutation_p.S1386F|CD109_ENST00000422508.2_Missense_Mutation_p.S1326F			Q6YHK3	CD109_HUMAN	CD109 molecule	1403					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)	p.S1403F(1)		NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AAGCTGTCCTCCTGTGACCTT	0.473																																					p.S1403F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4208T	6						.						144.0	124.0	131.0					6																	74533227		2203	4300	6503	74589947	SO:0001583	missense	135228	exon33			AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.4208C>T	6.37:g.74533227C>T	ENSP00000287097:p.Ser1403Phe	Somatic		Capture	Illumina HiSeq	Phase_I	74589947	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.741704	0.30865	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.32753	1.44;1.44;1.44	4.49	2.71	0.32032	Alpha-macroglobulin, receptor-binding (1);	217.367000	0.02888	U	0.133757	T	0.17492	0.0420	L	0.27053	0.805	0.26748	N	0.970269	D;B;P	0.61080	0.989;0.321;0.944	P;B;B	0.53593	0.73;0.138;0.396	T	0.22487	-1.0215	10	0.28530	T	0.3	.	9.2725	0.37679	0.0:0.8307:0.0:0.1693	.	1326;1386;1403	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	F	1386;1326;1403	ENSP00000388062:S1386F;ENSP00000404475:S1326F;ENSP00000287097:S1403F	ENSP00000287097:S1403F	S	+	2	0	CD109	74589947	0.021000	0.18746	0.520000	0.27837	0.045000	0.14185	0.410000	0.21098	0.635000	0.30488	0.467000	0.42956	TCC		0.473	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
TMEM30A	55754	broad.mit.edu	37	6	75994155	75994155	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:75994155C>T	ENST00000230461.6	-	1	529	c.200G>A	c.(199-201)gGc>gAc	p.G67D	TMEM30A_ENST00000475111.2_Missense_Mutation_p.G67D|RP1-234P15.4_ENST00000607221.1_lincRNA	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	67					drug transmembrane transport (GO:0006855)|phospholipid translocation (GO:0045332)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endosome (GO:0036010)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.G67D(1)		NS(1)|haematopoietic_and_lymphoid_tissue(8)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GACAAAAATGCCAATGCCGAT	0.572																																					p.G67D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G200A	6						.						80.0	67.0	72.0					6																	75994155		2203	4300	6503	76050875	SO:0001583	missense	55754	exon1			AK001718	CCDS4983.1, CCDS47453.1	6q14.1	2014-01-28	2004-06-17	2004-06-18	ENSG00000112697	ENSG00000112697			16667	protein-coding gene	gene with protein product		611028	"""chromosome 6 open reading frame 67"""	C6orf67		15375526	Standard	NM_001143958		Approved	FLJ10856, CDC50A	uc003phw.2	Q9NV96	OTTHUMG00000015050	ENST00000230461.6:c.200G>A	6.37:g.75994155C>T	ENSP00000230461:p.Gly67Asp	Somatic		Capture	Illumina HiSeq	Phase_I	76050875	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Missense_Mutation	SNP	ENST00000230461.6	37	CCDS4983.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.004388	0.93287	.	.	ENSG00000112697	ENST00000230461;ENST00000545449;ENST00000475111	.	.	.	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.60196	0.2250	L	0.33189	0.99	0.80722	D	1	D;P	0.89917	1.0;0.952	D;P	0.83275	0.996;0.829	T	0.59172	-0.7504	9	0.36615	T	0.2	.	18.5277	0.90978	0.0:1.0:0.0:0.0	.	67;67	Q9NV96-2;Q9NV96	.;CC50A_HUMAN	D	67;51;67	.	ENSP00000230461:G67D	G	-	2	0	TMEM30A	76050875	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.507000	0.81676	2.380000	0.81148	0.655000	0.94253	GGC		0.572	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247	
IMPG1	3617	broad.mit.edu	37	6	76744474	76744474	+	Missense_Mutation	SNP	C	C	T	rs200194885		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:76744474C>T	ENST00000369950.3	-	3	521	c.332G>A	c.(331-333)cGg>cAg	p.R111Q	IMPG1_ENST00000369963.3_Missense_Mutation_p.R33Q	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1									p.R111Q(1)		breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				CAGAAAGATCCGATATGCTTC	0.488																																					p.R111Q	Pancreas(37;839 1141 2599 26037)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G332A	6						.						92.0	83.0	86.0					6																	76744474		2203	4300	6503	76801194	SO:0001583	missense	3617	exon3			AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"""sialoprotein associated with cones and rods"""	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.332G>A	6.37:g.76744474C>T	ENSP00000358966:p.Arg111Gln	Somatic		Capture	Illumina HiSeq	Phase_I	76801194	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	C	36	5.711068	0.96821	.	.	ENSG00000112706	ENST00000369950;ENST00000369963	T;T	0.81163	-1.34;-1.46	5.77	5.77	0.91146	.	0.000000	0.64402	D	0.000016	D	0.89382	0.6699	M	0.80982	2.52	0.53688	D	0.999976	D	0.89917	1.0	D	0.85130	0.997	D	0.88377	0.2999	9	.	.	.	.	19.9944	0.97379	0.0:1.0:0.0:0.0	.	111	Q17R60	IMPG1_HUMAN	Q	111;33	ENSP00000358966:R111Q;ENSP00000358980:R33Q	.	R	-	2	0	IMPG1	76801194	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.076000	0.50081	2.720000	0.93068	0.557000	0.71058	CGG		0.488	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563	
HTR1B	3351	broad.mit.edu	37	6	78172393	78172393	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:78172393G>A	ENST00000369947.2	-	1	1097	c.728C>T	c.(727-729)aCg>aTg	p.T243M		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	243					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|bone remodeling (GO:0046849)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to temperature stimulus (GO:0071502)|drinking behavior (GO:0042756)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.T243M(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	25		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Methysergide(DB00247)|Naratriptan(DB00952)|Olanzapine(DB00334)|Ondansetron(DB00904)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	CCTGTTGGGCGTCTGTTTCAA	0.612																																					p.T243M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C728T	6						.						53.0	60.0	58.0					6																	78172393		2203	4300	6503	78229112	SO:0001583	missense	3351	exon1			BC069065	CCDS4986.1	6q13	2012-08-08	2012-02-03		ENSG00000135312	ENSG00000135312		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5287	protein-coding gene	gene with protein product		182131	"""5-hydroxytryptamine (serotonin) receptor 1B"""			1348246, 11247661	Standard	NM_000863		Approved	S12, 5-HT1B, HTR1D2, 5-HT1DB	uc003pil.1	P28222	OTTHUMG00000015066	ENST00000369947.2:c.728C>T	6.37:g.78172393G>A	ENSP00000358963:p.Thr243Met	Somatic		Capture	Illumina HiSeq	Phase_I	78229112	NM_000863	Q4VAY7	Missense_Mutation	SNP	ENST00000369947.2	37	CCDS4986.1	.	.	.	.	.	.	.	.	.	.	G	19.65	3.867036	0.72065	.	.	ENSG00000135312	ENST00000369947	T	0.35789	1.29	5.3	5.3	0.74995	GPCR, rhodopsin-like superfamily (1);	0.289076	0.33477	N	0.004877	T	0.35098	0.0920	N	0.22421	0.69	0.54753	D	0.999983	D	0.71674	0.998	D	0.65874	0.939	T	0.04307	-1.0961	9	.	.	.	.	18.1271	0.89589	0.0:0.0:1.0:0.0	.	243	P28222	5HT1B_HUMAN	M	243	ENSP00000358963:T243M	.	T	-	2	0	HTR1B	78229112	1.000000	0.71417	0.996000	0.52242	0.924000	0.55760	9.503000	0.97984	2.762000	0.94881	0.555000	0.69702	ACG		0.612	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863	
IBTK	25998	broad.mit.edu	37	6	82900844	82900844	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:82900844C>A	ENST00000306270.7	-	25	4070	c.3521G>T	c.(3520-3522)aGc>aTc	p.S1174I	IBTK_ENST00000503631.1_Missense_Mutation_p.S973I|IBTK_ENST00000510291.1_Missense_Mutation_p.S1159I	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	1174					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)	p.S1174I(1)		central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		TGTTTCCATGCTATTCATTCC	0.328																																					p.S1174I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3521T	6						.						115.0	108.0	110.0					6																	82900844		2202	4299	6501	82957563	SO:0001583	missense	25998	exon25			AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	17853	protein-coding gene	gene with protein product		606457	"""Bruton agammaglobulinemia tyrosine kinase inhibitor"""	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.3521G>T	6.37:g.82900844C>A	ENSP00000305721:p.Ser1174Ile	Somatic		Capture	Illumina HiSeq	Phase_I	82957563	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	37	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.026918	0.35797	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.38887	1.55;1.11;1.53	5.81	3.07	0.35406	.	0.468385	0.25509	N	0.030193	T	0.27866	0.0686	L	0.53249	1.67	0.09310	N	1	B;B;P;B	0.51240	0.342;0.019;0.943;0.019	B;B;P;B	0.53861	0.103;0.01;0.736;0.01	T	0.09015	-1.0694	10	0.42905	T	0.14	-0.5278	3.8208	0.08835	0.1206:0.491:0.2534:0.1349	.	973;1159;125;1174	E9PDR5;E7EPI0;B3KX60;Q9P2D0	.;.;.;IBTK_HUMAN	I	1174;973;1159	ENSP00000305721:S1174I;ENSP00000422762:S973I;ENSP00000426405:S1159I	ENSP00000305721:S1174I	S	-	2	0	IBTK	82957563	0.000000	0.05858	0.742000	0.31022	0.986000	0.74619	-0.176000	0.09811	0.793000	0.33875	0.650000	0.86243	AGC		0.328	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525	
DOPEY1	23033	broad.mit.edu	37	6	83819938	83819938	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:83819938C>T	ENST00000349129.2	+	6	846	c.586C>T	c.(586-588)Cgt>Tgt	p.R196C	DOPEY1_ENST00000237163.5_Missense_Mutation_p.R196C|DOPEY1_ENST00000536812.1_Missense_Mutation_p.R196C|DOPEY1_ENST00000369739.3_Missense_Mutation_p.R196C	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	196					protein transport (GO:0015031)			p.R196C(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TCCTGCTGTGCGTTTACCTGG	0.443																																					p.R196C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C586T	6						.						185.0	164.0	171.0					6																	83819938		2203	4300	6503	83876657	SO:0001583	missense	23033	exon6			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.586C>T	6.37:g.83819938C>T	ENSP00000195654:p.Arg196Cys	Somatic		Capture	Illumina HiSeq	Phase_I	83876657	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.605033	0.87157	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000536812;ENST00000369739	T;T;T	0.62498	0.09;0.11;0.02	5.73	5.73	0.89815	Dopey, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.82549	0.5061	H	0.94771	3.58	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.86338	0.1703	10	0.87932	D	0	.	15.0302	0.71701	0.1422:0.8578:0.0:0.0	.	196;196;196	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	C	196	ENSP00000195654:R196C;ENSP00000237163:R196C;ENSP00000358754:R196C	ENSP00000237163:R196C	R	+	1	0	DOPEY1	83876657	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	4.341000	0.59335	2.861000	0.98227	0.655000	0.94253	CGT		0.443	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
DOPEY1	23033	broad.mit.edu	37	6	83877655	83877655	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:83877655C>T	ENST00000349129.2	+	39	7427	c.7167C>T	c.(7165-7167)acC>acT	p.T2389T	PGM3_ENST00000513973.1_3'UTR|PGM3_ENST00000512866.1_Intron|DOPEY1_ENST00000237163.5_Silent_p.T2293T|DOPEY1_ENST00000369739.3_Silent_p.T2400T|DOPEY1_ENST00000484282.1_3'UTR	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2389					protein transport (GO:0015031)			p.T2389T(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CCATCTGCACCGTGCGCAGTA	0.512																																					p.T2389T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C7167T	6						.						60.0	54.0	56.0					6																	83877655		2203	4300	6503	83934374	SO:0001819	synonymous_variant	23033	exon39			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.7167C>T	6.37:g.83877655C>T		Somatic		Capture	Illumina HiSeq	Phase_I	83934374	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Silent	SNP	ENST00000349129.2	37	CCDS4996.1																																																																																				0.512	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
SNAP91	9892	broad.mit.edu	37	6	84372086	84372086	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:84372086delA	ENST00000439399.2	-	4	645	c.329delT	c.(328-330)ttgfs	p.L110fs	SNAP91_ENST00000520213.1_Frame_Shift_Del_p.L110fs|SNAP91_ENST00000428679.2_Frame_Shift_Del_p.L110fs|SNAP91_ENST00000520302.1_Frame_Shift_Del_p.L110fs|SNAP91_ENST00000521743.1_Frame_Shift_Del_p.L110fs|SNAP91_ENST00000437520.1_Frame_Shift_Del_p.L110fs|SNAP91_ENST00000195649.6_Frame_Shift_Del_p.L110fs|SNAP91_ENST00000369694.2_Frame_Shift_Del_p.L110fs|SNAP91_ENST00000521485.1_Frame_Shift_Del_p.L110fs	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	110	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)	p.L110fs*15(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		ACTTTTGTCCAAAAAATTGCT	0.274																																					p.L110fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.329delT	6						.						29.0	28.0	28.0					6																	84372086		1784	4035	5819	84428805	SO:0001589	frameshift_variant	9892	exon4			AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"""synaptosomal-associated protein, 91 kDa (mouse) homolog"", ""synaptosomal-associated protein, 91kDa homolog (mouse)"""			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.329delT	6.37:g.84372086delA	ENSP00000400459:p.Leu110fs	Somatic		Capture	Illumina HiSeq	Phase_I	84428805	NM_014841	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Frame_Shift_Del	DEL	ENST00000439399.2	37	CCDS47455.1																																																																																				0.274	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1		
GJB7	375519	broad.mit.edu	37	6	87993980	87993980	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:87993980delT	ENST00000525899.1	-	3	996	c.651delA	c.(649-651)aaafs	p.K217fs	GJB7_ENST00000296882.3_Frame_Shift_Del_p.K217fs	NM_198568.2	NP_940970.1	Q6PEY0	CXB7_HUMAN	gap junction protein, beta 7, 25kDa	217					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)		p.K217fs*>7(1)		endometrium(2)|large_intestine(3)	5		all_cancers(76;1.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;7.38e-10)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00323)		BRCA - Breast invasive adenocarcinoma(108;0.0167)		GGACTTGAGGTTTTTTTAAAT	0.413																																					p.K217fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.651delA	6						.						66.0	67.0	67.0					6																	87993980		2203	4300	6503	88050699	SO:0001589	frameshift_variant	375519	exon3			AJ414563	CCDS5008.1	6q15	2008-02-05	2007-11-06			ENSG00000164411		"""Ion channels / Gap junction proteins (connexins)"""	16690	protein-coding gene	gene with protein product	"""connexin 25"""	611921	"""gap junction protein, beta 7"""				Standard	NM_198568		Approved	CX25, bA136M9.1	uc003plo.2	Q6PEY0		ENST00000525899.1:c.651delA	6.37:g.87993980delT	ENSP00000435355:p.Lys217fs	Somatic		Capture	Illumina HiSeq	Phase_I	88050699	NM_198568	B3KXL0|Q96KP0	Frame_Shift_Del	DEL	ENST00000525899.1	37	CCDS5008.1																																																																																				0.413	GJB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394780.1		
CNR1	1268	broad.mit.edu	37	6	88853864	88853864	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:88853864G>A	ENST00000537554.1	-	2	4692	c.1130C>T	c.(1129-1131)aCg>aTg	p.T377M	CNR1_ENST00000535130.1_Missense_Mutation_p.T377M|CNR1_ENST00000468898.1_Missense_Mutation_p.T344M|CNR1_ENST00000549890.1_Missense_Mutation_p.T377M|CNR1_ENST00000428600.2_Missense_Mutation_p.T377M|CNR1_ENST00000362094.5_3'UTR|CNR1_ENST00000369499.2_Missense_Mutation_p.T377M|CNR1_ENST00000549716.1_Missense_Mutation_p.T316M|CNR1_ENST00000369501.2_Missense_Mutation_p.T377M	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	377					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)	p.T377M(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	TGCAAACACCGTCTTAATGAG	0.522																																					p.T377M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1130T	6						.						129.0	124.0	126.0					6																	88853864		2203	4300	6503	88910583	SO:0001583	missense	1268	exon2			AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"""GPCR / Class A : Cannabinoid receptors"""	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.1130C>T	6.37:g.88853864G>A	ENSP00000441046:p.Thr377Met	Somatic		Capture	Illumina HiSeq	Phase_I	88910583	NM_001160259	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Missense_Mutation	SNP	ENST00000537554.1	37	CCDS5015.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.812190	0.50527	.	.	ENSG00000118432	ENST00000369501;ENST00000535130;ENST00000537554;ENST00000369499;ENST00000549890;ENST00000468898;ENST00000428600;ENST00000549716	T;T;T;T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18	6.05	6.05	0.98169	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.49270	0.1547	L	0.43646	1.37	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.98	T	0.42032	-0.9475	10	0.62326	D	0.03	.	20.6086	0.99469	0.0:0.0:1.0:0.0	.	344;377	P21554-3;P21554	.;CNR1_HUMAN	M	377;377;377;377;377;344;377;316	ENSP00000358513:T377M;ENSP00000442689:T377M;ENSP00000441046:T377M;ENSP00000358511:T377M;ENSP00000446819:T377M;ENSP00000420188:T344M;ENSP00000412192:T377M;ENSP00000449549:T316M	ENSP00000358511:T377M	T	-	2	0	CNR1	88910583	1.000000	0.71417	1.000000	0.80357	0.630000	0.37929	7.876000	0.87215	2.880000	0.98712	0.655000	0.94253	ACG		0.522	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2		
MDN1	23195	broad.mit.edu	37	6	90410546	90410546	+	Silent	SNP	T	T	C	rs369622870		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:90410546T>C	ENST00000369393.3	-	56	8572	c.8457A>G	c.(8455-8457)caA>caG	p.Q2819Q	MDN1_ENST00000428876.1_Silent_p.Q2819Q			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2819					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.Q2819Q(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GGACCTTCAGTTGTGAAAAAC	0.468																																					p.Q2819Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A8457G	6						.	T		0,4406		0,0,2203	62.0	58.0	60.0		8457	-6.6	0.0	6		60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MDN1	NM_014611.1		0,1,6502	CC,CT,TT		0.0116,0.0,0.0077		2819/5597	90410546	1,13005	2203	4300	6503	90467267	SO:0001819	synonymous_variant	23195	exon56			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.8457A>G	6.37:g.90410546T>C		Somatic		Capture	Illumina HiSeq	Phase_I	90467267	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																				0.468	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
MDN1	23195	broad.mit.edu	37	6	90415853	90415853	+	Frame_Shift_Del	DEL	A	A	-	rs35107588		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:90415853delA	ENST00000369393.3	-	53	8188	c.8073delT	c.(8071-8073)tttfs	p.F2691fs	MDN1_ENST00000428876.1_Frame_Shift_Del_p.F2691fs			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2691					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.F2691fs*7(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CACAAAGTTCAAAAAAAGCAG	0.418																																					p.F2691fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.8073delT	6						.						94.0	88.0	90.0					6																	90415853		2203	4300	6503	90472574	SO:0001589	frameshift_variant	23195	exon53			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.8073delT	6.37:g.90415853delA	ENSP00000358400:p.Phe2691fs	Somatic		Capture	Illumina HiSeq	Phase_I	90472574	NM_014611	O15019|Q5T794	Frame_Shift_Del	DEL	ENST00000369393.3	37	CCDS5024.1																																																																																				0.418	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
MDN1	23195	broad.mit.edu	37	6	90457144	90457144	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:90457144T>C	ENST00000369393.3	-	27	3923	c.3808A>G	c.(3808-3810)Atc>Gtc	p.I1270V	MDN1_ENST00000428876.1_Missense_Mutation_p.I1270V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1270					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.I1270V(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CGAAGGGTGATGAAGCCCTGC	0.468																																					p.I1270V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3808G	6						.						90.0	80.0	83.0					6																	90457144		2203	4300	6503	90513865	SO:0001583	missense	23195	exon27			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.3808A>G	6.37:g.90457144T>C	ENSP00000358400:p.Ile1270Val	Somatic		Capture	Illumina HiSeq	Phase_I	90513865	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.295115	0.60086	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.39229	1.09;1.09	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.29850	0.0746	M	0.64170	1.965	0.52099	D	0.999948	B	0.21225	0.053	B	0.25291	0.059	T	0.17715	-1.0360	10	0.45353	T	0.12	.	15.0686	0.72017	0.0:0.0:0.0:1.0	.	1270	Q9NU22	MDN1_HUMAN	V	1270	ENSP00000358400:I1270V;ENSP00000413970:I1270V	ENSP00000358400:I1270V	I	-	1	0	MDN1	90513865	1.000000	0.71417	0.997000	0.53966	0.891000	0.51852	7.526000	0.81920	1.961000	0.56991	0.454000	0.30748	ATC		0.468	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
GJA10	84694	broad.mit.edu	37	6	90604334	90604334	+	Silent	SNP	G	G	A	rs566486758		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:90604334G>A	ENST00000369352.1	+	1	147	c.147G>A	c.(145-147)caG>caA	p.Q49Q		NM_032602.1	NP_115991.1	P57773	CXA9_HUMAN	gap junction protein, alpha 10, 62kDa	49					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)		p.Q49Q(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|skin(3)|urinary_tract(1)	37		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		ATGATGAACAGTCAGCATTTG	0.483																																					p.Q49Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G147A	6						.						151.0	121.0	131.0					6																	90604334		2203	4300	6503	90661055	SO:0001819	synonymous_variant	84694	exon1			AF296766	CCDS5025.1	6q15-q16	2008-02-05			ENSG00000135355	ENSG00000135355		"""Ion channels / Gap junction proteins (connexins)"""	16995	protein-coding gene	gene with protein product	"""connexin 62"""	611924					Standard	NM_032602		Approved	CX62	uc011eaa.2	Q969M2	OTTHUMG00000015210	ENST00000369352.1:c.147G>A	6.37:g.90604334G>A		Somatic		Capture	Illumina HiSeq	Phase_I	90661055	NM_032602	B2R722|B3KVQ2|Q5TA63|Q96KG0	Silent	SNP	ENST00000369352.1	37	CCDS5025.1																																																																																				0.483	GJA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041505.1	NM_032602	
TMEM200A	114801	broad.mit.edu	37	6	130762428	130762428	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:130762428delT	ENST00000296978.3	+	3	1732	c.861delT	c.(859-861)gctfs	p.A287fs	TMEM200A_ENST00000545622.1_Frame_Shift_Del_p.A287fs|TMEM200A_ENST00000392429.1_Frame_Shift_Del_p.A287fs	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	287						integral component of membrane (GO:0016021)		p.F288fs*5(2)		NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		CCATCAGTGCTTTTACATTGC	0.413																																					p.A287fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.861delT	6						.						150.0	148.0	148.0					6																	130762428		2203	4300	6503	130804121	SO:0001589	frameshift_variant	114801	exon2			AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"""KIAA1913"""	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.861delT	6.37:g.130762428delT	ENSP00000296978:p.Ala287fs	Somatic		Capture	Illumina HiSeq	Phase_I	130804121	NM_052913	Q96PX5	Frame_Shift_Del	DEL	ENST00000296978.3	37	CCDS5140.1																																																																																				0.413	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913	
OR2A4	79541	broad.mit.edu	37	6	132022371	132022371	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:132022371delG	ENST00000315453.2	-	1	264	c.171delC	c.(169-171)cccfs	p.P57fs	ENPP3_ENST00000358229.5_Intron|ENPP3_ENST00000414305.1_Intron|ENPP3_ENST00000357639.3_Intron	NM_030908.1	NP_112170.1	O95047	OR2A4_HUMAN	olfactory receptor, family 2, subfamily A, member 4	57					positive regulation of cytokinesis (GO:0032467)|regulation of actin cytoskeleton organization (GO:0032956)	cleavage furrow (GO:0032154)|Flemming body (GO:0090543)|integral component of membrane (GO:0016021)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M58fs*25(1)		large_intestine(1)|ovary(1)|skin(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.018)|OV - Ovarian serous cystadenocarcinoma(155;0.041)		AGAAGTACATGGGGGCGTGCA	0.607																																					p.P57fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.171delC	6						.						9.0	10.0	10.0					6																	132022371		2002	4030	6032	132064064	SO:0001589	frameshift_variant	79541	exon1			AC005587	CCDS5149.1	6q23	2012-08-09	2003-05-22		ENSG00000180658	ENSG00000180658		"""GPCR / Class A : Olfactory receptors"""	14729	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 10"""	OR2A10			Standard	NM_030908		Approved		uc011ecd.2	O95047	OTTHUMG00000016316	ENST00000315453.2:c.171delC	6.37:g.132022371delG	ENSP00000319546:p.Pro57fs	Somatic		Capture	Illumina HiSeq	Phase_I	132064064	NM_030908	Q0VAR3|Q6IF18|Q9NQN0	Frame_Shift_Del	DEL	ENST00000315453.2	37	CCDS5149.1																																																																																				0.607	OR2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109221.1	NM_030908	
GRM1	2911	broad.mit.edu	37	6	146755387	146755387	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:146755387delC	ENST00000282753.1	+	8	3275	c.3040delC	c.(3040-3042)cccfs	p.P1016fs	GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000361719.2_Frame_Shift_Del_p.P1016fs|GRM1_ENST00000492807.2_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000507907.1_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1016	Gln/Pro-rich.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.P1015fs*16(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CAAGGGCTTGCCCCCTCCTCT	0.672																																					p.P1014fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3040delC	6						.						54.0	64.0	61.0					6																	146755387		2203	4299	6502	146797080	SO:0001589	frameshift_variant	2911	exon9			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.3040delC	6.37:g.146755387delC	ENSP00000282753:p.Pro1016fs	Somatic		Capture	Illumina HiSeq	Phase_I	146797080	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Frame_Shift_Del	DEL	ENST00000282753.1	37	CCDS5209.1																																																																																				0.672	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
SMOC2	64094	broad.mit.edu	37	6	169053881	169053881	+	Missense_Mutation	SNP	G	G	A	rs201624579		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr6:169053881G>A	ENST00000356284.2	+	11	1478	c.1258G>A	c.(1258-1260)Ggc>Agc	p.G420S	SMOC2_ENST00000354536.5_Missense_Mutation_p.G431S	NM_001166412.1	NP_001159884.1	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	420					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.G431S(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	32		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		GAAAGAGGACGGCAAAGCGGA	0.532													G|||	1	0.000199681	0.0	0.0	5008	,	,		17701	0.0		0.001	False		,,,				2504	0.0				p.G420S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1258A	6						.						117.0	107.0	110.0					6																	169053881		2203	4300	6503	168795806	SO:0001583	missense	64094	exon11			AB014730	CCDS5307.1, CCDS55076.1	6q27	2013-01-10			ENSG00000112562	ENSG00000112562		"""EF-hand domain containing"""	20323	protein-coding gene	gene with protein product		607223				12031507	Standard	NM_022138		Approved	SMAP2	uc003qwr.2	Q9H3U7	OTTHUMG00000016050	ENST00000356284.2:c.1258G>A	6.37:g.169053881G>A	ENSP00000348630:p.Gly420Ser	Somatic		Capture	Illumina HiSeq	Phase_I	168795806	NM_001166412	B3KPS7|Q4G169|Q5TAT7|Q5TAT8|Q86VV9|Q96SF3|Q9H1L3|Q9H1L4|Q9H3U0|Q9H4F7|Q9HCV2	Missense_Mutation	SNP	ENST00000356284.2	37	CCDS55076.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.73	1.432574	0.25813	.	.	ENSG00000112562	ENST00000356284;ENST00000354536;ENST00000366793;ENST00000392101;ENST00000538593;ENST00000417208	T;T	0.35236	1.32;1.32	4.92	4.05	0.47172	EF-hand-like domain (1);	0.287375	0.32918	N	0.005486	T	0.09512	0.0234	L	0.27053	0.805	0.46376	D	0.999014	P;P	0.46656	0.676;0.882	B;B	0.37508	0.154;0.252	T	0.06862	-1.0803	10	0.14656	T	0.56	0.0482	10.4801	0.44689	0.0899:0.0:0.91:0.0	.	420;431	Q9H3U7;Q9H3U7-2	SMOC2_HUMAN;.	S	420;431;420;97;97;40	ENSP00000348630:G420S;ENSP00000346537:G431S	ENSP00000346537:G431S	G	+	1	0	SMOC2	168795806	1.000000	0.71417	0.003000	0.11579	0.023000	0.10783	3.974000	0.56852	1.056000	0.40484	0.655000	0.94253	GGC		0.532	SMOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043201.1		
FBXO24	26261	broad.mit.edu	37	7	100198307	100198307	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:100198307C>T	ENST00000241071.6	+	10	1850	c.1528C>T	c.(1528-1530)Cag>Tag	p.Q510*	PCOLCE-AS1_ENST00000446022.1_RNA|PCOLCE_ENST00000223061.5_5'Flank|FBXO24_ENST00000427939.2_Nonsense_Mutation_p.Q548*|PCOLCE-AS1_ENST00000442166.2_RNA|PCOLCE-AS1_ENST00000544873.1_RNA|FBXO24_ENST00000360609.2_3'UTR|FBXO24_ENST00000468962.1_Nonsense_Mutation_p.Q498*	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	510					protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.Q510*(1)		NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					CAGAGCACCCCAGGACCCCGG	0.662																																					p.Q498X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1492T	7						.						40.0	40.0	40.0					7																	100198307		2203	4300	6503	100036243	SO:0001587	stop_gained	26261	exon10			AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336		"""F-boxes /  ""other"""""	13595	protein-coding gene	gene with protein product		609097	"""F-box only protein 24"""			10531035, 10531037	Standard	NM_012172		Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.1528C>T	7.37:g.100198307C>T	ENSP00000241071:p.Gln510*	Somatic		Capture	Illumina HiSeq	Phase_I	100036243	NM_001163499	A4D2D4|B4DX91|B4DY42|Q9H0G1	Nonsense_Mutation	SNP	ENST00000241071.6	37	CCDS5698.1	.	.	.	.	.	.	.	.	.	.	c	20.3	3.967729	0.74131	.	.	ENSG00000106336	ENST00000241071;ENST00000468962;ENST00000427939	.	.	.	4.44	4.44	0.53790	.	0.128634	0.33515	N	0.004823	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-8.1137	14.6423	0.68734	0.0:1.0:0.0:0.0	.	.	.	.	X	510;498;548	.	ENSP00000241071:Q510X	Q	+	1	0	FBXO24	100036243	0.993000	0.37304	0.985000	0.45067	0.507000	0.33981	2.331000	0.43894	2.299000	0.77371	0.552000	0.68991	CAG		0.662	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1		
ZAN	7455	broad.mit.edu	37	7	100358152	100358152	+	RNA	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:100358152G>A	ENST00000348028.3	+	0	4000				ZAN_ENST00000349350.6_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000427578.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V1279M(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			GTATGTTACTGTGTCCAGGTA	0.602																																					p.V1279M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3835A	7						.						69.0	78.0	75.0					7																	100358152		2186	4269	6455	100196088			7455	exon19			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"""zonadhesin"""			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100358152G>A		Somatic		Capture	Illumina HiSeq	Phase_I	100196088	NM_173059	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	G	15.97	2.989949	0.54041	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585	T;T;T	0.61392	0.11;0.11;0.11	4.72	3.84	0.44239	von Willebrand factor, type D domain (3);	0.174698	0.27744	N	0.018039	T	0.76730	0.4028	M	0.92833	3.35	0.80722	D	1	D;D	0.63046	0.99;0.992	P;D	0.63192	0.857;0.912	T	0.78984	-0.1988	10	0.46703	T	0.11	.	9.4657	0.38811	0.1018:0.0:0.8982:0.0	.	1279;1279	F5H0T8;Q9Y493	.;ZAN_HUMAN	M	1279	ENSP00000445943:V1279M;ENSP00000445091:V1279M;ENSP00000444427:V1279M	ENSP00000423579:V1279M	V	+	1	0	ZAN	100196088	0.997000	0.39634	0.798000	0.32154	0.574000	0.36063	2.962000	0.49176	1.311000	0.45024	0.555000	0.69702	GTG		0.602	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386	
SRRT	51593	broad.mit.edu	37	7	100485388	100485388	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:100485388A>G	ENST00000347433.4	+	17	2392	c.2234A>G	c.(2233-2235)aAg>aGg	p.K745R	SRRT_ENST00000432932.1_Missense_Mutation_p.K744R|SRRT_ENST00000457580.2_Missense_Mutation_p.K745R|SRRT_ENST00000388793.4_Missense_Mutation_p.K744R			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	745					cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.K745R(1)		breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						GAAGTGAAAAAGGAAGTCGCG	0.522																																					p.K744R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2231G	7						.						112.0	118.0	116.0					7																	100485388		2203	4300	6503	100323324	SO:0001583	missense	51593	exon17				CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"""arsenite resistance protein"""	614469	"""serrate RNA effector molecule homolog (Arabidopsis)"""			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.2234A>G	7.37:g.100485388A>G	ENSP00000314491:p.Lys745Arg	Somatic		Capture	Illumina HiSeq	Phase_I	100323324	NM_001128852	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Missense_Mutation	SNP	ENST00000347433.4	37	CCDS34709.1	.	.	.	.	.	.	.	.	.	.	A	13.65	2.301987	0.40694	.	.	ENSG00000087087	ENST00000457580;ENST00000388793;ENST00000342198;ENST00000432932;ENST00000347433;ENST00000448764;ENST00000445337	.	.	.	4.94	4.94	0.65067	Arsenite-resistance protein 2 (1);	0.000000	0.85682	D	0.000000	T	0.67277	0.2876	M	0.68952	2.095	0.53005	D	0.999967	B;P;P;D	0.56287	0.035;0.859;0.859;0.975	B;P;P;P	0.56648	0.01;0.473;0.473;0.803	T	0.67260	-0.5715	9	0.37606	T	0.19	.	12.5696	0.56328	1.0:0.0:0.0:0.0	.	744;744;745;745	Q9BXP5-3;Q9BXP5-4;Q9BXP5-2;Q9BXP5	.;.;.;SRRT_HUMAN	R	745;744;110;744;745;375;22	.	ENSP00000344670:K110R	K	+	2	0	SRRT	100323324	1.000000	0.71417	0.988000	0.46212	0.442000	0.32017	6.567000	0.73983	2.073000	0.62155	0.260000	0.18958	AAG		0.522	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908	
ZNHIT1	10467	broad.mit.edu	37	7	100867021	100867021	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:100867021G>A	ENST00000305105.2	+	4	869	c.341G>A	c.(340-342)cGc>cAc	p.R114H	ZNHIT1_ENST00000492315.1_3'UTR	NM_006349.2	NP_006340.1	O43257	ZNHI1_HUMAN	zinc finger, HIT-type containing 1	114					negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of histone deacetylation (GO:0031063)|regulation of T cell proliferation (GO:0042129)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)	p.R114H(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(2)	11	Lung NSC(181;0.168)|all_lung(186;0.215)					CGGCCCCAGCGCCCCTTCTGT	0.657																																					p.R114H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G341A	7						.						52.0	54.0	53.0					7																	100867021		2203	4300	6503	100653741	SO:0001583	missense	10467	exon4			AF093571	CCDS5716.1	7q22.1	2010-09-15	2010-09-15	2003-08-08	ENSG00000106400	ENSG00000106400		"""Zinc fingers, HIT-type"""	21688	protein-coding gene	gene with protein product	"""putative cyclin G1 interacting protein"""		"""zinc finger protein, subfamily 4A (HIT domain containing), member 1"", ""zinc finger, HIT domain containing 1"""	ZNFN4A1			Standard	NM_006349		Approved	CG1I, H_DJ0747G18.14	uc003uye.3	O43257	OTTHUMG00000157113	ENST00000305105.2:c.341G>A	7.37:g.100867021G>A	ENSP00000304593:p.Arg114His	Somatic		Capture	Illumina HiSeq	Phase_I	100653741	NM_006349	Q6IB12	Missense_Mutation	SNP	ENST00000305105.2	37	CCDS5716.1	.	.	.	.	.	.	.	.	.	.	G	32	5.178366	0.94846	.	.	ENSG00000106400	ENST00000305105	T	0.54279	0.58	5.26	4.37	0.52481	Zinc finger, HIT-type (1);	0.000000	0.85682	D	0.000000	T	0.76849	0.4045	M	0.93062	3.375	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.81514	-0.0898	10	0.62326	D	0.03	-27.0126	12.135	0.53966	0.0863:0.0:0.9137:0.0	.	114	O43257	ZNHI1_HUMAN	H	114	ENSP00000304593:R114H	ENSP00000304593:R114H	R	+	2	0	ZNHIT1	100653741	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.947000	0.75959	2.475000	0.83589	0.549000	0.68633	CGC		0.657	ZNHIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347488.1	NM_006349	
CUX1	1523	broad.mit.edu	37	7	101845482	101845482	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:101845482A>G	ENST00000292535.7	+	18	2943	c.2905A>G	c.(2905-2907)Aag>Gag	p.K969E	CUX1_ENST00000547394.2_Intron|CUX1_ENST00000556210.1_Missense_Mutation_p.K811E|CUX1_ENST00000549414.2_Missense_Mutation_p.K947E|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000360264.3_Missense_Mutation_p.K980E|CUX1_ENST00000546411.2_Missense_Mutation_p.K867E|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000550008.2_Missense_Mutation_p.K913E	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	969					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)	p.K969E(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						CTTCGGGGAGAAGGTAAGGGA	0.547																																					p.K969E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2905G	7						.						64.0	70.0	68.0					7																	101845482		2203	4300	6503	101632202	SO:0001583	missense	1523	exon18			M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.2905A>G	7.37:g.101845482A>G	ENSP00000292535:p.Lys969Glu	Somatic		Capture	Illumina HiSeq	Phase_I	101632202	NM_181552	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	37	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.070992	0.76301	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T	0.63096	-0.0;0.0;-0.01;-0.02;-0.0;-0.01	5.4	5.4	0.78164	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.000000	0.64402	D	0.000001	T	0.74496	0.3724	L	0.59436	1.845	0.80722	D	1	D;D	0.71674	0.992;0.998	D;D	0.78314	0.987;0.991	T	0.73649	-0.3916	10	0.37606	T	0.19	-31.146	14.0126	0.64507	1.0:0.0:0.0:0.0	.	969;980	P39880;P39880-3	CUX1_HUMAN;.	E	980;969;947;913;867;811	ENSP00000353401:K980E;ENSP00000292535:K969E;ENSP00000446630:K947E;ENSP00000447373:K913E;ENSP00000450125:K867E;ENSP00000451558:K811E	ENSP00000292535:K969E	K	+	1	0	CUX1	101632202	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.962000	0.93254	2.061000	0.61500	0.533000	0.62120	AAG		0.547	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913	
SH2B2	10603	broad.mit.edu	37	7	101957772	101957772	+	Silent	SNP	G	G	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:101957772G>C	ENST00000536178.1	+	8	1461	c.1416G>C	c.(1414-1416)ggG>ggC	p.G472G	SH2B2_ENST00000306803.8_Silent_p.G434G			O14492	SH2B2_HUMAN	SH2B adaptor protein 2	435	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191, ECO:0000305}.				actin cytoskeleton organization (GO:0030036)|antigen receptor-mediated signaling pathway (GO:0050851)|B-1 B cell homeostasis (GO:0001922)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cytokine-mediated signaling pathway (GO:0019221)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|regulation of JAK-STAT cascade (GO:0046425)|regulation of metabolic process (GO:0019222)|regulation of Ras protein signal transduction (GO:0046578)|signal transduction (GO:0007165)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stress fiber (GO:0001725)	JAK pathway signal transduction adaptor activity (GO:0008269)|SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)	p.G472G(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	9						TGGCAGGGGGGCCCCGGAACC	0.627																																					p.A392P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1174C	7						.						28.0	32.0	31.0					7																	101957772		1945	4128	6073	101744492	SO:0001819	synonymous_variant	10603	exon5			AB000520		7q22.1	2013-02-14			ENSG00000160999	ENSG00000160999		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	17381	protein-coding gene	gene with protein product	"""adaptor protein with pleckstrin homology and src"""	605300				9233773	Standard	XM_005276976		Approved	APS	uc011kko.2	O14492	OTTHUMG00000150652	ENST00000536178.1:c.1416G>C	7.37:g.101957772G>C		Somatic		Capture	Illumina HiSeq	Phase_I	101744492	NM_020979	A6ND74	Silent	SNP	ENST00000536178.1	37		.	.	.	.	.	.	.	.	.	.	.	0.491	-0.875555	0.02550	.	.	ENSG00000160999	ENST00000432527	D	0.96856	-4.15	4.66	-6.88	0.01665	.	0.000000	0.85682	D	0.000000	D	0.91898	0.7435	.	.	.	.	.	.	.	.	.	.	.	.	D	0.84020	0.0353	6	0.56958	D	0.05	-46.9534	1.1427	0.01769	0.3042:0.3252:0.117:0.2535	.	.	.	.	A	40	ENSP00000415306:G40A	ENSP00000415306:G40A	G	+	2	0	SH2B2	101744492	0.000000	0.05858	0.324000	0.25361	0.158000	0.22134	-2.157000	0.01282	-1.039000	0.03275	-0.921000	0.02739	GGC		0.627	SH2B2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_020979	
NAPEPLD	222236	broad.mit.edu	37	7	102760646	102760646	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:102760646G>A	ENST00000417955.1	-	3	473	c.319C>T	c.(319-321)Ctt>Ttt	p.L107F	NAPEPLD_ENST00000465647.1_Missense_Mutation_p.L107F|NAPEPLD_ENST00000427257.1_Missense_Mutation_p.L107F|NAPEPLD_ENST00000455523.2_Missense_Mutation_p.L180F|NAPEPLD_ENST00000341533.4_Missense_Mutation_p.L107F			Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D	107					phospholipid catabolic process (GO:0009395)	extracellular vesicular exosome (GO:0070062)|photoreceptor outer segment membrane (GO:0042622)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|zinc ion binding (GO:0008270)	p.L107F(1)		endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TATGGCTTAAGCACTGGGAGT	0.398																																					p.L107F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C319T	7						.						92.0	92.0	92.0					7																	102760646		2203	4300	6503	102547882	SO:0001583	missense	222236	exon3			BC037350, AY357337	CCDS5729.1	7q22.1	2014-03-14			ENSG00000161048	ENSG00000161048	3.1.4.54		21683	protein-coding gene	gene with protein product	"""chromosome 7 open reading frame 18, N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D"""	612334				14634025, 15820312, 18067139	Standard	NM_198990		Approved	FMP30, C7orf18, NAPE-PLD	uc003vbd.2	Q6IQ20	OTTHUMG00000157204	ENST00000417955.1:c.319C>T	7.37:g.102760646G>A	ENSP00000407112:p.Leu107Phe	Somatic		Capture	Illumina HiSeq	Phase_I	102547882	NM_198990	Q5CZ87|Q769K1	Missense_Mutation	SNP	ENST00000417955.1	37	CCDS5729.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.456063	0.43634	.	.	ENSG00000161048	ENST00000341533;ENST00000417955;ENST00000465647;ENST00000427257;ENST00000455523;ENST00000418294	D;D;D;D;D;D	0.95171	-3.63;-3.63;-3.63;-3.63;-3.63;-3.63	6.02	3.08	0.35506	.	0.377411	0.31092	N	0.008280	D	0.93226	0.7842	L	0.58428	1.81	0.23043	N	0.998385	P;B	0.45011	0.848;0.017	P;B	0.50231	0.635;0.04	D	0.85012	0.0906	10	0.13853	T	0.58	-50.0065	10.1517	0.42799	0.0865:0.5338:0.3796:0.0	.	180;107	B4E3B0;Q6IQ20	.;NAPEP_HUMAN	F	107;107;107;107;180;107	ENSP00000340093:L107F;ENSP00000407112:L107F;ENSP00000419188:L107F;ENSP00000392775:L107F;ENSP00000414364:L180F;ENSP00000404391:L107F	ENSP00000340093:L107F	L	-	1	0	NAPEPLD	102547882	0.962000	0.33011	0.998000	0.56505	0.990000	0.78478	1.249000	0.32839	0.838000	0.34948	0.655000	0.94253	CTT		0.398	NAPEPLD-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347904.1	NM_198990	
DNAJC2	27000	broad.mit.edu	37	7	102956230	102956230	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:102956230C>T	ENST00000379263.3	-	15	1867	c.1617G>A	c.(1615-1617)acG>acA	p.T539T	PMPCB_ENST00000420236.2_Intron|DNAJC2_ENST00000249270.7_Silent_p.T486T	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	539					'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)	p.T497T(1)|p.T486T(1)		endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						GTTCTGAAGGCGTTGCGTTGT	0.378																																					p.T486T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1458A	7						.						185.0	166.0	172.0					7																	102956230		1900	4110	6010	102743466	SO:0001819	synonymous_variant	27000	exon13			X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"""Heat shock proteins / DNAJ (HSP40)"""	13192	protein-coding gene	gene with protein product		605502	"""zuotin related factor 1"""	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.1617G>A	7.37:g.102956230C>T		Somatic		Capture	Illumina HiSeq	Phase_I	102743466	NM_001129887	A4VCI0|Q9BVX1	Silent	SNP	ENST00000379263.3	37	CCDS43628.1																																																																																				0.378	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1		
RELN	5649	broad.mit.edu	37	7	103214651	103214651	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:103214651C>A	ENST00000428762.1	-	30	4558	c.4399G>T	c.(4399-4401)Ggt>Tgt	p.G1467C	RELN_ENST00000424685.2_Missense_Mutation_p.G1467C|RELN_ENST00000343529.5_Missense_Mutation_p.G1467C	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1467					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.G1467C(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		ACCTGGGCACCTGTTATCTTG	0.517																																					p.G1467C	NSCLC(146;835 1944 15585 22231 52158)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4399T	7						.						141.0	120.0	127.0					7																	103214651		2203	4300	6503	103001887	SO:0001583	missense	5649	exon30				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.4399G>T	7.37:g.103214651C>A	ENSP00000392423:p.Gly1467Cys	Somatic		Capture	Illumina HiSeq	Phase_I	103001887	NM_005045	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.175752	0.78564	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.48522	1.4;0.81;1.4	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.70037	0.3178	M	0.76727	2.345	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.69824	0.966;0.929	T	0.73043	-0.4107	10	0.87932	D	0	.	19.4429	0.94831	0.0:1.0:0.0:0.0	.	1467;1467	P78509-2;P78509	.;RELN_HUMAN	C	1467	ENSP00000392423:G1467C;ENSP00000345694:G1467C;ENSP00000388446:G1467C	ENSP00000345694:G1467C	G	-	1	0	RELN	103001887	1.000000	0.71417	0.153000	0.22517	0.789000	0.44602	7.445000	0.80570	2.669000	0.90835	0.655000	0.94253	GGT		0.517	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
NRCAM	4897	broad.mit.edu	37	7	107820720	107820720	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:107820720C>A	ENST00000425651.2	-	22	2797	c.2798G>T	c.(2797-2799)gGg>gTg	p.G933V	NRCAM_ENST00000379022.4_Missense_Mutation_p.G933V|NRCAM_ENST00000413765.2_Missense_Mutation_p.G914V|NRCAM_ENST00000351718.4_Missense_Mutation_p.G917V|NRCAM_ENST00000379028.3_Missense_Mutation_p.G933V|NRCAM_ENST00000379024.4_Missense_Mutation_p.G914V	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	933	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)	p.G917V(1)		breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						CTCCCCTTTCCCATTGACCAC	0.522																																					p.G933V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2798T	7						.						87.0	77.0	80.0					7																	107820720		2203	4300	6503	107607956	SO:0001583	missense	4897	exon22				CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.2798G>T	7.37:g.107820720C>A	ENSP00000401244:p.Gly933Val	Somatic		Capture	Illumina HiSeq	Phase_I	107607956	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.179221	0.78564	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022	T;T;T;T;T;T	0.60797	0.16;0.16;0.16;0.16;0.16;0.16	5.56	5.56	0.83823	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.207707	0.50627	D	0.000113	T	0.72961	0.3526	L	0.52206	1.635	0.80722	D	1	D;D;D;D;D	0.71674	0.997;0.998;0.997;0.991;0.99	D;D;D;D;D	0.76575	0.977;0.988;0.987;0.973;0.977	T	0.74300	-0.3710	10	0.72032	D	0.01	.	19.5187	0.95176	0.0:1.0:0.0:0.0	.	933;914;914;917;933	Q92823-5;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;NRCAM_HUMAN	V	933;933;914;933;917;914;933;933	ENSP00000368314:G933V;ENSP00000407858:G914V;ENSP00000325269:G917V;ENSP00000368310:G914V;ENSP00000401244:G933V;ENSP00000368308:G933V	ENSP00000325269:G917V	G	-	2	0	NRCAM	107607956	0.991000	0.36638	0.997000	0.53966	0.993000	0.82548	3.244000	0.51399	2.609000	0.88269	0.563000	0.77884	GGG		0.522	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
LRRN3	54674	broad.mit.edu	37	7	110764590	110764590	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:110764590G>T	ENST00000422987.3	+	2	2593	c.1762G>T	c.(1762-1764)Gag>Tag	p.E588*	IMMP2L_ENST00000415362.1_Intron|LRRN3_ENST00000451085.1_Nonsense_Mutation_p.E588*|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000331762.3_Intron|IMMP2L_ENST00000405709.2_Intron|LRRN3_ENST00000308478.5_Nonsense_Mutation_p.E588*	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	588	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E588*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		TCCATCAACTGAGTATAAAAT	0.363																																					p.E588X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1762T	7						.						46.0	45.0	45.0					7																	110764590		2203	4300	6503	110551826	SO:0001587	stop_gained	54674	exon2			AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17200	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 5"""					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.1762G>T	7.37:g.110764590G>T	ENSP00000412417:p.Glu588*	Somatic		Capture	Illumina HiSeq	Phase_I	110551826	NM_018334	O43377|Q6I9V8|Q8IYQ6	Nonsense_Mutation	SNP	ENST00000422987.3	37	CCDS5754.1	.	.	.	.	.	.	.	.	.	.	G	43	10.314091	0.99381	.	.	ENSG00000173114	ENST00000308478;ENST00000451085;ENST00000422987	.	.	.	5.59	5.59	0.84812	.	0.000000	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	20.0377	0.97569	0.0:0.0:1.0:0.0	.	.	.	.	X	588	.	ENSP00000312001:E588X	E	+	1	0	LRRN3	110551826	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	6.889000	0.75627	2.822000	0.97130	0.650000	0.86243	GAG		0.363	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334	
TMEM168	64418	broad.mit.edu	37	7	112424313	112424313	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:112424313G>A	ENST00000312814.6	-	2	1128	c.568C>T	c.(568-570)Ctg>Ttg	p.L190L	TMEM168_ENST00000454074.1_Silent_p.L190L	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	190						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)		p.L190L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						TCAATAATCAGCATAGCCAGA	0.368																																					p.L190L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C568T	7						.						47.0	48.0	48.0					7																	112424313		2202	4300	6502	112211549	SO:0001819	synonymous_variant	64418	exon2				CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.568C>T	7.37:g.112424313G>A		Somatic		Capture	Illumina HiSeq	Phase_I	112211549	NM_022484	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Silent	SNP	ENST00000312814.6	37	CCDS5757.1																																																																																				0.368	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484	
PPP1R3A	5506	broad.mit.edu	37	7	113518658	113518658	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:113518658T>C	ENST00000284601.3	-	4	2557	c.2489A>G	c.(2488-2490)aAg>aGg	p.K830R		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	830					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)		p.K830R(1)		NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						GTCATGTGTCTTCCTAGGATT	0.363																																					p.K830R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2489G	7						.						173.0	152.0	159.0					7																	113518658		2203	4300	6503	113305894	SO:0001583	missense	5506	exon4			AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9291	protein-coding gene	gene with protein product	"""glycogen-associated regulatory subunit of protein phosphatase-1"", ""protein phosphatase 1 regulatory subunit GM"""	600917	"""protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)"", ""protein phosphatase 1, regulatory (inhibitor) subunit 3A"""	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.2489A>G	7.37:g.113518658T>C	ENSP00000284601:p.Lys830Arg	Somatic		Capture	Illumina HiSeq	Phase_I	113305894	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	T	8.950	0.968043	0.18659	.	.	ENSG00000154415	ENST00000284601	T	0.17213	2.29	5.81	5.81	0.92471	.	0.286793	0.30510	N	0.009471	T	0.20700	0.0498	M	0.62723	1.935	0.09310	N	1	P	0.38922	0.651	B	0.33521	0.165	T	0.19192	-1.0313	10	0.62326	D	0.03	-0.536	16.1536	0.81640	0.0:0.0:0.0:1.0	.	830	Q16821	PPR3A_HUMAN	R	830	ENSP00000284601:K830R	ENSP00000284601:K830R	K	-	2	0	PPP1R3A	113305894	0.020000	0.18652	0.063000	0.19743	0.052000	0.14988	1.519000	0.35888	2.203000	0.70933	0.528000	0.53228	AAG		0.363	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711	
ST7	7982	broad.mit.edu	37	7	116778506	116778506	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:116778506T>C	ENST00000393446.2	+	8	1117	c.814T>C	c.(814-816)Ttg>Ctg	p.L272L	ST7-AS2_ENST00000442719.1_RNA|ST7_ENST00000422922.1_Silent_p.L226L|ST7_ENST00000393449.1_Silent_p.L295L|ST7_ENST00000432298.1_Silent_p.L249L|ST7-AS2_ENST00000434993.1_RNA|ST7_ENST00000487459.1_3'UTR|ST7_ENST00000393444.3_Silent_p.L229L|ST7-AS2_ENST00000432541.1_RNA|ST7_ENST00000265437.5_Silent_p.L295L|ST7_ENST00000393451.3_Silent_p.L272L|ST7_ENST00000323984.3_Silent_p.L295L|ST7_ENST00000393447.4_Silent_p.L252L|ST7_ENST00000393443.1_Silent_p.L222L			Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)	p.L295L(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		CACCAATGTCTTGGTGTACAT	0.408																																					p.L272L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T814C	7						.						164.0	152.0	156.0					7																	116778506		2203	4300	6503	116565742	SO:0001819	synonymous_variant	7982	exon8			AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000393446.2:c.814T>C	7.37:g.116778506T>C		Somatic		Capture	Illumina HiSeq	Phase_I	116565742	NM_018412	A8K137|B4DRQ2	Silent	SNP	ENST00000393446.2	37																																																																																					0.408	ST7-013	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000319687.1	NM_021908	
CPED1	79974	broad.mit.edu	37	7	120629709	120629709	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:120629709C>T	ENST00000310396.5	+	2	501	c.34C>T	c.(34-36)Cga>Tga	p.R12*	CPED1_ENST00000450913.2_Nonsense_Mutation_p.R12*|CPED1_ENST00000340646.5_Nonsense_Mutation_p.R12*|CPED1_ENST00000495036.1_3'UTR	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	12						endoplasmic reticulum (GO:0005783)		p.R12*(1)									TTGTCGTCGGCGATTTTGCCC	0.562																																					p.R12X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C34T	7						.						128.0	114.0	119.0					7																	120629709		2203	4300	6503	120416945	SO:0001587	stop_gained	79974	exon2				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.34C>T	7.37:g.120629709C>T	ENSP00000309772:p.Arg12*	Somatic		Capture	Illumina HiSeq	Phase_I	120416945	NM_024913	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Nonsense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	C	37	6.496659	0.97616	.	.	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000340646	.	.	.	5.64	4.75	0.60458	.	0.198839	0.33057	N	0.005338	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.3463	0.49563	0.0:0.9173:0.0:0.0827	.	.	.	.	X	12	.	ENSP00000309772:R12X	R	+	1	2	C7orf58	120416945	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.247000	0.51422	2.662000	0.90505	0.655000	0.94253	CGA		0.562	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
PTPRZ1	5803	broad.mit.edu	37	7	121616230	121616230	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:121616230C>T	ENST00000393386.2	+	5	871	c.460C>T	c.(460-462)Caa>Taa	p.Q154*	PTPRZ1_ENST00000449182.1_Nonsense_Mutation_p.Q154*	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	154	Alpha-carbonic anhydrase.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.Q154*(2)		NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TTTATAGATGCAAATCTACTG	0.303																																					p.Q154X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C460T	7						.						95.0	89.0	91.0					7																	121616230		2203	4296	6499	121403466	SO:0001587	stop_gained	5803	exon5			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.460C>T	7.37:g.121616230C>T	ENSP00000377047:p.Gln154*	Somatic		Capture	Illumina HiSeq	Phase_I	121403466	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Nonsense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	C	37	6.557712	0.97663	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	.	.	.	5.43	5.43	0.79202	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.2396	0.93875	0.0:1.0:0.0:0.0	.	.	.	.	X	154	.	ENSP00000377047:Q154X	Q	+	1	0	PTPRZ1	121403466	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.079000	0.76829	2.561000	0.86390	0.543000	0.68304	CAA		0.303	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
RNF148	378925	broad.mit.edu	37	7	122341990	122341990	+	Missense_Mutation	SNP	C	C	T	rs377391654		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:122341990C>T	ENST00000434824.1	-	1	1031	c.815G>A	c.(814-816)cGc>cAc	p.R272H	CADPS2_ENST00000449022.2_Intron|RNF133_ENST00000340112.2_5'Flank|CADPS2_ENST00000412584.2_Intron|RNF148_ENST00000447240.1_3'UTR|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000313070.7_Intron	NM_198085.1	NP_932351.1	Q8N7C7	RN148_HUMAN	ring finger protein 148	272						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.R272H(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(7)	16						AGTTAAAATGCGTACTACATC	0.418																																					p.R272H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G815A	7						.						140.0	131.0	134.0					7																	122341990		1904	4134	6038	122129226	SO:0001583	missense	378925	exon1			BC029264	CCDS47692.1	7q31.33	2013-01-09			ENSG00000235631	ENSG00000235631		"""RING-type (C3HC4) zinc fingers"""	22411	protein-coding gene	gene with protein product						8744354	Standard	NM_198085		Approved	MGC35222	uc003vkk.1	Q8N7C7	OTTHUMG00000157099	ENST00000434824.1:c.815G>A	7.37:g.122341990C>T	ENSP00000388207:p.Arg272His	Somatic		Capture	Illumina HiSeq	Phase_I	122129226	NM_198085	A4D0X4|Q8N308	Missense_Mutation	SNP	ENST00000434824.1	37	CCDS47692.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676053	0.67928	.	.	ENSG00000235631	ENST00000434824	T	0.45668	0.89	5.51	5.51	0.81932	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	.	.	.	.	T	0.64091	0.2567	M	0.78223	2.4	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.67719	-0.5598	9	0.87932	D	0	.	12.3868	0.55336	0.0:0.9223:0.0:0.0777	.	272	Q8N7C7	RN148_HUMAN	H	272	ENSP00000388207:R272H	ENSP00000388207:R272H	R	-	2	0	RNF148	122129226	0.994000	0.37717	1.000000	0.80357	0.996000	0.88848	2.677000	0.46892	2.580000	0.87095	0.655000	0.94253	CGC		0.418	RNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347424.1	NM_198085	
GRM8	2918	broad.mit.edu	37	7	126883205	126883205	+	Silent	SNP	G	G	A	rs368194397		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:126883205G>A	ENST00000339582.2	-	2	862	c.54C>T	c.(52-54)acC>acT	p.T18T	GRM8_ENST00000405249.1_Silent_p.T18T|GRM8_ENST00000444921.2_Silent_p.T18T|GRM8_ENST00000358373.3_Silent_p.T18T			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	18					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.T18T(2)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				AGAACTTGGCGGTCAAGAGGA	0.483										HNSCC(24;0.065)																											p.T18T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C54T	7						.	G	,	0,4406		0,0,2203	85.0	82.0	83.0		54,54	-12.3	0.0	7		83	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	GRM8	NM_000845.2,NM_001127323.1	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	18/909,18/909	126883205	2,13004	2203	4300	6503	126670441	SO:0001819	synonymous_variant	2918	exon2				CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.54C>T	7.37:g.126883205G>A		Somatic		Capture	Illumina HiSeq	Phase_I	126670441	NM_001127323	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Silent	SNP	ENST00000339582.2	37	CCDS5794.1																																																																																				0.483	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		
FLNC	2318	broad.mit.edu	37	7	128484941	128484941	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:128484941C>T	ENST00000325888.8	+	21	3683	c.3422C>T	c.(3421-3423)cCt>cTt	p.P1141L	FLNC_ENST00000346177.6_Missense_Mutation_p.P1141L	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1141					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)	p.P1141L(1)		biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GCCCACATCCCTGGCTCGCCC	0.632																																					p.P1141L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3422T	7						.						89.0	95.0	93.0					7																	128484941		2156	4272	6428	128272177	SO:0001583	missense	2318	exon21			AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.3422C>T	7.37:g.128484941C>T	ENSP00000327145:p.Pro1141Leu	Somatic		Capture	Illumina HiSeq	Phase_I	128272177	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831938	0.91036	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.85629	-2.01;-2.01	5.56	5.56	0.83823	Immunoglobulin-like fold (1);	0.057214	0.64402	D	0.000001	D	0.94742	0.8303	M	0.93854	3.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95612	0.8673	10	0.87932	D	0	.	19.5273	0.95212	0.0:1.0:0.0:0.0	.	1141;1141	Q14315-2;Q14315	.;FLNC_HUMAN	L	1141	ENSP00000327145:P1141L;ENSP00000344002:P1141L	ENSP00000327145:P1141L	P	+	2	0	FLNC	128272177	1.000000	0.71417	0.985000	0.45067	0.948000	0.59901	7.818000	0.86416	2.615000	0.88500	0.555000	0.69702	CCT		0.632	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
IRF5	3663	broad.mit.edu	37	7	128588852	128588852	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:128588852C>T	ENST00000402030.2	+	9	1549	c.1477C>T	c.(1477-1479)Cac>Tac	p.H493Y	IRF5_ENST00000477535.1_Missense_Mutation_p.H407Y|IRF5_ENST00000473745.1_Missense_Mutation_p.H493Y|IRF5_ENST00000357234.5_Missense_Mutation_p.H509Y|IRF5_ENST00000249375.4_Missense_Mutation_p.H493Y	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	493					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H499Y(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|prostate(1)	15						CTGGCCTATGCACCCAGCTGG	0.652																																					p.H493Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1477T	7						.						41.0	44.0	43.0					7																	128588852		2203	4300	6503	128376088	SO:0001583	missense	3663	exon9				CCDS5808.1, CCDS43645.1, CCDS56512.1	7q32	2008-07-18			ENSG00000128604	ENSG00000128604			6120	protein-coding gene	gene with protein product		607218					Standard	XM_005250317		Approved		uc003vog.3	Q13568	OTTHUMG00000158410	ENST00000402030.2:c.1477C>T	7.37:g.128588852C>T	ENSP00000385352:p.His493Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	128376088	NM_001098627	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	Missense_Mutation	SNP	ENST00000402030.2	37	CCDS5808.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.492115	0.84962	.	.	ENSG00000128604	ENST00000357234;ENST00000477535;ENST00000402030;ENST00000249375;ENST00000473745;ENST00000412326	D;D;D;D;D	0.97752	-4.52;-4.48;-4.51;-4.51;-4.51	5.87	5.87	0.94306	.	2.128040	0.02078	N	0.052141	D	0.98667	0.9553	L	0.54323	1.7	0.45087	D	0.998101	D;D;D	0.71674	0.963;0.998;0.991	P;P;D	0.69307	0.63;0.813;0.963	D	0.91331	0.5090	10	0.87932	D	0	-6.1999	17.712	0.88324	0.0:1.0:0.0:0.0	.	407;493;509	E7EW54;Q13568;Q13568-2	.;IRF5_HUMAN;.	Y	509;407;493;493;493;483	ENSP00000349770:H509Y;ENSP00000419950:H407Y;ENSP00000385352:H493Y;ENSP00000249375:H493Y;ENSP00000419149:H493Y	ENSP00000249375:H493Y	H	+	1	0	IRF5	128376088	1.000000	0.71417	1.000000	0.80357	0.656000	0.38851	2.666000	0.46799	2.785000	0.95823	0.655000	0.94253	CAC		0.652	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627	
PODXL	5420	broad.mit.edu	37	7	131195812	131195812	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:131195812T>C	ENST00000378555.3	-	2	728	c.481A>G	c.(481-483)Aaa>Gaa	p.K161E	PODXL_ENST00000537928.1_Missense_Mutation_p.K161E|PODXL_ENST00000541194.1_Missense_Mutation_p.K163E|PODXL_ENST00000322985.9_Missense_Mutation_p.K161E|PODXL_ENST00000465001.1_5'Flank			O00592	PODXL_HUMAN	podocalyxin-like	161	Thr-rich.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)		p.K161E(1)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					TGGCTGCTTTTCCCCCCAGAG	0.527																																					p.K161E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A481G	7						.						337.0	295.0	309.0					7																	131195812		2203	4300	6503	130846352	SO:0001583	missense	5420	exon2				CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.481A>G	7.37:g.131195812T>C	ENSP00000367817:p.Lys161Glu	Somatic		Capture	Illumina HiSeq	Phase_I	130846352	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	37	CCDS34755.1	.	.	.	.	.	.	.	.	.	.	T	6.671	0.492398	0.12702	.	.	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000544955;ENST00000378555;ENST00000322985	T;T;T;T	0.11821	2.89;2.74;2.9;2.94	3.29	-1.21	0.09524	.	2505.650000	0.00166	N	0.000000	T	0.07279	0.0184	N	0.08118	0	0.09310	N	1	B;B	0.24426	0.103;0.063	B;B	0.22386	0.039;0.017	T	0.33954	-0.9848	10	0.06099	T	0.92	1.7909	10.91	0.47103	0.0:0.0:0.2482:0.7518	.	161;161	O00592-2;O00592	.;PODXL_HUMAN	E	163;161;151;161;161	ENSP00000440518:K163E;ENSP00000442655:K161E;ENSP00000367817:K161E;ENSP00000319782:K161E	ENSP00000319782:K161E	K	-	1	0	PODXL	130846352	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.020000	0.12525	-0.265000	0.09352	-0.249000	0.11873	AAA		0.527	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
PLXNA4	91584	broad.mit.edu	37	7	131848975	131848975	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:131848975C>T	ENST00000359827.3	-	24	5388	c.4426G>A	c.(4426-4428)Gcc>Acc	p.A1476T	PLXNA4_ENST00000321063.4_Missense_Mutation_p.A1476T			Q9HCM2	PLXA4_HUMAN	plexin A4	1476					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.A1476T(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CCCGTGATGGCGTCAATGGGG	0.587																																					p.A1476T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4426A	7						.						75.0	77.0	76.0					7																	131848975		2203	4300	6503	131499515	SO:0001583	missense	91584	exon24			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.4426G>A	7.37:g.131848975C>T	ENSP00000352882:p.Ala1476Thr	Somatic		Capture	Illumina HiSeq	Phase_I	131499515	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.445626	0.63178	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.16196	2.36;2.36	5.45	5.45	0.79879	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.052319	0.85682	D	0.000000	T	0.40222	0.1108	M	0.82630	2.6	0.46167	D	0.998905	D	0.60575	0.988	P	0.58721	0.844	T	0.36648	-0.9739	10	0.87932	D	0	.	13.356	0.60627	0.2641:0.7359:0.0:0.0	.	1476	Q9HCM2	PLXA4_HUMAN	T	1476	ENSP00000323194:A1476T;ENSP00000352882:A1476T	ENSP00000323194:A1476T	A	-	1	0	PLXNA4	131499515	0.560000	0.26570	0.963000	0.40424	0.687000	0.40016	1.194000	0.32174	2.550000	0.86006	0.655000	0.94253	GCC		0.587	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
PLXNA4	91584	broad.mit.edu	37	7	131864526	131864526	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:131864526C>T	ENST00000359827.3	-	20	4756	c.3794G>A	c.(3793-3795)cGc>cAc	p.R1265H	PLXNA4_ENST00000321063.4_Missense_Mutation_p.R1265H			Q9HCM2	PLXA4_HUMAN	plexin A4	1265					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.R1265H(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						GTCACTTTCGCGGGACTTGCG	0.607																																					p.R1265H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3794A	7						.						49.0	48.0	49.0					7																	131864526		2203	4300	6503	131515066	SO:0001583	missense	91584	exon20			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3794G>A	7.37:g.131864526C>T	ENSP00000352882:p.Arg1265His	Somatic		Capture	Illumina HiSeq	Phase_I	131515066	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.180365	0.78677	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.01084	5.36;5.36	4.82	4.82	0.62117	.	0.049297	0.85682	D	0.000000	T	0.02380	0.0073	M	0.74881	2.28	0.80722	D	1	P	0.41498	0.752	B	0.34779	0.189	T	0.55835	-0.8078	10	0.52906	T	0.07	.	18.0686	0.89398	0.0:1.0:0.0:0.0	.	1265	Q9HCM2	PLXA4_HUMAN	H	1265	ENSP00000323194:R1265H;ENSP00000352882:R1265H	ENSP00000323194:R1265H	R	-	2	0	PLXNA4	131515066	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.904000	0.69886	2.524000	0.85096	0.484000	0.47621	CGC		0.607	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
PLXNA4	91584	broad.mit.edu	37	7	132192309	132192309	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:132192309C>T	ENST00000359827.3	-	2	2106	c.1144G>A	c.(1144-1146)Gac>Aac	p.D382N	PLXNA4_ENST00000423507.2_Missense_Mutation_p.D382N|PLXNA4_ENST00000321063.4_Missense_Mutation_p.D382N|PLXNA4_ENST00000378539.5_Missense_Mutation_p.D382N			Q9HCM2	PLXA4_HUMAN	plexin A4	382	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.D382N(3)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CAGGCCAGGTCCAGCGTGCCC	0.597																																					p.D382N												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G1144A	7						.						58.0	48.0	52.0					7																	132192309		2203	4300	6503	131842849	SO:0001583	missense	91584	exon3			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.1144G>A	7.37:g.132192309C>T	ENSP00000352882:p.Asp382Asn	Somatic		Capture	Illumina HiSeq	Phase_I	131842849	NM_181775	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.150238	0.37923	.	.	ENSG00000221866	ENST00000321063;ENST00000359827;ENST00000423507;ENST00000378539	T;T;T;T	0.09817	2.94;2.94;2.94;2.94	5.96	5.96	0.96718	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.64402	U	0.000004	T	0.17577	0.0422	N	0.25485	0.75	0.80722	D	1	P;P;B	0.51057	0.864;0.941;0.086	P;P;B	0.57009	0.503;0.811;0.133	T	0.05582	-1.0876	10	0.10636	T	0.68	.	20.4123	0.99019	0.0:1.0:0.0:0.0	.	382;382;382	Q9HCM2-2;A4D1N6;Q9HCM2	.;.;PLXA4_HUMAN	N	382	ENSP00000323194:D382N;ENSP00000352882:D382N;ENSP00000392772:D382N;ENSP00000367800:D382N	ENSP00000323194:D382N	D	-	1	0	PLXNA4	131842849	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.814000	0.86154	2.824000	0.97209	0.655000	0.94253	GAC		0.597	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
SLC13A4	26266	broad.mit.edu	37	7	135377113	135377113	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:135377113C>T	ENST00000354042.4	-	11	1867	c.1178G>A	c.(1177-1179)cGg>cAg	p.R393Q	C7orf73_ENST00000422968.1_3'UTR	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	393					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)	p.R393Q(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						GCCAGGCTCCCGGGTAAACCA	0.443																																					p.R393Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1178A	7						.						64.0	73.0	70.0					7																	135377113		2203	4300	6503	135027653	SO:0001583	missense	26266	exon11			AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"""Solute carriers"""	15827	protein-coding gene	gene with protein product	"""sulphate transporter 1"""	604309	"""solute carrier family 13 (sodium/sulphate symporters), member 4"""			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.1178G>A	7.37:g.135377113C>T	ENSP00000297282:p.Arg393Gln	Somatic		Capture	Illumina HiSeq	Phase_I	135027653	NM_012450	A4D1Q4|Q8N631	Missense_Mutation	SNP	ENST00000354042.4	37	CCDS5840.1	.	.	.	.	.	.	.	.	.	.	C	35	5.594924	0.96602	.	.	ENSG00000164707	ENST00000354042	T	0.03035	4.07	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.21590	0.0520	M	0.86268	2.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00715	-1.1597	10	0.87932	D	0	-15.5	16.1696	0.81793	0.0:1.0:0.0:0.0	.	262;393	Q59HF0;Q9UKG4	.;S13A4_HUMAN	Q	393	ENSP00000297282:R393Q	ENSP00000297282:R393Q	R	-	2	0	SLC13A4	135027653	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.416000	0.81992	0.561000	0.74099	CGG		0.443	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450	
SLC37A3	84255	broad.mit.edu	37	7	140058440	140058440	+	Splice_Site	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:140058440C>T	ENST00000326232.9	-	6	724	c.521G>A	c.(520-522)gGa>gAa	p.G174E	SLC37A3_ENST00000340308.3_Splice_Site_p.G174E|SLC37A3_ENST00000429996.2_Intron|SLC37A3_ENST00000447932.2_Splice_Site_p.G174E|SLC37A3_ENST00000461089.1_5'UTR	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	174					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.G174E(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					AGTGGCATACCCGGCTTTCCC	0.483																																					p.G174E	Esophageal Squamous(133;211 1716 4665 11387 37873)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G521A	7						.						126.0	130.0	129.0					7																	140058440		2203	4300	6503	139704909	SO:0001630	splice_region_variant	84255	exon6			AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"""Solute carriers"""	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.521+1G>A	7.37:g.140058440C>T		Somatic		Capture	Illumina HiSeq	Phase_I	139704909	NM_032295	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	37	CCDS5859.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.5|29.5	5.010860|5.010860	0.93346|0.93346	.|.	.|.	ENSG00000157800|ENSG00000157800	ENST00000485861|ENST00000340308;ENST00000447932;ENST00000326232;ENST00000539816	.|T;T;T	.|0.51071	.|0.72;0.72;0.72	5.28|5.28	5.28|5.28	0.74379|0.74379	.|Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.|0.109633	.|0.64402	.|D	.|0.000007	T|T	0.46034|0.46034	0.1372|0.1372	L|L	0.28400|0.28400	0.85|0.85	0.80722|0.80722	D|D	1|1	.|B;B;B;P;B	.|0.41188	.|0.392;0.34;0.12;0.741;0.242	.|P;B;B;P;B	.|0.46718	.|0.475;0.257;0.142;0.525;0.159	T|T	0.23691|0.23691	-1.0181|-1.0181	5|9	.|.	.|.	.|.	-15.2563|-15.2563	17.4631|17.4631	0.87625|0.87625	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|146;174;174;174;174	.|B4DKF5;F5H743;Q8NCC5-2;Q8NCC5-3;Q8NCC5	.|.;.;.;.;SPX3_HUMAN	N|E	99|174	.|ENSP00000343358:G174E;ENSP00000397481:G174E;ENSP00000321498:G174E	.|.	D|G	-|-	1|2	0|0	SLC37A3|SLC37A3	139704909|139704909	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.956000|0.956000	0.61745|0.61745	7.608000|7.608000	0.82898|0.82898	2.624000|2.624000	0.88883|0.88883	0.655000|0.655000	0.94253|0.94253	GAC|GGA		0.483	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295	Missense_Mutation
CLCN1	1180	broad.mit.edu	37	7	143013439	143013439	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:143013439G>T	ENST00000343257.2	+	1	221	c.134G>T	c.(133-135)aGg>aTg	p.R45M		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	45					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.R45M(1)		breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					CTCCAGCACAGGCTCCGGAAG	0.607																																					p.R45M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G134T	7						.						76.0	69.0	72.0					7																	143013439		2203	4300	6503	142723561	SO:0001583	missense	1180	exon1			Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"""Ion channels / Chloride channels : Voltage-sensitive"""	2019	protein-coding gene	gene with protein product	"""Thomsen disease, autosomal dominant"""	118425	"""chloride channel 1, skeletal muscle"""			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.134G>T	7.37:g.143013439G>T	ENSP00000339867:p.Arg45Met	Somatic		Capture	Illumina HiSeq	Phase_I	142723561	NM_000083	A4D2H5|Q2M202	Missense_Mutation	SNP	ENST00000343257.2	37	CCDS5881.1	.	.	.	.	.	.	.	.	.	.	.	22.9	4.350014	0.82132	.	.	ENSG00000188037	ENST00000343257	D	0.87491	-2.26	5.19	5.19	0.71726	.	0.282328	0.27645	N	0.018449	D	0.90703	0.7083	M	0.62723	1.935	0.33553	D	0.596354	D	0.63880	0.993	P	0.56700	0.804	D	0.94009	0.7282	10	0.66056	D	0.02	.	16.5819	0.84717	0.0:0.0:1.0:0.0	.	45	P35523	CLCN1_HUMAN	M	45	ENSP00000339867:R45M	ENSP00000339867:R45M	R	+	2	0	CLCN1	142723561	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	3.874000	0.56101	2.427000	0.82271	0.650000	0.86243	AGG		0.607	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083	
EZH2	2146	broad.mit.edu	37	7	148524346	148524346	+	Missense_Mutation	SNP	C	C	T	rs377467108		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:148524346C>T	ENST00000460911.1	-	7	726	c.638G>A	c.(637-639)cGc>cAc	p.R213H	EZH2_ENST00000476773.1_Missense_Mutation_p.R204H|EZH2_ENST00000320356.2_Missense_Mutation_p.R213H|EZH2_ENST00000541220.1_Missense_Mutation_p.R204H|EZH2_ENST00000478654.1_Missense_Mutation_p.R204H|EZH2_ENST00000483967.1_Missense_Mutation_p.R204H|EZH2_ENST00000350995.2_Missense_Mutation_p.R174H|EZH2_ENST00000536783.1_Missense_Mutation_p.R104H			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	213	Interaction with DNMT1, DNMT3A and DNMT3B.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)	p.R213H(1)|p.R174H(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			CCGAGGTGGGCGGCTTTCTTT	0.333			Mis		DLBCL																																p.R174H			Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G521A	7						.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405		0,1,2202	88.0	96.0	93.0		638,611,611,638,521	2.3	0.1	7		93	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	EZH2	NM_001203247.1,NM_001203248.1,NM_001203249.1,NM_004456.4,NM_152998.2	29,29,29,29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign,benign,benign	213/747,204/738,204/696,213/752,174/708	148524346	1,13005	2203	4300	6503	148155279	SO:0001583	missense	2146	exon6				CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"""Chromatin-modifying enzymes / K-methyltransferases"""	3527	protein-coding gene	gene with protein product		601573	"""enhancer of zeste (Drosophila) homolog 2"", ""enhancer of zeste homolog 2 (Drosophila)"""			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.638G>A	7.37:g.148524346C>T	ENSP00000419711:p.Arg213His	Somatic		Capture	Illumina HiSeq	Phase_I	148155279	NM_152998	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	.	.	.	.	.	.	.	.	.	.	a	12.71	2.019550	0.35606	2.27E-4	0.0	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967;ENST00000536783	D;D;D;D;D;D;D;T	0.93953	-3.28;-3.32;-3.32;-3.32;-3.28;-3.28;-3.32;0.94	5.6	2.29	0.28610	SANT domain, DNA binding (1);	0.904107	0.09772	N	0.757885	T	0.81823	0.4904	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001;0.0	B;B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0;0.001	T	0.70594	-0.4829	10	0.32370	T	0.25	.	5.6098	0.17398	0.0:0.3737:0.0:0.6263	.	213;204;204;213;174;213	B7Z8K5;Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;.;EZH2_HUMAN;.;.	H	204;213;213;174;204;204;204;104	ENSP00000417062:R204H;ENSP00000320147:R213H;ENSP00000419711:R213H;ENSP00000223193:R174H;ENSP00000443219:R204H;ENSP00000419050:R204H;ENSP00000419856:R204H;ENSP00000439305:R104H	ENSP00000320147:R213H	R	-	2	0	EZH2	148155279	0.010000	0.17322	0.120000	0.21714	0.980000	0.70556	0.727000	0.25999	0.661000	0.30985	0.650000	0.86243	CGC		0.333	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456	
ZNF746	155061	broad.mit.edu	37	7	149174766	149174766	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:149174766C>T	ENST00000340622.3	-	5	881	c.601G>A	c.(601-603)Gcc>Acc	p.A201T	ZNF746_ENST00000458143.2_Missense_Mutation_p.A201T			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	201					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.A201T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			ACGCCCAGGGCCTGCTGCTCC	0.662																																					p.A201T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G601A	7						.						26.0	29.0	28.0					7																	149174766		2203	4300	6503	148805699	SO:0001583	missense	155061	exon5			AK055975	CCDS5897.1, CCDS55180.1	7q36.1	2013-01-08			ENSG00000181220	ENSG00000181220		"""Zinc fingers, C2H2-type"", ""-"""	21948	protein-coding gene	gene with protein product		613914					Standard	NM_152557		Approved	FLJ31413	uc010lpi.2	Q6NUN9	OTTHUMG00000158972	ENST00000340622.3:c.601G>A	7.37:g.149174766C>T	ENSP00000345140:p.Ala201Thr	Somatic		Capture	Illumina HiSeq	Phase_I	148805699	NM_001163474	A8K6Z9|Q6ZRF9	Missense_Mutation	SNP	ENST00000340622.3	37	CCDS5897.1	.	.	.	.	.	.	.	.	.	.	C	15.77	2.930349	0.52866	.	.	ENSG00000181220	ENST00000340622;ENST00000458143	T;T	0.10192	2.9;2.9	4.7	2.72	0.32119	.	0.308092	0.23247	N	0.050298	T	0.07369	0.0186	L	0.36672	1.1	0.30746	N	0.745633	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.002	T	0.25882	-1.0119	10	0.12766	T	0.61	-5.2302	7.0394	0.25010	0.1988:0.6088:0.1924:0.0	.	201;201	Q6NUN9-2;Q6NUN9	.;ZN746_HUMAN	T	201	ENSP00000345140:A201T;ENSP00000395007:A201T	ENSP00000345140:A201T	A	-	1	0	ZNF746	148805699	0.120000	0.22244	0.885000	0.34714	0.318000	0.28184	1.413000	0.34725	0.956000	0.37904	0.563000	0.77884	GCC		0.662	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557	
ASIC3	9311	broad.mit.edu	37	7	150749793	150749793	+	3'UTR	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:150749793C>A	ENST00000349064.5	+	0	1848				ASIC3_ENST00000297512.8_3'UTR|ASIC3_ENST00000357922.4_Missense_Mutation_p.L531M	NM_004769.3|NM_020321.3	NP_004760.1|NP_064717.1	Q9UHC3	ASIC3_HUMAN	acid-sensing (proton-gated) ion channel 3						cation transmembrane transport (GO:0098655)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ion transmembrane transport (GO:0034220)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|response to heat (GO:0009408)|sensory perception (GO:0007600)|sensory perception of sour taste (GO:0050915)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|enterobactin transporter activity (GO:0042931)|ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)	p.L531M(1)									CATGCCTAGCCTGCACGTAGC	0.572																																					p.L531M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1591A	7						.						291.0	248.0	263.0					7																	150749793		2203	4300	6503	150380726	SO:0001624	3_prime_UTR_variant	9311	exon10			AB010575	CCDS5914.1, CCDS5915.1, CCDS5916.1	7q35	2012-02-23	2012-02-22	2012-02-22	ENSG00000213199	ENSG00000213199		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	101	protein-coding gene	gene with protein product	"""testis sodium channel 1"""	611741	"""amiloride-sensitive cation channel 3, testis"", ""amiloride-sensitive cation channel 3"""	ACCN3		9571199, 9744806	Standard	NM_004769		Approved	TNaC1, DRASIC	uc003wio.3	Q9UHC3	OTTHUMG00000158685	ENST00000349064.5:c.*54C>A	7.37:g.150749793C>A		Somatic		Capture	Illumina HiSeq	Phase_I	150380726	NM_020322	B2R9V0|O60263|O75906|Q59FN9|Q9UER8|Q9UHC4	Missense_Mutation	SNP	ENST00000349064.5	37	CCDS5916.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.936210	0.73442	.	.	ENSG00000213199	ENST00000357922	T	0.68765	-0.35	4.73	1.62	0.23740	.	.	.	.	.	T	0.61400	0.2344	.	.	.	0.09310	N	1	P	0.44195	0.828	P	0.48400	0.576	T	0.51364	-0.8715	8	0.46703	T	0.11	.	3.3475	0.07141	0.2009:0.5592:0.0:0.24	.	531	Q9UHC3-2	.	M	531	ENSP00000350600:L531M	ENSP00000350600:L531M	L	+	1	2	ACCN3	150380726	0.000000	0.05858	0.001000	0.08648	0.751000	0.42716	0.052000	0.14163	0.231000	0.21079	0.561000	0.74099	CTG		0.572	ASIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351725.1	NM_004769	
NOM1	64434	broad.mit.edu	37	7	156761801	156761801	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:156761801G>A	ENST00000275820.3	+	10	2334	c.2319G>A	c.(2317-2319)ttG>ttA	p.L773L		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	773						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.L773L(1)		endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		TCAGTGAATTGGACAAACCCA	0.333																																					p.L773L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2319A	7						.						73.0	75.0	74.0					7																	156761801		2203	4300	6503	156454562	SO:0001819	synonymous_variant	64434	exon10			AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 113"""	611269	"""chromosome 7 open reading frame 3"""	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.2319G>A	7.37:g.156761801G>A		Somatic		Capture	Illumina HiSeq	Phase_I	156454562	NM_138400	Q96I08	Silent	SNP	ENST00000275820.3	37	CCDS34787.1																																																																																				0.333	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
HEATR2	54919	broad.mit.edu	37	7	769436	769436	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:769436C>T	ENST00000297440.6	+	2	752	c.732C>T	c.(730-732)gaC>gaT	p.D244D	PRKAR1B_ENST00000403562.1_5'Flank|PRKAR1B_ENST00000488474.1_5'Flank|PRKAR1B_ENST00000537384.1_5'Flank|HEATR2_ENST00000313147.5_Silent_p.D244D|HEATR2_ENST00000438961.1_3'UTR	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	244						cytoplasm (GO:0005737)		p.D244D(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		AGTCCGTGGACGACGTGCTTT	0.577																																					p.D244D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C732T	7						.						147.0	120.0	129.0					7																	769436		2203	4300	6503	735962	SO:0001819	synonymous_variant	54919	exon2			AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.732C>T	7.37:g.769436C>T		Somatic		Capture	Illumina HiSeq	Phase_I	735962	NM_017802	Q69YL1|Q96FI9|Q9NX75	Silent	SNP	ENST00000297440.6	37	CCDS34580.1	.	.	.	.	.	.	.	.	.	.	C	7.612	0.675029	0.14841	.	.	ENSG00000164818	ENST00000440747	.	.	.	5.19	-1.6	0.08426	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-35.1048	12.2889	0.54807	0.0:0.3743:0.0:0.6257	.	.	.	.	X	46	.	.	R	+	1	2	HEATR2	735962	0.902000	0.30710	0.881000	0.34555	0.736000	0.42039	-0.084000	0.11268	-0.739000	0.04809	-0.812000	0.03155	CGA		0.577	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802	
HEATR2	54919	broad.mit.edu	37	7	813801	813801	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:813801C>T	ENST00000297440.6	+	10	2068	c.2048C>T	c.(2047-2049)gCg>gTg	p.A683V	HEATR2_ENST00000403952.3_Missense_Mutation_p.A108V|HEATR2_ENST00000313147.5_Missense_Mutation_p.A683V	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	683						cytoplasm (GO:0005737)		p.A683V(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		TGCCTCTGGGCGCTCACCAGC	0.711																																					p.A683V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2048T	7						.						35.0	38.0	37.0					7																	813801		2202	4298	6500	780327	SO:0001583	missense	54919	exon10			AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.2048C>T	7.37:g.813801C>T	ENSP00000297440:p.Ala683Val	Somatic		Capture	Illumina HiSeq	Phase_I	780327	NM_017802	Q69YL1|Q96FI9|Q9NX75	Missense_Mutation	SNP	ENST00000297440.6	37	CCDS34580.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.705566	0.89018	.	.	ENSG00000164818	ENST00000297440;ENST00000313147;ENST00000537862;ENST00000403952	T;T;T	0.66460	-0.21;-0.21;-0.21	5.44	5.44	0.79542	Armadillo-like helical (1);Armadillo-type fold (1);	0.102602	0.64402	D	0.000003	T	0.66046	0.2750	L	0.45352	1.415	0.46499	D	0.999078	D;P;D	0.76494	0.999;0.895;0.998	P;B;P	0.50860	0.632;0.244;0.652	T	0.66814	-0.5828	10	0.46703	T	0.11	-31.1351	12.262	0.54655	0.0:0.9212:0.0:0.0788	.	683;108;429	Q86Y56;E9PGY2;F5H8D4	HEAT2_HUMAN;.;.	V	683;683;429;108	ENSP00000297440:A683V;ENSP00000321451:A683V;ENSP00000384884:A108V	ENSP00000297440:A683V	A	+	2	0	HEATR2	780327	0.996000	0.38824	0.950000	0.38849	0.976000	0.68499	3.656000	0.54467	2.550000	0.86006	0.561000	0.74099	GCG		0.711	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802	
EIF3B	8662	broad.mit.edu	37	7	2415031	2415031	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:2415031G>A	ENST00000360876.4	+	14	1953	c.1897G>A	c.(1897-1899)Ggt>Agt	p.G633S	EIF3B_ENST00000397011.2_Missense_Mutation_p.G633S	NM_001037283.1	NP_001032360.1			eukaryotic translation initiation factor 3, subunit B									p.G633S(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	24		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		CAGTATGAACGGTGCCTTAGC	0.582																																					p.G633S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1897A	7						.						235.0	167.0	190.0					7																	2415031		2203	4300	6503	2381557	SO:0001583	missense	8662	exon14			U62583	CCDS5332.1	7p22	2013-02-12	2007-07-27	2007-07-27	ENSG00000106263	ENSG00000106263		"""RNA binding motif (RRM) containing"""	3280	protein-coding gene	gene with protein product		603917	"""eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa"""	EIF3S9		8995410	Standard	NM_001037283		Approved	PRT1, eIF3b	uc003sly.3	P55884	OTTHUMG00000022839	ENST00000360876.4:c.1897G>A	7.37:g.2415031G>A	ENSP00000354125:p.Gly633Ser	Somatic		Capture	Illumina HiSeq	Phase_I	2381557	NM_003751		Missense_Mutation	SNP	ENST00000360876.4	37	CCDS5332.1	.	.	.	.	.	.	.	.	.	.	G	12.86	2.065951	0.36470	.	.	ENSG00000106263	ENST00000314800;ENST00000360876;ENST00000397011;ENST00000489558	T;T	0.10860	2.83;2.83	5.46	4.59	0.56863	Translation initiation factor 2A, beta propellor-like domain (1);Six-bladed beta-propeller, TolB-like (1);	0.140353	0.64402	D	0.000004	T	0.21718	0.0523	L	0.50847	1.595	0.58432	D	0.999998	D	0.65815	0.995	P	0.57846	0.828	T	0.00778	-1.1570	10	0.36615	T	0.2	-24.9881	13.8681	0.63600	0.0744:0.0:0.9256:0.0	.	633	P55884	EIF3B_HUMAN	S	633;633;633;557	ENSP00000354125:G633S;ENSP00000380206:G633S	ENSP00000316638:G633S	G	+	1	0	EIF3B	2381557	1.000000	0.71417	0.106000	0.21319	0.690000	0.40134	9.664000	0.98607	1.319000	0.45190	-0.136000	0.14681	GGT		0.582	EIF3B-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207006.1		
CHST12	55501	broad.mit.edu	37	7	2473211	2473211	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:2473211G>A	ENST00000258711.6	+	2	1072	c.937G>A	c.(937-939)Gag>Aag	p.E313K		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	313					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)	p.E313K(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		CCCGCACACGGAGAAGCTGGC	0.657																																					p.E313K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G937A	7						.						40.0	43.0	42.0					7																	2473211		2203	4300	6503	2439737	SO:0001583	missense	55501	exon2			AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"""Sulfotransferases, membrane-bound"""	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.937G>A	7.37:g.2473211G>A	ENSP00000258711:p.Glu313Lys	Somatic		Capture	Illumina HiSeq	Phase_I	2439737	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	37	CCDS5333.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.834014	0.71373	.	.	ENSG00000136213	ENST00000258711	T	0.74526	-0.85	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.85991	0.5826	M	0.74647	2.275	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84588	0.0665	10	0.34782	T	0.22	-4.4299	18.8686	0.92303	0.0:0.0:1.0:0.0	.	313	Q9NRB3	CHSTC_HUMAN	K	313	ENSP00000258711:E313K	ENSP00000258711:E313K	E	+	1	0	CHST12	2439737	1.000000	0.71417	0.989000	0.46669	0.534000	0.34807	7.630000	0.83225	2.464000	0.83262	0.462000	0.41574	GAG		0.657	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641	
CARD11	84433	broad.mit.edu	37	7	2946386	2946386	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:2946386G>A	ENST00000396946.4	-	25	3754	c.3351C>T	c.(3349-3351)taC>taT	p.Y1117Y		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	1117	Guanylate kinase-like.				Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)	p.Y1110Y(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CCACCGTGGCGTACAGGCACG	0.647			Mis		DLBCL																																p.Y1117Y			Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3351T	7						.						68.0	53.0	58.0					7																	2946386		2203	4300	6503	2912912	SO:0001819	synonymous_variant	84433	exon25			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.3351C>T	7.37:g.2946386G>A		Somatic		Capture	Illumina HiSeq	Phase_I	2912912	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	ENST00000396946.4	37	CCDS5336.2																																																																																				0.647	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
SDK1	221935	broad.mit.edu	37	7	4277367	4277367	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:4277367C>T	ENST00000404826.2	+	42	6220	c.6081C>T	c.(6079-6081)ttC>ttT	p.F2027F	SDK1_ENST00000389531.3_Silent_p.F2007F|SDK1_ENST00000466611.1_3'UTR	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	2027					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.F2027F(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TGGTGGTGTTCGCCCTCGTCC	0.567																																					p.F2027F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C6081T	7						.						200.0	171.0	181.0					7																	4277367		2203	4300	6503	4243893	SO:0001819	synonymous_variant	221935	exon42			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.6081C>T	7.37:g.4277367C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4243893	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																				0.567	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
TNRC18	84629	broad.mit.edu	37	7	5355650	5355650	+	Missense_Mutation	SNP	C	C	T	rs369654719		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:5355650C>T	ENST00000430969.1	-	25	7147	c.6799G>A	c.(6799-6801)Gga>Aga	p.G2267R	TNRC18_ENST00000399537.4_Missense_Mutation_p.G2267R	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2267							chromatin binding (GO:0003682)	p.G2267R(2)|p.G99R(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CCCGTGTCTCCGTCGTCAAAC	0.602																																					p.G2267R												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G6799A	7						.	C	ARG/GLY	0,3136		0,0,1568	56.0	51.0	53.0		6799	4.5	0.8	7		53	1,7163		0,1,3581	no	missense	TNRC18	NM_001080495.2	125	0,1,5149	TT,TC,CC		0.014,0.0,0.0097	probably-damaging	2267/2969	5355650	1,10299	1568	3582	5150	5322176	SO:0001583	missense	84629	exon25			U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.6799G>A	7.37:g.5355650C>T	ENSP00000395538:p.Gly2267Arg	Somatic		Capture	Illumina HiSeq	Phase_I	5322176	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	18.66|18.66	3.672588|3.672588	0.67928|0.67928	0.0|0.0	1.4E-4|1.4E-4	ENSG00000182095|ENSG00000182095	ENST00000399537;ENST00000430969|ENST00000328270	T;T|.	0.59906|.	0.23;0.23|.	4.46|4.46	4.46|4.46	0.54185|0.54185	.|.	.|.	.|.	.|.	.|.	T|T	0.74084|0.74084	0.3670|0.3670	M|M	0.72353|0.72353	2.195|2.195	0.49582|0.49582	D|D	0.9998|0.9998	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.75393|0.75393	-0.3333|-0.3333	9|5	0.72032|.	D|.	0.01|.	.|.	16.6933|16.6933	0.85327|0.85327	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	2267|.	O15417|.	TNC18_HUMAN|.	R|Q	2267|80	ENSP00000382452:G2267R;ENSP00000395538:G2267R|.	ENSP00000382452:G2267R|.	G|R	-|-	1|2	0|0	TNRC18|TNRC18	5322176|5322176	1.000000|1.000000	0.71417|0.71417	0.803000|0.803000	0.32268|0.32268	0.286000|0.286000	0.27126|0.27126	7.420000|7.420000	0.80191|0.80191	2.010000|2.010000	0.58986|0.58986	0.511000|0.511000	0.50034|0.50034	GGA|CGG		0.602	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
RNF216	54476	broad.mit.edu	37	7	5754798	5754798	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:5754798G>A	ENST00000425013.2	-	11	1772	c.1548C>T	c.(1546-1548)cgC>cgT	p.R516R	RNF216_ENST00000389902.3_Silent_p.R573R	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	516					apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R573R(1)	FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		CATAGCAGCAGCGACACTCAA	0.522																																					p.R516R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1548T	7						.						206.0	192.0	197.0					7																	5754798		2203	4300	6503	5721324	SO:0001819	synonymous_variant	54476	exon11			AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"""RING-type (C3HC4) zinc fingers"""	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.1548C>T	7.37:g.5754798G>A		Somatic		Capture	Illumina HiSeq	Phase_I	5721324	NM_207116	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Silent	SNP	ENST00000425013.2	37	CCDS34595.1																																																																																				0.522	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111	
ICA1	3382	broad.mit.edu	37	7	8198251	8198251	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:8198251delT	ENST00000402384.3	-	7	877	c.611delA	c.(610-612)aacfs	p.N204fs	ICA1_ENST00000422063.2_Frame_Shift_Del_p.N204fs|ICA1_ENST00000265577.7_Frame_Shift_Del_p.N203fs|ICA1_ENST00000401396.1_Frame_Shift_Del_p.N192fs|ICA1_ENST00000396675.3_Frame_Shift_Del_p.N204fs|ICA1_ENST00000406470.2_Frame_Shift_Del_p.N204fs|ICA1_ENST00000407906.1_Frame_Shift_Del_p.N204fs			Q05084	ICA69_HUMAN	islet cell autoantigen 1, 69kDa	204	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|secretory granule membrane (GO:0030667)|synaptic vesicle membrane (GO:0030672)		p.N204fs*5(3)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	23		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		TTTGTCAAAGTTTTTTTTTGC	0.378																																					p.N204fs												.	.	3	Deletion - Frameshift(3)	large_intestine(3)	c.611delA	7						.						143.0	125.0	131.0					7																	8198251		2203	4300	6503	8164776	SO:0001589	frameshift_variant	3382	exon7				CCDS34602.1, CCDS64595.1	7p22	2006-12-13	2002-08-29		ENSG00000003147	ENSG00000003147			5343	protein-coding gene	gene with protein product		147625	"""islet cell autoantigen 1 (69kD)"""			7918678, 8777998	Standard	NM_001276478		Approved	ICAp69	uc003srm.3	Q05084	OTTHUMG00000152008	ENST00000402384.3:c.611delA	7.37:g.8198251delT	ENSP00000385570:p.Asn204fs	Somatic		Capture	Illumina HiSeq	Phase_I	8164776	NM_004968	A8K7U1|B3FTQ2|P78506|Q13824|Q96HG3	Frame_Shift_Del	DEL	ENST00000402384.3	37	CCDS34602.1																																																																																				0.378	ICA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324793.1	NM_004968	
SNX13	23161	broad.mit.edu	37	7	17930008	17930008	+	Missense_Mutation	SNP	C	C	T	rs368160651		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:17930008C>T	ENST00000409389.1	-	5	590	c.418G>A	c.(418-420)Gca>Aca	p.A140T	SNX13_ENST00000428135.3_Missense_Mutation_p.A140T|SNX13_ENST00000409604.1_Missense_Mutation_p.A140T			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	140	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.A140T(1)		breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					TGAATGAGTGCGTTTTGAAGA	0.358																																					p.A140T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G418A	7						.	C	THR/ALA	0,3678		0,0,1839	87.0	83.0	84.0		418	5.9	1.0	7		84	1,8169		0,1,4084	no	missense	SNX13	NM_015132.4	58	0,1,5923	TT,TC,CC		0.0122,0.0,0.0084	possibly-damaging	140/958	17930008	1,11847	1839	4085	5924	17896533	SO:0001583	missense	23161	exon5			AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"""Sorting nexins"""	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.418G>A	7.37:g.17930008C>T	ENSP00000386705:p.Ala140Thr	Somatic		Capture	Illumina HiSeq	Phase_I	17896533	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Missense_Mutation	SNP	ENST00000409389.1	37		.	.	.	.	.	.	.	.	.	.	C	34	5.354258	0.95830	0.0	1.22E-4	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044;ENST00000409604	T;T	0.21734	1.99;2.25	5.93	5.93	0.95920	Phox-associated domain (2);PX-associated, sorting nexin 13 (1);	0.096535	0.64402	D	0.000001	T	0.42921	0.1224	L	0.47716	1.5	0.80722	D	1	D;P;P;P	0.89917	1.0;0.889;0.66;0.919	D;B;B;B	0.85130	0.997;0.302;0.274;0.2	T	0.02064	-1.1220	10	0.37606	T	0.19	-11.8719	20.3368	0.98748	0.0:1.0:0.0:0.0	.	140;140;140;140	Q9NSH0;Q9Y5W8;B8ZZT9;Q9Y5W8-2	.;SNX13_HUMAN;.;.	T	140;140;188;140	ENSP00000386705:A140T;ENSP00000398789:A140T	ENSP00000242044:A188T	A	-	1	0	SNX13	17896533	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	7.193000	0.77780	2.805000	0.96524	0.655000	0.94253	GCA		0.358	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132	
DNAH11	8701	broad.mit.edu	37	7	21646115	21646115	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:21646115T>C	ENST00000409508.3	+	19	3751	c.3720T>C	c.(3718-3720)caT>caC	p.H1240H	DNAH11_ENST00000328843.6_Silent_p.H1240H	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1240	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.H1240H(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						CACCTCTCCATAATGCGGAAG	0.363									Kartagener syndrome																												p.H1240H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3720C	7						.						80.0	76.0	77.0					7																	21646115		1860	4101	5961	21612640	SO:0001819	synonymous_variant	8701	exon19	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.3720T>C	7.37:g.21646115T>C		Somatic		Capture	Illumina HiSeq	Phase_I	21612640	NM_003777	Q9UJ82	Silent	SNP	ENST00000409508.3	37																																																																																					0.363	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777	
DNAH11	8701	broad.mit.edu	37	7	21675631	21675631	+	Missense_Mutation	SNP	G	G	T	rs199538599		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:21675631G>T	ENST00000409508.3	+	26	4674	c.4643G>T	c.(4642-4644)aGc>aTc	p.S1548I	DNAH11_ENST00000328843.6_Missense_Mutation_p.S1553I|DNAH11_ENST00000465593.1_3'UTR	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1553	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.S1553I(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						CACCTGGAAAGCATTTTTGTC	0.403									Kartagener syndrome																												p.S1553I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4658T	7						.						84.0	80.0	81.0					7																	21675631		1870	4108	5978	21642156	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.4643G>T	7.37:g.21675631G>T	ENSP00000475939:p.Ser1548Ile	Somatic		Capture	Illumina HiSeq	Phase_I	21642156	NM_003777	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	28.5	4.928878	0.92389	.	.	ENSG00000105877	ENST00000328843	T	0.62498	0.02	5.56	5.56	0.83823	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	D	0.000000	T	0.79540	0.4463	.	.	.	0.80722	D	1	D	0.61080	0.989	D	0.65573	0.936	T	0.81573	-0.0871	9	0.72032	D	0.01	.	18.2896	0.90124	0.0:0.0:1.0:0.0	.	1553	Q96DT5	DYH11_HUMAN	I	1553	ENSP00000330671:S1553I	ENSP00000330671:S1553I	S	+	2	0	DNAH11	21642156	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.267000	0.78462	2.596000	0.87737	0.650000	0.86243	AGC		0.403	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777	
DNAH11	8701	broad.mit.edu	37	7	21784170	21784170	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:21784170G>T	ENST00000409508.3	+	50	8300	c.8269G>T	c.(8269-8271)Gat>Tat	p.D2757Y	DNAH11_ENST00000328843.6_Missense_Mutation_p.D2764Y	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2764					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.D2764Y(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						AAAAGATTGTGATTTGTTTCA	0.368									Kartagener syndrome																												p.X2764L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8291T	7						.						115.0	113.0	114.0					7																	21784170		1846	4098	5944	21750695	SO:0001583	missense	8701	exon50	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.8269G>T	7.37:g.21784170G>T	ENSP00000475939:p.Asp2757Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	21750695	NM_003777	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	17.21	3.332198	0.60853	.	.	ENSG00000105877	ENST00000328843	T	0.39592	1.07	5.91	3.17	0.36434	.	0.103488	0.64402	D	0.000004	T	0.47637	0.1456	.	.	.	0.43250	D	0.995171	D	0.53151	0.958	P	0.51016	0.656	T	0.43278	-0.9401	9	0.62326	D	0.03	.	9.0908	0.36610	0.3399:0.0:0.6601:0.0	.	2764	Q96DT5	DYH11_HUMAN	Y	2764	ENSP00000330671:D2764Y	ENSP00000330671:D2764Y	D	+	1	0	DNAH11	21750695	0.122000	0.22280	0.924000	0.36721	0.957000	0.61999	0.417000	0.21214	0.421000	0.25980	-0.136000	0.14681	GAT		0.368	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777	
CDCA7L	55536	broad.mit.edu	37	7	21942715	21942715	+	Frame_Shift_Del	DEL	G	G	-	rs201829504		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:21942715delG	ENST00000406877.3	-	9	1494	c.1215delC	c.(1213-1215)cccfs	p.P405fs	CDCA7L_ENST00000373934.4_Frame_Shift_Del_p.P359fs|CDCA7L_ENST00000465490.1_5'Flank|CDCA7L_ENST00000356195.5_Frame_Shift_Del_p.P371fs	NM_018719.4	NP_061189.2	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like	405					positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.C406fs*46(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	29						TCCCACGACAGGGGGGACACA	0.517																																					p.P359fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1077delC	7						.						53.0	49.0	50.0					7																	21942715		2203	4300	6503	21909240	SO:0001589	frameshift_variant	55536	exon8				CCDS5374.1, CCDS47558.1, CCDS47559.1	7p15.3	2007-04-27			ENSG00000164649	ENSG00000164649			30777	protein-coding gene	gene with protein product		609685				16829576	Standard	NM_018719		Approved	RAM2, R1, JPO2	uc010kuk.3	Q96GN5	OTTHUMG00000128429	ENST00000406877.3:c.1215delC	7.37:g.21942715delG	ENSP00000383986:p.Pro405fs	Somatic		Capture	Illumina HiSeq	Phase_I	21909240	NM_001127371	A4D141|A6NF50|B3KTR5|B4DUT3|C9K0Y1|Q6PIL4|Q86YT0|Q8IXN5|Q96C70|Q9H9A2|Q9NPV2	Frame_Shift_Del	DEL	ENST00000406877.3	37	CCDS5374.1																																																																																				0.517	CDCA7L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250218.4	NM_018719	
GPNMB	10457	broad.mit.edu	37	7	23293803	23293803	+	Missense_Mutation	SNP	C	C	T	rs145407985	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:23293803C>T	ENST00000381990.2	+	3	400	c.239C>T	c.(238-240)gCg>gTg	p.A80V	GPNMB_ENST00000453162.2_Missense_Mutation_p.A80V|GPNMB_ENST00000258733.4_Missense_Mutation_p.A80V|GPNMB_ENST00000539136.1_Intron|GPNMB_ENST00000409458.3_Missense_Mutation_p.A80V	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	80					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)	p.A80V(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			CGTGTGCAGGCGGTCCTGACC	0.458													C|||	2	0.000399361	0.0	0.0	5008	,	,		16129	0.002		0.0	False		,,,				2504	0.0				p.A80V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C239T	7						.	C	VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	108.0	113.0	111.0		239,239	5.3	0.9	7	dbSNP_134	111	0,8600		0,0,4300	no	missense,missense	GPNMB	NM_001005340.1,NM_002510.2	64,64	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	80/573,80/561	23293803	1,13005	2203	4300	6503	23260328	SO:0001583	missense	10457	exon3			X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"""transmembrane glycoprotein"", ""glycoprotein NMB"", ""glycoprotein nmb-like protein"", ""osteoactivin"""	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.239C>T	7.37:g.23293803C>T	ENSP00000371420:p.Ala80Val	Somatic		Capture	Illumina HiSeq	Phase_I	23260328	NM_001005340	A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	ENST00000381990.2	37	CCDS34610.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.396907	0.42512	2.27E-4	0.0	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000409458;ENST00000453162	T;T;T	0.13420	2.59;2.61;2.62	6.17	5.3	0.74995	.	0.073610	0.56097	D	0.000028	T	0.29158	0.0725	L	0.57536	1.79	0.35035	D	0.759118	D;D;P;D	0.89917	0.999;1.0;0.58;1.0	D;D;B;D	0.87578	0.964;0.998;0.126;0.998	T	0.20605	-1.0270	10	0.02654	T	1	-21.0265	15.6955	0.77494	0.0:0.9348:0.0:0.0652	.	80;80;80;80	F5GY20;Q14956;Q14956-2;Q96F58	.;GPNMB_HUMAN;.;.	V	80;115;80;80;80	ENSP00000258733:A80V;ENSP00000371420:A80V;ENSP00000405586:A80V	ENSP00000258733:A80V	A	+	2	0	GPNMB	23260328	0.981000	0.34729	0.916000	0.36221	0.167000	0.22549	2.490000	0.45294	1.625000	0.50366	0.655000	0.94253	GCG		0.458	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340	
OSBPL3	26031	broad.mit.edu	37	7	24874171	24874171	+	Silent	SNP	G	G	A	rs201551833		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:24874171G>A	ENST00000313367.2	-	15	2131	c.1680C>T	c.(1678-1680)tgC>tgT	p.C560C	OSBPL3_ENST00000396431.1_Silent_p.C529C|OSBPL3_ENST00000353930.1_Silent_p.C524C|OSBPL3_ENST00000409069.1_Silent_p.C493C|OSBPL3_ENST00000431825.2_Silent_p.C493C|OSBPL3_ENST00000396429.1_Silent_p.C524C|OSBPL3_ENST00000352860.1_Silent_p.C529C	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	560					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)	p.C560C(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						CCAGCTCCTCGCAGAGCCTCT	0.622													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16542	0.0		0.0	False		,,,				2504	0.0				p.C524C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1572T	7						.						74.0	68.0	70.0					7																	24874171		2203	4300	6503	24840696	SO:0001819	synonymous_variant	26031	exon14			AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.1680C>T	7.37:g.24874171G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24840696	NM_145321	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Silent	SNP	ENST00000313367.2	37	CCDS5390.1																																																																																				0.622	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		
HOXA1	3198	broad.mit.edu	37	7	27135411	27135411	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:27135411C>T	ENST00000343060.4	-	1	182	c.121G>A	c.(121-123)Gcg>Acg	p.A41T	HOTAIRM1_ENST00000495032.1_RNA|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000429611.3_RNA|HOXA1_ENST00000355633.5_Missense_Mutation_p.A41T	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	41					abducens nerve formation (GO:0021599)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|artery morphogenesis (GO:0048844)|central nervous system neuron differentiation (GO:0021953)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|cognition (GO:0050890)|embryonic neurocranium morphogenesis (GO:0048702)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|inner ear development (GO:0048839)|motor neuron axon guidance (GO:0008045)|multicellular organismal development (GO:0007275)|neuromuscular process (GO:0050905)|optokinetic behavior (GO:0007634)|outer ear morphogenesis (GO:0042473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of behavior (GO:0050795)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|semicircular canal formation (GO:0060876)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.A41T(1)		endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GCGCTGACCGCGCACGACTGG	0.637											OREG0003750	type=REGULATORY REGION|Gene=BC031342|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.A41T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G121A	7						.						59.0	65.0	63.0					7																	27135411		2203	4300	6503	27101936	SO:0001583	missense	3198	exon1				CCDS5401.1, CCDS5402.2	7p15.2	2011-06-20	2005-12-22		ENSG00000105991	ENSG00000105991		"""Homeoboxes / ANTP class : HOXL subclass"""	5099	protein-coding gene	gene with protein product		142955	"""homeo box A1"""	HOX1F, HOX1		1973146	Standard	NM_153620		Approved		uc003sye.3	P49639	OTTHUMG00000023207	ENST00000343060.4:c.121G>A	7.37:g.27135411C>T	ENSP00000343246:p.Ala41Thr	Somatic	792	Capture	Illumina HiSeq	Phase_I	27101936	NM_153620	A4D184|B2R8U7|O43363	Missense_Mutation	SNP	ENST00000343060.4	37	CCDS5401.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.212381	0.79240	.	.	ENSG00000105991	ENST00000343060;ENST00000355633	T;T	0.35421	1.31;1.31	5.15	4.21	0.49690	.	0.200729	0.41001	D	0.000978	T	0.54447	0.1859	L	0.60455	1.87	0.58432	D	0.999992	D;D	0.89917	0.989;1.0	B;D	0.87578	0.422;0.998	T	0.55730	-0.8095	10	0.56958	D	0.05	.	13.3343	0.60507	0.1589:0.8411:0.0:0.0	.	41;41	P49639;E7ERT8	HXA1_HUMAN;.	T	41	ENSP00000343246:A41T;ENSP00000347851:A41T	ENSP00000343246:A41T	A	-	1	0	HOXA1	27101936	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	1.617000	0.36943	2.398000	0.81561	0.297000	0.19635	GCG		0.637	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1		
JAZF1	221895	broad.mit.edu	37	7	27872428	27872428	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:27872428C>T	ENST00000283928.5	-	5	888	c.723G>A	c.(721-723)atG>atA	p.M241I	JAZF1_ENST00000466516.1_5'UTR	NM_175061.3	NP_778231.2	Q86VZ6	JAZF1_HUMAN	JAZF zinc finger 1	241					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transcription corepressor activity (GO:0003714)	p.M241I(1)	JAZF1/SUZ12(133)	endometrium(1)|large_intestine(1)|lung(4)	6						GTTATTGCTGCATCTTCCTGA	0.493			T	SUZ12	endometrial stromal tumours																																p.M241I			Dom	yes		7	7p15.2-p15.1	221895	juxtaposed with another zinc finger gene 1		M	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G723A	7						.						144.0	135.0	138.0					7																	27872428		2203	4300	6503	27838953	SO:0001583	missense	221895	exon5			BC047229	CCDS5416.1	7p15.2-p15.1	2010-04-14			ENSG00000153814	ENSG00000153814		"""Zinc fingers, C2H2-type"""	28917	protein-coding gene	gene with protein product		606246				8401585	Standard	XM_006715656		Approved	TIP27, DKFZp761K2222, ZNF802	uc003szn.3	Q86VZ6	OTTHUMG00000128545	ENST00000283928.5:c.723G>A	7.37:g.27872428C>T	ENSP00000283928:p.Met241Ile	Somatic		Capture	Illumina HiSeq	Phase_I	27838953	NM_175061	A4D195|Q8N3L7	Missense_Mutation	SNP	ENST00000283928.5	37	CCDS5416.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.49|11.49	1.654700|1.654700	0.29425|0.29425	.|.	.|.	ENSG00000153814|ENSG00000153814	ENST00000427814|ENST00000283928	.|T	.|0.76578	.|-1.03	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	.|0.104630	.|0.85682	.|D	.|0.000000	T|T	0.65995|0.65995	0.2745|0.2745	N|N	0.14661|0.14661	0.345|0.345	0.58432|0.58432	D|D	0.999999|0.999999	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.58387|0.58387	-0.7645|-0.7645	5|10	.|0.19590	.|T;T	.|0.45;0.45	-24.4678|-24.4678	20.8794|20.8794	0.99867|0.99867	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|241	.|Q86VZ6	.|JAZF1_HUMAN	Y|I	228|241	.|ENSP00000283928:M241I	.|ENSP00000283928:M241I;ENSP00000283928:M241I	C|M	-|-	2|3	0|0	JAZF1|JAZF1	27838953|27838953	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.747000|3.747000	0.55134|0.55134	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	TGC|ATG		0.493	JAZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250382.2	NM_175061	
CCDC129	223075	broad.mit.edu	37	7	31614300	31614300	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:31614300G>A	ENST00000407970.3	+	7	580	c.542G>A	c.(541-543)cGt>cAt	p.R181H	CCDC129_ENST00000451887.2_Missense_Mutation_p.R207H|CCDC129_ENST00000319386.3_Missense_Mutation_p.R181H|CCDC129_ENST00000409210.1_Missense_Mutation_p.R89H	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	181								p.R181H(2)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						ATCAACATCCGTGTTTTTCTT	0.507																																					p.R181H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G542A	7						.						92.0	85.0	87.0					7																	31614300		2203	4300	6503	31580825	SO:0001583	missense	223075	exon7			AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.542G>A	7.37:g.31614300G>A	ENSP00000384416:p.Arg181His	Somatic		Capture	Illumina HiSeq	Phase_I	31580825	NM_194300	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	G	21.2	4.109488	0.77096	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.23950	1.91;2.15;2.13;1.88	5.4	-0.698	0.11280	.	0.407506	0.21322	N	0.076457	T	0.18759	0.0450	L	0.55103	1.725	0.22066	N	0.999384	B;B;B;B	0.34255	0.14;0.445;0.445;0.445	B;B;B;B	0.22386	0.017;0.039;0.039;0.039	T	0.08576	-1.0715	9	.	.	.	-0.3517	11.7075	0.51605	0.4879:0.0:0.5121:0.0	.	207;191;181;181	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	H	181;181;207;191;89	ENSP00000313062:R181H;ENSP00000384416:R181H;ENSP00000395835:R207H;ENSP00000387214:R89H	.	R	+	2	0	CCDC129	31580825	0.019000	0.18553	0.967000	0.41034	0.989000	0.77384	-0.182000	0.09726	-0.484000	0.06763	0.563000	0.77884	CGT		0.507	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
AOAH	313	broad.mit.edu	37	7	36570112	36570112	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:36570112C>T	ENST00000258749.5	-	19	1833	c.1434G>A	c.(1432-1434)gaG>gaA	p.E478E	AOAH_ENST00000491444.1_5'UTR|AOAH_ENST00000535891.1_Silent_p.E446E|AOAH_ENST00000538464.1_Silent_p.E200E|AOAH_ENST00000431169.1_Silent_p.E478E	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	478					inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|lipopolysaccharide metabolic process (GO:0008653)|negative regulation of inflammatory response (GO:0050728)	extracellular region (GO:0005576)	acyloxyacyl hydrolase activity (GO:0050528)|catalytic activity (GO:0003824)|lipoprotein lipase activity (GO:0004465)	p.E478E(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(21)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	41						TGGAGAGTTGCTCTGCTCTCT	0.388																																					p.E478E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1434A	7						.						80.0	78.0	79.0					7																	36570112		2202	4300	6502	36536637	SO:0001819	synonymous_variant	313	exon19			BC025698	CCDS5448.1, CCDS55102.1, CCDS75584.1	7p14-p12	2014-03-14			ENSG00000136250	ENSG00000136250	3.1.1.77		548	protein-coding gene	gene with protein product		102593				1883828	Standard	NM_001637		Approved		uc022abu.1	P28039	OTTHUMG00000023566	ENST00000258749.5:c.1434G>A	7.37:g.36570112C>T		Somatic		Capture	Illumina HiSeq	Phase_I	36536637	NM_001637	A4D1Y5|B7Z490|Q53F13	Silent	SNP	ENST00000258749.5	37	CCDS5448.1																																																																																				0.388	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637	
VPS41	27072	broad.mit.edu	37	7	38796483	38796483	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:38796483A>G	ENST00000310301.4	-	19	1704	c.1650T>C	c.(1648-1650)agT>agC	p.S550S	VPS41_ENST00000395969.2_Silent_p.S525S	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	550					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)	p.S550S(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						CCTTGATAGAACTGAAAAGAT	0.284																																					p.S550S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1650C	7						.						95.0	96.0	96.0					7																	38796483		2202	4294	6496	38763008	SO:0001819	synonymous_variant	27072	exon19			U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.1650T>C	7.37:g.38796483A>G		Somatic		Capture	Illumina HiSeq	Phase_I	38763008	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Silent	SNP	ENST00000310301.4	37	CCDS5457.1																																																																																				0.284	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
POU6F2	11281	broad.mit.edu	37	7	39247175	39247175	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:39247175C>T	ENST00000403058.1	+	5	621	c.467C>T	c.(466-468)gCt>gTt	p.A156V	POU6F2_ENST00000517348.1_3'UTR|POU6F2_ENST00000518318.2_Missense_Mutation_p.A156V|POU6F2_ENST00000559001.1_Missense_Mutation_p.A148V	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	156					central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A156V(1)		NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						GTGGCAGCAGCTGCAGCCGGA	0.537																																					p.A156V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C467T	7						.						37.0	35.0	36.0					7																	39247175		2203	4300	6503	39213700	SO:0001583	missense	11281	exon5			U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"""Homeoboxes / POU class"""	21694	protein-coding gene	gene with protein product	"""Retina-derived POU-domain factor-1"""	609062	"""POU domain, class 6, transcription factor 2"""			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.467C>T	7.37:g.39247175C>T	ENSP00000384004:p.Ala156Val	Somatic		Capture	Illumina HiSeq	Phase_I	39213700	NM_007252	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Missense_Mutation	SNP	ENST00000403058.1	37	CCDS34620.2	.	.	.	.	.	.	.	.	.	.	C	27.9	4.876439	0.91664	.	.	ENSG00000106536	ENST00000403058;ENST00000518318	D;D	0.86956	-2.12;-2.19	6.17	6.17	0.99709	.	0.440677	0.23472	N	0.047817	D	0.91942	0.7448	L	0.44542	1.39	0.54753	D	0.99998	D;D	0.89917	1.0;0.997	D;D	0.85130	0.997;0.985	D	0.91517	0.5231	10	0.72032	D	0.01	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	156;156	P78424-2;P78424	.;PO6F2_HUMAN	V	156	ENSP00000384004:A156V;ENSP00000430514:A156V	ENSP00000384004:A156V	A	+	2	0	POU6F2	39213700	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.402000	0.79972	2.941000	0.99782	0.655000	0.94253	GCT		0.537	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252	
CDK13	8621	broad.mit.edu	37	7	40102523	40102523	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:40102523G>A	ENST00000181839.4	+	8	3304	c.2699G>A	c.(2698-2700)tGt>tAt	p.C900Y	CDK13_ENST00000484589.1_3'UTR|CDK13_ENST00000340829.5_Missense_Mutation_p.C900Y	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	900	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.C900Y(1)		cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						GTATGGAGCTGTGGGTAAGAT	0.383																																					p.C900Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2699A	7						.						256.0	260.0	259.0					7																	40102523		2203	4300	6503	40069048	SO:0001583	missense	8621	exon8			M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"""Cyclin-dependent kinases"""	1733	protein-coding gene	gene with protein product	"""cholinesterase-related cell division controller"""	603309	"""cell division cycle 2-like 5 (cholinesterase-related cell division controller)"""	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.2699G>A	7.37:g.40102523G>A	ENSP00000181839:p.Cys900Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	40069048	NM_003718	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	De_novo_Start_OutOfFrame	SNP	ENST00000181839.4	37	CCDS5461.1	.	.	.	.	.	.	.	.	.	.	.	19.51	3.841166	0.71488	.	.	ENSG00000065883	ENST00000181839;ENST00000340829	T;T	0.64991	-0.13;-0.13	5.52	5.52	0.82312	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.69233	0.3088	N	0.21194	0.64	0.80722	D	1	D;D;D	0.89917	0.997;1.0;0.999	D;D;D	0.87578	0.974;0.998;0.99	T	0.66200	-0.5983	8	.	.	.	-9.0227	19.8265	0.96619	0.0:0.0:1.0:0.0	.	286;900;900	Q9BVE2;Q14004-2;Q14004	.;.;CDK13_HUMAN	Y	900	ENSP00000181839:C900Y;ENSP00000340557:C900Y	.	C	+	2	0	CDK13	40069048	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.835000	0.99442	2.770000	0.95276	0.563000	0.77884	TGT		0.383	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718	
GLI3	2737	broad.mit.edu	37	7	42188023	42188023	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:42188023C>T	ENST00000395925.3	-	3	253	c.169G>A	c.(169-171)Gca>Aca	p.A57T	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	57					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A57T(1)		NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						ATAGTGATTGCGTTTCTTCTC	0.418									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.A57T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G169A	7						.						143.0	124.0	130.0					7																	42188023		2203	4300	6503	42154548	SO:0001583	missense	2737	exon3	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.169G>A	7.37:g.42188023C>T	ENSP00000379258:p.Ala57Thr	Somatic		Capture	Illumina HiSeq	Phase_I	42154548	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.276921	0.80580	.	.	ENSG00000106571	ENST00000395925;ENST00000448703	T	0.17054	2.3	5.82	5.82	0.92795	.	0.053701	0.85682	D	0.000000	T	0.11879	0.0289	N	0.17082	0.46	0.80722	D	1	D	0.58620	0.983	B	0.37239	0.244	T	0.06734	-1.0810	10	0.34782	T	0.22	.	20.0966	0.97849	0.0:1.0:0.0:0.0	.	57	P10071	GLI3_HUMAN	T	57	ENSP00000379258:A57T	ENSP00000379258:A57T	A	-	1	0	GLI3	42154548	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.626000	0.61269	2.753000	0.94483	0.557000	0.71058	GCA		0.418	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
POLM	27434	broad.mit.edu	37	7	44113470	44113470	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:44113470C>T	ENST00000242248.5	-	9	1327	c.1226G>A	c.(1225-1227)tGc>tAc	p.C409Y	POLM_ENST00000492971.1_5'Flank|POLM_ENST00000335195.6_Missense_Mutation_p.C372Y|POLM_ENST00000395831.3_Missense_Mutation_p.C329Y	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	409					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.C409Y(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(3)|skin(2)	22						CCAGGATGGGCAGGGCCTCGT	0.602								DNA polymerases (catalytic subunits)																													p.C409Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1226A	7						.						61.0	70.0	67.0					7																	44113470		2203	4300	6503	44079995	SO:0001583	missense	27434	exon9			AF176097	CCDS34625.1, CCDS64635.1, CCDS64636.1	7p13	2012-05-18			ENSG00000122678	ENSG00000122678		"""DNA polymerases"""	9185	protein-coding gene	gene with protein product	"""Pol iota"""	606344				10982892	Standard	XM_005249708		Approved	Tdt-N	uc003tjt.3	Q9NP87	OTTHUMG00000155353	ENST00000242248.5:c.1226G>A	7.37:g.44113470C>T	ENSP00000242248:p.Cys409Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	44079995	NM_013284	D3DVK4|Q6P5X8|Q86WQ9	Missense_Mutation	SNP	ENST00000242248.5	37	CCDS34625.1	.	.	.	.	.	.	.	.	.	.	C	0.801	-0.755451	0.03019	.	.	ENSG00000122678	ENST00000335195;ENST00000242248;ENST00000395831	T;T;T	0.41400	1.0;1.0;1.0	4.32	2.36	0.29203	DNA-directed DNA polymerase X (1);	1.231750	0.05411	N	0.542456	T	0.42471	0.1204	L	0.60455	1.87	0.09310	N	1	P;B;B	0.50272	0.933;0.327;0.116	P;B;B	0.46510	0.519;0.036;0.034	T	0.26326	-1.0106	10	0.18276	T	0.48	-6.6676	5.5054	0.16850	0.0:0.6862:0.2038:0.11	.	329;372;409	Q86WQ9;Q6P5X8;Q9NP87	.;.;DPOLM_HUMAN	Y	372;409;329	ENSP00000335141:C372Y;ENSP00000242248:C409Y;ENSP00000379174:C329Y	ENSP00000242248:C409Y	C	-	2	0	POLM	44079995	0.000000	0.05858	0.004000	0.12327	0.037000	0.13140	0.014000	0.13333	1.192000	0.43071	0.650000	0.86243	TGC		0.602	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284	
MYO1G	64005	broad.mit.edu	37	7	45005396	45005396	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:45005396G>A	ENST00000258787.7	-	17	2357	c.2221C>T	c.(2221-2223)Cgc>Tgc	p.R741C		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	741						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R741C(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						CGGAACCAGCGCATGATGGTG	0.652																																					p.R741C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2221T	7						.						50.0	50.0	50.0					7																	45005396		2203	4300	6503	44971921	SO:0001583	missense	64005	exon17			AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"""Myosins / Myosin superfamily : Class I"""	13880	protein-coding gene	gene with protein product	"""minor histocompatibility antigen HA-2"""	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.2221C>T	7.37:g.45005396G>A	ENSP00000258787:p.Arg741Cys	Somatic		Capture	Illumina HiSeq	Phase_I	44971921	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	37	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454937	0.63290	.	.	ENSG00000136286	ENST00000258787	T	0.72394	-0.65	4.22	0.995	0.19838	.	0.487702	0.15151	U	0.277712	T	0.70334	0.3212	M	0.62723	1.935	0.41357	D	0.987403	D	0.59767	0.986	P	0.48571	0.582	T	0.71130	-0.4682	10	0.62326	D	0.03	.	10.3412	0.43879	0.0:0.3419:0.533:0.1251	.	741	B0I1T2	MYO1G_HUMAN	C	741	ENSP00000258787:R741C	ENSP00000258787:R741C	R	-	1	0	MYO1G	44971921	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	0.999000	0.29757	0.306000	0.22856	0.462000	0.41574	CGC		0.652	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2		
ABCA13	154664	broad.mit.edu	37	7	48266938	48266938	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:48266938T>G	ENST00000435803.1	+	6	572	c.548T>G	c.(547-549)cTt>cGt	p.L183R		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	183					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.L183R(1)|p.L128R(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GATTTTCTACTTTTACTGCCG	0.418																																					p.F129V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T385G	7						.						125.0	128.0	127.0					7																	48266938		1884	4111	5995	48237484	SO:0001583	missense	154664	exon4			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.548T>G	7.37:g.48266938T>G	ENSP00000411096:p.Leu183Arg	Somatic		Capture	Illumina HiSeq	Phase_I	48237484	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	T	4.145	0.025216	0.08054	.	.	ENSG00000179869	ENST00000435803	T	0.36340	1.26	5.37	-0.36	0.12568	.	0.945772	0.08630	N	0.917101	T	0.19604	0.0471	L	0.29908	0.895	0.25256	N	0.98963	B;B	0.15719	0.014;0.01	B;B	0.13407	0.008;0.009	T	0.31668	-0.9935	10	0.06365	T	0.9	.	4.6215	0.12455	0.3689:0.0:0.3013:0.3298	.	183;183	Q86UQ4;Q86UQ4-2	ABCAD_HUMAN;.	R	183	ENSP00000411096:L183R	ENSP00000409268:L183R	L	+	2	0	ABCA13	48237484	0.007000	0.16637	0.027000	0.17364	0.220000	0.24768	0.009000	0.13219	0.022000	0.15160	0.455000	0.32223	CTT		0.418	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
IKZF1	10320	broad.mit.edu	37	7	50468219	50468219	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:50468219G>A	ENST00000331340.3	+	8	1609	c.1454G>A	c.(1453-1455)gGc>gAc	p.G485D	IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000343574.5_Missense_Mutation_p.G398D|IKZF1_ENST00000359197.5_Missense_Mutation_p.G443D|IKZF1_ENST00000438033.1_Missense_Mutation_p.G398D|IKZF1_ENST00000349824.4_Missense_Mutation_p.G342D|IKZF1_ENST00000439701.1_Missense_Mutation_p.G443D|IKZF1_ENST00000357364.4_Missense_Mutation_p.G398D|IKZF1_ENST00000346667.4_Missense_Mutation_p.G255D	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	485					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(28)|p.G485D(1)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				GGCTGCCACGGCTTCCGTGAT	0.587			"""D,T"""	BCL6	"""ALL, DLBCL"""																																p.G485D			"""Rec,Dom"""	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	.	29	Unknown(28)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(28)|large_intestine(1)	c.G1454A	7						.						48.0	55.0	52.0					7																	50468219		2192	4296	6488	50435713	SO:0001583	missense	10320	exon8			U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13176	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 92"""	603023	"""zinc finger protein, subfamily 1A, 1 (Ikaros)"""	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.1454G>A	7.37:g.50468219G>A	ENSP00000331614:p.Gly485Asp	Somatic		Capture	Illumina HiSeq	Phase_I	50435713	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Missense_Mutation	SNP	ENST00000331340.3	37		.	.	.	.	.	.	.	.	.	.	G	34	5.346351	0.95807	.	.	ENSG00000185811	ENST00000346667;ENST00000343574;ENST00000359197;ENST00000349824;ENST00000357364;ENST00000331340;ENST00000438033;ENST00000439701	T;T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.69260	0.3091	.	.	.	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.72097	-0.4393	9	0.87932	D	0	-5.2298	19.9376	0.97146	0.0:0.0:1.0:0.0	.	398;255;398;443;485	Q13422-2;Q13422-6;Q13422-3;Q13422-7;Q13422	.;.;.;.;IKZF1_HUMAN	D	255;398;443;342;398;485;398;443	ENSP00000340080:G255D;ENSP00000342750:G398D;ENSP00000352123:G443D;ENSP00000342485:G342D;ENSP00000349928:G398D;ENSP00000331614:G485D;ENSP00000396554:G398D;ENSP00000413025:G443D	ENSP00000331614:G485D	G	+	2	0	IKZF1	50435713	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.899000	0.87370	2.711000	0.92665	0.655000	0.94253	GGC		0.587	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060	
ZNF680	340252	broad.mit.edu	37	7	63981871	63981871	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:63981871G>A	ENST00000309683.6	-	4	1412	c.1261C>T	c.(1261-1263)Ctt>Ttt	p.L421F	ZNF680_ENST00000476563.1_5'Flank	NM_178558.4	NP_848653.2	Q8NEM1	ZN680_HUMAN	zinc finger protein 680	421					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L421F(1)		breast(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	27		Lung NSC(55;0.118)|all_lung(88;0.243)				TGTCGAGTAAGGCTGGAGCAC	0.373																																					p.L421F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1261T	7						.						33.0	35.0	34.0					7																	63981871		2202	4297	6499	63619306	SO:0001583	missense	340252	exon4			AK074911	CCDS34644.1, CCDS47594.1	7q11.21	2013-01-08			ENSG00000173041	ENSG00000173041		"""Zinc fingers, C2H2-type"", ""-"""	26897	protein-coding gene	gene with protein product	"""hypothetical protein FLJ90430"""					12477932	Standard	NM_178558		Approved	FLJ90430	uc003tta.2	Q8NEM1	OTTHUMG00000156542	ENST00000309683.6:c.1261C>T	7.37:g.63981871G>A	ENSP00000309330:p.Leu421Phe	Somatic		Capture	Illumina HiSeq	Phase_I	63619306	NM_178558	B3KVJ4|Q6ZNF3|Q8NC79	Missense_Mutation	SNP	ENST00000309683.6	37	CCDS34644.1	.	.	.	.	.	.	.	.	.	.	g	11.20	1.567265	0.28003	.	.	ENSG00000173041	ENST00000309683	T	0.52057	0.68	1.32	1.32	0.21799	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.50497	0.1619	M	0.76938	2.355	0.09310	N	0.999996	B	0.28233	0.204	B	0.36959	0.237	T	0.53746	-0.8395	9	0.72032	D	0.01	.	5.9779	0.19391	0.0:0.0:1.0:0.0	.	421	Q8NEM1	ZN680_HUMAN	F	421	ENSP00000309330:L421F	ENSP00000309330:L421F	L	-	1	0	ZNF680	63619306	0.756000	0.28383	0.004000	0.12327	0.037000	0.13140	1.553000	0.36255	0.696000	0.31696	0.485000	0.47835	CTT		0.373	ZNF680-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344568.1	NM_178558	
AUTS2	26053	broad.mit.edu	37	7	70255333	70255333	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:70255333G>A	ENST00000342771.4	+	19	3452	c.3131G>A	c.(3130-3132)cGc>cAc	p.R1044H	AUTS2_ENST00000406775.2_Missense_Mutation_p.R1020H	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	1044								p.R1044H(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)		GACAGGACTCGCATGATGACC	0.662																																					p.R1044H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3131A	7						.						34.0	39.0	37.0					7																	70255333		2203	4300	6503	69893269	SO:0001583	missense	26053	exon19			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.3131G>A	7.37:g.70255333G>A	ENSP00000344087:p.Arg1044His	Somatic		Capture	Illumina HiSeq	Phase_I	69893269	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	g	26.3	4.720602	0.89205	.	.	ENSG00000158321	ENST00000406775;ENST00000342771	T;T	0.66638	-0.22;-0.17	4.62	4.62	0.57501	.	0.100240	0.64402	D	0.000001	T	0.76919	0.4055	L	0.46157	1.445	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.996	T	0.76198	-0.3047	9	.	.	.	-28.0047	17.4889	0.87698	0.0:0.0:1.0:0.0	.	496;1020;1044	B4DLG0;Q8WXX7-2;Q8WXX7	.;.;AUTS2_HUMAN	H	1020;1044	ENSP00000385263:R1020H;ENSP00000344087:R1044H	.	R	+	2	0	AUTS2	69893269	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.355000	0.97087	2.115000	0.64714	0.651000	0.88453	CGC		0.662	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2		
POM121	9883	broad.mit.edu	37	7	72413626	72413626	+	Missense_Mutation	SNP	G	G	A	rs201571911		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:72413626G>A	ENST00000434423.2	+	11	3094	c.3094G>A	c.(3094-3096)Ggt>Agt	p.G1032S	POM121_ENST00000257622.4_Missense_Mutation_p.G767S|POM121_ENST00000358357.3_Missense_Mutation_p.G767S|POM121_ENST00000395270.1_Missense_Mutation_p.G767S|POM121_ENST00000446813.1_Missense_Mutation_p.G767S			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	1032	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.G767S(2)		NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				TATCTTTGGCGGTGCCACGCA	0.637																																					p.G767S												.	.	2	Substitution - Missense(2)	large_intestine(1)|skin(1)	c.G2299A	7						.	G	SER/GLY	0,4406		0,0,2203	87.0	83.0	84.0		2299	-3.6	0.0	7		84	1,8599	1.2+/-3.3	0,1,4299	no	missense	POM121	NM_172020.2	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	767/985	72413626	1,13005	2203	4300	6503	72051562	SO:0001583	missense	9883	exon13			AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.3094G>A	7.37:g.72413626G>A	ENSP00000405562:p.Gly1032Ser	Somatic		Capture	Illumina HiSeq	Phase_I	72051562	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		.	.	.	.	.	.	.	.	.	.	G	0.395	-0.921239	0.02396	0.0	1.16E-4	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.03831	3.85;3.79;3.85;3.79;4.07	2.55	-3.64	0.04515	.	0.630018	0.13123	N	0.412044	T	0.01156	0.0038	N	0.00793	-1.18	0.09310	N	1	B;B	0.19073	0.033;0.003	B;B	0.12837	0.008;0.003	T	0.43845	-0.9366	10	0.02654	T	1	.	8.1528	0.31152	0.506:0.0:0.4939:0.0	.	767;1032	A8MXF9;Q96HA1	.;P121A_HUMAN	S	767;767;767;767;1032	ENSP00000393020:G767S;ENSP00000257622:G767S;ENSP00000378687:G767S;ENSP00000351124:G767S;ENSP00000405562:G1032S	ENSP00000257622:G767S	G	+	1	0	POM121	72051562	0.011000	0.17503	0.000000	0.03702	0.013000	0.08279	0.617000	0.24359	-0.594000	0.05836	0.173000	0.16961	GGT		0.637	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
BAZ1B	9031	broad.mit.edu	37	7	72892057	72892057	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:72892057C>T	ENST00000339594.4	-	7	2072	c.1734G>A	c.(1732-1734)aaG>aaA	p.K578K	BAZ1B_ENST00000404251.1_Silent_p.K578K	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	578	Lys-rich.				cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)	p.K578K(1)		NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				CCTCATACCGCTTCTGTTTTT	0.438																																					p.K578K	Esophageal Squamous(112;1167 1561 21085 43672 48228)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1734A	7						.						158.0	175.0	169.0					7																	72892057		2203	4294	6497	72529993	SO:0001819	synonymous_variant	9031	exon7			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"""Zinc fingers, PHD-type"""	961	protein-coding gene	gene with protein product	"""Williams-Beuren syndrome chromosome region 9"", ""Williams-Beuren syndrome chromosome region 10"", ""transcription factor WSTF"""	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.1734G>A	7.37:g.72892057C>T		Somatic		Capture	Illumina HiSeq	Phase_I	72529993	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Silent	SNP	ENST00000339594.4	37	CCDS5549.1																																																																																				0.438	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	
PTPN12	5782	broad.mit.edu	37	7	77265164	77265164	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:77265164G>A	ENST00000248594.6	+	15	2412	c.2140G>A	c.(2140-2142)Gaa>Aaa	p.E714K	PTPN12_ENST00000435495.2_Missense_Mutation_p.E584K|PTPN12_ENST00000415482.2_Missense_Mutation_p.E595K	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	714					protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)	p.E714K(1)		breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						AAAAAAGTCTGAAGTAAGTCC	0.333																																					p.E584K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1750A	7						.						51.0	49.0	50.0					7																	77265164		2203	4297	6500	77103100	SO:0001583	missense	5782	exon14				CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.2140G>A	7.37:g.77265164G>A	ENSP00000248594:p.Glu714Lys	Somatic		Capture	Illumina HiSeq	Phase_I	77103100	NM_001131009	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	G	11.18	1.561825	0.27915	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000435495;ENST00000407343	T;T;T;T	0.38887	3.83;3.25;3.25;1.11	5.06	3.26	0.37387	.	0.162693	0.40818	N	0.001005	T	0.29288	0.0729	L	0.56769	1.78	0.25305	N	0.989242	P	0.52316	0.952	B	0.40741	0.339	T	0.27331	-1.0077	10	0.05620	T	0.96	.	5.7745	0.18271	0.1762:0.1587:0.665:0.0	.	714	Q05209	PTN12_HUMAN	K	714;595;584;196	ENSP00000248594:E714K;ENSP00000392429:E595K;ENSP00000397991:E584K;ENSP00000385079:E196K	ENSP00000248594:E714K	E	+	1	0	PTPN12	77103100	0.989000	0.36119	0.992000	0.48379	0.436000	0.31835	1.114000	0.31196	0.664000	0.31047	0.655000	0.94253	GAA		0.333	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3		
PCLO	27445	broad.mit.edu	37	7	82586181	82586181	+	Missense_Mutation	SNP	G	G	A	rs370195239		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:82586181G>A	ENST00000333891.9	-	5	4425	c.4088C>T	c.(4087-4089)aCg>aTg	p.T1363M	PCLO_ENST00000423517.2_Missense_Mutation_p.T1363M	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.T1363M(2)|p.T1294M(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						AGAATATCCCGTGTCGCTCAG	0.428																																					p.T1363M												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.C4088T	7						.						54.0	52.0	53.0					7																	82586181		1856	4089	5945	82424117	SO:0001583	missense	27445	exon5			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.4088C>T	7.37:g.82586181G>A	ENSP00000334319:p.Thr1363Met	Somatic		Capture	Illumina HiSeq	Phase_I	82424117	NM_033026		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	13.17	2.156894	0.38119	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.23754	1.89;1.9	5.67	5.67	0.87782	.	.	.	.	.	T	0.54870	0.1885	M	0.75777	2.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.56685	-0.7938	9	0.87932	D	0	.	19.7654	0.96337	0.0:0.0:1.0:0.0	.	1363;1363	Q9Y6V0-5;Q9Y6V0-6	.;.	M	1294;1363;1363	ENSP00000334319:T1363M;ENSP00000388393:T1363M	ENSP00000334319:T1363M	T	-	2	0	PCLO	82424117	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.524000	0.81866	2.659000	0.90383	0.655000	0.94253	ACG		0.428	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
PCLO	27445	broad.mit.edu	37	7	82764324	82764324	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:82764324G>A	ENST00000333891.9	-	3	2879	c.2542C>T	c.(2542-2544)Ccc>Tcc	p.P848S	PCLO_ENST00000423517.2_Missense_Mutation_p.P848S	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.P848S(2)|p.P794S(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTTTGTACGGGGTCAACTTGT	0.458																																					p.P848S												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.C2542T	7						.						154.0	156.0	155.0					7																	82764324		1918	4130	6048	82602260	SO:0001583	missense	27445	exon3			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.2542C>T	7.37:g.82764324G>A	ENSP00000334319:p.Pro848Ser	Somatic		Capture	Illumina HiSeq	Phase_I	82602260	NM_033026		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	8.650	0.897945	0.17686	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.34072	1.38;1.74	5.98	3.22	0.36961	.	.	.	.	.	T	0.27063	0.0663	L	0.36672	1.1	0.80722	D	1	B;B	0.15930	0.015;0.015	B;B	0.16289	0.015;0.015	T	0.06481	-1.0824	9	0.87932	D	0	.	7.2842	0.26328	0.1943:0.1204:0.6853:0.0	.	848;848	Q9Y6V0-5;Q9Y6V0-6	.;.	S	794;848;848	ENSP00000334319:P848S;ENSP00000388393:P848S	ENSP00000334319:P848S	P	-	1	0	PCLO	82602260	0.998000	0.40836	0.747000	0.31113	0.845000	0.48019	1.005000	0.29834	0.424000	0.26061	0.655000	0.94253	CCC		0.458	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
SEMA3D	223117	broad.mit.edu	37	7	84694783	84694783	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:84694783G>A	ENST00000284136.6	-	6	718	c.675C>T	c.(673-675)caC>caT	p.H225H	SEMA3D_ENST00000444867.1_Silent_p.H225H	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	225	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.H225H(1)		NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						TGATGTAGTGGTGGTCATGAG	0.403																																					p.H225H	Ovarian(63;442 1191 17318 29975 31528)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C675T	7						.						129.0	113.0	118.0					7																	84694783		2203	4300	6503	84532719	SO:0001819	synonymous_variant	223117	exon6			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"""Semaphorins"", ""Immunoglobulin superfamily / V-set domain containing"""	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.675C>T	7.37:g.84694783G>A		Somatic		Capture	Illumina HiSeq	Phase_I	84532719	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Silent	SNP	ENST00000284136.6	37	CCDS34676.1																																																																																				0.403	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754	
SEMA3D	223117	broad.mit.edu	37	7	84702334	84702334	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:84702334C>T	ENST00000284136.6	-	4	482	c.439G>A	c.(439-441)Gga>Aga	p.G147R	SEMA3D_ENST00000444867.1_Missense_Mutation_p.G147R	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	147	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.G147R(1)		NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						GCTCCAGTTCCACACACATAT	0.333																																					p.G147R	Ovarian(63;442 1191 17318 29975 31528)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G439A	7						.						111.0	103.0	106.0					7																	84702334		2203	4300	6503	84540270	SO:0001583	missense	223117	exon4			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"""Semaphorins"", ""Immunoglobulin superfamily / V-set domain containing"""	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.439G>A	7.37:g.84702334C>T	ENSP00000284136:p.Gly147Arg	Somatic		Capture	Illumina HiSeq	Phase_I	84540270	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.787793	0.90367	.	.	ENSG00000153993	ENST00000284136;ENST00000444867	T;T	0.70986	-0.53;-0.53	5.07	5.07	0.68467	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	D	0.89876	0.6842	H	0.97051	3.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.994	D	0.93353	0.6720	10	0.72032	D	0.01	.	18.4481	0.90693	0.0:1.0:0.0:0.0	.	147;147	C9JYT6;O95025	.;SEM3D_HUMAN	R	147	ENSP00000284136:G147R;ENSP00000401366:G147R	ENSP00000284136:G147R	G	-	1	0	SEMA3D	84540270	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.938000	0.75904	2.331000	0.79229	0.557000	0.71058	GGA		0.333	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754	
KIAA1324L	222223	broad.mit.edu	37	7	86547810	86547810	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:86547810G>A	ENST00000450689.2	-	12	1726	c.1541C>T	c.(1540-1542)aCa>aTa	p.T514I	KIAA1324L_ENST00000416314.1_Missense_Mutation_p.T347I|KIAA1324L_ENST00000444627.1_Missense_Mutation_p.T514I|KIAA1324L_ENST00000297222.6_Missense_Mutation_p.T274I|KIAA1324L_ENST00000490995.1_5'UTR	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	514						integral component of membrane (GO:0016021)		p.T274I(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					AAAGACAAATGTTATTCTTCC	0.398																																					p.T347I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1040T	7						.						134.0	114.0	120.0					7																	86547810		2203	4300	6503	86385746	SO:0001583	missense	222223	exon11			AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"""EIG121-like"""	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.1541C>T	7.37:g.86547810G>A	ENSP00000413445:p.Thr514Ile	Somatic		Capture	Illumina HiSeq	Phase_I	86385746	NM_152748	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Missense_Mutation	SNP	ENST00000450689.2	37	CCDS47632.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.021840	0.75275	.	.	ENSG00000164659	ENST00000450689;ENST00000297222;ENST00000444627;ENST00000416314	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	5.84	3.94	0.45596	Growth factor, receptor (1);	0.102562	0.64402	D	0.000003	T	0.66157	0.2761	M	0.78637	2.42	0.80722	D	1	D;P;P	0.62365	0.991;0.836;0.836	D;P;P	0.65443	0.935;0.603;0.603	T	0.71262	-0.4645	10	0.72032	D	0.01	.	12.6345	0.56675	0.0713:0.1275:0.8012:0.0	.	514;274;347	A8MWY0;A8MWY0-2;B4DJV3	K132L_HUMAN;.;.	I	514;274;514;347	ENSP00000413445:T514I;ENSP00000297222:T274I;ENSP00000397377:T514I;ENSP00000402390:T347I	ENSP00000297222:T274I	T	-	2	0	KIAA1324L	86385746	1.000000	0.71417	0.918000	0.36340	0.920000	0.55202	6.624000	0.74243	1.492000	0.48499	0.655000	0.94253	ACA		0.398	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748	
DMTF1	9988	broad.mit.edu	37	7	86817542	86817542	+	Missense_Mutation	SNP	C	C	T	rs199931097		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:86817542C>T	ENST00000394703.5	+	15	1899	c.1336C>T	c.(1336-1338)Cgc>Tgc	p.R446C	DMTF1_ENST00000414194.2_Missense_Mutation_p.R180C|DMTF1_ENST00000413276.2_Intron|DMTF1_ENST00000331242.7_Missense_Mutation_p.R446C|DMTF1_ENST00000432937.2_Missense_Mutation_p.R358C	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	446	Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R446C(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					AAGAGTTGCCCGCTTGGAAGA	0.433													C|||	1	0.000199681	0.0	0.0	5008	,	,		17921	0.0		0.001	False		,,,				2504	0.0				p.R446C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1336T	7						.						169.0	161.0	164.0					7																	86817542		2203	4300	6503	86655478	SO:0001583	missense	9988	exon13			AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"""cyclin D-binding Myb-like protein"""	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.1336C>T	7.37:g.86817542C>T	ENSP00000378193:p.Arg446Cys	Somatic		Capture	Illumina HiSeq	Phase_I	86655478	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Missense_Mutation	SNP	ENST00000394703.5	37	CCDS5601.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	27.0	4.794106	0.90453	.	.	ENSG00000135164	ENST00000331242;ENST00000432937;ENST00000394703;ENST00000414194	T;T;T;T	0.52754	0.72;0.73;0.72;0.65	5.57	5.57	0.84162	.	0.104042	0.64402	D	0.000002	T	0.37073	0.0990	N	0.14661	0.345	0.58432	D	0.999999	D	0.60575	0.988	B	0.43225	0.412	T	0.38802	-0.9644	10	0.62326	D	0.03	-0.965	18.9103	0.92481	0.0:1.0:0.0:0.0	.	446	Q9Y222	DMTF1_HUMAN	C	446;358;446;180	ENSP00000332171:R446C;ENSP00000412532:R358C;ENSP00000378193:R446C;ENSP00000415910:R180C	ENSP00000332171:R446C	R	+	1	0	DMTF1	86655478	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.807000	0.75201	2.780000	0.95670	0.655000	0.94253	CGC		0.433	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145	
AKAP9	10142	broad.mit.edu	37	7	91570448	91570448	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:91570448C>T	ENST00000359028.2	+	1	260	c.35C>T	c.(34-36)gCc>gTc	p.A12V	AKAP9_ENST00000358100.2_Missense_Mutation_p.A12V|AKAP9_ENST00000394564.1_Missense_Mutation_p.A12V|AKAP9_ENST00000356239.3_Missense_Mutation_p.A12V			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	12					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.A12V(2)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AAGCTGGAGGCCGGCAAAGCC	0.652			T	BRAF	papillary thyroid																																p.A12V			Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C35T	7						.						86.0	87.0	87.0					7																	91570448		2203	4300	6503	91408384	SO:0001583	missense	10142	exon1			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.35C>T	7.37:g.91570448C>T	ENSP00000351922:p.Ala12Val	Somatic		Capture	Illumina HiSeq	Phase_I	91408384	NM_147185	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	C	21.7	4.194593	0.78902	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565;ENST00000394564	T;T;T;T	0.13901	2.55;3.25;3.22;2.55	4.63	4.63	0.57726	.	.	.	.	.	T	0.31513	0.0799	L	0.50333	1.59	0.42510	D	0.992964	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.87578	0.998;0.998;0.998;0.996	T	0.01810	-1.1269	9	0.66056	D	0.02	.	14.8557	0.70335	0.0:1.0:0.0:0.0	.	12;12;12;12	Q99996-2;Q99996-3;A4D1E4;Q6PJH3	.;.;.;.	V	12	ENSP00000348573:A12V;ENSP00000351922:A12V;ENSP00000350813:A12V;ENSP00000378065:A12V	ENSP00000348573:A12V	A	+	2	0	AKAP9	91408384	0.995000	0.38212	1.000000	0.80357	0.995000	0.86356	2.627000	0.46469	2.562000	0.86427	0.655000	0.94253	GCC		0.652	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
ANKIB1	54467	broad.mit.edu	37	7	91936914	91936914	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:91936914delA	ENST00000265742.3	+	3	806	c.430delA	c.(430-432)aaafs	p.K145fs		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	145							zinc ion binding (GO:0008270)	p.N146fs*12(2)		cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TGTTGATAACAAAAAAAACAC	0.363																																					p.K144fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.430delA	7						.						61.0	59.0	60.0					7																	91936914		1881	4106	5987	91774850	SO:0001589	frameshift_variant	54467	exon3			AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"""Ankyrin repeat domain containing"""	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.430delA	7.37:g.91936914delA	ENSP00000265742:p.Lys145fs	Somatic		Capture	Illumina HiSeq	Phase_I	91774850	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Frame_Shift_Del	DEL	ENST00000265742.3	37	CCDS47639.1																																																																																				0.363	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1		
ANKIB1	54467	broad.mit.edu	37	7	92017328	92017328	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:92017328G>A	ENST00000265742.3	+	14	2255	c.1879G>A	c.(1879-1881)Gag>Aag	p.E627K		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	627							zinc ion binding (GO:0008270)	p.E627K(1)		cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AGAAAAGATGGAGCAATTGAG	0.303																																					p.E627K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1879A	7						.						45.0	40.0	42.0					7																	92017328		1808	4062	5870	91855264	SO:0001583	missense	54467	exon14			AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"""Ankyrin repeat domain containing"""	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.1879G>A	7.37:g.92017328G>A	ENSP00000265742:p.Glu627Lys	Somatic		Capture	Illumina HiSeq	Phase_I	91855264	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Missense_Mutation	SNP	ENST00000265742.3	37	CCDS47639.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.338758	0.81911	.	.	ENSG00000001629	ENST00000265742	T	0.12255	2.7	5.47	5.47	0.80525	Zinc finger, RING-type (1);	0.000000	0.85682	D	0.000000	T	0.16599	0.0399	L	0.39397	1.21	0.58432	D	0.999998	P	0.36438	0.553	B	0.38655	0.278	T	0.01245	-1.1407	10	0.52906	T	0.07	.	17.8694	0.88807	0.0:0.0:1.0:0.0	.	627	Q9P2G1	AKIB1_HUMAN	K	627	ENSP00000265742:E627K	ENSP00000265742:E627K	E	+	1	0	ANKIB1	91855264	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.306000	0.78905	2.729000	0.93468	0.655000	0.94253	GAG		0.303	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1		
PON1	5444	broad.mit.edu	37	7	94937362	94937362	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:94937362A>G	ENST00000222381.3	-	6	890	c.659T>C	c.(658-660)tTt>tCt	p.F220S	PON1_ENST00000542556.1_Missense_Mutation_p.F220S	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	220					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)	p.F220S(1)		autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	AGCAAAATCAAATCCTTCTGC	0.413																																					p.F220S	GBM(119;715 1622 17358 22490 33240)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T659C	7						.						130.0	109.0	116.0					7																	94937362		2203	4300	6503	94775298	SO:0001583	missense	5444	exon6			AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"""Paraoxonases"""	9204	protein-coding gene	gene with protein product	"""esterase A"", ""arylesterase 1"""	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.659T>C	7.37:g.94937362A>G	ENSP00000222381:p.Phe220Ser	Somatic		Capture	Illumina HiSeq	Phase_I	94775298	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	CCDS5638.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.181287	0.38511	.	.	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.51574	0.7;0.7	4.95	3.78	0.43462	Six-bladed beta-propeller, TolB-like (1);	0.218007	0.48767	D	0.000164	T	0.74068	0.3668	M	0.94142	3.5	0.43152	D	0.994928	D;D	0.89917	1.0;0.999	D;D	0.85130	0.995;0.997	T	0.78685	-0.2108	10	0.87932	D	0	-10.3427	9.5365	0.39226	0.7186:0.0:0.0:0.2814	.	220;220	F5H4W9;P27169	.;PON1_HUMAN	S	220	ENSP00000222381:F220S;ENSP00000444854:F220S	ENSP00000222381:F220S	F	-	2	0	PON1	94775298	1.000000	0.71417	0.517000	0.27799	0.260000	0.26232	1.618000	0.36954	1.003000	0.39130	0.402000	0.26972	TTT		0.413	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446	
PON2	5445	broad.mit.edu	37	7	95039289	95039289	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:95039289A>G	ENST00000222572.3	-	6	865	c.619T>C	c.(619-621)Tac>Cac	p.Y207H	PON2_ENST00000536183.1_Missense_Mutation_p.Y228H|PON2_ENST00000433091.2_Missense_Mutation_p.Y195H|PON2_ENST00000483292.1_5'UTR			Q15165	PON2_HUMAN	paraoxonase 2	207					aromatic compound catabolic process (GO:0019439)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arylesterase activity (GO:0004064)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.Y207H(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			TTTGGACTGTAGTAAACAACA	0.363																																					p.Y207H	GBM(42;803 823 13649 23368 31463)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T619C	7						.						163.0	159.0	160.0					7																	95039289		2203	4300	6503	94877225	SO:0001583	missense	5445	exon6			M63012, AF001601	CCDS5640.1, CCDS47644.1	7q21.3	2014-03-14			ENSG00000105854	ENSG00000105854	3.1.1.2	"""Paraoxonases"""	9205	protein-coding gene	gene with protein product	"""paraoxonase nirs"", ""arylesterase 2"""	602447				8661009, 9714608	Standard	XM_005250453		Approved		uc003unv.3	Q15165	OTTHUMG00000153948	ENST00000222572.3:c.619T>C	7.37:g.95039289A>G	ENSP00000222572:p.Tyr207His	Somatic		Capture	Illumina HiSeq	Phase_I	94877225	NM_000305	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Missense_Mutation	SNP	ENST00000222572.3	37	CCDS5640.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.596931	0.87055	.	.	ENSG00000105854	ENST00000536183;ENST00000355659;ENST00000433091;ENST00000222572	T;T;T	0.61392	0.11;0.11;0.11	4.97	4.97	0.65823	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.80854	0.4703	M	0.92604	3.325	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.84259	0.0482	10	0.45353	T	0.12	-16.4818	15.1215	0.72447	1.0:0.0:0.0:0.0	.	207;207	A4D1H7;Q15165	.;PON2_HUMAN	H	228;205;195;207	ENSP00000440282:Y228H;ENSP00000404622:Y195H;ENSP00000222572:Y207H	ENSP00000222572:Y207H	Y	-	1	0	PON2	94877225	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.529000	0.90602	2.222000	0.72286	0.528000	0.53228	TAC		0.363	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305	
TRRAP	8295	broad.mit.edu	37	7	98533270	98533270	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:98533270A>G	ENST00000359863.4	+	28	4292	c.4083A>G	c.(4081-4083)tcA>tcG	p.S1361S	TRRAP_ENST00000446306.3_Silent_p.S1360S|TRRAP_ENST00000355540.3_Silent_p.S1361S	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	1361					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.S1361S(2)		NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GCCTTCCGTCACTCGTACCTT	0.378																																					p.S1361S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A4083G	7						.						89.0	82.0	85.0					7																	98533270		2203	4300	6503	98371206	SO:0001819	synonymous_variant	8295	exon28			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.4083A>G	7.37:g.98533270A>G		Somatic		Capture	Illumina HiSeq	Phase_I	98371206	NM_003496	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	A	0.459	-0.890012	0.02511	.	.	ENSG00000196367	ENST00000456197	.	.	.	6.17	-12.3	0.00002	.	.	.	.	.	T	0.44244	0.1284	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59768	-0.7392	4	.	.	.	.	8.0766	0.30720	0.238:0.0666:0.4983:0.1972	.	.	.	.	R	1076	.	.	H	+	2	0	TRRAP	98371206	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-2.580000	0.00907	-3.544000	0.00144	-1.763000	0.00667	CAC		0.378	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
TRRAP	8295	broad.mit.edu	37	7	98606078	98606078	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:98606078A>G	ENST00000359863.4	+	69	10999	c.10790A>G	c.(10789-10791)tAc>tGc	p.Y3597C	TRRAP_ENST00000446306.3_Missense_Mutation_p.Y3586C|TRRAP_ENST00000355540.3_Missense_Mutation_p.Y3568C	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	3597	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.Y3568C(1)|p.Y3597C(1)		NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GTGGAGATCTACAAGCAGCGC	0.607																																					p.Y3568C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A10703G	7						.						138.0	122.0	128.0					7																	98606078		2203	4300	6503	98444014	SO:0001583	missense	8295	exon68			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.10790A>G	7.37:g.98606078A>G	ENSP00000352925:p.Tyr3597Cys	Somatic		Capture	Illumina HiSeq	Phase_I	98444014	NM_003496	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.6|26.6	4.749958|4.749958	0.89753|0.89753	.|.	.|.	ENSG00000196367|ENSG00000196367	ENST00000456197|ENST00000359863;ENST00000355540;ENST00000446306	.|D;D	.|0.82344	.|-1.6;-1.6	5.54|5.54	5.54|5.54	0.83059|0.83059	.|Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.92450|0.92450	0.7603|0.7603	M|M	0.89840|0.89840	3.065|3.065	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.73708	.|0.974;0.981;0.979	D|D	0.93961|0.93961	0.7240|0.7240	5|10	.|0.87932	.|D	.|0	.|.	15.6762|15.6762	0.77326|0.77326	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|3568;3325;3597	.|Q9Y4A5-2;Q59FH1;Q9Y4A5	.|.;.;TRRAP_HUMAN	A|C	3326|3597;3568;3585	.|ENSP00000352925:Y3597C;ENSP00000347733:Y3568C	.|ENSP00000347733:Y3568C	T|Y	+|+	1|2	0|0	TRRAP|TRRAP	98444014|98444014	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.331000|9.331000	0.96430|0.96430	2.102000|2.102000	0.63906|0.63906	0.533000|0.533000	0.62120|0.62120	ACA|TAC		0.607	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
PTCD1	26024	broad.mit.edu	37	7	99030929	99030929	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:99030929A>C	ENST00000292478.4	-	3	816	c.566T>G	c.(565-567)cTg>cGg	p.L189R	PTCD1_ENST00000485746.1_5'UTR|ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.L238R|ATP5J2-PTCD1_ENST00000437572.1_5'Flank|PTCD1_ENST00000555673.1_Missense_Mutation_p.L238R	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	189					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)	p.L189R(1)		endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			GGCCTTCTTCAGGTAGCCAAC	0.612																																					p.L189R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T566G	7						.						142.0	136.0	138.0					7																	99030929		2203	4300	6503	98868865	SO:0001583	missense	26024	exon3			AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.566T>G	7.37:g.99030929A>C	ENSP00000292478:p.Leu189Arg	Somatic		Capture	Illumina HiSeq	Phase_I	98868865	NM_015545	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	37	CCDS34691.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.575855	0.86645	.	.	ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000555673;ENST00000413834	T;T;T	0.69040	-0.37;-0.37;-0.37	5.23	5.23	0.72850	.	0.265417	0.31051	N	0.008342	T	0.82038	0.4950	M	0.80508	2.5	0.43819	D	0.996387	D;D	0.89917	1.0;1.0	D;D	0.77004	0.988;0.989	D	0.84263	0.0484	10	0.56958	D	0.05	-11.2881	15.1208	0.72441	1.0:0.0:0.0:0.0	.	238;189	G3V325;O75127	.;PTCD1_HUMAN	R	189;238;238	ENSP00000292478:L189R;ENSP00000450995:L238R;ENSP00000400168:L238R	ENSP00000400168:L238R	L	-	2	0	ATP5J2-PTCD1;PTCD1	98868865	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	7.576000	0.82467	1.973000	0.57446	0.482000	0.46254	CTG		0.612	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545	
ZNF394	84124	broad.mit.edu	37	7	99091608	99091608	+	Silent	SNP	G	G	A	rs142908024		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:99091608G>A	ENST00000337673.6	-	3	1433	c.1230C>T	c.(1228-1230)ggC>ggT	p.G410G	ZNF394_ENST00000394177.3_5'Flank|ZNF394_ENST00000426306.2_3'UTR|ZNF789_ENST00000493485.1_Intron|ZNF789_ENST00000494186.1_Intron	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	410					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G410G(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					ACGGCTTCTCGCCTGTGTGTG	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		19500	0.001		0.0	False		,,,				2504	0.0				p.G410G	Ovarian(24;589 697 9939 12704 40742)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1230T	7						.	G		0,4406		0,0,2203	98.0	98.0	98.0		1230	-7.1	0.1	7	dbSNP_134	98	7,8593	5.7+/-21.5	1,5,4294	no	coding-synonymous	ZNF394	NM_032164.2		1,5,6497	AA,AG,GG		0.0814,0.0,0.0538		410/562	99091608	7,12999	2203	4300	6503	98929544	SO:0001819	synonymous_variant	84124	exon3			BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.1230C>T	7.37:g.99091608G>A		Somatic		Capture	Illumina HiSeq	Phase_I	98929544	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Silent	SNP	ENST00000337673.6	37	CCDS5666.1																																																																																				0.493	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164	
AP4M1	9179	broad.mit.edu	37	7	99703094	99703094	+	Silent	SNP	C	C	T	rs142325884	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:99703094C>T	ENST00000359593.4	+	11	1019	c.861C>T	c.(859-861)tcC>tcT	p.S287S	AP4M1_ENST00000422582.1_Silent_p.S159S|AP4M1_ENST00000421755.1_Silent_p.S287S|AP4M1_ENST00000429084.1_Silent_p.S294S	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	287	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|Golgi trans cisterna (GO:0000138)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)	p.S287S(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACCAACTCTCCGATGACCTCC	0.587													C|||	3	0.000599042	0.0008	0.0	5008	,	,		18582	0.001		0.001	False		,,,				2504	0.0				p.S287S	Pancreas(174;1182 2812 29595 49511)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C861T	7						.	C		2,4404	4.2+/-10.8	0,2,2201	120.0	99.0	106.0		861	-6.8	0.9	7	dbSNP_134	106	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	AP4M1	NM_004722.3		0,4,6499	TT,TC,CC		0.0233,0.0454,0.0308		287/454	99703094	4,13002	2203	4300	6503	99541030	SO:0001819	synonymous_variant	9179	exon11			Y08387	CCDS5685.1	7q22.1	2012-06-29			ENSG00000221838	ENSG00000221838			574	protein-coding gene	gene with protein product	"""mu-adaptin-related protein-2"", ""mu subunit of AP-4"", ""AP-4 adapter complex mu subunit"", ""adaptor-related protein complex AP-4 mu4 subunit"""	602296				9013859, 10066790, 21620353	Standard	NM_004722		Approved	MU-ARP2, MU-4, SPG50	uc003utb.4	O00189	OTTHUMG00000154722	ENST00000359593.4:c.861C>T	7.37:g.99703094C>T		Somatic		Capture	Illumina HiSeq	Phase_I	99541030	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Silent	SNP	ENST00000359593.4	37	CCDS5685.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	7.367	0.625946	0.14257	4.54E-4	2.33E-4	ENSG00000221838	ENST00000445295	.	.	.	5.38	-6.76	0.01732	.	.	.	.	.	T	0.48484	0.1502	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52983	-0.8502	4	.	.	.	-6.7416	8.423	0.32712	0.3823:0.5078:0.0:0.1099	.	.	.	.	L	13	.	.	P	+	2	0	AP4M1	99541030	0.104000	0.21937	0.922000	0.36590	0.582000	0.36321	-0.821000	0.04452	-1.026000	0.03330	-1.087000	0.02190	CCG		0.587	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722	
BCAP29	55973	broad.mit.edu	37	7	107234540	107234540	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:107234540delT	ENST00000005259.4	+	4	673	c.334delT	c.(334-336)tttfs	p.F113fs	BCAP29_ENST00000379119.2_Frame_Shift_Del_p.F113fs|BCAP29_ENST00000494086.1_3'UTR|BCAP29_ENST00000465919.1_Frame_Shift_Del_p.F19fs|BCAP29_ENST00000379117.2_Frame_Shift_Del_p.F113fs|BCAP29_ENST00000379121.2_Frame_Shift_Del_p.F19fs|BCAP29_ENST00000445771.2_Frame_Shift_Del_p.F113fs	NM_018844.3	NP_061332.2	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein 29	113					apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.W114fs*2(2)		cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	14						ATTTTCCCTATTTTTTTGGCT	0.328																																					p.F112fs												.	.	2	Deletion - Frameshift(2)	ovary(1)|large_intestine(1)	c.334delT	7						.						49.0	54.0	52.0					7																	107234540		2203	4300	6503	107021776	SO:0001589	frameshift_variant	55973	exon3				CCDS34730.1, CCDS34731.1	7q22.3	2012-09-20			ENSG00000075790	ENSG00000075790			24131	protein-coding gene	gene with protein product						12477932	Standard	NM_018844		Approved	BAP29, DKFZp686M2086	uc011kma.1	Q9UHQ4	OTTHUMG00000154770	ENST00000005259.4:c.334delT	7.37:g.107234540delT	ENSP00000005259:p.Phe113fs	Somatic		Capture	Illumina HiSeq	Phase_I	107021776	NM_001008405	G5E9L4|O95003	Frame_Shift_Del	DEL	ENST00000005259.4	37	CCDS34731.1																																																																																				0.328	BCAP29-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337011.2	NM_018844	
ESYT2	57488	broad.mit.edu	37	7	158528237	158528237	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr7:158528237T>C	ENST00000251527.5	-	20	2608	c.2543A>G	c.(2542-2544)aAc>aGc	p.N848S	ESYT2_ENST00000435514.2_Missense_Mutation_p.N283S	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	876	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)	p.N848S(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						GCCGCCACTGTTCTTCACGGC	0.448																																					p.N848S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2543G	7						.						161.0	168.0	166.0					7																	158528237		2203	4300	6503	158220998	SO:0001583	missense	57488	exon20			AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2543A>G	7.37:g.158528237T>C	ENSP00000251527:p.Asn848Ser	Somatic		Capture	Illumina HiSeq	Phase_I	158220998	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	37	CCDS34791.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.494127	0.44352	.	.	ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000435514	T;T;T	0.07800	3.16;3.16;3.16	5.59	5.59	0.84812	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.15435	0.0372	L	0.35487	1.065	0.58432	D	0.999999	D;P	0.53312	0.959;0.778	P;P	0.57152	0.805;0.814	T	0.02042	-1.1224	10	0.38643	T	0.18	-30.6804	14.9432	0.71009	0.0:0.0:0.0:1.0	.	848;876	A0FGR8-2;A0FGR8	.;ESYT2_HUMAN	S	848;897;839;283	ENSP00000251527:N848S;ENSP00000275418:N839S;ENSP00000411488:N283S	ENSP00000251527:N848S	N	-	2	0	ESYT2	158220998	1.000000	0.71417	1.000000	0.80357	0.035000	0.12851	7.535000	0.82014	2.132000	0.65825	0.533000	0.62120	AAC		0.448	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
RIMS2	9699	broad.mit.edu	37	8	104831793	104831794	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:104831793_104831794insT	ENST00000507740.1	+	1	294_295	c.58_59insT	c.(58-60)gttfs	p.V20fs	RIMS2_ENST00000262231.10_Frame_Shift_Ins_p.V20fs|RIMS2_ENST00000522174.1_3'UTR|RIMS2_ENST00000406091.3_Intron	NM_014677.4	NP_055492.3	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	0					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.S22fs*10(1)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TTTTCATGGGGTTTTTTCATCC	0.347										HNSCC(12;0.0054)																											p.V20fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.58_59insT	8						.																																			104900970	SO:0001589	frameshift_variant	9699	exon1			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000507740.1:c.64dupT	8.37:g.104831799_104831799dupT	ENSP00000423559:p.Val20fs	Somatic		Capture	Illumina HiSeq	Phase_I	104900969	NM_014677	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Frame_Shift_Ins	INS	ENST00000507740.1	37	CCDS43761.1																																																																																				0.347	RIMS2-005	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367215.1	NM_001100117	
DOCK5	80005	broad.mit.edu	37	8	25182988	25182989	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:25182988_25182989insC	ENST00000276440.7	+	18	1872_1873	c.1828_1829insC	c.(1828-1830)accfs	p.T610fs		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	610	DHR-1.				positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.S612fs*4(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		GGTCACCTTCACCCCAAGCAAG	0.46																																					p.T610fs	Pancreas(145;34 1887 3271 10937 30165)											.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1828_1829insC	8						.																																			25238906	SO:0001589	frameshift_variant	80005	exon18				CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.1832dupC	8.37:g.25182992_25182992dupC	ENSP00000276440:p.Thr610fs	Somatic		Capture	Illumina HiSeq	Phase_I	25238905	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Frame_Shift_Ins	INS	ENST00000276440.7	37	CCDS6047.1																																																																																				0.460	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
PREX2	80243	broad.mit.edu	37	8	68992683	68992684	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:68992683_68992684insA	ENST00000288368.4	+	16	1925_1926	c.1648_1649insA	c.(1648-1650)gaafs	p.E550fs	RP11-403D15.2_ENST00000526901.1_RNA|PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	550	DEP 2. {ECO:0000255|PROSITE- ProRule:PRU00066}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.S552fs*6(2)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TGTAGTCCTTGAAAAAAGCGAA	0.342																																					p.E550fs												.	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.1648_1649insA	8						.																																			69155238	SO:0001589	frameshift_variant	80243	exon16			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1654dupA	8.37:g.68992689_68992689dupA	ENSP00000288368:p.Glu550fs	Somatic		Capture	Illumina HiSeq	Phase_I	69155237	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Frame_Shift_Ins	INS	ENST00000288368.4	37	CCDS6201.1																																																																																				0.342	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
VPS13B	157680	broad.mit.edu	37	8	100866185	100866185	+	Missense_Mutation	SNP	A	A	G	rs398124326		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:100866185A>G	ENST00000358544.2	+	56	10754	c.10643A>G	c.(10642-10644)tAc>tGc	p.Y3548C	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.Y3523C	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3548					protein transport (GO:0015031)			p.Y3523C(1)|p.Y3548C(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TTTGACACCTACCTTCCTAAC	0.473																																					p.Y3523C	Colon(161;2205 2542 7338 31318)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A10568G	8						.						102.0	104.0	103.0					8																	100866185		2203	4300	6503	100935361	SO:0001583	missense	157680	exon56			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.10643A>G	8.37:g.100866185A>G	ENSP00000351346:p.Tyr3548Cys	Somatic		Capture	Illumina HiSeq	Phase_I	100935361	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.956231	0.73902	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.69306	-0.39;-0.39	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.68979	0.3060	N	0.13043	0.29	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.984;0.997	T	0.71411	-0.4601	10	0.38643	T	0.18	.	15.6676	0.77242	1.0:0.0:0.0:0.0	.	3523;3548	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	C	3523;3548	ENSP00000349685:Y3523C;ENSP00000351346:Y3548C	ENSP00000349685:Y3523C	Y	+	2	0	VPS13B	100935361	1.000000	0.71417	0.998000	0.56505	0.938000	0.57974	6.732000	0.74790	2.098000	0.63641	0.454000	0.30748	TAC		0.473	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
SOX7	83595	broad.mit.edu	37	8	10583859	10583859	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:10583859C>A	ENST00000304501.1	-	2	634	c.556G>T	c.(556-558)Ggc>Tgc	p.G186C	SOX7_ENST00000554914.1_Missense_Mutation_p.G238C|SOX7_ENST00000553390.1_Missense_Mutation_p.G238C|CTD-2135J3.3_ENST00000506149.2_RNA	NM_031439.2	NP_113627.1	Q9BT81	SOX7_HUMAN	SRY (sex determining region Y)-box 7	186					endoderm formation (GO:0001706)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|regulation of canonical Wnt signaling pathway (GO:0060828)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.G186C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		CCGCCGCCGCCACCACCAGCC	0.716																																					p.G186C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G556T	8						.						13.0	15.0	14.0					8																	10583859		2141	4189	6330	10621269	SO:0001583	missense	83595	exon2			AJ409320	CCDS5977.1	8p22	2013-01-25			ENSG00000171056	ENSG00000171056		"""SRY (sex determining region Y)-boxes"""	18196	protein-coding gene	gene with protein product		612202				11691915	Standard	NM_031439		Approved		uc003wtf.3	Q9BT81	OTTHUMG00000090585	ENST00000304501.1:c.556G>T	8.37:g.10583859C>A	ENSP00000301921:p.Gly186Cys	Somatic		Capture	Illumina HiSeq	Phase_I	10621269	NM_031439	B4DKV0|Q53YD0	Missense_Mutation	SNP	ENST00000304501.1	37	CCDS5977.1	.	.	.	.	.	.	.	.	.	.	C	8.669	0.902459	0.17760	.	.	ENSG00000171056;ENSG00000171056;ENSG00000258724	ENST00000304501;ENST00000553390;ENST00000554914	D;D;D	0.99466	-5.03;-5.95;-5.95	1.16	-1.39	0.08997	.	0.216636	0.23284	U	0.049877	D	0.97848	0.9293	N	0.14661	0.345	0.20074	N	0.999938	D;D	0.76494	0.999;0.986	D;P	0.70935	0.971;0.756	D	0.94026	0.7297	10	0.38643	T	0.18	.	3.2394	0.06776	0.5213:0.4787:0.0:0.0	.	238;186	B4DKV0;Q9BT81	.;SOX7_HUMAN	C	186;238;238	ENSP00000301921:G186C;ENSP00000452017:G238C;ENSP00000451145:G238C	ENSP00000346908:G238C	G	-	1	0	SOX7;CTD-2135J3.4	10621269	0.093000	0.21703	0.039000	0.18376	0.758000	0.43043	0.878000	0.28126	0.202000	0.20498	0.205000	0.17691	GGC		0.716	SOX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207131.1		
FAM167A	83648	broad.mit.edu	37	8	11282090	11282090	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:11282090C>A	ENST00000528897.1	-	3	1056	c.437G>T	c.(436-438)gGc>gTc	p.G146V	C8orf12_ENST00000529305.1_Intron|FAM167A_ENST00000531564.1_5'UTR|FAM167A_ENST00000284486.4_Missense_Mutation_p.G146V|C8orf12_ENST00000284481.3_Intron|FAM167A_ENST00000534308.1_Missense_Mutation_p.G146V			Q96KS9	F167A_HUMAN	family with sequence similarity 167, member A	146								p.G146V(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)	9						GTTGATGTCGCCACGCAGGCG	0.627																																					p.G146V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G437T	8						.						102.0	77.0	85.0					8																	11282090		2203	4300	6503	11319500	SO:0001583	missense	83648	exon3				CCDS5981.1	8p23-p22	2010-08-27	2008-06-11	2008-06-11	ENSG00000154319	ENSG00000154319			15549	protein-coding gene	gene with protein product		610085	"""chromosome 8 open reading frame 13"""	C8orf13			Standard	NM_053279		Approved		uc003wtw.2	Q96KS9	OTTHUMG00000129361	ENST00000528897.1:c.437G>T	8.37:g.11282090C>A	ENSP00000436655:p.Gly146Val	Somatic		Capture	Illumina HiSeq	Phase_I	11319500	NM_053279	A8K3T9|Q3SXY1|Q3SXY3|Q8N3M3|Q9NSR0	Missense_Mutation	SNP	ENST00000528897.1	37	CCDS5981.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.076516	0.55753	.	.	ENSG00000154319	ENST00000284486;ENST00000534308;ENST00000528897	T;T;T	0.29917	1.55;1.55;1.55	4.91	4.91	0.64330	.	0.210963	0.48767	D	0.000170	T	0.27629	0.0679	N	0.08118	0	0.58432	D	0.999999	P	0.51147	0.942	P	0.51777	0.679	T	0.14587	-1.0467	10	0.41790	T	0.15	-0.7158	17.3188	0.87231	0.0:1.0:0.0:0.0	.	146	Q96KS9	F167A_HUMAN	V	146	ENSP00000284486:G146V;ENSP00000432232:G146V;ENSP00000436655:G146V	ENSP00000284486:G146V	G	-	2	0	FAM167A	11319500	1.000000	0.71417	0.160000	0.22671	0.225000	0.24961	5.426000	0.66476	2.558000	0.86282	0.555000	0.69702	GGC		0.627	FAM167A-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000383901.1		
BLK	640	broad.mit.edu	37	8	11412389	11412389	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:11412389C>T	ENST00000259089.4	+	7	1202	c.610C>T	c.(610-612)Cac>Tac	p.H204Y	RP11-148O21.6_ENST00000602626.1_lincRNA|RP11-148O21.3_ENST00000527922.1_RNA|RP11-148O21.4_ENST00000528629.1_RNA|BLK_ENST00000529894.1_Missense_Mutation_p.H133Y	NM_001715.2	NP_001706.2	P51451	BLK_HUMAN	BLK proto-oncogene, Src family tyrosine kinase	204	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				B cell receptor signaling pathway (GO:0050853)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of insulin secretion (GO:0032024)	plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.H204Y(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(4)|stomach(1)	27			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)		CCTGGTGCAGCACTATTCTAG	0.582																																					p.H204Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C610T	8						.						30.0	29.0	29.0					8																	11412389		2203	4300	6503	11449798	SO:0001583	missense	640	exon7			BC004473	CCDS5982.1	8p23-p22	2014-06-25	2014-06-25		ENSG00000136573	ENSG00000136573		"""SH2 domain containing"""	1057	protein-coding gene	gene with protein product		191305	"""B lymphoid tyrosine kinase"""			7845672	Standard	NM_001715		Approved	MGC10442	uc003wty.3	P51451	OTTHUMG00000090729	ENST00000259089.4:c.610C>T	8.37:g.11412389C>T	ENSP00000259089:p.His204Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	11449798	NM_001715	Q16291|Q96IN1	Missense_Mutation	SNP	ENST00000259089.4	37	CCDS5982.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.137973	0.37728	.	.	ENSG00000136573	ENST00000259089;ENST00000427279;ENST00000529894	T;T	0.26067	1.76;1.76	4.57	3.7	0.42460	SH2 motif (5);	0.000000	0.45606	D	0.000349	T	0.23210	0.0561	L	0.33624	1.015	0.80722	D	1	B	0.32717	0.381	B	0.41646	0.362	T	0.05068	-1.0908	10	0.37606	T	0.19	.	8.5061	0.33188	0.0:0.8216:0.0:0.1784	.	204	P51451	BLK_HUMAN	Y	204;204;133	ENSP00000259089:H204Y;ENSP00000433663:H133Y	ENSP00000259089:H204Y	H	+	1	0	BLK	11449798	0.487000	0.25988	1.000000	0.80357	0.914000	0.54420	0.754000	0.26390	1.050000	0.40346	0.462000	0.41574	CAC		0.582	BLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207460.1		
PABPC1	26986	broad.mit.edu	37	8	101724923	101724923	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:101724923C>T	ENST00000318607.5	-	6	1961	c.833G>A	c.(832-834)cGc>cAc	p.R278H	PABPC1_ENST00000522387.1_Missense_Mutation_p.R246H|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000519004.1_Missense_Mutation_p.R233H	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	278	CSDE1-binding.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)	p.R278H(1)		breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TTCAAATTTGCGCTTAAGTTC	0.408																																					p.R278H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G833A	8						.						153.0	143.0	146.0					8																	101724923		2203	4300	6503	101794099	SO:0001583	missense	26986	exon6			Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.833G>A	8.37:g.101724923C>T	ENSP00000313007:p.Arg278His	Somatic		Capture	Illumina HiSeq	Phase_I	101794099	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.5|22.5	4.301453|4.301453	0.81136|0.81136	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000517403;ENST00000519100|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387	.|T;T;T	.|0.06371	.|3.31;3.31;3.31	5.57|5.57	5.57|5.57	0.84162|0.84162	.|.	.|0.000000	.|0.64402	.|D	.|0.000008	T|T	0.10121|0.10121	0.0248|0.0248	L|L	0.55834|0.55834	1.745|1.745	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.30686	.|0.073;0.29;0.29	.|B;B;B	.|0.25884	.|0.021;0.043;0.064	T|T	0.04551|0.04551	-1.0943|-1.0943	5|10	.|0.56958	.|D	.|0.05	.|.	19.9103|19.9103	0.97024|0.97024	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|246;278;278	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	T|H	23;147|278;278;233;246	.|ENSP00000313007:R278H;ENSP00000429594:R233H;ENSP00000429395:R246H	.|ENSP00000313007:R278H	A|R	-|-	1|2	0|0	PABPC1|PABPC1	101794099|101794099	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.789000|7.789000	0.85783|0.85783	2.779000|2.779000	0.95612|0.95612	0.655000|0.655000	0.94253|0.94253	GCA|CGC		0.408	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
ENPP2	5168	broad.mit.edu	37	8	120608091	120608091	+	Intron	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:120608091T>G	ENST00000075322.6	-	12	1031				ENPP2_ENST00000427067.2_Intron|ENPP2_ENST00000522826.1_Intron|ENPP2_ENST00000522167.1_5'Flank|ENPP2_ENST00000259486.6_Missense_Mutation_p.D375A	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2						cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.D375A(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			ACTTACTTTGTCCTGACGAGT	0.448																																					p.D375A	Melanoma(20;305 879 2501 4818 31020)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1124C	8						.						139.0	139.0	139.0					8																	120608091		2203	4300	6503	120677272	SO:0001627	intron_variant	5168	exon12			D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.973-1991A>C	8.37:g.120608091T>G		Somatic		Capture	Illumina HiSeq	Phase_I	120677272	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.284178	0.40394	.	.	ENSG00000136960	ENST00000259486	T	0.72394	-0.65	6.07	6.07	0.98685	.	0.000000	0.42821	D	0.000659	T	0.56572	0.1994	.	.	.	0.80722	D	1	B	0.26809	0.16	B	0.28305	0.088	T	0.54070	-0.8348	9	0.10111	T	0.7	.	15.2117	0.73230	0.0:0.0:0.0:1.0	.	375	Q13822-2	.	A	375	ENSP00000259486:D375A	ENSP00000259486:D375A	D	-	2	0	ENPP2	120677272	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.896000	0.63222	2.326000	0.78906	0.533000	0.62120	GAC		0.448	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
EFR3A	23167	broad.mit.edu	37	8	133014008	133014008	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:133014008T>C	ENST00000254624.5	+	20	2385	c.2160T>C	c.(2158-2160)gtT>gtC	p.V720V	EFR3A_ENST00000334503.4_Silent_p.V720V|EFR3A_ENST00000521940.1_3'UTR|EFR3A_ENST00000519656.1_Silent_p.V684V	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	720						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)		p.V720V(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			TTCTCTAGGTTAGTAACACTG	0.308																																					p.V720V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2160C	8						.						127.0	134.0	131.0					8																	133014008		2203	4300	6503	133083190	SO:0001819	synonymous_variant	23167	exon20			D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.2160T>C	8.37:g.133014008T>C		Somatic		Capture	Illumina HiSeq	Phase_I	133083190	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Silent	SNP	ENST00000254624.5	37	CCDS34942.2																																																																																				0.308	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137	
PHF20L1	51105	broad.mit.edu	37	8	133848922	133848922	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:133848922C>T	ENST00000395386.2	+	16	2346	c.2047C>T	c.(2047-2049)Cga>Tga	p.R683*	AF230666.2_ENST00000608375.1_RNA|PHF20L1_ENST00000395390.2_Nonsense_Mutation_p.R658*|PHF20L1_ENST00000220847.7_Nonsense_Mutation_p.R70*|AF230666.2_ENST00000429151.1_RNA	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	683							zinc ion binding (GO:0008270)	p.R657*(2)		breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TGAAATTGTGCGATGTATTTG	0.408																																					p.R683X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C2047T	8						.						190.0	183.0	185.0					8																	133848922		1969	4147	6116	133918104	SO:0001587	stop_gained	51105	exon16			AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24280	protein-coding gene	gene with protein product	"""tudor domain containing 20B"""					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.2047C>T	8.37:g.133848922C>T	ENSP00000378784:p.Arg683*	Somatic		Capture	Illumina HiSeq	Phase_I	133918104	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Nonsense_Mutation	SNP	ENST00000395386.2	37	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	C	38	7.083629	0.98051	.	.	ENSG00000129292	ENST00000395386;ENST00000220847;ENST00000395390	.	.	.	5.14	3.02	0.34903	.	0.103999	0.38111	U	0.001810	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6783	12.4875	0.55881	0.3889:0.6111:0.0:0.0	.	.	.	.	X	683;70;658	.	ENSP00000220847:R70X	R	+	1	2	PHF20L1	133918104	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	2.219000	0.42899	1.289000	0.44618	0.544000	0.68410	CGA		0.408	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018	
TG	7038	broad.mit.edu	37	8	133948010	133948010	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:133948010G>A	ENST00000220616.4	+	25	4982	c.4942G>A	c.(4942-4944)Gca>Aca	p.A1648T	TG_ENST00000542445.1_Missense_Mutation_p.A82T|TG_ENST00000377869.1_Missense_Mutation_p.A1591T	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1648					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.A1648T(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GAAACGAGATGCACTGGGGAA	0.453																																					p.A1648T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4942A	8						.						94.0	82.0	86.0					8																	133948010		2203	4300	6503	134017192	SO:0001583	missense	7038	exon25			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4942G>A	8.37:g.133948010G>A	ENSP00000220616:p.Ala1648Thr	Somatic		Capture	Illumina HiSeq	Phase_I	134017192	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.23|11.23	1.578533|1.578533	0.28180|0.28180	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445|ENST00000519178	T;T;T|.	0.68765|.	-0.35;-0.35;-0.35|.	6.16|6.16	-0.176|-0.176	0.13311|0.13311	.|.	0.593799|.	0.17049|.	N|.	0.189009|.	T|T	0.24774|0.24774	0.0601|0.0601	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	1|1	B;B|.	0.17268|.	0.021;0.016|.	B;B|.	0.16289|.	0.015;0.009|.	T|T	0.26052|0.26052	-1.0114|-1.0114	10|5	0.36615|.	T|.	0.2|.	.|.	4.3227|4.3227	0.11025|0.11025	0.4619:0.0:0.382:0.1561|0.4619:0.0:0.382:0.1561	.|.	82;1648|.	F5GWW5;P01266|.	.;THYG_HUMAN|.	T|Y	1591;454;1648;82|167	ENSP00000367100:A1591T;ENSP00000220616:A1648T;ENSP00000441693:A82T|.	ENSP00000220616:A1648T|.	A|C	+|+	1|2	0|0	TG|TG	134017192|134017192	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.069000|0.069000	0.16628|0.16628	0.077000|0.077000	0.14738|0.14738	-0.096000|-0.096000	0.12329|0.12329	0.650000|0.650000	0.86243|0.86243	GCA|TGC		0.453	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
TG	7038	broad.mit.edu	37	8	134034346	134034346	+	Silent	SNP	C	C	T	rs140927008		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:134034346C>T	ENST00000220616.4	+	40	7027	c.6987C>T	c.(6985-6987)atC>atT	p.I2329I	TG_ENST00000542445.1_Silent_p.I699I|TG_ENST00000377869.1_Silent_p.I2272I|TG_ENST00000519543.1_Silent_p.I462I	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2329					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.I2329I(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GCAACCTCATCGTGGTCACTG	0.597																																					p.I2329I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C6987T	8						.	C		0,4406		0,0,2203	158.0	140.0	146.0		6987	-2.0	1.0	8	dbSNP_134	146	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TG	NM_003235.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		2329/2769	134034346	1,13005	2203	4300	6503	134103528	SO:0001819	synonymous_variant	7038	exon40			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.6987C>T	8.37:g.134034346C>T		Somatic		Capture	Illumina HiSeq	Phase_I	134103528	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	C	11.15	1.555220	0.27739	0.0	1.16E-4	ENSG00000042832	ENST00000519178;ENST00000518108	.	.	.	5.93	-2.05	0.07321	.	.	.	.	.	T	0.51007	0.1649	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43956	-0.9359	4	.	.	.	.	7.0804	0.25227	0.1092:0.4679:0.0:0.4229	.	.	.	.	C	785;125	.	.	R	+	1	0	TG	134103528	0.002000	0.14202	0.987000	0.45799	0.966000	0.64601	-1.443000	0.02405	-0.295000	0.08960	0.561000	0.74099	CGT		0.597	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
KHDRBS3	10656	broad.mit.edu	37	8	136561025	136561025	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:136561025C>T	ENST00000355849.5	+	4	763	c.353C>T	c.(352-354)gCg>gTg	p.A118V	KHDRBS3_ENST00000520981.1_Intron	NM_006558.1	NP_006549.1	O75525	KHDR3_HUMAN	KH domain containing, RNA binding, signal transduction associated 3	118	KH.				regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A118V(1)		NS(1)|endometrium(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	26	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.247)			AGTGGAGAAGCGAAGTACTTC	0.363																																					p.A118V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C353T	8						.						73.0	60.0	64.0					8																	136561025		2203	4300	6503	136630207	SO:0001583	missense	10656	exon4			AF069681	CCDS6374.1	8q24.23	2008-05-15			ENSG00000131773	ENSG00000131773			18117	protein-coding gene	gene with protein product		610421				10332027, 10564820	Standard	XR_242372		Approved	T-STAR, Etle, etoile, SALP, SLM2, SLM-2	uc003yuv.3	O75525	OTTHUMG00000164164	ENST00000355849.5:c.353C>T	8.37:g.136561025C>T	ENSP00000348108:p.Ala118Val	Somatic		Capture	Illumina HiSeq	Phase_I	136630207	NM_006558	Q6NUL8|Q9UPA8	Missense_Mutation	SNP	ENST00000355849.5	37	CCDS6374.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.2|25.2	4.612550|4.612550	0.87258|0.87258	.|.	.|.	ENSG00000131773|ENSG00000131773	ENST00000355849;ENST00000524199;ENST00000517394|ENST00000524282	T;T;T|.	0.20200|.	2.09;2.09;2.09|.	5.91|5.91	5.91|5.91	0.95273|0.95273	K Homology (1);|.	0.048033|.	0.85682|.	D|.	0.000000|.	T|.	0.67420|.	0.2891|.	L|L	0.41236|0.41236	1.265|1.265	0.80722|0.80722	D|D	1|1	D;P|.	0.69078|.	0.997;0.582|.	P;B|.	0.56514|.	0.8;0.119|.	T|.	0.61083|.	-0.7134|.	10|.	0.72032|.	D|.	0.01|.	-23.8349|-23.8349	19.2892|19.2892	0.94092|0.94092	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	118;118|.	O75525-2;O75525|.	.;KHDR3_HUMAN|.	V|X	118;90;91|33	ENSP00000348108:A118V;ENSP00000431022:A90V;ENSP00000430284:A91V|.	ENSP00000348108:A118V|.	A|R	+|+	2|1	0|2	KHDRBS3|KHDRBS3	136630207|136630207	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.990000|0.990000	0.78478|0.78478	4.763000|4.763000	0.62257|0.62257	2.804000|2.804000	0.96469|0.96469	0.650000|0.650000	0.86243|0.86243	GCG|CGA		0.363	KHDRBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377529.1		
FAM135B	51059	broad.mit.edu	37	8	139151337	139151337	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:139151337A>G	ENST00000395297.1	-	18	3963	c.3793T>C	c.(3793-3795)Tta>Cta	p.L1265L		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1265								p.L1265L(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			ATGAGCCATAAGCCTAGGaag	0.373										HNSCC(54;0.14)																											p.L1265L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T3793C	8						.						89.0	83.0	85.0					8																	139151337		1833	4092	5925	139220519	SO:0001819	synonymous_variant	51059	exon18			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3793T>C	8.37:g.139151337A>G		Somatic		Capture	Illumina HiSeq	Phase_I	139220519	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																				0.373	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
FAM135B	51059	broad.mit.edu	37	8	139164067	139164067	+	Missense_Mutation	SNP	C	C	T	rs143605493	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:139164067C>T	ENST00000395297.1	-	13	2821	c.2651G>A	c.(2650-2652)cGc>cAc	p.R884H		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	884								p.R884H(4)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TGCTATGACGCGTGGTATTTT	0.463										HNSCC(54;0.14)			C|||	3	0.000599042	0.0008	0.0014	5008	,	,		20098	0.001		0.0	False		,,,				2504	0.0				p.R884H												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G2651A	8						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	118.0	110.0	112.0		2651	-0.4	0.0	8	dbSNP_134	112	0,8600		0,0,4300	yes	missense	FAM135B	NM_015912.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	884/1407	139164067	1,13005	2203	4300	6503	139233249	SO:0001583	missense	51059	exon13			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.2651G>A	8.37:g.139164067C>T	ENSP00000378710:p.Arg884His	Somatic		Capture	Illumina HiSeq	Phase_I	139233249	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.093	1.002180	0.19121	2.27E-4	0.0	ENSG00000147724	ENST00000395297	T	0.13538	2.58	5.33	-0.4	0.12411	.	1.043410	0.07411	N	0.892363	T	0.07683	0.0193	N	0.17082	0.46	0.09310	N	1	B;B;B	0.17465	0.022;0.002;0.001	B;B;B	0.09377	0.004;0.003;0.001	T	0.40924	-0.9537	10	0.29301	T	0.29	0.2605	5.4294	0.16444	0.0:0.4851:0.1443:0.3706	.	884;884;884	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	H	884	ENSP00000378710:R884H	ENSP00000276737:R884H	R	-	2	0	FAM135B	139233249	0.000000	0.05858	0.003000	0.11579	0.011000	0.07611	-1.754000	0.01816	-0.014000	0.14175	0.655000	0.94253	CGC		0.463	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
TSNARE1	203062	broad.mit.edu	37	8	143427172	143427172	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:143427172A>G	ENST00000307180.3	-	3	287	c.170T>C	c.(169-171)gTg>gCg	p.V57A	TSNARE1_ENST00000524325.1_Missense_Mutation_p.V57A|TSNARE1_ENST00000519651.1_Intron|TSNARE1_ENST00000520166.1_Missense_Mutation_p.V57A	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	57					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)	p.V57A(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					GTCCTTCCCCACACAGCGGTT	0.612																																					p.V57A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T170C	8						.						108.0	90.0	96.0					8																	143427172		2203	4300	6503	143425079	SO:0001583	missense	203062	exon3					8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.170T>C	8.37:g.143427172A>G	ENSP00000303437:p.Val57Ala	Somatic		Capture	Illumina HiSeq	Phase_I	143425079	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	37	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	A	12.65	2.001552	0.35320	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000520462;ENST00000518720	T;T;T;T;T	0.32753	2.35;2.35;2.35;1.49;1.44	2.62	1.46	0.22682	.	0.348573	0.16515	U	0.211092	T	0.15825	0.0381	L	0.27053	0.805	0.09310	N	1	B;B;B	0.32717	0.381;0.381;0.381	B;B;B	0.20384	0.029;0.029;0.029	T	0.15780	-1.0425	10	0.87932	D	0	-0.0878	4.4312	0.11529	0.8412:0.0:0.1588:0.0	.	57;57;57	B7ZLB0;Q96NA8;A0AVG3	.;TSNA1_HUMAN;.	A	57;57;57;57;73	ENSP00000428763:V57A;ENSP00000303437:V57A;ENSP00000427770:V57A;ENSP00000429626:V57A;ENSP00000430789:V73A	ENSP00000303437:V57A	V	-	2	0	TSNARE1	143425079	0.000000	0.05858	0.074000	0.20217	0.923000	0.55619	-0.023000	0.12456	0.431000	0.26258	0.528000	0.53228	GTG		0.612	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
CYP11B1	1584	broad.mit.edu	37	8	143958160	143958160	+	Missense_Mutation	SNP	C	C	T	rs148066255		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:143958160C>T	ENST00000292427.4	-	4	769	c.737G>A	c.(736-738)cGc>cAc	p.R246H	CYP11B1_ENST00000517471.1_Missense_Mutation_p.R246H|CYP11B1_ENST00000377675.3_Missense_Mutation_p.R317H	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	246					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)	p.R246H(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	GCTGGTCCAGCGAGACAGGCT	0.612									Familial Hyperaldosteronism type I																												p.R246H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G737A	8						.	C	HIS/ARG,HIS/ARG	2,4404		0,2,2201	48.0	43.0	45.0		737,737	3.6	0.2	8	dbSNP_134	45	0,8600		0,0,4300	no	missense,missense	CYP11B1	NM_000497.3,NM_001026213.1	29,29	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging	246/504,246/438	143958160	2,13004	2203	4300	6503	143955162	SO:0001583	missense	1584	exon4	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"""Cytochrome P450s"""	2591	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	610613	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"""	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.737G>A	8.37:g.143958160C>T	ENSP00000292427:p.Arg246His	Somatic		Capture	Illumina HiSeq	Phase_I	143955162	NM_001026213	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Missense_Mutation	SNP	ENST00000292427.4	37	CCDS6392.1	.	.	.	.	.	.	.	.	.	.	.	16.12	3.034217	0.54896	4.54E-4	0.0	ENSG00000160882	ENST00000292427;ENST00000517471;ENST00000377675	T;T;T	0.69685	-0.33;-0.42;-0.33	3.64	3.64	0.41730	.	0.144573	0.33235	N	0.005121	T	0.79009	0.4374	M	0.72894	2.215	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.987;0.987;0.99	T	0.69928	-0.5012	10	0.59425	D	0.04	.	13.1709	0.59597	0.0:1.0:0.0:0.0	.	317;246;246	Q4VAR0;Q4VAQ9;P15538	.;.;C11B1_HUMAN	H	246;246;317	ENSP00000292427:R246H;ENSP00000428043:R246H;ENSP00000366903:R317H	ENSP00000292427:R246H	R	-	2	0	CYP11B1	143955162	0.000000	0.05858	0.228000	0.23943	0.189000	0.23516	0.411000	0.21115	2.015000	0.59207	0.555000	0.69702	CGC		0.612	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2		
PARP10	84875	broad.mit.edu	37	8	145058571	145058571	+	Missense_Mutation	SNP	G	G	A	rs377189297		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:145058571G>A	ENST00000313028.7	-	6	1581	c.1487C>T	c.(1486-1488)gCg>gTg	p.A496V	PARP10_ENST00000525773.1_Missense_Mutation_p.A508V|PARP10_ENST00000533665.1_5'Flank|PARP10_ENST00000524918.1_Missense_Mutation_p.A496V	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	496					negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.A496V(2)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CTCCTCAGCCGCCTGGCAGGA	0.607																																					p.A496V												.	.	2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	c.C1487T	8						.		VAL/ALA	1,4403		0,1,2201	18.0	22.0	21.0		1487	2.5	0.2	8		21	1,8583		0,1,4291	no	missense	PARP10	NM_032789.3	64	0,2,6492	AA,AG,GG		0.0116,0.0227,0.0154	benign	496/1026	145058571	2,12986	2202	4292	6494	145130559	SO:0001583	missense	84875	exon6			AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"""Poly (ADP-ribose) polymerases"""	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.1487C>T	8.37:g.145058571G>A	ENSP00000325618:p.Ala496Val	Somatic		Capture	Illumina HiSeq	Phase_I	145130559	NM_032789	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Missense_Mutation	SNP	ENST00000313028.7	37	CCDS34960.1	.	.	.	.	.	.	.	.	.	.	G	7.151	0.583853	0.13749	2.27E-4	1.16E-4	ENSG00000178685	ENST00000524918;ENST00000534861;ENST00000313028;ENST00000525773	T;T;T	0.15017	2.46;2.48;2.48	4.35	2.55	0.30701	.	0.000000	0.45867	D	0.000323	T	0.13072	0.0317	L	0.40543	1.245	0.19300	N	0.99998	B;B	0.23490	0.086;0.008	B;B	0.15484	0.013;0.002	T	0.17684	-1.0361	10	0.48119	T	0.1	.	8.8729	0.35327	0.1781:0.0:0.8219:0.0	.	508;496	E9PNI7;Q53GL7	.;PAR10_HUMAN	V	496;202;496;508	ENSP00000431620:A496V;ENSP00000325618:A496V;ENSP00000434776:A508V	ENSP00000325618:A496V	A	-	2	0	PARP10	145130559	0.023000	0.18921	0.182000	0.23118	0.008000	0.06430	0.659000	0.24994	0.309000	0.22966	-0.821000	0.03111	GCG		0.607	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789	
CPSF1	29894	broad.mit.edu	37	8	145624202	145624202	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:145624202C>T	ENST00000349769.3	-	17	1699	c.1605G>A	c.(1603-1605)atG>atA	p.M535I	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	535					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)	p.M535I(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			TGACTGTCCACATGTCATAGC	0.637																																					p.M535I	NSCLC(133;1088 1848 27708 34777 35269)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1605A	8						.						87.0	95.0	92.0					8																	145624202		2203	4300	6503	145595010	SO:0001583	missense	29894	exon17			U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.1605G>A	8.37:g.145624202C>T	ENSP00000339353:p.Met535Ile	Somatic		Capture	Illumina HiSeq	Phase_I	145595010	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	37	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867400	0.91511	.	.	ENSG00000071894	ENST00000349769	T	0.38560	1.13	5.94	5.94	0.96194	.	0.040041	0.85682	D	0.000000	T	0.41073	0.1143	L	0.37697	1.125	0.80722	D	1	B	0.27594	0.182	B	0.37091	0.241	T	0.13150	-1.0520	10	0.19590	T	0.45	-14.3976	17.8483	0.88737	0.0:1.0:0.0:0.0	.	535	Q10570	CPSF1_HUMAN	I	535	ENSP00000339353:M535I	ENSP00000339353:M535I	M	-	3	0	CPSF1	145595010	1.000000	0.71417	1.000000	0.80357	0.705000	0.40729	7.050000	0.76620	2.817000	0.96982	0.655000	0.94253	ATG		0.637	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
TDRP	157695	broad.mit.edu	37	8	442406	442406	+	Missense_Mutation	SNP	G	G	A	rs372438854		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:442406G>A	ENST00000324079.6	-	3	791	c.551C>T	c.(550-552)gCg>gTg	p.A184V	TDRP_ENST00000524229.1_5'Flank|TDRP_ENST00000427263.2_Intron|TDRP_ENST00000523656.1_Intron			Q86YL5	TDRP_HUMAN	testis development related protein	184					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.A184V(1)									CCCTCACTCCGCCTCCTCCGG	0.587																																					p.A184V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C551T	8						.	G	VAL/ALA	0,4110		0,0,2055	9.0	10.0	10.0		551	-2.7	0.0	8		10	1,8397		0,1,4198	no	missense	C8orf42	NM_175075.3	64	0,1,6253	AA,AG,GG		0.0119,0.0,0.0080	benign	184/186	442406	1,12507	2055	4199	6254	432406	SO:0001583	missense	157695	exon3			AY194292	CCDS47759.1, CCDS59090.1	8p23.3	2013-06-03	2013-06-03	2013-06-03	ENSG00000180190	ENSG00000180190			26951	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 42"""	C8orf42		20170638	Standard	NM_175075		Approved	INM01, TDRP1, TDRP2		Q86YL5	OTTHUMG00000163593	ENST00000324079.6:c.551C>T	8.37:g.442406G>A	ENSP00000315111:p.Ala184Val	Somatic		Capture	Illumina HiSeq	Phase_I	432406	NM_175075	B6VF03|B9EG53	Missense_Mutation	SNP	ENST00000324079.6	37	CCDS47759.1	.	.	.	.	.	.	.	.	.	.	G	5.608	0.296952	0.10622	0.0	1.19E-4	ENSG00000180190	ENST00000324079	.	.	.	6.08	-2.67	0.06059	.	0.534812	0.19108	N	0.122535	T	0.15176	0.0366	N	0.08118	0	0.09310	N	0.999999	B	0.10296	0.003	B	0.06405	0.002	T	0.09100	-1.0690	9	0.38643	T	0.18	.	7.9634	0.30085	0.4976:0.1122:0.3902:0.0	.	184	Q86YL5	CH042_HUMAN	V	184	.	ENSP00000315111:A184V	A	-	2	0	C8orf42	432406	0.977000	0.34250	0.001000	0.08648	0.011000	0.07611	1.897000	0.39799	-1.003000	0.03425	-1.814000	0.00607	GCG		0.587	TDRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374442.1	NM_175075	
ARHGEF10	9639	broad.mit.edu	37	8	1814761	1814761	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:1814761G>T	ENST00000398564.1	+	6	690	c.690G>T	c.(688-690)tgG>tgT	p.W230C	ARHGEF10_ENST00000349830.3_Missense_Mutation_p.W205C|ARHGEF10_ENST00000398560.1_Missense_Mutation_p.W230C|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.W230C|ARHGEF10_ENST00000520359.1_Missense_Mutation_p.W206C|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.W230C			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	230					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.W230C(1)		endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		ACACAGCCTGGATGGAGAGTA	0.582																																					p.W205C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G615T	8						.						83.0	92.0	89.0					8																	1814761		2203	4300	6503	1802168	SO:0001583	missense	9639	exon6			AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.690G>T	8.37:g.1814761G>T	ENSP00000381571:p.Trp230Cys	Somatic		Capture	Illumina HiSeq	Phase_I	1802168	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	37		.	.	.	.	.	.	.	.	.	.	G	25.0	4.596235	0.86953	.	.	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398560;ENST00000398564;ENST00000262112	T;T;T;T;T;T	0.75260	-0.2;-0.51;-0.22;-0.92;-0.22;-0.27	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.85168	0.5635	M	0.63843	1.955	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.942;0.999;0.974	D	0.86582	0.1854	10	0.87932	D	0	-7.2713	18.8403	0.92182	0.0:0.0:1.0:0.0	.	230;230;230;206;205	O15013-4;O15013-6;E9PB39;O15013-7;O15013-5	.;.;.;.;.	C	205;206;230;230;230;230	ENSP00000340297:W205C;ENSP00000427909:W206C;ENSP00000431012:W230C;ENSP00000381568:W230C;ENSP00000381571:W230C;ENSP00000262112:W230C	ENSP00000262112:W230C	W	+	3	0	ARHGEF10	1802168	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.939000	0.92951	2.511000	0.84671	0.585000	0.79938	TGG		0.582	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
PCM1	5108	broad.mit.edu	37	8	17869275	17869275	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:17869275A>T	ENST00000519253.1	+	34	5677	c.5426A>T	c.(5425-5427)gAt>gTt	p.D1809V	PCM1_ENST00000325083.8_Missense_Mutation_p.D1817V|PCM1_ENST00000524226.1_Missense_Mutation_p.D1763V|PCM1_ENST00000327578.8_Missense_Mutation_p.D516V			Q15154	PCM1_HUMAN	pericentriolar material 1	1817					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)	p.D1817V(1)	PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		GGCCCTGTGGATGTCCAGACT	0.408			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""																																p.D1817V			Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A5450T	8						.						134.0	139.0	137.0					8																	17869275		1915	4130	6045	17913555	SO:0001583	missense	5108	exon34				CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.5426A>T	8.37:g.17869275A>T	ENSP00000431099:p.Asp1809Val	Somatic		Capture	Illumina HiSeq	Phase_I	17913555	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.1|21.1	4.095886|4.095886	0.76870|0.76870	.|.	.|.	ENSG00000078674|ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226;ENST00000327578|ENST00000522275	T;T;T;T|.	0.70986|.	-0.53;-0.53;-0.53;-0.53|.	5.32|5.32	5.32|5.32	0.75619|0.75619	.|.	0.236082|.	0.45867|.	D|.	0.000340|.	T|T	0.70395|0.70395	0.3219|0.3219	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;0.999;1.0|.	D;D;D;D;D;D;D|.	0.85130|.	0.997;0.997;0.997;0.997;0.984;0.991;0.997|.	T|T	0.69292|0.69292	-0.5183|-0.5183	10|5	0.87932|.	D|.	0|.	-26.0778|-26.0778	15.5958|15.5958	0.76578|0.76578	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1809;1817;616;1809;1762;1763;1817|.	B9EIS5;D3DSQ0;B4DJ00;E7ETA6;Q15154-2;E7EV56;Q15154|.	.;.;.;.;.;.;PCM1_HUMAN|.	V|L	1817;1809;1763;516|557	ENSP00000327077:D1817V;ENSP00000431099:D1809V;ENSP00000430521:D1763V;ENSP00000328332:D516V|.	ENSP00000327077:D1817V|.	D|M	+|+	2|1	0|0	PCM1|PCM1	17913555|17913555	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.742000|0.742000	0.42306|0.42306	8.661000|8.661000	0.91125|0.91125	2.146000|2.146000	0.66826|0.66826	0.533000|0.533000	0.62120|0.62120	GAT|ATG		0.408	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
ASAH1	427	broad.mit.edu	37	8	17922014	17922014	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:17922014delA	ENST00000262097.6	-	6	720	c.409delT	c.(409-411)tatfs	p.Y137fs	ASAH1_ENST00000381733.4_Frame_Shift_Del_p.Y153fs|ASAH1_ENST00000520781.1_Intron|ASAH1_ENST00000314146.10_Frame_Shift_Del_p.Y131fs|ASAH1_ENST00000417108.2_Intron	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1	137					cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)	p.Y153fs*10(1)|p.Y137fs*10(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		AATAATTCATAAAAAATATTG	0.308																																					p.Y153fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.457delT	8						.						27.0	27.0	27.0					8																	17922014		2202	4296	6498	17966294	SO:0001589	frameshift_variant	427	exon6			U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763			735	protein-coding gene	gene with protein product		613468	"""N-acylsphingosine amidohydrolase (acid ceramidase)"""	ASAH		8955159, 10610716	Standard	NM_004315		Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997	ENST00000262097.6:c.409delT	8.37:g.17922014delA	ENSP00000262097:p.Tyr137fs	Somatic		Capture	Illumina HiSeq	Phase_I	17966294	NM_004315	E9PDS0|Q6W898|Q96AS2	Frame_Shift_Del	DEL	ENST00000262097.6	37	CCDS6006.1																																																																																				0.308	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	
XPO7	23039	broad.mit.edu	37	8	21835304	21835304	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:21835304C>T	ENST00000252512.9	+	8	887	c.787C>T	c.(787-789)Cag>Tag	p.Q263*	XPO7_ENST00000434536.1_Nonsense_Mutation_p.Q272*|XPO7_ENST00000433566.4_Nonsense_Mutation_p.Q264*	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	263				Missing (in Ref. 3; BAA34465). {ECO:0000305}.	mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)	p.Q263*(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		TTCAACCTTGCAGCTGTTTTT	0.403																																					p.Q263X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C787T	8						.						232.0	201.0	211.0					8																	21835304		1844	4088	5932	21891250	SO:0001587	stop_gained	23039	exon8			AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227		"""Exportins"""	14108	protein-coding gene	gene with protein product		606140	"""RAN binding protein 16"""	RANBP16		11024021, 9872452	Standard	NM_015024		Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.787C>T	8.37:g.21835304C>T	ENSP00000252512:p.Gln263*	Somatic		Capture	Illumina HiSeq	Phase_I	21891250	NM_015024	O94846|Q6PJK9|Q8NEK7	Nonsense_Mutation	SNP	ENST00000252512.9	37	CCDS47818.1	.	.	.	.	.	.	.	.	.	.	C	38	7.152402	0.98099	.	.	ENSG00000130227	ENST00000434536;ENST00000252512;ENST00000433566	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	-12.6349	19.2998	0.94140	0.0:1.0:0.0:0.0	.	.	.	.	X	272;263;264	.	ENSP00000252512:Q263X	Q	+	1	0	XPO7	21891250	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.544000	0.67231	2.732000	0.93576	0.563000	0.77884	CAG		0.403	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024	
XPO7	23039	broad.mit.edu	37	8	21844722	21844722	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:21844722A>G	ENST00000252512.9	+	14	1748	c.1648A>G	c.(1648-1650)Atg>Gtg	p.M550V	XPO7_ENST00000434536.1_Missense_Mutation_p.M559V|XPO7_ENST00000433566.4_Missense_Mutation_p.M551V	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	550					mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)	p.M550V(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		AGAGTTGGCCATGCTGAGCTT	0.478																																					p.M550V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1648G	8						.						144.0	146.0	145.0					8																	21844722		1939	4125	6064	21900668	SO:0001583	missense	23039	exon14			AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227		"""Exportins"""	14108	protein-coding gene	gene with protein product		606140	"""RAN binding protein 16"""	RANBP16		11024021, 9872452	Standard	NM_015024		Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.1648A>G	8.37:g.21844722A>G	ENSP00000252512:p.Met550Val	Somatic		Capture	Illumina HiSeq	Phase_I	21900668	NM_015024	O94846|Q6PJK9|Q8NEK7	Missense_Mutation	SNP	ENST00000252512.9	37	CCDS47818.1	.	.	.	.	.	.	.	.	.	.	A	11.99	1.804915	0.31961	.	.	ENSG00000130227	ENST00000434536;ENST00000252512;ENST00000433566	T;T;T	0.64260	-0.09;-0.09;-0.09	5.78	5.78	0.91487	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.53270	0.1786	L	0.38175	1.15	0.80722	D	1	B;B;B	0.13145	0.007;0.001;0.0	B;B;B	0.06405	0.002;0.002;0.002	T	0.46857	-0.9161	10	0.30078	T	0.28	-20.9834	15.7876	0.78319	1.0:0.0:0.0:0.0	.	551;559;550	E7ESC6;E9PEN8;Q9UIA9	.;.;XPO7_HUMAN	V	559;550;551	ENSP00000404853:M559V;ENSP00000252512:M550V;ENSP00000410249:M551V	ENSP00000252512:M550V	M	+	1	0	XPO7	21900668	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.350000	0.79385	2.206000	0.71126	0.533000	0.62120	ATG		0.478	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024	
HR	55806	broad.mit.edu	37	8	21986514	21986514	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:21986514G>A	ENST00000381418.4	-	2	1650	c.170C>T	c.(169-171)cCa>cTa	p.P57L	HR_ENST00000518377.1_5'Flank|HR_ENST00000312841.8_Missense_Mutation_p.P57L	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	57					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P57L(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CCAGGAGTCTGGGGTGCTCAG	0.677																																					p.P57L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C170T	8						.						36.0	40.0	39.0					8																	21986514		2203	4299	6502	22042459	SO:0001583	missense	55806	exon2			AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.170C>T	8.37:g.21986514G>A	ENSP00000370826:p.Pro57Leu	Somatic		Capture	Illumina HiSeq	Phase_I	22042459	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.162912	0.78226	.	.	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.77358	-1.07;-1.09	4.8	4.8	0.61643	.	0.157080	0.30142	N	0.010302	T	0.81725	0.4883	L	0.34521	1.04	0.44754	D	0.997752	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.997	D	0.83363	0.0003	10	0.87932	D	0	-1.0168	13.2272	0.59921	0.0:0.0:1.0:0.0	.	57;57;57	A6NCE3;O43593-2;O43593	.;.;HAIR_HUMAN	L	57	ENSP00000370826:P57L;ENSP00000326765:P57L	ENSP00000326765:P57L	P	-	2	0	HR	22042459	0.989000	0.36119	1.000000	0.80357	0.863000	0.49368	1.793000	0.38764	2.492000	0.84095	0.561000	0.74099	CCA		0.677	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
LGI3	203190	broad.mit.edu	37	8	22006190	22006190	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:22006190G>A	ENST00000306317.2	-	8	1419	c.1130C>T	c.(1129-1131)aCc>aTc	p.T377I	LGI3_ENST00000424267.2_Missense_Mutation_p.T353I	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	377					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)	p.T377I(1)		endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		CTCCAGGTCGGTGTCACGGTG	0.642																																					p.T377I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1130T	8						.						78.0	63.0	68.0					8																	22006190		2203	4300	6503	22062135	SO:0001583	missense	203190	exon8			AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.1130C>T	8.37:g.22006190G>A	ENSP00000302297:p.Thr377Ile	Somatic		Capture	Illumina HiSeq	Phase_I	22062135	NM_139278	A5PLP2|Q86TL4|Q8N296	Missense_Mutation	SNP	ENST00000306317.2	37	CCDS6025.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.440590	0.63067	.	.	ENSG00000168481	ENST00000306317;ENST00000424267	T;T	0.80033	-1.33;-1.33	5.13	5.13	0.70059	Six-bladed beta-propeller, TolB-like (1);	0.058167	0.64402	D	0.000002	T	0.79563	0.4467	M	0.61703	1.905	0.47276	D	0.999374	B;B	0.28291	0.206;0.206	B;B	0.28916	0.096;0.054	T	0.79344	-0.1842	10	0.59425	D	0.04	-26.1478	16.0848	0.81038	0.0:0.0:1.0:0.0	.	353;377	A5PLP2;Q8N145	.;LGI3_HUMAN	I	377;353	ENSP00000302297:T377I;ENSP00000399121:T353I	ENSP00000302297:T377I	T	-	2	0	LGI3	22062135	1.000000	0.71417	0.906000	0.35671	0.774000	0.43823	6.719000	0.74718	2.366000	0.80165	0.561000	0.74099	ACC		0.642	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1		
CCAR2	57805	broad.mit.edu	37	8	22471738	22471738	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:22471738C>T	ENST00000308511.4	+	9	1087	c.838C>T	c.(838-840)Cgg>Tgg	p.R280W	CCAR2_ENST00000389279.3_Missense_Mutation_p.R280W|CCAR2_ENST00000520861.1_5'UTR|RP11-582J16.5_ENST00000521025.1_RNA			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	280					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)	p.R280W(1)									TCATCCAAGCCGGATCCAGGT	0.562																																					p.R280W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C838T	8						.						53.0	49.0	50.0					8																	22471738		2203	4300	6503	22527683	SO:0001583	missense	57805	exon9			AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"""deleted in breast cancer"""	607359	"""KIAA1967"""	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.838C>T	8.37:g.22471738C>T	ENSP00000310670:p.Arg280Trp	Somatic		Capture	Illumina HiSeq	Phase_I	22527683	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	37	CCDS34863.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.945924	0.73672	.	.	ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000522599	T;T;T	0.46063	1.46;1.46;0.88	5.47	5.47	0.80525	.	0.084777	0.49916	D	0.000129	T	0.50137	0.1598	N	0.22421	0.69	0.80722	D	1	D	0.89917	1.0	D	0.70016	0.967	T	0.44406	-0.9330	10	0.38643	T	0.18	-22.8046	16.6012	0.84816	0.0:1.0:0.0:0.0	.	280	Q8N163	K1967_HUMAN	W	280;280;98	ENSP00000310670:R280W;ENSP00000373930:R280W;ENSP00000429739:R98W	ENSP00000310670:R280W	R	+	1	2	KIAA1967	22527683	1.000000	0.71417	0.998000	0.56505	0.940000	0.58332	2.961000	0.49168	2.723000	0.93209	0.655000	0.94253	CGG		0.562	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174	
BIN3	55909	broad.mit.edu	37	8	22481559	22481559	+	Nonsense_Mutation	SNP	G	G	A	rs539144238		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:22481559G>A	ENST00000276416.6	-	8	552	c.484C>T	c.(484-486)Cga>Tga	p.R162*	BIN3_ENST00000519335.1_5'UTR|BIN3_ENST00000399977.4_Nonsense_Mutation_p.R114*|BIN3_ENST00000519513.1_Nonsense_Mutation_p.R108*	NM_018688.4	NP_061158.1	Q9NQY0	BIN3_HUMAN	bridging integrator 3	162	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				actin filament organization (GO:0007015)|barrier septum assembly (GO:0000917)|cytokinesis (GO:0000910)|myoblast migration involved in skeletal muscle regeneration (GO:0014839)|protein localization (GO:0008104)|regulation of lamellipodium assembly (GO:0010591)|skeletal muscle fiber development (GO:0048741)|unidimensional cell growth (GO:0009826)	actin filament (GO:0005884)|cytoplasm (GO:0005737)	cytoskeletal adaptor activity (GO:0008093)	p.R162*(1)		kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	9		Prostate(55;0.0424)|Breast(100;0.102)|all_epithelial(46;0.143)		BRCA - Breast invasive adenocarcinoma(99;0.00664)|Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		AGCTCCTCTCGTGCCTAGGGA	0.627													G|||	1	0.000199681	0.0	0.0	5008	,	,		16684	0.0		0.0	False		,,,				2504	0.001				p.R162X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C484T	8						.						29.0	34.0	32.0					8																	22481559		2019	4171	6190	22537504	SO:0001587	stop_gained	55909	exon8				CCDS47825.1	8p21.2	2008-07-04			ENSG00000147439	ENSG00000147439			1054	protein-coding gene	gene with protein product		606396				16524918	Standard	NM_018688		Approved		uc003xcl.3	Q9NQY0	OTTHUMG00000163844	ENST00000276416.6:c.484C>T	8.37:g.22481559G>A	ENSP00000276416:p.Arg162*	Somatic		Capture	Illumina HiSeq	Phase_I	22537504	NM_018688	Q9BVG2|Q9NVY9	Nonsense_Mutation	SNP	ENST00000276416.6	37	CCDS47825.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.838927	0.51057	.	.	ENSG00000147439	ENST00000276416;ENST00000519513;ENST00000399977	.	.	.	5.29	5.29	0.74685	.	0.062088	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-12.8694	16.4518	0.83993	0.0:0.0:1.0:0.0	.	.	.	.	X	162;108;114	.	ENSP00000276416:R162X	R	-	1	2	BIN3	22537504	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	5.731000	0.68554	2.478000	0.83669	0.561000	0.74099	CGA		0.627	BIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375895.1		
CLU	1191	broad.mit.edu	37	8	27457434	27457434	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:27457434C>T	ENST00000316403.10	-	7	1432	c.1027G>A	c.(1027-1029)Gag>Aag	p.E343K	CLU_ENST00000523500.1_Missense_Mutation_p.E343K|CLU_ENST00000405140.3_Missense_Mutation_p.E343K|CLU_ENST00000560366.1_Missense_Mutation_p.E395K|CLU_ENST00000546343.1_Missense_Mutation_p.E354K			P10909	CLUS_HUMAN	clusterin	343					blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)	p.E395K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		TTTAGCAGCTCGTTGTATTTC	0.577																																					p.E354K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1060A	8						.						129.0	107.0	114.0					8																	27457434		2203	4300	6503	27513351	SO:0001583	missense	1191	exon7			M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"""complement lysis inhibitor"", ""sulfated glycoprotein 2"", ""testosterone-repressed prostate message 2"", ""apolipoprotein J"""	185430	"""clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"""	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.1027G>A	8.37:g.27457434C>T	ENSP00000315130:p.Glu343Lys	Somatic		Capture	Illumina HiSeq	Phase_I	27513351	NM_001171138	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Missense_Mutation	SNP	ENST00000316403.10	37	CCDS47832.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.97|13.97	2.395881|2.395881	0.42512|0.42512	.|.	.|.	ENSG00000120885|ENSG00000120885	ENST00000316403;ENST00000546343;ENST00000405140;ENST00000523500;ENST00000380446;ENST00000520012|ENST00000522098	T;T;T|.	0.23754|.	1.89;1.89;1.89|.	5.62|5.62	1.57|1.57	0.23409|0.23409	Clusterin, C-terminal (1);|.	0.431454|.	0.28688|.	N|.	0.014477|.	T|T	0.50205|0.50205	0.1602|0.1602	L|L	0.48642|0.48642	1.525|1.525	0.26709|0.26709	N|N	0.971006|0.971006	D;D;D;D|.	0.58268|.	0.982;0.982;0.972;0.977|.	P;B;P;P|.	0.51777|.	0.679;0.351;0.469;0.504|.	T|T	0.45556|0.45556	-0.9253|-0.9253	10|5	0.35671|.	T|.	0.21|.	-12.343|-12.343	16.3933|16.3933	0.83546|0.83546	0.0:0.4604:0.5396:0.0|0.0:0.4604:0.5396:0.0	.|.	208;395;354;343|.	E7ETA7;P10909-2;P10909-5;P10909|.	.;.;.;CLUS_HUMAN|.	K|Q	395;354;343;343;168;208|205	ENSP00000446413:E354K;ENSP00000385419:E343K;ENSP00000429620:E343K|.	ENSP00000315130:E395K|.	E|R	-|-	1|2	0|0	CLU|CLU	27513351|27513351	0.004000|0.004000	0.15560|0.15560	0.052000|0.052000	0.19188|0.19188	0.196000|0.196000	0.23810|0.23810	0.777000|0.777000	0.26718|0.26718	0.004000|0.004000	0.14682|0.14682	0.655000|0.655000	0.94253|0.94253	GAG|CGA		0.577	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831	
GOLGA7	51125	broad.mit.edu	37	8	41363526	41363526	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:41363526C>T	ENST00000357743.4	+	3	562	c.361C>T	c.(361-363)Cga>Tga	p.R121*	GOLGA7_ENST00000518270.1_Nonsense_Mutation_p.R121*|GOLGA7_ENST00000405786.2_Nonsense_Mutation_p.R121*|GOLGA7_ENST00000521417.1_3'UTR|GOLGA7_ENST00000520817.1_Nonsense_Mutation_p.R121*	NM_001002296.1	NP_001002296.1	Q7Z5G4	GOGA7_HUMAN	golgin A7	121					Golgi to plasma membrane protein transport (GO:0043001)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|intrinsic component of Golgi membrane (GO:0031228)|palmitoyltransferase complex (GO:0002178)		p.R121*(1)		breast(1)|large_intestine(1)	2	Ovarian(28;0.014)|Colorectal(14;0.0234)|Lung SC(25;0.211)	all_lung(54;0.000771)|Lung NSC(58;0.0031)|Hepatocellular(245;0.014)|Esophageal squamous(32;0.0559)	Colorectal(10;0.0014)|OV - Ovarian serous cystadenocarcinoma(14;0.00596)|LUSC - Lung squamous cell carcinoma(45;0.0137)|COAD - Colon adenocarcinoma(11;0.0147)			GCGAGGACTGCGAGTTGTATC	0.393																																					p.R121X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C361T	8						.						81.0	78.0	79.0					8																	41363526		2203	4300	6503	41482683	SO:0001587	stop_gained	51125	exon4			AF125102	CCDS34887.1, CCDS55226.1	8p11.21	2011-10-25	2010-02-12		ENSG00000147533	ENSG00000147533			24876	protein-coding gene	gene with protein product		609453	"""golgi autoantigen, golgin subfamily a, 7"""			11042152	Standard	NM_001174124		Approved	GCP16, HSPC041, GOLGA3AP1, GOLGA7A	uc003xnu.3	Q7Z5G4	OTTHUMG00000164077	ENST00000357743.4:c.361C>T	8.37:g.41363526C>T	ENSP00000350378:p.Arg121*	Somatic		Capture	Illumina HiSeq	Phase_I	41482683	NM_016099	D3DSX9|J3KQ24|Q96EQ4|Q9P1S0|Q9Y5U7	Nonsense_Mutation	SNP	ENST00000357743.4	37	CCDS34887.1	.	.	.	.	.	.	.	.	.	.	C	37	6.367558	0.97511	.	.	ENSG00000147533	ENST00000518270;ENST00000520817;ENST00000405786;ENST00000357743	.	.	.	5.34	4.4	0.53042	.	0.122747	0.53938	D	0.000046	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.8716	12.8806	0.58014	0.2345:0.7655:0.0:0.0	.	.	.	.	X	121	.	ENSP00000276530:R121X	R	+	1	2	GOLGA7	41482683	0.983000	0.35010	1.000000	0.80357	0.971000	0.66376	1.943000	0.40253	2.481000	0.83766	0.655000	0.94253	CGA		0.393	GOLGA7-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377142.1	NM_016099	
ANK1	286	broad.mit.edu	37	8	41581082	41581082	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:41581082G>A	ENST00000347528.4	-	8	864	c.781C>T	c.(781-783)Cgg>Tgg	p.R261W	ANK1_ENST00000396945.1_Missense_Mutation_p.R261W|ANK1_ENST00000396942.1_Missense_Mutation_p.R261W|ANK1_ENST00000352337.4_Missense_Mutation_p.R261W|ANK1_ENST00000289734.7_Missense_Mutation_p.R261W|ANK1_ENST00000379758.2_Missense_Mutation_p.R261W|ANK1_ENST00000265709.8_Missense_Mutation_p.R294W	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	261	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.R261W(1)		breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			TGGGCTCCCCGATCCAGCAGC	0.652																																					p.R261W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C781T	8						.						116.0	86.0	96.0					8																	41581082		2203	4300	6503	41700239	SO:0001583	missense	286	exon8			M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.781C>T	8.37:g.41581082G>A	ENSP00000339620:p.Arg261Trp	Somatic		Capture	Illumina HiSeq	Phase_I	41700239	NM_020475	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	G	17.25	3.341903	0.61073	.	.	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.58	4.61	0.57282	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.59115	0.2170	M	0.73430	2.235	0.80722	D	1	B;B;P;P;B	0.45594	0.32;0.444;0.652;0.862;0.209	B;B;B;B;B	0.34346	0.171;0.157;0.135;0.18;0.171	T	0.66885	-0.5810	10	0.87932	D	0	.	14.0484	0.64719	0.0782:0.0:0.9218:0.0	.	294;261;261;261;261	P16157-21;P16157-4;P16157;P16157-5;P16157-3	.;.;ANK1_HUMAN;.;.	W	261;261;261;261;261;261;294;261	ENSP00000339620:R261W;ENSP00000289734:R261W;ENSP00000369082:R261W;ENSP00000380149:R261W;ENSP00000380147:R261W;ENSP00000309131:R261W;ENSP00000265709:R294W	ENSP00000265709:R294W	R	-	1	2	ANK1	41700239	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.898000	0.48672	1.189000	0.43028	0.655000	0.94253	CGG		0.652	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
POTEA	340441	broad.mit.edu	37	8	43152506	43152506	+	RNA	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:43152506T>C	ENST00000522175.2	+	0	494							Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A									p.Y164Y(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(27)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CAGATATGTATGGGAATACTG	0.393																																					p.Y164Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T492C	8						.						95.0	95.0	95.0					8																	43152506		2201	4299	6500	43271663			340441	exon3			AY462869		8p11.1	2013-01-11	2008-11-26	2008-11-26	ENSG00000188877	ENSG00000188877		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33893	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 3"""	608915	"""ANKRD26-like family A, member 1"""	A26A1			Standard	NM_001002920		Approved	POTE8, POTE-8, CT104.3	uc003xpz.1	Q6S8J7	OTTHUMG00000164111		8.37:g.43152506T>C		Somatic		Capture	Illumina HiSeq	Phase_I	43271663	NM_001005365	A6ND17|A6ND71|Q6S8J6	Silent	SNP	ENST00000522175.2	37																																																																																					0.393	POTEA-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000383492.1	NM_001002920	
SPIDR	23514	broad.mit.edu	37	8	48626149	48626149	+	Missense_Mutation	SNP	A	A	G	rs374494194		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:48626149A>G	ENST00000297423.4	+	16	2671	c.2287A>G	c.(2287-2289)Atg>Gtg	p.M763V	SPIDR_ENST00000518074.1_Missense_Mutation_p.M703V|SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Missense_Mutation_p.M693V|SPIDR_ENST00000517693.1_Missense_Mutation_p.M238V	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	763					cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)		p.M763V(1)									TGGCCCGGTGATGCTCGACAG	0.517																																					p.M763V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2287G	8						.	A	VAL/MET	0,4152		0,0,2076	101.0	103.0	102.0		2287	2.6	0.0	8		102	1,8429		0,1,4214	no	missense	KIAA0146	NM_001080394.2	21	0,1,6290	GG,GA,AA		0.0119,0.0,0.0079	benign	763/916	48626149	1,12581	2076	4215	6291	48788702	SO:0001583	missense	23514	exon16			AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"""KIAA0146"""	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.2287A>G	8.37:g.48626149A>G	ENSP00000297423:p.Met763Val	Somatic		Capture	Illumina HiSeq	Phase_I	48788702	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Missense_Mutation	SNP	ENST00000297423.4	37	CCDS43737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	2.960|2.960	-0.214891|-0.214891	0.06101|0.06101	0.0|0.0	1.19E-4|1.19E-4	ENSG00000164808|ENSG00000164808	ENST00000297423;ENST00000518074;ENST00000541342;ENST00000519141;ENST00000517693;ENST00000519362;ENST00000522321;ENST00000521056|ENST00000519401	.|.	.|.	.|.	5.08|5.08	2.63|2.63	0.31362|0.31362	.|.	0.743675|.	0.13016|.	N|.	0.420427|.	T|.	0.11110|.	0.0271|.	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	B;B;B;B;B;B|.	0.15930|.	0.015;0.015;0.003;0.0;0.015;0.0|.	B;B;B;B;B;B|.	0.12837|.	0.008;0.008;0.001;0.001;0.005;0.001|.	T|.	0.30534|.	-0.9975|.	9|.	0.23302|.	T|.	0.38|.	.|.	5.002|5.002	0.14269|0.14269	0.6817:0.1562:0.1621:0.0|0.6817:0.1562:0.1621:0.0	.|.	253;268;703;693;238;763|.	B4DZY2;B4DWT8;B4E0Y6;B4DFV2;B3KP42;Q14159|.	.;.;.;.;.;K0146_HUMAN|.	V|W	763;703;693;268;238;238;124;124|444	.|.	ENSP00000297423:M763V|.	M|X	+|+	1|3	0|0	KIAA0146|KIAA0146	48788702|48788702	0.698000|0.698000	0.27777|0.27777	0.005000|0.005000	0.12908|0.12908	0.011000|0.011000	0.07611|0.07611	1.389000|1.389000	0.34453|0.34453	0.264000|0.264000	0.21851|0.21851	0.482000|0.482000	0.46254|0.46254	ATG|TGA		0.517	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394	
PRKDC	5591	broad.mit.edu	37	8	48746884	48746884	+	Silent	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:48746884A>C	ENST00000314191.2	-	60	8078	c.8022T>G	c.(8020-8022)tcT>tcG	p.S2674S	PRKDC_ENST00000338368.3_Silent_p.S2674S|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	2675	KIP-binding.				B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)	p.S2675S(1)|p.S2674S(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	GCAAGGAGTCAGATGAGGGAC	0.537								Non-homologous end-joining																													p.L2675R	Esophageal Squamous(79;1091 1253 12329 31680 40677)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T8024G	8						.						142.0	155.0	151.0					8																	48746884		2169	4281	6450	48909437	SO:0001819	synonymous_variant	5591	exon59				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.8022T>G	8.37:g.48746884A>C		Somatic		Capture	Illumina HiSeq	Phase_I	48909437	NM_001081640	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Silent	SNP	ENST00000314191.2	37																																																																																					0.537	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640	
PXDNL	137902	broad.mit.edu	37	8	52252255	52252255	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:52252255delT	ENST00000356297.4	-	21	4175	c.4075delA	c.(4075-4077)acafs	p.T1359fs	PXDNL_ENST00000543296.1_Intron	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1359					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.T1359fs*25(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GAGAACTTTGTTTTTGCCAGA	0.363																																					p.T1359fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.4075delA	8						.						152.0	145.0	147.0					8																	52252255		1862	4087	5949	52414808	SO:0001589	frameshift_variant	137902	exon21				CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.4075delA	8.37:g.52252255delT	ENSP00000348645:p.Thr1359fs	Somatic		Capture	Illumina HiSeq	Phase_I	52414808	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Frame_Shift_Del	DEL	ENST00000356297.4	37	CCDS47855.1																																																																																				0.363	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
PXDNL	137902	broad.mit.edu	37	8	52370063	52370063	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:52370063A>C	ENST00000356297.4	-	9	1077	c.977T>G	c.(976-978)cTt>cGt	p.L326R	PXDNL_ENST00000543296.1_Missense_Mutation_p.L326R	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	326					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.L326R(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TTTACCTGGAAGACTGGAGTA	0.408																																					p.L326R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T977G	8						.						88.0	85.0	86.0					8																	52370063		1873	4116	5989	52532616	SO:0001583	missense	137902	exon9				CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.977T>G	8.37:g.52370063A>C	ENSP00000348645:p.Leu326Arg	Somatic		Capture	Illumina HiSeq	Phase_I	52532616	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	A	1.588	-0.529819	0.04112	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.68181	-0.28;-0.31	3.71	-4.87	0.03123	.	.	.	.	.	T	0.35158	0.0922	N	0.11756	0.17	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18650	-1.0330	9	0.15952	T	0.53	.	0.521	0.00612	0.4238:0.134:0.1838:0.2583	.	326	A1KZ92	PXDNL_HUMAN	R	326	ENSP00000348645:L326R;ENSP00000444865:L326R	ENSP00000348645:L326R	L	-	2	0	PXDNL	52532616	0.016000	0.18221	0.000000	0.03702	0.000000	0.00434	0.853000	0.27777	-1.967000	0.01008	-1.874000	0.00550	CTT		0.408	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
NPBWR1	2831	broad.mit.edu	37	8	53852612	53852612	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:53852612G>A	ENST00000331251.3	+	1	1622	c.145G>A	c.(145-147)Gcc>Acc	p.A49T		NM_005285.3	NP_005276.2	P48145	NPBW1_HUMAN	neuropeptides B/W receptor 1	49					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)|regulation of metabolic process (GO:0019222)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)	p.A49T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)	17		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				GGTGATCTGCGCCGTGGGTCT	0.697																																					p.A49T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G145A	8						.						33.0	30.0	31.0					8																	53852612		2202	4298	6500	54015165	SO:0001583	missense	2831	exon1			BC033145	CCDS6151.1	8p22-q21.13	2012-08-08	2006-02-15	2006-02-15		ENSG00000183729		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4522	protein-coding gene	gene with protein product		600730	"""G protein-coupled receptor 7"""	GPR7		7590751, 12401809	Standard	NM_005285		Approved		uc011ldu.2	P48145		ENST00000331251.3:c.145G>A	8.37:g.53852612G>A	ENSP00000330284:p.Ala49Thr	Somatic		Capture	Illumina HiSeq	Phase_I	54015165	NM_005285	Q6NTC7	Missense_Mutation	SNP	ENST00000331251.3	37	CCDS6151.1	.	.	.	.	.	.	.	.	.	.	G	36	5.903824	0.97087	.	.	ENSG00000183729	ENST00000331251	T	0.37235	1.21	4.74	4.74	0.60224	.	0.115150	0.36815	N	0.002381	T	0.38558	0.1045	N	0.08118	0	0.58432	D	0.999998	D	0.76494	0.999	P	0.62435	0.902	T	0.49826	-0.8898	10	0.52906	T	0.07	.	17.9109	0.88934	0.0:0.0:1.0:0.0	.	49	P48145	NPBW1_HUMAN	T	49	ENSP00000330284:A49T	ENSP00000330284:A49T	A	+	1	0	NPBWR1	54015165	1.000000	0.71417	0.987000	0.45799	0.935000	0.57460	7.403000	0.79983	2.457000	0.83068	0.655000	0.94253	GCC		0.697	NPBWR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378047.1	NM_005285	
ATP6V1H	51606	broad.mit.edu	37	8	54684663	54684663	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:54684663C>T	ENST00000359530.2	-	10	1198	c.935G>A	c.(934-936)tGc>tAc	p.C312Y	ATP6V1H_ENST00000355221.3_Missense_Mutation_p.C294Y|ATP6V1H_ENST00000520188.1_Missense_Mutation_p.C272Y|ATP6V1H_ENST00000396774.2_Missense_Mutation_p.C312Y|ATP6V1H_ENST00000523899.1_5'Flank	NM_015941.3	NP_057025.2	Q9UI12	VATH_HUMAN	ATPase, H+ transporting, lysosomal 50/57kDa, V1 subunit H	312					ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|endocytosis (GO:0006897)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|regulation of catalytic activity (GO:0050790)|regulation of defense response to virus by virus (GO:0050690)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V1 domain (GO:0000221)	enzyme regulator activity (GO:0030234)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)	p.C294Y(1)		endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	18		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)			CAGAACTTTGCACTGAATCAT	0.368																																					p.C312Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G935A	8						.						102.0	93.0	96.0					8																	54684663		2203	4300	6503	54847216	SO:0001583	missense	51606	exon10			AF132945	CCDS6153.1, CCDS6154.1	8q11.2	2011-05-24	2002-08-29		ENSG00000047249	ENSG00000047249		"""ATPases / V-type"""	18303	protein-coding gene	gene with protein product	"""vacuolar ATP synthase subunit H"""	608861	"""ATPase, H+ transporting, lysosomal 50/57kD, V1 subunit H"""			9620685, 10810093	Standard	NM_015941		Approved	CGI-11, SFD, VMA13, SFDalpha, SFDbeta	uc003xrm.4	Q9UI12	OTTHUMG00000164231	ENST00000359530.2:c.935G>A	8.37:g.54684663C>T	ENSP00000352522:p.Cys312Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	54847216	NM_015941	B3KMR0|Q6PK44|Q9H3E3|Q9Y300	Missense_Mutation	SNP	ENST00000359530.2	37	CCDS6153.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.642083	0.87859	.	.	ENSG00000047249	ENST00000355221;ENST00000520188;ENST00000359530;ENST00000396774	.	.	.	5.21	5.21	0.72293	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.75852	0.3906	M	0.72353	2.195	0.80722	D	1	P;P	0.47604	0.767;0.898	P;P	0.57548	0.661;0.823	T	0.74163	-0.3754	9	0.37606	T	0.19	-17.2037	19.1196	0.93357	0.0:1.0:0.0:0.0	.	294;312	Q9UI12-2;Q9UI12	.;VATH_HUMAN	Y	294;272;312;312	.	ENSP00000347359:C294Y	C	-	2	0	ATP6V1H	54847216	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.445000	0.80570	2.581000	0.87130	0.609000	0.83330	TGC		0.368	ATP6V1H-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377865.1	NM_015941	
LYPLA1	10434	broad.mit.edu	37	8	54963680	54963680	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:54963680A>G	ENST00000316963.3	-	8	724	c.531T>C	c.(529-531)gtT>gtC	p.V177V	LYPLA1_ENST00000343231.6_Silent_p.V161V|LYPLA1_ENST00000522007.1_Missense_Mutation_p.F57S|LYPLA1_ENST00000519926.1_5'Flank	NM_001279360.1|NM_006330.2	NP_001266289.1|NP_006321.1	O75608	LYPA1_HUMAN	lysophospholipase I	177					fatty acid metabolic process (GO:0006631)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|nitric oxide metabolic process (GO:0046209)|protein depalmitoylation (GO:0002084)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	lysophospholipase activity (GO:0004622)|palmitoyl-(protein) hydrolase activity (GO:0008474)	p.V177V(1)		central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)	6		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)			ACATCAGGGGAACCAAAGGGT	0.408																																					p.V177V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T531C	8						.						87.0	83.0	84.0					8																	54963680		2203	4300	6503	55126233	SO:0001819	synonymous_variant	10434	exon8			AF081281	CCDS6157.1, CCDS64899.1, CCDS75738.1, CCDS75739.1	8q11.23-q12.1	2008-05-15			ENSG00000120992	ENSG00000120992	3.1.1.5		6737	protein-coding gene	gene with protein product		605599				10064899	Standard	NM_006330		Approved	LPL1	uc003xry.3	O75608	OTTHUMG00000164313	ENST00000316963.3:c.531T>C	8.37:g.54963680A>G		Somatic		Capture	Illumina HiSeq	Phase_I	55126233	NM_006330	O43202|Q9UQF9	Silent	SNP	ENST00000316963.3	37	CCDS6157.1	.	.	.	.	.	.	.	.	.	.	A	8.794	0.931320	0.18131	.	.	ENSG00000120992	ENST00000522007	.	.	.	4.88	2.49	0.30216	.	.	.	.	.	T	0.46171	0.1379	.	.	.	0.27126	N	0.962026	.	.	.	.	.	.	T	0.40683	-0.9550	5	0.87932	D	0	-24.9145	9.8445	0.41019	0.8835:0.0:0.1165:0.0	.	.	.	.	S	57	.	ENSP00000427967:F57S	F	-	2	0	LYPLA1	55126233	1.000000	0.71417	1.000000	0.80357	0.490000	0.33462	2.445000	0.44899	0.317000	0.23160	0.528000	0.53228	TTC		0.408	LYPLA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378238.1		
SOX17	64321	broad.mit.edu	37	8	55370935	55370935	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:55370935T>C	ENST00000297316.4	+	1	441	c.237T>C	c.(235-237)gcT>gcC	p.A79A		NM_022454.3	NP_071899.1	Q9H6I2	SOX17_HUMAN	SRY (sex determining region Y)-box 17	79					angiogenesis (GO:0001525)|canonical Wnt signaling pathway (GO:0060070)|cardiac cell fate determination (GO:0060913)|cardiogenic plate morphogenesis (GO:0003142)|cell migration involved in gastrulation (GO:0042074)|common bile duct development (GO:0061009)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cell differentiation (GO:0060956)|endocardium formation (GO:0060214)|endoderm formation (GO:0001706)|endodermal cell fate determination (GO:0007493)|endodermal digestive tract morphogenesis (GO:0061031)|gall bladder development (GO:0061010)|heart formation (GO:0060914)|heart looping (GO:0001947)|inner cell mass cellular morphogenesis (GO:0001828)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell growth (GO:0030308)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell differentiation (GO:0045597)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein destabilization (GO:0031648)|protein stabilization (GO:0050821)|regulation of cardiac cell fate specification (GO:2000043)|regulation of embryonic development (GO:0045995)|regulation of stem cell division (GO:2000035)|regulation of stem cell proliferation (GO:0072091)|regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification (GO:0060807)|regulation of transcription, DNA-templated (GO:0006355)|renal system development (GO:0072001)|rostrocaudal neural tube patterning (GO:0021903)|signal transduction involved in regulation of gene expression (GO:0023019)|spermatogenesis (GO:0007283)|stem cell fate specification (GO:0048866)|vasculogenesis (GO:0001570)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A79A(1)		endometrium(6)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)	18		Lung NSC(129;0.109)|all_epithelial(80;0.176)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;1.9e-07)|Epithelial(17;1.7e-05)|all cancers(17;0.000159)			TGGTGTGGGCTAAGGACGAGC	0.697																																					p.A79A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T237C	8						.						24.0	29.0	27.0					8																	55370935		2201	4298	6499	55533488	SO:0001819	synonymous_variant	64321	exon1			AB073988	CCDS6159.1	8q11.23	2014-09-04			ENSG00000164736	ENSG00000164736		"""SRY (sex determining region Y)-boxes"""	18122	protein-coding gene	gene with protein product		610928				11786926	Standard	NM_022454		Approved		uc003xsb.4	Q9H6I2	OTTHUMG00000164377	ENST00000297316.4:c.237T>C	8.37:g.55370935T>C		Somatic		Capture	Illumina HiSeq	Phase_I	55533488	NM_022454		Silent	SNP	ENST00000297316.4	37	CCDS6159.1																																																																																				0.697	SOX17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378526.2		
RP1	6101	broad.mit.edu	37	8	55541377	55541377	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:55541377delT	ENST00000220676.1	+	4	5083	c.4935delT	c.(4933-4935)tctfs	p.S1645fs		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1645					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.P1648fs*62(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TCAAACCATCTTTTTTTCCTG	0.378																																					p.S1645fs	Colon(91;1014 1389 7634 14542 40420)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.4935delT	8						.						96.0	100.0	99.0					8																	55541377		2202	4299	6501	55703930	SO:0001589	frameshift_variant	6101	exon4			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.4935delT	8.37:g.55541377delT	ENSP00000220676:p.Ser1645fs	Somatic		Capture	Illumina HiSeq	Phase_I	55703930	NM_006269		Frame_Shift_Del	DEL	ENST00000220676.1	37	CCDS6160.1																																																																																				0.378	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
LYN	4067	broad.mit.edu	37	8	56922493	56922493	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:56922493G>A	ENST00000519728.1	+	13	1659	c.1363G>A	c.(1363-1365)Gcc>Acc	p.A455T	LYN_ENST00000520220.2_Missense_Mutation_p.A434T	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	455	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to heat (GO:0034605)|cellular response to retinoic acid (GO:0071300)|cytokine secretion (GO:0050663)|dendritic cell differentiation (GO:0097028)|erythrocyte differentiation (GO:0030218)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|histamine secretion by mast cell (GO:0002553)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of immune response (GO:0050777)|negative regulation of intracellular signal transduction (GO:1902532)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell proliferation (GO:0070667)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|neuron projection development (GO:0031175)|oligodendrocyte development (GO:0014003)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oligodendrocyte progenitor proliferation (GO:0070447)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of stress-activated protein kinase signaling cascade (GO:0070304)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cytokine production (GO:0001817)|regulation of cytokine secretion (GO:0050707)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of erythrocyte differentiation (GO:0045646)|regulation of inflammatory response (GO:0050727)|regulation of mast cell activation (GO:0033003)|regulation of mast cell degranulation (GO:0043304)|regulation of monocyte chemotaxis (GO:0090025)|regulation of platelet aggregation (GO:0090330)|regulation of protein phosphorylation (GO:0001932)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to carbohydrate (GO:0009743)|response to drug (GO:0042493)|response to hormone (GO:0009725)|response to insulin (GO:0032868)|response to organic cyclic compound (GO:0014070)|response to sterol depletion (GO:0006991)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|T cell costimulation (GO:0031295)|tolerance induction to self antigen (GO:0002513)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integrin alpha2-beta1 complex (GO:0034666)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycosphingolipid binding (GO:0043208)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)	p.A455T(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)		Bosutinib(DB06616)|Ponatinib(DB08901)	CGTGATGACCGCCCTGTCCCA	0.502																																					p.A455T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1363A	8						.						67.0	63.0	65.0					8																	56922493		2203	4300	6503	57085047	SO:0001583	missense	4067	exon13			M16038	CCDS6162.1, CCDS47859.1	8q13	2014-06-25	2014-06-25		ENSG00000254087	ENSG00000254087		"""SH2 domain containing"""	6735	protein-coding gene	gene with protein product		165120	"""v-yes-1 Yamaguchi sarcoma viral related oncogene homolog"""			3561390	Standard	NM_002350		Approved	JTK8	uc003xsk.4	P07948	OTTHUMG00000044345	ENST00000519728.1:c.1363G>A	8.37:g.56922493G>A	ENSP00000428924:p.Ala455Thr	Somatic		Capture	Illumina HiSeq	Phase_I	57085047	NM_002350	A0AVQ5	Missense_Mutation	SNP	ENST00000519728.1	37	CCDS6162.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.039277	0.75617	.	.	ENSG00000254087	ENST00000519728;ENST00000520220	T;T	0.11821	2.74;2.74	5.92	5.05	0.67936	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.157235	0.56097	D	0.000022	T	0.16727	0.0402	L	0.47716	1.5	0.48040	D	0.999578	D;P	0.53619	0.961;0.896	B;B	0.43386	0.418;0.29	T	0.01127	-1.1443	10	0.59425	D	0.04	.	15.2089	0.73202	0.0674:0.0:0.9326:0.0	.	525;455	Q6NUK7;P07948	.;LYN_HUMAN	T	455;434	ENSP00000428924:A455T;ENSP00000428424:A434T	ENSP00000428924:A455T	A	+	1	0	LYN	57085047	0.994000	0.37717	0.997000	0.53966	0.961000	0.63080	3.140000	0.50585	1.512000	0.48834	0.655000	0.94253	GCC		0.502	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378155.1	NM_002350	
CHD7	55636	broad.mit.edu	37	8	61734401	61734401	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:61734401C>T	ENST00000423902.2	+	10	3229	c.2750C>T	c.(2749-2751)aCg>aTg	p.T917M	CHD7_ENST00000525508.1_Missense_Mutation_p.T917M|CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	917	Chromo 2. {ECO:0000255|PROSITE- ProRule:PRU00053}.		T -> M (in a patient with CHARGES; unknown pathological significance). {ECO:0000269|PubMed:21158681}.		adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.T917M(2)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			GAAGACAGCACGTGGGAGCGG	0.458																																					p.T917M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2750T	8						.						55.0	54.0	54.0					8																	61734401		1904	4138	6042	61896955	SO:0001583	missense	55636	exon10			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.2750C>T	8.37:g.61734401C>T	ENSP00000392028:p.Thr917Met	Somatic		Capture	Illumina HiSeq	Phase_I	61896955	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.717967	0.89205	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000525508	D;D	0.81908	-1.55;-1.55	5.53	5.53	0.82687	Chromo domain (1);Chromo domain/shadow (2);	0.000000	0.85682	D	0.000000	D	0.94473	0.8221	H	0.96015	3.755	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	D	0.95613	0.8674	10	0.87932	D	0	-17.126	19.8195	0.96586	0.0:1.0:0.0:0.0	.	917;917	Q9P2D1-2;Q9P2D1	.;CHD7_HUMAN	M	917	ENSP00000392028:T917M;ENSP00000436027:T917M	ENSP00000307304:T917M	T	+	2	0	CHD7	61896955	1.000000	0.71417	0.970000	0.41538	0.953000	0.61014	7.818000	0.86416	2.756000	0.94617	0.655000	0.94253	ACG		0.458	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
PDE7A	5150	broad.mit.edu	37	8	66647077	66647077	+	Silent	SNP	G	G	A	rs139866507	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:66647077G>A	ENST00000401827.3	-	7	1091	c.648C>T	c.(646-648)caC>caT	p.H216H	PDE7A_ENST00000396642.3_Silent_p.H216H|PDE7A_ENST00000518667.1_5'UTR|PDE7A_ENST00000379419.4_Silent_p.H190H	NM_001242318.2	NP_001229247.1	Q13946	PDE7A_HUMAN	phosphodiesterase 7A	216	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)	p.H190H(1)|p.H216H(1)		large_intestine(5)|lung(3)|stomach(1)|urinary_tract(1)	10			Epithelial(68;0.0509)|BRCA - Breast invasive adenocarcinoma(89;0.111)|all cancers(69;0.168)|OV - Ovarian serous cystadenocarcinoma(28;0.238)		Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	CATCCGCAGCGTGGACTGCGT	0.373																																					p.H190H												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C570T	8						.	G	,	0,4406		0,0,2203	173.0	161.0	165.0		648,570	-4.0	1.0	8	dbSNP_134	165	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous	PDE7A	NM_001242318.2,NM_002603.3	,	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	,	216/483,190/457	66647077	3,13003	2203	4300	6503	66809631	SO:0001819	synonymous_variant	5150	exon7			L12052	CCDS34901.1, CCDS56538.1	8q13	2008-03-18				ENSG00000205268	3.1.4.17	"""Phosphodiesterases"""	8791	protein-coding gene	gene with protein product		171885				8389765, 9521885	Standard	NM_001242318		Approved	HCP1	uc003xvq.3	Q13946		ENST00000401827.3:c.648C>T	8.37:g.66647077G>A		Somatic		Capture	Illumina HiSeq	Phase_I	66809631	NM_002603	A0AVH6|A8K436|A8K9G5|O15380|Q96T72	Silent	SNP	ENST00000401827.3	37	CCDS56538.1																																																																																				0.373	PDE7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378905.1		
MSC	9242	broad.mit.edu	37	8	72756190	72756190	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:72756190G>T	ENST00000325509.4	-	1	513	c.224C>A	c.(223-225)cCc>cAc	p.P75H	RP11-383H13.1_ENST00000524152.1_Intron|MSC_ENST00000518440.1_5'Flank|RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000521467.1_Intron	NM_005098.3	NP_005089.2	O60682	MUSC_HUMAN	musculin	75					branchiomeric skeletal muscle development (GO:0014707)|diaphragm development (GO:0060539)|palate development (GO:0060021)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P75H(1)		endometrium(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(4)|skin(2)	26	Breast(64;0.176)		Epithelial(68;0.137)|BRCA - Breast invasive adenocarcinoma(89;0.203)			AGCCACACGGGGCCGCTTCCT	0.721											OREG0018826	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P75H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C224A	8						.						3.0	5.0	4.0					8																	72756190		1787	3760	5547	72918744	SO:0001583	missense	9242	exon1				CCDS43746.1	8q13.3	2013-06-07	2010-04-28		ENSG00000178860	ENSG00000178860		"""Basic helix-loop-helix proteins"""	7321	protein-coding gene	gene with protein product	"""activated B-cell factor-1"""	603628	"""musculin (activated B-cell factor-1)"""			9584154, 10198176	Standard	NM_005098		Approved	ABF-1, bHLHa22	uc003xyx.1	O60682	OTTHUMG00000164489	ENST00000325509.4:c.224C>A	8.37:g.72756190G>T	ENSP00000321445:p.Pro75His	Somatic	1140	Capture	Illumina HiSeq	Phase_I	72918744	NM_005098	O75946|Q53XZ2|Q9BRE7	Missense_Mutation	SNP	ENST00000325509.4	37	CCDS43746.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.866202	0.32977	.	.	ENSG00000178860	ENST00000325509	D	0.97731	-4.51	4.25	3.35	0.38373	.	4.579620	0.00780	N	0.001268	D	0.94345	0.8182	N	0.19112	0.55	0.21020	N	0.9998	B	0.32693	0.38	B	0.34038	0.174	D	0.88998	0.3419	10	0.15952	T	0.53	.	8.2982	0.31997	0.1114:0.0:0.8886:0.0	.	75	O60682	MUSC_HUMAN	H	75	ENSP00000321445:P75H	ENSP00000321445:P75H	P	-	2	0	MSC	72918744	0.000000	0.05858	0.648000	0.29521	0.729000	0.41735	0.260000	0.18424	0.970000	0.38263	0.561000	0.74099	CCC		0.721	MSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378974.1	NM_005098	
TRPA1	8989	broad.mit.edu	37	8	72987616	72987616	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:72987616C>T	ENST00000262209.4	-	1	236	c.29G>A	c.(28-30)cGc>cAc	p.R10H		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	10					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)	p.R10H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	TTCTCCAGGGCGCCACATCTT	0.642																																					p.R10H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G29A	8						.						83.0	87.0	86.0					8																	72987616		2203	4300	6503	73150170	SO:0001583	missense	8989	exon1			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.29G>A	8.37:g.72987616C>T	ENSP00000262209:p.Arg10His	Somatic		Capture	Illumina HiSeq	Phase_I	73150170	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	C	8.447	0.852219	0.17106	.	.	ENSG00000104321	ENST00000262209	T	0.41400	1.0	4.58	2.74	0.32292	.	0.432388	0.24523	N	0.037782	T	0.28400	0.0702	L	0.51422	1.61	0.09310	N	1	P	0.51653	0.947	B	0.39027	0.288	T	0.16748	-1.0392	10	0.30854	T	0.27	-1.2497	3.6369	0.08153	0.1885:0.5738:0.0:0.2377	.	10	O75762	TRPA1_HUMAN	H	10	ENSP00000262209:R10H	ENSP00000262209:R10H	R	-	2	0	TRPA1	73150170	0.025000	0.19082	0.389000	0.26208	0.058000	0.15608	-0.032000	0.12266	0.626000	0.30322	0.591000	0.81541	CGC		0.642	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
RDH10	157506	broad.mit.edu	37	8	74235200	74235200	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:74235200A>G	ENST00000240285.5	+	6	1633	c.955A>G	c.(955-957)Aag>Gag	p.K319E	RDH10_ENST00000519380.1_Missense_Mutation_p.K154E|RP11-434I12.2_ENST00000514599.1_RNA|RP11-434I12.2_ENST00000517475.1_RNA	NM_172037.4	NP_742034.1	Q8IZV5	RDH10_HUMAN	retinol dehydrogenase 10 (all-trans)	319					bud elongation involved in lung branching (GO:0060449)|ear development (GO:0043583)|embryonic camera-type eye development (GO:0031076)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|gonad development (GO:0008406)|in utero embryonic development (GO:0001701)|metanephros development (GO:0001656)|neural crest cell development (GO:0014032)|nose development (GO:0043584)|phototransduction, visible light (GO:0007603)|primary lung bud formation (GO:0060431)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	cell body (GO:0044297)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)	p.K319E(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)	11	Breast(64;0.0954)		Epithelial(68;0.0105)|all cancers(69;0.0465)|BRCA - Breast invasive adenocarcinoma(89;0.0608)			AGGAGCGGACAAGTGTATGTA	0.368																																					p.K319E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A955G	8						.						82.0	73.0	76.0					8																	74235200		2203	4300	6503	74397754	SO:0001583	missense	157506	exon6			AF456765	CCDS6213.1	8q21.11	2011-09-20			ENSG00000121039	ENSG00000121039	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	19975	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 16C, member 4"""	607599				12407145, 19027726	Standard	NM_172037		Approved	SDR16C4	uc003xzi.3	Q8IZV5	OTTHUMG00000164492	ENST00000240285.5:c.955A>G	8.37:g.74235200A>G	ENSP00000240285:p.Lys319Glu	Somatic		Capture	Illumina HiSeq	Phase_I	74397754	NM_172037		Missense_Mutation	SNP	ENST00000240285.5	37	CCDS6213.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.095053	0.56075	.	.	ENSG00000121039	ENST00000240285;ENST00000519380	D;T	0.84298	-1.83;-0.04	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.73087	0.3542	L	0.29908	0.895	0.80722	D	1	P	0.34864	0.473	B	0.24848	0.056	T	0.72516	-0.4269	10	0.07175	T	0.84	.	15.577	0.76400	1.0:0.0:0.0:0.0	.	319	Q8IZV5	RDH10_HUMAN	E	319;154	ENSP00000240285:K319E;ENSP00000428132:K154E	ENSP00000240285:K319E	K	+	1	0	RDH10	74397754	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.139000	0.94554	2.267000	0.75376	0.383000	0.25322	AAG		0.368	RDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378982.1		
HNF4G	3174	broad.mit.edu	37	8	76465424	76465424	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:76465424G>A	ENST00000354370.1	+	6	766	c.496G>A	c.(496-498)Gat>Aat	p.D166N	HNF4G_ENST00000396423.2_Missense_Mutation_p.D203N			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	166					endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.D166N(2)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	37	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			ATTACCATTGGATGATCAGGT	0.323																																					p.D203N												.	.	2	Substitution - Missense(2)	large_intestine(1)|skin(1)	c.G607A	8						.						101.0	99.0	100.0					8																	76465424		2203	4300	6503	76627979	SO:0001583	missense	3174	exon5				CCDS6220.2	8q21-q22	2013-01-16			ENSG00000164749	ENSG00000164749		"""Nuclear hormone receptors"""	5026	protein-coding gene	gene with protein product		605966				8622695, 12220494	Standard	NM_004133		Approved	NR2A2	uc003yar.3	Q14541	OTTHUMG00000149920	ENST00000354370.1:c.496G>A	8.37:g.76465424G>A	ENSP00000346339:p.Asp166Asn	Somatic		Capture	Illumina HiSeq	Phase_I	76627979	NM_004133	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	37		.	.	.	.	.	.	.	.	.	.	G	33	5.237373	0.95240	.	.	ENSG00000164749	ENST00000354370;ENST00000396423	D;D	0.94828	-3.53;-3.53	5.5	5.5	0.81552	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.087270	0.85682	D	0.000000	D	0.95809	0.8636	M	0.74258	2.255	0.80722	D	1	B;P	0.41546	0.052;0.754	B;P	0.48840	0.112;0.592	D	0.94710	0.7891	9	.	.	.	.	19.5916	0.95514	0.0:0.0:1.0:0.0	.	203;166	F1D8Q4;Q14541	.;HNF4G_HUMAN	N	166;203	ENSP00000346339:D166N;ENSP00000379701:D203N	.	D	+	1	0	HNF4G	76627979	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.167000	0.94773	2.861000	0.98227	0.655000	0.94253	GAT		0.323	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133	
HNF4G	3174	broad.mit.edu	37	8	76471053	76471053	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:76471053G>A	ENST00000354370.1	+	9	1033	c.763G>A	c.(763-765)Gat>Aat	p.D255N	HNF4G_ENST00000396423.2_Missense_Mutation_p.D292N			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	255					endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.D255H(1)|p.D255N(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	37	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			AGGGCTAAGCGATCCAGTAAA	0.398																																					p.D292N												.	.	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	c.G874A	8						.						63.0	61.0	62.0					8																	76471053		2203	4300	6503	76633608	SO:0001583	missense	3174	exon8				CCDS6220.2	8q21-q22	2013-01-16			ENSG00000164749	ENSG00000164749		"""Nuclear hormone receptors"""	5026	protein-coding gene	gene with protein product		605966				8622695, 12220494	Standard	NM_004133		Approved	NR2A2	uc003yar.3	Q14541	OTTHUMG00000149920	ENST00000354370.1:c.763G>A	8.37:g.76471053G>A	ENSP00000346339:p.Asp255Asn	Somatic		Capture	Illumina HiSeq	Phase_I	76633608	NM_004133	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	37		.	.	.	.	.	.	.	.	.	.	G	10.26	1.302447	0.23736	.	.	ENSG00000164749	ENST00000354370;ENST00000396423	D;D	0.94537	-3.45;-3.45	5.62	5.62	0.85841	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.133574	0.64402	D	0.000002	D	0.88865	0.6553	L	0.31845	0.965	0.58432	D	0.999998	B;B	0.10296	0.001;0.003	B;B	0.13407	0.003;0.009	T	0.82295	-0.0528	10	0.09843	T	0.71	.	10.7311	0.46098	0.1157:0.0:0.8843:0.0	.	292;255	F1D8Q4;Q14541	.;HNF4G_HUMAN	N	255;292	ENSP00000346339:D255N;ENSP00000379701:D292N	ENSP00000346339:D255N	D	+	1	0	HNF4G	76633608	1.000000	0.71417	0.983000	0.44433	0.483000	0.33249	6.426000	0.73374	2.648000	0.89879	0.655000	0.94253	GAT		0.398	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133	
ZFAND1	79752	broad.mit.edu	37	8	82626171	82626171	+	Silent	SNP	G	G	A	rs370810052		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:82626171G>A	ENST00000220669.5	-	6	480	c.462C>T	c.(460-462)ggC>ggT	p.G154G	ZFAND1_ENST00000522520.1_Silent_p.G47G|ZFAND1_ENST00000517588.1_Silent_p.G47G|ZFAND1_ENST00000519523.1_Silent_p.G154G|ZFAND1_ENST00000523096.1_Silent_p.G154G|ZFAND1_ENST00000521895.1_Silent_p.G47G|ZFAND1_ENST00000521287.1_Silent_p.G47G	NM_024699.2	NP_078975.2	Q8TCF1	ZFAN1_HUMAN	zinc finger, AN1-type domain 1	154							zinc ion binding (GO:0008270)	p.G154G(1)		kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						ATGACTTATCGCCATCAGCAT	0.363																																					p.G154G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C462T	8						.	G	,,	1,4405	2.1+/-5.4	0,1,2202	179.0	157.0	165.0		462,462,462	-2.9	1.0	8		165	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ZFAND1	NM_001170796.1,NM_001170797.1,NM_024699.2	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	154/262,154/228,154/269	82626171	1,13005	2203	4300	6503	82788726	SO:0001819	synonymous_variant	79752	exon6				CCDS6232.1, CCDS55250.1, CCDS55251.1	8q21.13	2006-07-07						"""Zinc fingers, AN1-type domain containing"""	25858	protein-coding gene	gene with protein product						12477932	Standard	NM_024699		Approved	FLJ14007	uc003ycj.2	Q8TCF1		ENST00000220669.5:c.462C>T	8.37:g.82626171G>A		Somatic		Capture	Illumina HiSeq	Phase_I	82788726	NM_001170797	E5RIG0|E5RJ99|Q658R7|Q6IA32|Q6PGQ6|Q9H810	Silent	SNP	ENST00000220669.5	37	CCDS6232.1																																																																																				0.363	ZFAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379739.1	NM_024699	
CA2	760	broad.mit.edu	37	8	86386635	86386635	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:86386635delT	ENST00000285379.5	+	4	664	c.434delT	c.(433-435)attfs	p.I145fs		NM_000067.2	NP_000058.1	P00918	CAH2_HUMAN	carbonic anhydrase II	145					angiotensin-activated signaling pathway (GO:0038166)|bicarbonate transport (GO:0015701)|kidney development (GO:0001822)|morphogenesis of an epithelium (GO:0002009)|odontogenesis of dentin-containing tooth (GO:0042475)|one-carbon metabolic process (GO:0006730)|positive regulation of bone resorption (GO:0045780)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of dipeptide transmembrane transport (GO:2001150)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of anion transport (GO:0044070)|regulation of chloride transport (GO:2001225)|regulation of intracellular pH (GO:0051453)|response to estrogen (GO:0043627)|response to pH (GO:0009268)|response to zinc ion (GO:0010043)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.L147fs*1(1)		central_nervous_system(2)|cervix(1)|large_intestine(2)|lung(5)|prostate(1)	11					Acetazolamide(DB00819)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Diclofenamide(DB01144)|Dorzolamide(DB00869)|Ethinamate(DB01031)|Furosemide(DB00695)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Topiramate(DB00273)|Trichlormethiazide(DB01021)|Zonisamide(DB00909)	GTTCTAGGTATTTTTTTGAAG	0.388																																					p.I145fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.434delT	8						.						144.0	154.0	151.0					8																	86386635		2203	4300	6503	86573887	SO:0001589	frameshift_variant	760	exon4			J03037	CCDS6239.1	8q21.2	2012-10-02			ENSG00000104267	ENSG00000104267	4.2.1.1	"""Carbonic anhydrases"""	1373	protein-coding gene	gene with protein product		611492				3107918	Standard	NM_000067		Approved	Car2, CA-II, CAII	uc003ydk.2	P00918	OTTHUMG00000164944	ENST00000285379.5:c.434delT	8.37:g.86386635delT	ENSP00000285379:p.Ile145fs	Somatic		Capture	Illumina HiSeq	Phase_I	86573887	NM_000067	B2R7G8|Q6FI12|Q96ET9	Frame_Shift_Del	DEL	ENST00000285379.5	37	CCDS6239.1																																																																																				0.388	CA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381097.2	NM_000067	
PSKH2	85481	broad.mit.edu	37	8	87076537	87076537	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:87076537C>A	ENST00000276616.2	-	2	583	c.509G>T	c.(508-510)gGg>gTg	p.G170V	PSKH2_ENST00000517981.1_5'UTR	NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	170	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.G170V(1)		NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			ATACCTAATCCCATCAGCAAC	0.463																																					p.G170V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G509T	8						.						68.0	72.0	70.0					8																	87076537		2203	4300	6503	87145653	SO:0001583	missense	85481	exon2			AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.509G>T	8.37:g.87076537C>A	ENSP00000276616:p.Gly170Val	Somatic		Capture	Illumina HiSeq	Phase_I	87145653	NM_033126	A0AV22	Missense_Mutation	SNP	ENST00000276616.2	37	CCDS6240.1	.	.	.	.	.	.	.	.	.	.	C	19.54	3.846137	0.71603	.	.	ENSG00000147613	ENST00000276616	T	0.57595	0.39	5.32	5.32	0.75619	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.72637	0.3485	M	0.74467	2.265	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.76152	-0.3064	9	0.87932	D	0	.	16.4854	0.84183	0.0:1.0:0.0:0.0	.	170	Q96QS6	KPSH2_HUMAN	V	170	ENSP00000276616:G170V	ENSP00000276616:G170V	G	-	2	0	PSKH2	87145653	1.000000	0.71417	0.693000	0.30195	0.608000	0.37181	7.212000	0.77941	2.460000	0.83146	0.655000	0.94253	GGG		0.463	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126	
RUNX1T1	862	broad.mit.edu	37	8	92982958	92982958	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:92982958C>T	ENST00000523629.1	-	11	1921	c.1467G>A	c.(1465-1467)acG>acA	p.T489T	RUNX1T1_ENST00000396218.1_Silent_p.T462T|RUNX1T1_ENST00000360348.2_Silent_p.T452T|RUNX1T1_ENST00000436581.2_Silent_p.T500T|RUNX1T1_ENST00000520724.1_Silent_p.T452T|RUNX1T1_ENST00000265814.3_Silent_p.T489T|RUNX1T1_ENST00000518844.1_Silent_p.T462T|RUNX1T1_ENST00000422361.2_Silent_p.T452T	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	489					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T500T(1)|p.T489T(1)|p.T452T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			CCTCGGCGACCGTGCGCTCCA	0.602																																					p.T489T												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.G1467A	8						.						77.0	65.0	69.0					8																	92982958		2203	4300	6503	93052134	SO:0001819	synonymous_variant	862	exon12			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"""Zinc fingers, MYND-type"""	1535	protein-coding gene	gene with protein product		133435	"""core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"""	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.1467G>A	8.37:g.92982958C>T		Somatic		Capture	Illumina HiSeq	Phase_I	93052134	NM_001198626	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Silent	SNP	ENST00000523629.1	37	CCDS6256.1																																																																																				0.602	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635	
KIAA1429	25962	broad.mit.edu	37	8	95503934	95503934	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:95503934A>G	ENST00000297591.5	-	22	5087	c.5012T>C	c.(5011-5013)aTa>aCa	p.I1671T	KIAA1429_ENST00000437199.1_3'UTR	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	1671					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.I1671T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TGGTGGAGGTATTCCATCTTG	0.448																																					p.I1671T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T5012C	8						.						186.0	166.0	173.0					8																	95503934		2203	4300	6503	95573110	SO:0001583	missense	25962	exon22			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.5012T>C	8.37:g.95503934A>G	ENSP00000297591:p.Ile1671Thr	Somatic		Capture	Illumina HiSeq	Phase_I	95573110	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	37	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	A	17.11	3.304635	0.60305	.	.	ENSG00000164944	ENST00000297591	T	0.42900	0.96	5.36	5.36	0.76844	.	0.107337	0.64402	D	0.000008	T	0.32734	0.0839	N	0.22421	0.69	0.80722	D	1	B	0.25609	0.13	B	0.25759	0.063	T	0.13683	-1.0500	10	0.59425	D	0.04	-14.6648	15.3555	0.74423	1.0:0.0:0.0:0.0	.	1671	Q69YN4	VIR_HUMAN	T	1671	ENSP00000297591:I1671T	ENSP00000297591:I1671T	I	-	2	0	KIAA1429	95573110	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.962000	0.93254	2.039000	0.60335	0.528000	0.53228	ATA		0.448	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
KIAA1429	25962	broad.mit.edu	37	8	95538910	95538910	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:95538910delA	ENST00000297591.5	-	8	1637	c.1562delT	c.(1561-1563)ttafs	p.L521fs	KIAA1429_ENST00000421249.2_Frame_Shift_Del_p.L521fs|KIAA1429_ENST00000437199.1_Frame_Shift_Del_p.L521fs	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	521					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.L521fs*1(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			CCTACCTCTTAAAAAAGCTTC	0.373																																					p.L521X												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1562delT	8						.						63.0	64.0	64.0					8																	95538910		2203	4300	6503	95608086	SO:0001589	frameshift_variant	25962	exon8			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.1562delT	8.37:g.95538910delA	ENSP00000297591:p.Leu521fs	Somatic		Capture	Illumina HiSeq	Phase_I	95608086	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Frame_Shift_Del	DEL	ENST00000297591.5	37	CCDS34923.1																																																																																				0.373	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
STK3	6788	broad.mit.edu	37	8	99591934	99591934	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:99591934A>G	ENST00000419617.2	-	8	1046	c.906T>C	c.(904-906)caT>caC	p.H302H	STK3_ENST00000523601.1_Silent_p.H330H	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	302					apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)	p.H302H(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		GCTGTTCCTCATGTCTTTTAG	0.323																																					p.H302H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T906C	8						.						186.0	180.0	182.0					8																	99591934		1817	4086	5903	99661110	SO:0001819	synonymous_variant	6788	exon8			BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"""serine/threonine kinase 3 (Ste20, yeast homolog)"""			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.906T>C	8.37:g.99591934A>G		Somatic		Capture	Illumina HiSeq	Phase_I	99661110	NM_006281	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Silent	SNP	ENST00000419617.2	37	CCDS47900.1																																																																																				0.323	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281	
COMMD5	28991	broad.mit.edu	37	8	146076508	146076508	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr8:146076508C>T	ENST00000305103.3	-	2	468	c.216G>A	c.(214-216)ggG>ggA	p.G72G	AF235103.1_ENST00000578937.1_RNA|COMMD5_ENST00000450361.2_Silent_p.G72G|COMMD5_ENST00000402718.3_Silent_p.G72G	NM_014066.3	NP_054785.2	Q9GZQ3	COMD5_HUMAN	COMM domain containing 5	72						nucleus (GO:0005634)		p.G72G(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|ovary(1)|pancreas(1)	11	all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			TGGCGCTGACCCCAAGACGCT	0.642																																					p.G72G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G216A	8						.						25.0	23.0	24.0					8																	146076508		2202	4298	6500	146047312	SO:0001819	synonymous_variant	28991	exon2			AK023070	CCDS6436.1	8q24.3	2006-11-06				ENSG00000170619			17902	protein-coding gene	gene with protein product		608216				15799966, 10918053	Standard	NM_014066		Approved	HT002, FLJ13008, HCaRG	uc003zem.3	Q9GZQ3		ENST00000305103.3:c.216G>A	8.37:g.146076508C>T		Somatic		Capture	Illumina HiSeq	Phase_I	146047312	NM_001081004	D3DWN7|Q9NVN6|Q9UHX5	Silent	SNP	ENST00000305103.3	37	CCDS6436.1																																																																																				0.642	COMMD5-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382962.1	NM_014066	
GLIS3	169792	broad.mit.edu	37	9	3898647	3898648	+	Intron	INS	-	-	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:3898647_3898648insA	ENST00000324333.10	-	6	1857				GLIS3-AS1_ENST00000451340.2_RNA|GLIS3_ENST00000461870.1_Intron|GLIS3_ENST00000381971.3_Intron	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3						negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		GTAAAAGGCCTAAAAAAGGGTA	0.495																																					.												.	.	0			.	9						.		,	1,4263		0,1,2131					,	-3.0	0.0			39	0,8254		0,0,4127	no	intron,intron	GLIS3	NM_152629.3,NM_001042413.1	,	0,1,6258	A1A1,A1R,RR		0.0,0.0235,0.0080	,	,		1,12517				3888648	SO:0001627	intron_variant	169792	.			BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.1663+42->T	9.37:g.3898653_3898653dupA		Somatic		Capture	Illumina HiSeq	Phase_I	3888647	.	B1AL19|Q1PHK5	Frame_Shift_Ins	INS	ENST00000324333.10	37	CCDS6451.1																																																																																				0.495	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629	
GRIN3A	116443	broad.mit.edu	37	9	104375760	104375760	+	Silent	SNP	G	G	A	rs143542253		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:104375760G>A	ENST00000361820.3	-	6	3264	c.2664C>T	c.(2662-2664)tcC>tcT	p.S888S	GRIN3A_ENST00000479772.1_5'UTR	NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	888					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)	p.S888S(1)		breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	TGATTAGCTCGGATATGTTGG	0.463																																					p.S888S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2664T	9						.	G		1,4405	2.1+/-5.4	0,1,2202	196.0	158.0	171.0		2664	-10.3	0.9	9	dbSNP_134	171	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GRIN3A	NM_133445.2		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		888/1116	104375760	2,13004	2203	4300	6503	103415581	SO:0001819	synonymous_variant	116443	exon6				CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.2664C>T	9.37:g.104375760G>A		Somatic		Capture	Illumina HiSeq	Phase_I	103415581	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																				0.463	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
SLC44A1	23446	broad.mit.edu	37	9	108072052	108072052	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:108072052A>G	ENST00000374720.3	+	3	421	c.174A>G	c.(172-174)ctA>ctG	p.L58L	SLC44A1_ENST00000374723.1_Silent_p.L58L|SLC44A1_ENST00000374724.1_Silent_p.L58L|SLC44A1_ENST00000607692.1_3'UTR	NM_080546.3	NP_536856.2	Q8WWI5	CTL1_HUMAN	solute carrier family 44 (choline transporter), member 1	58					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)	p.L58L(1)		breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	38					Choline(DB00122)	CAGCAAGACTAGTGTCAGGAT	0.413																																					p.L58L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A174G	9						.						116.0	109.0	112.0					9																	108072052		2203	4300	6503	107111873	SO:0001819	synonymous_variant	23446	exon3			AJ420812	CCDS6763.1, CCDS75868.1	9q31.2	2014-01-28	2013-07-17	2005-09-06	ENSG00000070214	ENSG00000070214		"""CD molecules"", ""Solute carriers"""	18798	protein-coding gene	gene with protein product		606105	"""CDW92 antigen"""	CDW92		11698453, 10677542	Standard	NM_080546		Approved	CDw92, CTL1, CHTL1, CD92	uc004bcn.3	Q8WWI5	OTTHUMG00000020421	ENST00000374720.3:c.174A>G	9.37:g.108072052A>G		Somatic		Capture	Illumina HiSeq	Phase_I	107111873	NM_080546	A6NLZ9|Q5VUB3|Q8WVB0|Q96KU3|Q9NY69	Silent	SNP	ENST00000374720.3	37	CCDS6763.1																																																																																				0.413	SLC44A1-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053500.1	NM_080546	
RAD23B	5887	broad.mit.edu	37	9	110081108	110081108	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:110081108C>T	ENST00000358015.3	+	6	980	c.629C>T	c.(628-630)gCc>gTc	p.A210V	RAD23B_ENST00000416373.2_Missense_Mutation_p.A138V	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	210	UBA 1. {ECO:0000255|PROSITE- ProRule:PRU00212}.				DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)	p.A210V(1)		breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						GTAATTGCAGCCCTGAGAGCC	0.413								Direct reversal of damage;Nucleotide excision repair (NER)																													p.A210V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C629T	9						.						132.0	125.0	127.0					9																	110081108		2203	4300	6503	109120929	SO:0001583	missense	5887	exon6				CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"""XP-C repair complementing protein"", ""XP-C repair complementing complex 58 kDa"""	600062	"""RAD23 (S. cerevisiae) homolog B"""			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.629C>T	9.37:g.110081108C>T	ENSP00000350708:p.Ala210Val	Somatic		Capture	Illumina HiSeq	Phase_I	109120929	NM_002874	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Missense_Mutation	SNP	ENST00000358015.3	37	CCDS6769.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.218851|5.218851	0.95104|0.95104	.|.	.|.	ENSG00000119318|ENSG00000119318	ENST00000358015;ENST00000374678;ENST00000416373|ENST00000457811	T;T|.	0.64438|.	-0.1;-0.1|.	4.66|4.66	4.66|4.66	0.58398|0.58398	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88537|0.88537	0.6463|0.6463	H|H	0.97491|0.97491	4.015|4.015	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.997;1.0;1.0|.	D;D;D|.	0.91635|.	0.994;0.999;0.999|.	D|D	0.92993|0.92993	0.6416|0.6416	10|5	0.87932|.	D|.	0|.	-10.7463|-10.7463	17.9143|17.9143	0.88944|0.88944	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	189;210;210|.	B7Z4W4;B4DEA3;P54727|.	.;.;RD23B_HUMAN|.	V|S	210;138;138|80	ENSP00000350708:A210V;ENSP00000405623:A138V|.	ENSP00000350708:A210V|.	A|P	+|+	2|1	0|0	RAD23B|RAD23B	109120929|109120929	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.459000|7.459000	0.80802|0.80802	2.301000|2.301000	0.77427|0.77427	0.561000|0.561000	0.74099|0.74099	GCC|CCC		0.413	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874	
TMEM245	23731	broad.mit.edu	37	9	111812882	111812882	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:111812882C>T	ENST00000374586.3	-	13	1976	c.1945G>A	c.(1945-1947)Ggg>Agg	p.G649R		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	649						integral component of membrane (GO:0016021)		p.G649R(1)									AGGGCTGTCCCGCTGTAGAAG	0.458																																					p.G649R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1945A	9						.						130.0	128.0	129.0					9																	111812882		1992	4184	6176	110852703	SO:0001583	missense	23731	exon13			AF153415	CCDS43858.1	9q31	2012-03-06	2012-03-06	2012-03-06	ENSG00000106771	ENSG00000106771			1363	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 5"""	C9orf5		10564813	Standard	NM_032012		Approved	CG-2	uc004bdt.4	Q9H330	OTTHUMG00000020469	ENST00000374586.3:c.1945G>A	9.37:g.111812882C>T	ENSP00000363714:p.Gly649Arg	Somatic		Capture	Illumina HiSeq	Phase_I	110852703	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Missense_Mutation	SNP	ENST00000374586.3	37	CCDS43858.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.562326|5.562326	0.96527|0.96527	.|.	.|.	ENSG00000106771|ENSG00000106771	ENST00000374586;ENST00000223608|ENST00000413712	T|.	0.34667|.	1.35|.	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.82935|0.82935	0.5145|0.5145	M|M	0.83012|0.83012	2.62|2.62	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	T|T	0.82932|0.82932	-0.0212|-0.0212	10|5	0.72032|.	D|.	0.01|.	-16.0577|-16.0577	20.1356|20.1356	0.98028|0.98028	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	649;649|.	Q9H330-2;Q9H330|.	.;CI005_HUMAN|.	R|Q	649|241	ENSP00000363714:G649R|.	ENSP00000223608:G649R|.	G|R	-|-	1|2	0|0	C9orf5|C9orf5	110852703|110852703	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.974000|0.974000	0.67602|0.67602	7.800000|7.800000	0.85949|0.85949	2.755000|2.755000	0.94549|0.94549	0.650000|0.650000	0.86243|0.86243	GGG|CGG		0.458	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012	
ZNF483	158399	broad.mit.edu	37	9	114305371	114305371	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:114305371A>G	ENST00000309235.5	+	6	2314	c.2156A>G	c.(2155-2157)tAt>tGt	p.Y719C	ZNF483_ENST00000358151.4_Intron	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	719					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Y719C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						AGGAGAGAATATGAATGTAAC	0.393																																					p.Y719C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2156G	9						.						70.0	70.0	70.0					9																	114305371		2203	4300	6503	113345192	SO:0001583	missense	158399	exon6			AB075842	CCDS35105.1, CCDS35106.1	9q32	2013-01-09			ENSG00000173258	ENSG00000173258		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23384	protein-coding gene	gene with protein product							Standard	NM_001007169		Approved	ZKSCAN16, KIAA1962, ZSCAN48	uc004bff.2	Q8TF39	OTTHUMG00000020490	ENST00000309235.5:c.2156A>G	9.37:g.114305371A>G	ENSP00000311679:p.Tyr719Cys	Somatic		Capture	Illumina HiSeq	Phase_I	113345192	NM_133464	Q5VZN2|Q8NAE1	Missense_Mutation	SNP	ENST00000309235.5	37	CCDS35106.1	.	.	.	.	.	.	.	.	.	.	A	7.813	0.716096	0.15306	.	.	ENSG00000173258	ENST00000309235	T	0.25414	1.8	4.2	4.2	0.49525	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41194	D	0.000931	T	0.47173	0.1431	M	0.66506	2.035	0.49798	D	0.999825	D	0.89917	1.0	D	0.83275	0.996	T	0.49062	-0.8978	10	0.87932	D	0	-8.8301	11.891	0.52628	1.0:0.0:0.0:0.0	.	719	Q8TF39	ZN483_HUMAN	C	719	ENSP00000311679:Y719C	ENSP00000311679:Y719C	Y	+	2	0	ZNF483	113345192	0.009000	0.17119	0.039000	0.18376	0.048000	0.14542	0.748000	0.26305	2.134000	0.65973	0.482000	0.46254	TAT		0.393	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567	
FKBP15	23307	broad.mit.edu	37	9	115932015	115932015	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:115932015C>T	ENST00000238256.3	-	26	3091	c.2974G>A	c.(2974-2976)Gtc>Atc	p.V992I		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	992					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)		p.V1017I(1)|p.V992I(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						GGCAACGGGACAGCTTCCTCG	0.592																																					p.V992I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2974A	9						.						45.0	49.0	48.0					9																	115932015		2079	4207	6286	114971836	SO:0001583	missense	23307	exon26			AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.2974G>A	9.37:g.115932015C>T	ENSP00000238256:p.Val992Ile	Somatic		Capture	Illumina HiSeq	Phase_I	114971836	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	.	.	.	.	.	.	.	.	.	.	C	8.862	0.947154	0.18356	.	.	ENSG00000119321	ENST00000446284;ENST00000238256	T;T	0.21734	1.99;1.99	4.61	-0.243	0.13035	.	.	.	.	.	T	0.11024	0.0269	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34453	-0.9828	9	0.24483	T	0.36	7.0877	4.0514	0.09796	0.0:0.4544:0.1864:0.3592	.	573;992	B4DVS2;Q5T1M5	.;FKB15_HUMAN	I	1017;992	ENSP00000416158:V1017I;ENSP00000238256:V992I	ENSP00000238256:V992I	V	-	1	0	FKBP15	114971836	0.001000	0.12720	0.001000	0.08648	0.062000	0.15995	0.210000	0.17455	-0.079000	0.12707	0.491000	0.48974	GTC		0.592	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
FKBP15	23307	broad.mit.edu	37	9	115936836	115936836	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:115936836C>T	ENST00000238256.3	-	22	2368	c.2251G>A	c.(2251-2253)Gct>Act	p.A751T		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	751					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)		p.A776T(1)|p.A751T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						CGCTCTTGAGCTGACTTCTTT	0.453																																					p.A751T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2251A	9						.						94.0	91.0	92.0					9																	115936836		1895	4113	6008	114976657	SO:0001583	missense	23307	exon22			AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.2251G>A	9.37:g.115936836C>T	ENSP00000238256:p.Ala751Thr	Somatic		Capture	Illumina HiSeq	Phase_I	114976657	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	.	.	.	.	.	.	.	.	.	.	c	24.1	4.488148	0.84854	.	.	ENSG00000119321	ENST00000446284;ENST00000238256	T;T	0.24723	1.84;1.85	6.07	6.07	0.98685	.	.	.	.	.	T	0.44008	0.1273	L	0.54323	1.7	0.34912	D	0.747521	D;D	0.71674	0.998;0.979	D;P	0.65684	0.937;0.702	T	0.50550	-0.8815	9	0.45353	T	0.12	-14.9479	13.7005	0.62606	0.0:0.8457:0.1543:0.0	.	332;751	B4DVS2;Q5T1M5	.;FKB15_HUMAN	T	776;751	ENSP00000416158:A776T;ENSP00000238256:A751T	ENSP00000238256:A751T	A	-	1	0	FKBP15	114976657	0.346000	0.24844	0.991000	0.47740	0.986000	0.74619	1.319000	0.33655	2.890000	0.99128	0.586000	0.80456	GCT		0.453	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
BRINP1	1620	broad.mit.edu	37	9	121976289	121976289	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:121976289T>G	ENST00000265922.3	-	6	1291	c.830A>C	c.(829-831)aAc>aCc	p.N277T	BRINP1_ENST00000373964.2_Missense_Mutation_p.N277T	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	277					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)		p.N277T(1)									GATGGGGCAGTTGCACTGCGG	0.557																																					p.N277T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A830C	9						.						136.0	117.0	124.0					9																	121976289		2203	4300	6503	121016110	SO:0001583	missense	1620	exon6			AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"""deleted in bladder cancer chromosome region candidate 1"", ""deleted in bladder cancer 1"""	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.830A>C	9.37:g.121976289T>G	ENSP00000265922:p.Asn277Thr	Somatic		Capture	Illumina HiSeq	Phase_I	121016110	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	T	18.19	3.569040	0.65765	.	.	ENSG00000078725	ENST00000373969;ENST00000265922;ENST00000373964	T;T	0.54279	2.21;0.58	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.70979	0.3286	M	0.71206	2.165	0.80722	D	1	D;D	0.61080	0.989;0.981	D;D	0.70487	0.969;0.932	T	0.74399	-0.3678	10	0.72032	D	0.01	-29.2676	15.0119	0.71555	0.0:0.0:0.0:1.0	.	277;277	O60477-2;O60477	.;DBC1_HUMAN	T	277	ENSP00000265922:N277T;ENSP00000363075:N277T	ENSP00000265922:N277T	N	-	2	0	DBC1	121016110	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.698000	0.84413	2.147000	0.66899	0.460000	0.39030	AAC		0.557	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618	
PHF19	26147	broad.mit.edu	37	9	123636951	123636951	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:123636951C>T	ENST00000373896.3	-	2	321	c.69G>A	c.(67-69)aaG>aaA	p.K23K	PHF19_ENST00000312189.6_Silent_p.K23K	NM_015651.1	NP_056466.1	Q5T6S3	PHF19_HUMAN	PHD finger protein 19	23					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.K23K(2)		NS(2)|breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCAGGGCCCCCTTGTTGGGGA	0.567																																					p.K23K												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G69A	9						.						94.0	94.0	94.0					9																	123636951		2203	4300	6503	122676772	SO:0001819	synonymous_variant	26147	exon2			BX640713	CCDS35116.1, CCDS35117.1, CCDS69648.1, CCDS75889.1	9q34.11	2013-01-28			ENSG00000119403	ENSG00000119403		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24566	protein-coding gene	gene with protein product	"""polycomb-like 3"", ""tudor domain containing 19B"""	609740				15563832	Standard	XM_005251906		Approved	DKFZP727G051, PCL3, MTF2L1, TDRD19B	uc004bks.1	Q5T6S3	OTTHUMG00000020577	ENST00000373896.3:c.69G>A	9.37:g.123636951C>T		Somatic		Capture	Illumina HiSeq	Phase_I	122676772	NM_015651	Q32NF2|Q5T6S4|Q6N038|Q8TBL6|Q9UFS9	Silent	SNP	ENST00000373896.3	37	CCDS35116.1																																																																																				0.567	PHF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053838.3	XM_045308	
GSN	2934	broad.mit.edu	37	9	124094767	124094767	+	Silent	SNP	C	C	A	rs368986042		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:124094767C>A	ENST00000373818.4	+	17	2304	c.2235C>A	c.(2233-2235)acC>acA	p.T745T	GSN_ENST00000341272.2_Silent_p.T694T|GSN_ENST00000394353.2_Silent_p.T705T|GSN_ENST00000449733.1_Silent_p.T694T|GSN_ENST00000436847.1_Silent_p.T705T|GSN_ENST00000373823.3_Silent_p.T694T|GSN_ENST00000412819.1_Silent_p.T694T|GSN_ENST00000373806.1_Silent_p.T170T|GSN_ENST00000545652.1_Silent_p.T702T|GSN_ENST00000373808.2_Silent_p.T694T	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	745	Actin-binding, Ca-sensitive. {ECO:0000255}.				actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)	p.T694T(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						CGCCCATCACCGTGGTGAAGC	0.572											OREG0019445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T694T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2082A	9						.						156.0	133.0	141.0					9																	124094767		2203	4300	6503	123134588	SO:0001819	synonymous_variant	2934	exon19			X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"""amyloidosis, Finnish type"""	137350	"""gelsolin (amyloidosis, Finnish type)"""			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.2235C>A	9.37:g.124094767C>A		Somatic	1531	Capture	Illumina HiSeq	Phase_I	123134588	NM_001127664	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Silent	SNP	ENST00000373818.4	37	CCDS6828.1																																																																																				0.572	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177	
OR1Q1	158131	broad.mit.edu	37	9	125377667	125377667	+	Silent	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:125377667C>A	ENST00000297913.2	+	1	720	c.651C>A	c.(649-651)tcC>tcA	p.S217S	RP11-64P14.7_ENST00000431442.1_RNA	NM_012364.1	NP_036496.1	Q15612	OR1Q1_HUMAN	olfactory receptor, family 1, subfamily Q, member 1	217					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S217S(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	17						TTACTGCCTCCTATGCCTGCA	0.537																																					p.S217S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C651A	9						.						140.0	135.0	136.0					9																	125377667		2203	4300	6503	124417488	SO:0001819	synonymous_variant	158131	exon1				CCDS35125.1	9q33.2	2013-09-20			ENSG00000165202	ENSG00000165202		"""GPCR / Class A : Olfactory receptors"""	8223	protein-coding gene	gene with protein product				OR1Q2, OR1Q3			Standard	NM_012364		Approved	OST226, OR9-A, HSTPCR106, OST226OR9-A, TPCR106	uc011lyy.2	Q15612	OTTHUMG00000020615	ENST00000297913.2:c.651C>A	9.37:g.125377667C>A		Somatic		Capture	Illumina HiSeq	Phase_I	124417488	NM_012364	Q6IFN4|Q8NGR7|Q96R82	Silent	SNP	ENST00000297913.2	37	CCDS35125.1																																																																																				0.537	OR1Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053946.1		
RABGAP1	23637	broad.mit.edu	37	9	125832687	125832687	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:125832687C>T	ENST00000373647.4	+	15	2101	c.1967C>T	c.(1966-1968)gCt>gTt	p.A656V	RABGAP1_ENST00000373643.5_5'UTR|RABGAP1_ENST00000493854.1_3'UTR	NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	656	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)	p.A584V(1)|p.A656V(1)		breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						TTTCTTGCTGCTGTGCTCCTT	0.403																																					p.A656V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1967T	9						.						267.0	243.0	251.0					9																	125832687		2203	4300	6503	124872508	SO:0001583	missense	23637	exon15			AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"""rab6 GTPase activating protein (GAP and centrosome-associated)"", ""TBC1 domain family, member 11"""	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.1967C>T	9.37:g.125832687C>T	ENSP00000362751:p.Ala656Val	Somatic		Capture	Illumina HiSeq	Phase_I	124872508	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Missense_Mutation	SNP	ENST00000373647.4	37	CCDS6848.2	.	.	.	.	.	.	.	.	.	.	C	35	5.483331	0.96307	.	.	ENSG00000011454	ENST00000373647	T	0.16196	2.36	5.83	5.83	0.93111	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.53932	0.1827	M	0.91663	3.23	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.62737	-0.6791	10	0.87932	D	0	-15.0387	20.1271	0.97986	0.0:1.0:0.0:0.0	.	656	Q9Y3P9	RBGP1_HUMAN	V	656	ENSP00000362751:A656V	ENSP00000362751:A656V	A	+	2	0	RABGAP1	124872508	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.487000	0.81328	2.758000	0.94735	0.563000	0.77884	GCT		0.403	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197	
OLFML2A	169611	broad.mit.edu	37	9	127549350	127549350	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:127549350C>T	ENST00000373580.3	+	2	187	c.187C>T	c.(187-189)Cga>Tga	p.R63*		NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	63					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)	p.R63*(1)		endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						CGCGTGTAGCCGAGTGCGCAG	0.652																																					p.R63X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C187T	9						.						52.0	59.0	57.0					9																	127549350		2159	4268	6427	126589171	SO:0001587	stop_gained	169611	exon2			AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.187C>T	9.37:g.127549350C>T	ENSP00000362682:p.Arg63*	Somatic		Capture	Illumina HiSeq	Phase_I	126589171	NM_182487	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Nonsense_Mutation	SNP	ENST00000373580.3	37	CCDS6857.2	.	.	.	.	.	.	.	.	.	.	C	19.73	3.881694	0.72294	.	.	ENSG00000185585	ENST00000331715;ENST00000425732;ENST00000373580	.	.	.	5.73	3.85	0.44370	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.0104	0.64493	0.2753:0.7247:0.0:0.0	.	.	.	.	X	63	.	ENSP00000336425:R63X	R	+	1	2	OLFML2A	126589171	1.000000	0.71417	1.000000	0.80357	0.093000	0.18481	3.492000	0.53259	0.729000	0.32403	-0.181000	0.13052	CGA		0.652	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487	
LURAP1L	286343	broad.mit.edu	37	9	12821484	12821484	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:12821484A>G	ENST00000319264.3	+	2	1107	c.412A>G	c.(412-414)Att>Gtt	p.I138V		NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	141								p.I138V(1)									AAAAGCCACCATTACCAGCAG	0.532																																					p.I138V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A412G	9						.						82.0	84.0	83.0					9																	12821484		2203	4300	6503	12811484	SO:0001583	missense	286343	exon2			AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"""similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"""		"""chromosome 9 open reading frame 150"""	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.412A>G	9.37:g.12821484A>G	ENSP00000321026:p.Ile138Val	Somatic		Capture	Illumina HiSeq	Phase_I	12811484	NM_203403	Q5VZX7|Q8N923|Q8NCG2	Missense_Mutation	SNP	ENST00000319264.3	37	CCDS6473.1	.	.	.	.	.	.	.	.	.	.	A	5.089	0.202006	0.09652	.	.	ENSG00000153714	ENST00000319264	T	0.39997	1.05	5.59	1.9	0.25705	.	0.470122	0.20860	N	0.084376	T	0.21022	0.0506	N	0.11560	0.145	0.25787	N	0.984661	B	0.06786	0.001	B	0.04013	0.001	T	0.17776	-1.0358	10	0.23891	T	0.37	.	9.185	0.37165	0.6507:0.0:0.3493:0.0	.	141	Q8IV03	CI150_HUMAN	V	138	ENSP00000321026:I138V	ENSP00000321026:I138V	I	+	1	0	C9orf150	12811484	0.198000	0.23374	0.771000	0.31576	0.645000	0.38454	0.822000	0.27352	0.075000	0.16796	0.460000	0.39030	ATT		0.532	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403	
PPP6C	5537	broad.mit.edu	37	9	127911967	127911967	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:127911967C>T	ENST00000373547.4	-	7	1002	c.903G>A	c.(901-903)acG>acA	p.T301T	PPP6C_ENST00000373546.3_Silent_p.T154T|PPP6C_ENST00000415905.1_Silent_p.T279T|PPP6C_ENST00000451402.1_Silent_p.T338T	NM_002721.4	NP_002712.1	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit	301					G1/S transition of mitotic cell cycle (GO:0000082)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.T301T(2)		NS(2)|endometrium(1)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(3)	14						GGAAATATGGCGTTGTCGTTC	0.418																																					p.T279T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G837A	9						.						115.0	99.0	105.0					9																	127911967		2203	4300	6503	126951788	SO:0001819	synonymous_variant	5537	exon6			AF035158	CCDS6861.1, CCDS48018.1, CCDS48019.1	9q33.3	2010-03-17			ENSG00000119414	ENSG00000119414		"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9323	protein-coding gene	gene with protein product		612725				9143513	Standard	NM_002721		Approved	PP6	uc004bpg.4	O00743	OTTHUMG00000020671	ENST00000373547.4:c.903G>A	9.37:g.127911967C>T		Somatic		Capture	Illumina HiSeq	Phase_I	126951788	NM_001123369	B2R5V6|B7Z2W9|B7Z5K9|Q5U0A2|Q9UIC9	Silent	SNP	ENST00000373547.4	37	CCDS6861.1																																																																																				0.418	PPP6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054060.1	NM_016294	
LMX1B	4010	broad.mit.edu	37	9	129455432	129455432	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:129455432G>T	ENST00000373474.4	+	4	578	c.571G>T	c.(571-573)Gat>Tat	p.D191Y	LMX1B_ENST00000425646.2_Missense_Mutation_p.D168Y|LMX1B_ENST00000355497.5_Missense_Mutation_p.D191Y|LMX1B_ENST00000526117.1_Missense_Mutation_p.D191Y|LMX1B_ENST00000561065.1_Missense_Mutation_p.D168Y			O60663	LMX1B_HUMAN	LIM homeobox transcription factor 1, beta	191					cell proliferation (GO:0008283)|central nervous system neuron development (GO:0021954)|cerebellum morphogenesis (GO:0021587)|collagen fibril organization (GO:0030199)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral pattern formation (GO:0009953)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|organ growth (GO:0035265)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|trabecular meshwork development (GO:0002930)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.D168Y(1)		endometrium(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	15						GAAGAGCGAGGATGAAGATGG	0.682									Nail-Patella Syndrome																												p.D191Y	Pancreas(110;1796 2278 18357 20466)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G571T	9						.						27.0	23.0	24.0					9																	129455432		2188	4293	6481	128495253	SO:0001583	missense	4010	exon4	Familial Cancer Database	Osteo-Onychodysplasia, Turner-Kieser syndrome, Fong disease	U77457	CCDS6866.1, CCDS6866.2, CCDS55342.1, CCDS55343.1	9q33.3	2011-06-20			ENSG00000136944	ENSG00000136944		"""Homeoboxes / LIM class"""	6654	protein-coding gene	gene with protein product		602575		NPS1		9441763, 9590287	Standard	NM_002316		Approved		uc004bqj.3	O60663	OTTHUMG00000020692	ENST00000373474.4:c.571G>T	9.37:g.129455432G>T	ENSP00000362573:p.Asp191Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	128495253	NM_002316	F8W7W6|O75463|Q5JU95|Q6ISC9	Missense_Mutation	SNP	ENST00000373474.4	37	CCDS55342.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.172641	0.78452	.	.	ENSG00000136944	ENST00000526117;ENST00000373474;ENST00000355497;ENST00000425646	T;T;D;T	0.88124	-1.13;-1.13;-2.34;-1.13	4.85	4.85	0.62838	.	0.048012	0.85682	D	0.000000	D	0.92328	0.7566	M	0.68593	2.085	0.80722	D	1	D;D;D	0.89917	0.995;1.0;1.0	D;D;D	0.83275	0.94;0.99;0.996	D	0.91570	0.5271	10	0.36615	T	0.2	.	16.9347	0.86200	0.0:0.0:1.0:0.0	.	168;168;191	B7ZLH2;O60663;F8VYP0	.;LMX1B_HUMAN;.	Y	191;191;191;168	ENSP00000436930:D191Y;ENSP00000362573:D191Y;ENSP00000347684:D191Y;ENSP00000390923:D168Y	ENSP00000347684:D191Y	D	+	1	0	LMX1B	128495253	1.000000	0.71417	0.995000	0.50966	0.782000	0.44232	9.400000	0.97290	2.234000	0.73211	0.313000	0.20887	GAT		0.682	LMX1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054123.2		
FAM129B	64855	broad.mit.edu	37	9	130293979	130293979	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:130293979C>T	ENST00000373312.3	-	2	347	c.134G>A	c.(133-135)cGc>cAc	p.R45H	FAM129B_ENST00000373314.3_Missense_Mutation_p.R32H|FAM129B_ENST00000468379.1_5'UTR	NM_022833.2	NP_073744.2	Q96TA1	NIBL1_HUMAN	family with sequence similarity 129, member B	45					negative regulation of apoptotic process (GO:0043066)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R45H(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						AATCTCATGGCGCATGCTGTT	0.577																																					p.R45H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G134A	9						.						79.0	74.0	76.0					9																	130293979		2203	4300	6503	129333800	SO:0001583	missense	64855	exon2			AF151783	CCDS35144.1, CCDS35145.1	9q34.13	2010-02-01	2006-11-23	2006-11-23	ENSG00000136830	ENSG00000136830			25282	protein-coding gene	gene with protein product		614045	"""chromosome 9 open reading frame 88"""	C9orf88		14702039, 19362540	Standard	XM_005252135		Approved	DKFZP434H0820, FLJ13518, FLJ22151, FLJ22298, bA356B19.6, MINERVA	uc004brh.3	Q96TA1	OTTHUMG00000020705	ENST00000373312.3:c.134G>A	9.37:g.130293979C>T	ENSP00000362409:p.Arg45His	Somatic		Capture	Illumina HiSeq	Phase_I	129333800	NM_022833	Q4LE55|Q5VVW6|Q5VVW7|Q9BUS2|Q9NT35	Missense_Mutation	SNP	ENST00000373312.3	37	CCDS35145.1	.	.	.	.	.	.	.	.	.	.	c	28.6	4.930821	0.92389	.	.	ENSG00000136830	ENST00000373314;ENST00000373312	T;T	0.25749	1.78;1.81	4.88	4.88	0.63580	.	0.055998	0.64402	D	0.000001	T	0.49609	0.1567	M	0.68593	2.085	0.54753	D	0.999981	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.50363	-0.8837	10	0.66056	D	0.02	-35.4698	15.5765	0.76392	0.0:1.0:0.0:0.0	.	32;45	Q96TA1-2;Q96TA1	.;NIBL1_HUMAN	H	32;45	ENSP00000362411:R32H;ENSP00000362409:R45H	ENSP00000362409:R45H	R	-	2	0	FAM129B	129333800	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.165000	0.77544	2.539000	0.85634	0.556000	0.70494	CGC		0.577	FAM129B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054196.1	NM_022833	
SPTAN1	6709	broad.mit.edu	37	9	131370475	131370475	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:131370475G>A	ENST00000372731.4	+	34	4521	c.4411G>A	c.(4411-4413)Gaa>Aaa	p.E1471K	SPTAN1_ENST00000372739.3_Missense_Mutation_p.E1471K|SPTAN1_ENST00000358161.5_Missense_Mutation_p.E1471K	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1471					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.E1471K(1)		NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						CTTGAATACCGAAGACAAAGG	0.517																																					p.E1451K	NSCLC(120;833 1744 2558 35612 37579)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4351A	9						.						162.0	166.0	165.0					9																	131370475		2203	4300	6503	130410296	SO:0001583	missense	6709	exon33			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.4411G>A	9.37:g.131370475G>A	ENSP00000361816:p.Glu1471Lys	Somatic		Capture	Illumina HiSeq	Phase_I	130410296	NM_001195532	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.440708	0.83993	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.52983	0.64;0.64;0.64	5.54	5.54	0.83059	.	0.048330	0.85682	D	0.000000	T	0.55705	0.1937	M	0.82630	2.6	0.80722	D	1	P;B;B	0.38800	0.648;0.257;0.302	B;B;B	0.35655	0.207;0.04;0.066	T	0.64664	-0.6354	10	0.72032	D	0.01	.	19.8585	0.96775	0.0:0.0:1.0:0.0	.	1451;1471;1471	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	K	1471;1471;1471;1451	ENSP00000350882:E1471K;ENSP00000361816:E1471K;ENSP00000361824:E1471K	ENSP00000350882:E1471K	E	+	1	0	SPTAN1	130410296	1.000000	0.71417	0.942000	0.38095	0.941000	0.58515	9.420000	0.97426	2.760000	0.94817	0.655000	0.94253	GAA		0.517	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
PKN3	29941	broad.mit.edu	37	9	131480880	131480880	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:131480880G>A	ENST00000291906.4	+	18	2494	c.2101G>A	c.(2101-2103)Gca>Aca	p.A701T	ZDHHC12_ENST00000467312.1_5'Flank|PKN3_ENST00000485301.1_3'UTR	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	701	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)	p.A701T(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						CCTGAAGATCGCAGACTTTGG	0.562																																					p.A701T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2101A	9						.						96.0	96.0	96.0					9																	131480880		2203	4300	6503	130520701	SO:0001583	missense	29941	exon18			AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.2101G>A	9.37:g.131480880G>A	ENSP00000291906:p.Ala701Thr	Somatic		Capture	Illumina HiSeq	Phase_I	130520701	NM_013355	Q9UM03	Missense_Mutation	SNP	ENST00000291906.4	37	CCDS6908.1	.	.	.	.	.	.	.	.	.	.	G	35	5.424149	0.96111	.	.	ENSG00000160447	ENST00000291906	T	0.26223	1.75	5.85	5.85	0.93711	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.32436	0.0829	N	0.05012	-0.13	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.43540	-0.9385	9	0.62326	D	0.03	.	17.6554	0.88176	0.0:0.0:1.0:0.0	.	701	Q6P5Z2	PKN3_HUMAN	T	701	ENSP00000291906:A701T	ENSP00000291906:A701T	A	+	1	0	PKN3	130520701	1.000000	0.71417	0.937000	0.37676	0.974000	0.67602	9.119000	0.94362	2.772000	0.95346	0.655000	0.94253	GCA		0.562	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355	
LRRC8A	56262	broad.mit.edu	37	9	131670701	131670701	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:131670701C>T	ENST00000259324.5	+	3	1781	c.1258C>T	c.(1258-1260)Ctc>Ttc	p.L420F	LRRC8A_ENST00000372600.4_Missense_Mutation_p.L420F|LRRC8A_ENST00000372599.3_Missense_Mutation_p.L420F	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	420					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.L420F(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						CCGGCAGCGGCTCACCAAGAA	0.597																																					p.L420F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1258T	9						.						49.0	46.0	47.0					9																	131670701		2203	4300	6503	130710522	SO:0001583	missense	56262	exon3			AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"""leucine rich repeat containing 8"""	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.1258C>T	9.37:g.131670701C>T	ENSP00000259324:p.Leu420Phe	Somatic		Capture	Illumina HiSeq	Phase_I	130710522	NM_019594	Q6UXM2|Q8NCI0|Q9P2B1	Missense_Mutation	SNP	ENST00000259324.5	37	CCDS35155.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.417931	0.42918	.	.	ENSG00000136802	ENST00000372600;ENST00000372599;ENST00000259324	T;T;T	0.21734	1.99;1.99;1.99	5.21	4.25	0.50352	.	0.105878	0.64402	D	0.000005	T	0.28366	0.0701	M	0.62154	1.92	0.41375	D	0.987515	P	0.45634	0.863	P	0.46419	0.516	T	0.02232	-1.1191	10	0.45353	T	0.12	.	12.5238	0.56075	0.2704:0.7296:0.0:0.0	.	420	Q8IWT6	LRC8A_HUMAN	F	420	ENSP00000361682:L420F;ENSP00000361680:L420F;ENSP00000259324:L420F	ENSP00000259324:L420F	L	+	1	0	LRRC8A	130710522	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.560000	0.67332	2.595000	0.87683	0.561000	0.74099	CTC		0.597	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594	
C9orf50	375759	broad.mit.edu	37	9	132381845	132381845	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:132381845G>T	ENST00000372478.4	-	3	871	c.670C>A	c.(670-672)Ctg>Atg	p.L224M	NTMT1_ENST00000372486.1_Intron	NM_199350.3	NP_955382.3	Q5SZB4	CI050_HUMAN	chromosome 9 open reading frame 50	224								p.L224M(1)		central_nervous_system(1)|endometrium(4)|large_intestine(2)|ovary(1)|skin(1)|urinary_tract(1)	10		Ovarian(14;0.00556)				TCACCCTTCAGGGGCCCCAGA	0.527																																					p.L224M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C670A	9						.						105.0	103.0	104.0					9																	132381845		2203	4300	6503	131421666	SO:0001583	missense	375759	exon3			AK093122	CCDS35159.1	9q34.2	2012-03-15			ENSG00000179058	ENSG00000179058			23677	protein-coding gene	gene with protein product							Standard	NM_199350		Approved	FLJ35803	uc004byc.4	Q5SZB4	OTTHUMG00000020786	ENST00000372478.4:c.670C>A	9.37:g.132381845G>T	ENSP00000361556:p.Leu224Met	Somatic		Capture	Illumina HiSeq	Phase_I	131421666	NM_199350	Q2M1I2|Q8NA65	Missense_Mutation	SNP	ENST00000372478.4	37	CCDS35159.1	.	.	.	.	.	.	.	.	.	.	G	10.61	1.399814	0.25291	.	.	ENSG00000179058	ENST00000372478	T	0.21361	2.01	3.48	1.57	0.23409	.	0.823177	0.09924	N	0.738033	T	0.24160	0.0585	L	0.27053	0.805	0.09310	N	1	D	0.64830	0.994	P	0.59889	0.865	T	0.16571	-1.0398	10	0.35671	T	0.21	-2.2919	5.5273	0.16964	0.2598:0.0:0.7402:0.0	.	224	Q5SZB4	CI050_HUMAN	M	224	ENSP00000361556:L224M	ENSP00000361556:L224M	L	-	1	2	C9orf50	131421666	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	0.501000	0.22578	0.447000	0.26695	0.579000	0.79373	CTG		0.527	C9orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054593.1	NM_199350	
NTMT1	28989	broad.mit.edu	37	9	132396374	132396374	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:132396374T>C	ENST00000372486.1	+	3	553	c.204T>C	c.(202-204)tgT>tgC	p.C68C	NTMT1_ENST00000372481.3_Silent_p.C68C|NTMT1_ENST00000486391.2_3'UTR|NTMT1_ENST00000372480.1_Silent_p.C68C|NTMT1_ENST00000372483.4_Silent_p.C68C|NTMT1_ENST00000482347.1_5'UTR			Q9BV86	NTM1A_HUMAN	N-terminal Xaa-Pro-Lys N-methyltransferase 1	68					chromosome segregation (GO:0007059)|N-terminal peptidyl-proline dimethylation (GO:0018016)|N-terminal peptidyl-serine dimethylation (GO:0035572)|N-terminal peptidyl-serine trimethylation (GO:0035573)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein methyltransferase activity (GO:0008276)	p.C68C(1)									CCCTGGACTGTGGAGCTGGCA	0.572																																					p.C68C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T204C	9						.						77.0	76.0	76.0					9																	132396374		2203	4300	6503	131436195	SO:0001819	synonymous_variant	28989	exon3			AF110776	CCDS35160.1, CCDS69682.1, CCDS75918.1	9q34.2	2012-11-05	2012-06-12	2012-06-12	ENSG00000148335	ENSG00000148335	2.1.1.n5		23373	protein-coding gene	gene with protein product		613560	"""chromosome 9 open reading frame 32"", ""methyltransferase like 11A"""	C9orf32, METTL11A		20481588	Standard	XM_005251939		Approved	AD-003, HOMT1A	uc004byd.1	Q9BV86	OTTHUMG00000020785	ENST00000372486.1:c.204T>C	9.37:g.132396374T>C		Somatic		Capture	Illumina HiSeq	Phase_I	131436195	NM_014064	A8K4J2|A8K8G7|Q5SZB9|Q9UI28	Silent	SNP	ENST00000372486.1	37	CCDS35160.1																																																																																				0.572	NTMT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054589.1	NM_014064	
LAMC3	10319	broad.mit.edu	37	9	133943614	133943614	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:133943614C>T	ENST00000361069.4	+	15	2876	c.2743C>T	c.(2743-2745)Cgg>Tgg	p.R915W	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	915	Laminin EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)	p.R915W(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GAGGGGCTGCCGGAGGTAGGT	0.662																																					p.R915W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2743T	9						.						37.0	32.0	34.0					9																	133943614		2203	4299	6502	132933435	SO:0001583	missense	10319	exon15			AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.2743C>T	9.37:g.133943614C>T	ENSP00000354360:p.Arg915Trp	Somatic		Capture	Illumina HiSeq	Phase_I	132933435	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.510088	0.85282	.	.	ENSG00000050555	ENST00000361069;ENST00000355048	T	0.29655	1.56	5.12	4.16	0.48862	EGF-like, laminin (1);	0.591456	0.18224	N	0.147784	T	0.47040	0.1424	M	0.86343	2.81	0.33161	D	0.546942	D	0.64830	0.994	P	0.51657	0.676	T	0.65203	-0.6225	10	0.72032	D	0.01	.	8.2647	0.31806	0.1743:0.6569:0.1687:0.0	.	915	Q9Y6N6	LAMC3_HUMAN	W	915	ENSP00000354360:R915W	ENSP00000347156:R915W	R	+	1	2	LAMC3	132933435	0.984000	0.35163	0.968000	0.41197	0.946000	0.59487	1.111000	0.31159	2.544000	0.85801	0.644000	0.83932	CGG		0.662	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
GTF3C5	9328	broad.mit.edu	37	9	135926328	135926328	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:135926328A>G	ENST00000372097.5	+	4	1054	c.731A>G	c.(730-732)aAc>aGc	p.N244S	GTF3C5_ENST00000342018.8_Intron|GTF3C5_ENST00000372099.6_Missense_Mutation_p.N235S|GTF3C5_ENST00000372108.5_Missense_Mutation_p.N244S|GTF3C5_ENST00000372095.5_Missense_Mutation_p.N119S	NM_012087.3	NP_036219.2	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5, 63kDa	244					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.N244S(1)		endometrium(5)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)		GTCTGCACTAACCCCGTGGAC	0.632																																					p.N244S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A731G	9						.						38.0	31.0	33.0					9																	135926328		2203	4300	6503	134916149	SO:0001583	missense	9328	exon4			AF133124	CCDS6958.1, CCDS48050.1, CCDS75927.1	9q34.13	2010-03-23	2002-08-29		ENSG00000148308	ENSG00000148308		"""General transcription factors"""	4668	protein-coding gene	gene with protein product	"""transcription factor IIIC, 63 kD"""	604890	"""general transcription factor IIIC, polypeptide 5 (63kD)"""			10373544	Standard	NM_012087		Approved	TFiiiC2-63, TFIIIC63, TFIIICepsilon	uc004ccj.4	Q9Y5Q8	OTTHUMG00000020856	ENST00000372097.5:c.731A>G	9.37:g.135926328A>G	ENSP00000361169:p.Asn244Ser	Somatic		Capture	Illumina HiSeq	Phase_I	134916149	NM_001122823	A6NI44|A6NJB9|Q5T7U2|Q5T7U3|Q8N2U7|Q8N857|Q96GD9|Q9H4P2	Missense_Mutation	SNP	ENST00000372097.5	37	CCDS6958.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.3|22.3	4.277143|4.277143	0.80580|0.80580	.|.	.|.	ENSG00000148308|ENSG00000148308	ENST00000372097;ENST00000440319;ENST00000372099;ENST00000372095;ENST00000372089;ENST00000372108;ENST00000439697|ENST00000434175	T;T;T|.	0.47869|.	0.85;0.85;0.83|.	5.21|5.21	5.21|5.21	0.72293|0.72293	.|.	0.044706|.	0.85682|.	D|.	0.000000|.	T|T	0.64427|0.64427	0.2597|0.2597	L|L	0.55213|0.55213	1.73|1.73	0.47153|0.47153	D|D	0.999331|0.999331	P;D;D|.	0.65815|.	0.558;0.995;0.985|.	B;D;P|.	0.63877|.	0.276;0.919;0.831|.	T|T	0.62877|0.62877	-0.6761|-0.6761	10|5	0.45353|.	T|.	0.12|.	-45.4291|-45.4291	14.2553|14.2553	0.66048|0.66048	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	119;244;244|.	B7Z1V3;Q9Y5Q8-3;Q9Y5Q8|.	.;.;TF3C5_HUMAN|.	S|A	244;197;235;119;94;244;119|16	ENSP00000361169:N244S;ENSP00000361171:N235S;ENSP00000361180:N244S|.	ENSP00000361161:N94S|.	N|T	+|+	2|1	0|0	GTF3C5|GTF3C5	134916149|134916149	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.708000|0.708000	0.40852|0.40852	8.582000|8.582000	0.90791|0.90791	1.960000|1.960000	0.56953|0.56953	0.379000|0.379000	0.24179|0.24179	AAC|ACC		0.632	GTF3C5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054826.1	NM_001122823	
COL5A1	1289	broad.mit.edu	37	9	137711989	137711989	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:137711989G>A	ENST00000371817.3	+	58	4888	c.4474G>A	c.(4474-4476)Ggt>Agt	p.G1492S		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1492	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.G1492S(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CGGGCTCATCGGTCCTCCGGG	0.627																																					p.G1492S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4474A	9						.						104.0	98.0	100.0					9																	137711989		2203	4300	6503	136851810	SO:0001583	missense	1289	exon58			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4474G>A	9.37:g.137711989G>A	ENSP00000360882:p.Gly1492Ser	Somatic		Capture	Illumina HiSeq	Phase_I	136851810	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.675505	0.88445	.	.	ENSG00000130635	ENST00000371817;ENST00000355306	D	0.99607	-6.27	4.69	4.69	0.59074	.	0.000000	0.85682	U	0.000000	D	0.99743	0.9898	H	0.94306	3.52	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97075	0.9780	10	0.87932	D	0	.	17.6053	0.88036	0.0:0.0:1.0:0.0	.	1492	P20908	CO5A1_HUMAN	S	1492;29	ENSP00000360882:G1492S	ENSP00000347458:G29S	G	+	1	0	COL5A1	136851810	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.713000	0.98740	2.140000	0.66376	0.643000	0.83706	GGT		0.627	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
PPP1R26	9858	broad.mit.edu	37	9	138377544	138377544	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:138377544G>T	ENST00000356818.2	+	4	1737	c.1188G>T	c.(1186-1188)gaG>gaT	p.E396D	PPP1R26_ENST00000604351.1_Missense_Mutation_p.E396D|PPP1R26_ENST00000605660.1_Missense_Mutation_p.E396D|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000401470.3_Missense_Mutation_p.E396D|PPP1R26_ENST00000605286.1_Missense_Mutation_p.E396D	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	396					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)	p.E396D(1)									AACTCCGAGAGGAGAGAGCGC	0.607																																					p.E396D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1188T	9						.						37.0	40.0	39.0					9																	138377544		2203	4299	6502	137517365	SO:0001583	missense	9858	exon4			AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.1188G>T	9.37:g.138377544G>T	ENSP00000349274:p.Glu396Asp	Somatic		Capture	Illumina HiSeq	Phase_I	137517365	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	.	.	.	.	.	.	.	.	.	.	G	11.13	1.546745	0.27652	.	.	ENSG00000196422	ENST00000356818	T	0.10960	2.82	5.06	1.9	0.25705	.	0.731309	0.12614	N	0.453622	T	0.07007	0.0178	L	0.34521	1.04	0.09310	N	1	B	0.28783	0.222	B	0.28553	0.091	T	0.33727	-0.9857	10	0.30078	T	0.28	-12.9175	2.4585	0.04535	0.3672:0.0:0.3928:0.24	.	396	Q5T8A7	PPR26_HUMAN	D	396	ENSP00000349274:E396D	ENSP00000349274:E396D	E	+	3	2	KIAA0649	137517365	1.000000	0.71417	0.222000	0.23844	0.019000	0.09904	1.276000	0.33156	1.128000	0.42052	0.655000	0.94253	GAG		0.607	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
UBAC1	10422	broad.mit.edu	37	9	138831605	138831605	+	Splice_Site	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:138831605C>T	ENST00000371756.3	-	8	1094	c.877G>A	c.(877-879)Gcc>Acc	p.A293T	UBAC1_ENST00000465873.1_5'UTR	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	293	UBA 2. {ECO:0000255|PROSITE- ProRule:PRU00212}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.A293T(1)		NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		GAAATGACGGCCTAGAGGACA	0.627																																					p.A293T	NSCLC(78;973 1398 27381 29552 42415)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G877A	9						.						195.0	162.0	173.0					9																	138831605		2203	4300	6503	137971426	SO:0001630	splice_region_variant	10422	exon8			AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"""ubiquitin associated domain containing 1"""	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.877-1G>A	9.37:g.138831605C>T		Somatic		Capture	Illumina HiSeq	Phase_I	137971426	NM_016172	O75500|Q9UMW7	Missense_Mutation	SNP	ENST00000371756.3	37	CCDS35177.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789657	0.70337	.	.	ENSG00000130560	ENST00000371756	T	0.22743	1.94	5.01	5.01	0.66863	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.40862	0.1134	L	0.45470	1.425	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.21724	-1.0237	10	0.62326	D	0.03	-23.1257	17.3218	0.87238	0.0:1.0:0.0:0.0	.	293	Q9BSL1	UBAC1_HUMAN	T	293	ENSP00000360821:A293T	ENSP00000360821:A293T	A	-	1	0	UBAC1	137971426	1.000000	0.71417	0.945000	0.38365	0.015000	0.08874	7.135000	0.77276	2.334000	0.79466	0.561000	0.74099	GCC		0.627	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172	Missense_Mutation
NELFB	25920	broad.mit.edu	37	9	140157580	140157580	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:140157580G>A	ENST00000343053.4	+	5	1026	c.689G>A	c.(688-690)cGg>cAg	p.R230Q		NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B	230					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.R230Q(1)									CTGCGCACGCGGAATGTGCAC	0.617																																					p.R230Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G689A	9						.						206.0	151.0	169.0					9																	140157580		2203	4300	6503	139277401	SO:0001583	missense	25920	exon5			AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"""cofactor of BRCA1"""	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778	ENST00000343053.4:c.689G>A	9.37:g.140157580G>A	ENSP00000339495:p.Arg230Gln	Somatic		Capture	Illumina HiSeq	Phase_I	139277401	NM_015456	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Missense_Mutation	SNP	ENST00000343053.4	37	CCDS7040.1	.	.	.	.	.	.	.	.	.	.	G	31	5.083681	0.94050	.	.	ENSG00000188986	ENST00000343053	.	.	.	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.78407	0.4278	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.81075	-0.1097	9	0.66056	D	0.02	-48.1642	16.6026	0.84820	0.0:0.0:1.0:0.0	.	230	Q8WX92	NELFB_HUMAN	Q	230	.	ENSP00000339495:R230Q	R	+	2	0	COBRA1	139277401	1.000000	0.71417	0.621000	0.29145	0.948000	0.59901	9.711000	0.98735	2.231000	0.72958	0.305000	0.20034	CGG		0.617	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456	
KANK1	23189	broad.mit.edu	37	9	712566	712566	+	Silent	SNP	C	C	T	rs374777358		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:712566C>T	ENST00000382303.1	+	7	2452	c.1800C>T	c.(1798-1800)tgC>tgT	p.C600C	KANK1_ENST00000382297.2_Silent_p.C600C|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_Silent_p.C442C	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	600					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)	p.C600C(1)|p.C442C(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		TCAGCGTCTGCGAAACAGGCA	0.488																																					p.C442C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1326T	9						.	C	,	0,4406		0,0,2203	211.0	187.0	195.0		1800,1326	-11.0	0.1	9		195	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KANK1	NM_015158.2,NM_153186.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	600/1353,442/1195	712566	1,13005	2203	4300	6503	702566	SO:0001819	synonymous_variant	23189	exon2			AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.1800C>T	9.37:g.712566C>T		Somatic		Capture	Illumina HiSeq	Phase_I	702566	NM_153186	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Silent	SNP	ENST00000382303.1	37	CCDS34976.1																																																																																				0.488	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
GLIS3	169792	broad.mit.edu	37	9	4118781	4118781	+	Missense_Mutation	SNP	C	C	A	rs146067479		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:4118781C>A	ENST00000324333.10	-	3	425	c.232G>T	c.(232-234)Gcc>Tcc	p.A78S	GLIS3_ENST00000381971.3_Missense_Mutation_p.A233S	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	78	Ser-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A78S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		GAAGGGAGGGCCCTGTAGCCC	0.572																																					p.A78S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G232T	9						.						120.0	110.0	113.0					9																	4118781		2203	4300	6503	4108781	SO:0001583	missense	169792	exon3			BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.232G>T	9.37:g.4118781C>A	ENSP00000325494:p.Ala78Ser	Somatic		Capture	Illumina HiSeq	Phase_I	4108781	NM_152629	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	C	1.502	-0.551728	0.03996	.	.	ENSG00000107249	ENST00000324333;ENST00000381971;ENST00000477901;ENST00000478844;ENST00000481827;ENST00000478315;ENST00000462164	T;T	0.11930	2.73;2.73	5.59	-5.46	0.02608	.	0.859201	0.09933	N	0.736950	T	0.08223	0.0205	N	0.20685	0.6	0.18873	N	0.999987	B;B;B	0.19200	0.034;0.034;0.02	B;B;B	0.21708	0.036;0.036;0.01	T	0.35674	-0.9779	10	0.42905	T	0.14	.	11.034	0.47789	0.0:0.1696:0.0985:0.7319	.	108;233;78	Q1PHJ1;Q8NEA6-2;Q8NEA6	.;.;GLIS3_HUMAN	S	78;233;233;78;233;78;78	ENSP00000325494:A78S;ENSP00000371398:A233S	ENSP00000325494:A78S	A	-	1	0	GLIS3	4108781	0.039000	0.19947	0.007000	0.13788	0.060000	0.15804	0.043000	0.13971	-0.988000	0.03489	-0.136000	0.14681	GCC		0.572	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629	
GLDC	2731	broad.mit.edu	37	9	6556173	6556173	+	Missense_Mutation	SNP	C	C	T	rs386833542		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:6556173C>T	ENST00000321612.6	-	18	2332	c.2182G>A	c.(2182-2184)Ggg>Agg	p.G728R	GLDC_ENST00000460457.1_5'Flank	NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	728					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)	p.G728R(1)		cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	ATATTTGCCCCGTCTAGGTAG	0.443																																					p.G728R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2182A	9	GRCh37	CM061034	GLDC	M		.						105.0	91.0	96.0					9																	6556173		2203	4300	6503	6546173	SO:0001583	missense	2731	exon18			D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"""glycine cleavage system protein P"", ""glycine decarboxylase"""	238300	"""glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"""			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.2182G>A	9.37:g.6556173C>T	ENSP00000370737:p.Gly728Arg	Somatic		Capture	Illumina HiSeq	Phase_I	6546173	NM_000170	Q2M2F8	Missense_Mutation	SNP	ENST00000321612.6	37	CCDS34987.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.648511	0.87958	.	.	ENSG00000178445	ENST00000321612	D	0.94138	-3.36	5.36	5.36	0.76844	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aromatic amino acid beta-eliminating lyase/threonine aldolase (1);	0.000000	0.85682	D	0.000000	D	0.98365	0.9457	H	0.98786	4.33	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99521	1.0958	10	0.87932	D	0	-22.214	19.4633	0.94927	0.0:1.0:0.0:0.0	.	728	P23378	GCSP_HUMAN	R	728	ENSP00000370737:G728R	ENSP00000370737:G728R	G	-	1	0	GLDC	6546173	1.000000	0.71417	0.954000	0.39281	0.790000	0.44656	7.459000	0.80802	2.666000	0.90696	0.655000	0.94253	GGG		0.443	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170	
FREM1	158326	broad.mit.edu	37	9	14842520	14842520	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:14842520G>T	ENST00000380880.3	-	9	2315	c.1532C>A	c.(1531-1533)cCc>cAc	p.P511H	FREM1_ENST00000380881.4_Missense_Mutation_p.P512H|FREM1_ENST00000422223.2_Missense_Mutation_p.P511H			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	511					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.P512H(1)		breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		GACGTTGATGGGGAATTTGTG	0.502																																					p.P511H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1532A	9						.						148.0	148.0	148.0					9																	14842520		2035	4197	6232	14832520	SO:0001583	missense	158326	exon10			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.1532C>A	9.37:g.14842520G>T	ENSP00000370262:p.Pro511His	Somatic		Capture	Illumina HiSeq	Phase_I	14832520	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.017224	0.93404	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.52057	0.68;0.68;0.68	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.67711	0.2922	L	0.60904	1.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63659	-0.6587	10	0.45353	T	0.12	-14.2667	20.3539	0.98825	0.0:0.0:1.0:0.0	.	511	Q5H8C1	FREM1_HUMAN	H	512;511;511	ENSP00000370263:P512H;ENSP00000412940:P511H;ENSP00000370262:P511H	ENSP00000370257:P514H	P	-	2	0	FREM1	14832520	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.476000	0.97823	2.826000	0.97356	0.655000	0.94253	CCC		0.502	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
DENND4C	55667	broad.mit.edu	37	9	19342693	19342693	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:19342693C>T	ENST00000380432.2	+	17	2245	c.2212C>T	c.(2212-2214)Cct>Tct	p.P738S	DENND4C_ENST00000602925.1_Missense_Mutation_p.P974S|DENND4C_ENST00000434457.2_Missense_Mutation_p.P1023S			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	738					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.P738S(1)		breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						GCCTCACAGTCCTACTGAACC	0.423																																					p.P738S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2212T	9						.						115.0	105.0	108.0					9																	19342693		2203	4300	6503	19332693	SO:0001583	missense	55667	exon17			AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.2212C>T	9.37:g.19342693C>T	ENSP00000369797:p.Pro738Ser	Somatic		Capture	Illumina HiSeq	Phase_I	19332693	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37		.	.	.	.	.	.	.	.	.	.	C	14.04	2.417687	0.42918	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000540671;ENST00000380432	T;T;T	0.32988	1.74;1.43;1.66	4.98	3.1	0.35709	.	0.685021	0.14038	N	0.345636	T	0.30386	0.0763	L	0.59436	1.845	0.45261	D	0.998264	B;B	0.28419	0.075;0.211	B;B	0.26770	0.035;0.073	T	0.12604	-1.0541	10	0.42905	T	0.14	-12.1991	11.8771	0.52554	0.0:0.8549:0.0:0.1451	.	68;738	B7Z660;Q5VZ89	.;DEN4C_HUMAN	S	738;214;68;214	ENSP00000305795:P214S;ENSP00000443804:P68S;ENSP00000369797:P214S	ENSP00000305795:P214S	P	+	1	0	DENND4C	19332693	0.377000	0.25106	0.831000	0.32960	0.971000	0.66376	1.687000	0.37680	1.316000	0.45131	0.585000	0.79938	CCT		0.423	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
IFNA2	3440	broad.mit.edu	37	9	21384902	21384902	+	Missense_Mutation	SNP	T	T	C	rs373475123		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:21384902T>C	ENST00000380206.2	-	1	494	c.427A>G	c.(427-429)Agg>Ggg	p.R143G		NM_000605.3	NP_000596.2	P01563	IFNA2_HUMAN	interferon, alpha 2	143					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of gene expression (GO:0010629)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	type I interferon receptor binding (GO:0005132)	p.R143G(1)		breast(2)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	13				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		AAGTATTTCCTCACAGCCAGA	0.478																																					p.R143G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A427G	9						.	T	GLY/ARG	0,4406		0,0,2203	194.0	195.0	194.0		427	0.7	0.0	9		194	1,8599	1.2+/-3.3	0,1,4299	no	missense	IFNA2	NM_000605.3	125	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	143/189	21384902	1,13005	2203	4300	6503	21374902	SO:0001583	missense	3440	exon1				CCDS6506.1	9p22	2010-08-24			ENSG00000188379	ENSG00000188379		"""Interferons"""	5423	protein-coding gene	gene with protein product	"""alpha-2a interferon"", ""interferon alpha 2b"", ""interferon alpha A"""	147562				1385305	Standard	NM_000605		Approved	IFNA, IFN-alphaA	uc003zpb.3	P01563	OTTHUMG00000019674	ENST00000380206.2:c.427A>G	9.37:g.21384902T>C	ENSP00000369554:p.Arg143Gly	Somatic		Capture	Illumina HiSeq	Phase_I	21374902	NM_000605	H2DF54|H2DF55|P01564|Q14606|Q6DJX8|Q96KI6	Missense_Mutation	SNP	ENST00000380206.2	37	CCDS6506.1	.	.	.	.	.	.	.	.	.	.	T	12.74	2.029875	0.35797	0.0	1.16E-4	ENSG00000188379	ENST00000380206	T	0.51574	0.7	3.24	0.721	0.18219	.	0.336904	0.30383	N	0.009755	T	0.56587	0.1995	M	0.82630	2.6	0.09310	N	1	P	0.38827	0.649	P	0.50754	0.649	T	0.53690	-0.8403	10	0.87932	D	0	.	4.1194	0.10098	0.0:0.1199:0.2084:0.6717	.	143	Q6DJX8	.	G	143	ENSP00000369554:R143G	ENSP00000369554:R143G	R	-	1	2	IFNA2	21374902	0.771000	0.28555	0.003000	0.11579	0.030000	0.12068	1.887000	0.39698	-0.046000	0.13446	0.397000	0.26171	AGG		0.478	IFNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051903.1	NM_000605	
TAF1L	138474	broad.mit.edu	37	9	32631885	32631885	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:32631885delA	ENST00000242310.4	-	1	3782	c.3693delT	c.(3691-3693)tttfs	p.F1231fs	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1231					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.F1231fs*20(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GTTTTTCATCAAAAAGGGCAA	0.458																																					p.F1231fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3693delT	9						.						114.0	110.0	111.0					9																	32631885		2203	4300	6503	32621885	SO:0001589	frameshift_variant	138474	exon1			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3693delT	9.37:g.32631885delA	ENSP00000418379:p.Phe1231fs	Somatic		Capture	Illumina HiSeq	Phase_I	32621885	NM_153809	Q0VG57	Frame_Shift_Del	DEL	ENST00000242310.4	37	CCDS35003.1																																																																																				0.458	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
KIF24	347240	broad.mit.edu	37	9	34257623	34257623	+	Frame_Shift_Del	DEL	T	T	-	rs570788521	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:34257623delT	ENST00000402558.2	-	10	2006	c.1982delA	c.(1981-1983)aagfs	p.K661fs	KIF24_ENST00000379174.3_Frame_Shift_Del_p.K527fs|KIF24_ENST00000345050.2_Frame_Shift_Del_p.K527fs|KIF24_ENST00000379166.2_Frame_Shift_Del_p.K661fs			Q5T7B8	KIF24_HUMAN	kinesin family member 24	661					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K143fs*34(1)|p.K661fs*34(1)		breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			CTCTTCTGGCTTTTTTTTGGC	0.527													TTTTTTTT|TTTTTTTT|TTTTTTT|deletion	3	0.000599042	0.0	0.0043	5008	,	,		23710	0.0		0.0	False		,,,				2504	0.0				p.K661fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1982delA	9						.						65.0	65.0	65.0					9																	34257623		2203	4300	6503	34247623	SO:0001589	frameshift_variant	347240	exon11			AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"""Kinesins"", ""Sterile alpha motif (SAM) domain containing"""	19916	protein-coding gene	gene with protein product		613747	"""chromosome 9 open reading frame 48"""	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.1982delA	9.37:g.34257623delT	ENSP00000384433:p.Lys661fs	Somatic		Capture	Illumina HiSeq	Phase_I	34247623	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Frame_Shift_Del	DEL	ENST00000402558.2	37	CCDS6551.2																																																																																				0.527	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5		
KIAA1161	57462	broad.mit.edu	37	9	34371529	34371529	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:34371529C>T	ENST00000297625.7	-	2	1536	c.1311G>A	c.(1309-1311)ccG>ccA	p.P437P		NM_020702.3	NP_065753.2	Q6NSJ0	K1161_HUMAN	KIAA1161	471					carbohydrate metabolic process (GO:0005975)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of protein kinase B signaling (GO:0051897)|skeletal muscle fiber development (GO:0048741)	integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.P437P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.126)		TGAAGTCCCGCGGCAGGTAGC	0.692																																					p.P471P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1413A	9						.						12.0	16.0	15.0					9																	34371529		2055	4183	6238	34361529	SO:0001819	synonymous_variant	57462	exon2			AB032987		9p11.2	2009-11-06			ENSG00000164976	ENSG00000164976			19918	protein-coding gene	gene with protein product						10574461	Standard	XM_006716808		Approved	NET37	uc003zue.4	Q6NSJ0	OTTHUMG00000019816	ENST00000297625.7:c.1311G>A	9.37:g.34371529C>T		Somatic		Capture	Illumina HiSeq	Phase_I	34361529	NM_020702	Q5T587|Q5T588|Q9ULQ9	Silent	SNP	ENST00000297625.7	37																																																																																					0.692	KIAA1161-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000052158.1	XM_351807	
KIAA1161	57462	broad.mit.edu	37	9	34371720	34371720	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:34371720G>A	ENST00000297625.7	-	2	1345	c.1120C>T	c.(1120-1122)Cgc>Tgc	p.R374C		NM_020702.3	NP_065753.2	Q6NSJ0	K1161_HUMAN	KIAA1161	408					carbohydrate metabolic process (GO:0005975)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of protein kinase B signaling (GO:0051897)|skeletal muscle fiber development (GO:0048741)	integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.R374C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.126)		AACAGCTCGCGCTCCACGCCC	0.682																																					p.R408C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1222T	9						.						23.0	27.0	26.0					9																	34371720		2035	4158	6193	34361720	SO:0001583	missense	57462	exon2			AB032987		9p11.2	2009-11-06			ENSG00000164976	ENSG00000164976			19918	protein-coding gene	gene with protein product						10574461	Standard	XM_006716808		Approved	NET37	uc003zue.4	Q6NSJ0	OTTHUMG00000019816	ENST00000297625.7:c.1120C>T	9.37:g.34371720G>A	ENSP00000297625:p.Arg374Cys	Somatic		Capture	Illumina HiSeq	Phase_I	34361720	NM_020702	Q5T587|Q5T588|Q9ULQ9	Missense_Mutation	SNP	ENST00000297625.7	37		.	.	.	.	.	.	.	.	.	.	G	16.31	3.087456	0.55968	.	.	ENSG00000164976	ENST00000297625	T	0.44881	0.91	5.36	4.47	0.54385	Glycoside hydrolase, superfamily (1);	0.113392	0.56097	D	0.000034	T	0.62245	0.2412	M	0.79805	2.47	0.47065	D	0.999304	D	0.89917	1.0	D	0.66847	0.947	T	0.66160	-0.5993	10	0.72032	D	0.01	-18.2902	10.1511	0.42794	0.0:0.1488:0.6968:0.1544	.	408	Q6NSJ0	K1161_HUMAN	C	374	ENSP00000297625:R374C	ENSP00000297625:R374C	R	-	1	0	KIAA1161	34361720	0.994000	0.37717	1.000000	0.80357	0.946000	0.59487	1.646000	0.37249	1.272000	0.44329	-0.361000	0.07541	CGC		0.682	KIAA1161-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000052158.1	XM_351807	
KIAA1045	23349	broad.mit.edu	37	9	34971556	34971556	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:34971556C>T	ENST00000242315.3	+	2	343	c.261C>T	c.(259-261)ggC>ggT	p.G87G	KIAA1045_ENST00000544237.1_Silent_p.G87G|KIAA1045_ENST00000476115.2_Intron	NM_015297.1	NP_056112.1	Q9UPV7	K1045_HUMAN	KIAA1045	87							metal ion binding (GO:0046872)	p.G87G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			LUSC - Lung squamous cell carcinoma(32;0.00575)			ATGGGCGCGGCGTGGAGCCTG	0.617																																					p.G87G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C261T	9						.						79.0	94.0	89.0					9																	34971556		2009	4164	6173	34961556	SO:0001819	synonymous_variant	23349	exon2			AB028968	CCDS43796.1	9p13.2	2008-02-05			ENSG00000122733	ENSG00000122733			29180	protein-coding gene	gene with protein product						10470851	Standard	NM_015297		Approved		uc003zvr.3	Q9UPV7	OTTHUMG00000019844	ENST00000242315.3:c.261C>T	9.37:g.34971556C>T		Somatic		Capture	Illumina HiSeq	Phase_I	34961556	NM_015297	B7Z253|Q58FE9|Q5T662	Silent	SNP	ENST00000242315.3	37	CCDS43796.1																																																																																				0.617	KIAA1045-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052256.2	XM_048592	
PIGO	84720	broad.mit.edu	37	9	35091693	35091693	+	Frame_Shift_Del	DEL	G	G	-	rs148341577		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:35091693delG	ENST00000378617.3	-	7	2585	c.2191delC	c.(2191-2193)cgtfs	p.R731fs	PIGO_ENST00000298004.5_Intron|PIGO_ENST00000361778.2_Intron|PIGO_ENST00000341666.3_Frame_Shift_Del_p.R731fs	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O	731					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)	p.R731fs*17(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			ACCCGGAGACGGGGGGGAGCC	0.662																																					p.R731fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2191delC	9						.		,,	5,4057		0,5,2026	25.0	29.0	28.0		,,	5.4	1.0	9		28	12,7918		0,12,3953	no	intron,frameshift,intron	PIGO	NM_152850.3,NM_032634.3,NM_001201484.1	,,	0,17,5979	A1A1,A1R,RR		0.1513,0.1231,0.1418	,,	,,	35091693	17,11975	2145	4204	6349	35081693	SO:0001589	frameshift_variant	84720	exon7			AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"""Phosphatidylinositol glycan anchor biosynthesis"""	23215	protein-coding gene	gene with protein product		614730	"""phosphatidylinositol glycan, class O"""			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.2191delC	9.37:g.35091693delG	ENSP00000367880:p.Arg731fs	Somatic		Capture	Illumina HiSeq	Phase_I	35081693	NM_032634	B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	Frame_Shift_Del	DEL	ENST00000378617.3	37	CCDS6575.1																																																																																				0.662	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052284.1	NM_032634	
TESK1	7016	broad.mit.edu	37	9	35606966	35606966	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:35606966G>A	ENST00000336395.5	+	4	773	c.523G>A	c.(523-525)Gac>Aac	p.D175N	TESK1_ENST00000498522.1_3'UTR|MIR4667_ENST00000578933.1_RNA	NM_006285.2	NP_006276.2	Q15569	TESK1_HUMAN	testis-specific kinase 1	175	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell junction assembly (GO:0034329)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.D175N(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	27			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			ATTTCACCGCGACCTCACATC	0.567																																					p.D175N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G523A	9						.						31.0	26.0	28.0					9																	35606966		2203	4300	6503	35596966	SO:0001583	missense	7016	exon4			D50863	CCDS6580.1	9p13	2010-04-27			ENSG00000107140	ENSG00000107140	2.7.12.1		11731	protein-coding gene	gene with protein product	"""testis-specific kinase-1"", ""testis specific kinase-1"""	601782				8537404	Standard	NM_006285		Approved		uc003zxa.3	Q15569	OTTHUMG00000019863	ENST00000336395.5:c.523G>A	9.37:g.35606966G>A	ENSP00000338127:p.Asp175Asn	Somatic		Capture	Illumina HiSeq	Phase_I	35596966	NM_006285	Q8IXZ8	Missense_Mutation	SNP	ENST00000336395.5	37	CCDS6580.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444761	0.83993	.	.	ENSG00000107140	ENST00000336395	D	0.92965	-3.14	5.39	5.39	0.77823	Serine/threonine-protein kinase-like domain (1);Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.47852	D	0.000217	D	0.96626	0.8899	M	0.87269	2.87	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97190	0.9857	10	0.87932	D	0	-17.0878	18.1312	0.89602	0.0:0.0:1.0:0.0	.	175	Q15569	TESK1_HUMAN	N	175	ENSP00000338127:D175N	ENSP00000338127:D175N	D	+	1	0	TESK1	35596966	1.000000	0.71417	1.000000	0.80357	0.293000	0.27360	9.860000	0.99555	2.509000	0.84616	0.561000	0.74099	GAC		0.567	TESK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052314.1	NM_006285	
CD72	971	broad.mit.edu	37	9	35611807	35611807	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:35611807C>T	ENST00000396757.1	-	8	1108	c.944G>A	c.(943-945)cGc>cAc	p.R315H	CD72_ENST00000259633.4_Missense_Mutation_p.R315H|CD72_ENST00000490239.1_5'UTR			P21854	CD72_HUMAN	CD72 molecule	315	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor binding (GO:0005102)|transmembrane signaling receptor activity (GO:0004888)	p.R315H(1)		large_intestine(5)|liver(1)|lung(6)	12			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TTACCTAGTGCGTTGTGTATC	0.433											OREG0019172	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R315H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G944A	9						.						174.0	145.0	155.0					9																	35611807		2203	4300	6503	35601807	SO:0001583	missense	971	exon7				CCDS6581.1	9p	2008-07-21	2006-03-28		ENSG00000137101	ENSG00000137101		"""CD molecules"""	1696	protein-coding gene	gene with protein product		107272	"""CD72 antigen"""			2044654, 1711157	Standard	NM_001782		Approved	LYB2, CD72b	uc003zxb.2	P21854	OTTHUMG00000019870	ENST00000396757.1:c.944G>A	9.37:g.35611807C>T	ENSP00000379980:p.Arg315His	Somatic	856	Capture	Illumina HiSeq	Phase_I	35601807	NM_001782		Missense_Mutation	SNP	ENST00000396757.1	37	CCDS6581.1	.	.	.	.	.	.	.	.	.	.	C	0.024	-1.394128	0.01175	.	.	ENSG00000137101	ENST00000396757;ENST00000396759;ENST00000259633	T;T	0.16897	2.31;2.31	3.45	-6.9	0.01655	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	22.624000	0.00166	N	0.000000	T	0.07279	0.0184	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.20075	-1.0286	10	0.27082	T	0.32	11.4207	2.8508	0.05556	0.5665:0.1704:0.1116:0.1516	.	315	P21854	CD72_HUMAN	H	315	ENSP00000379980:R315H;ENSP00000259633:R315H	ENSP00000259633:R315H	R	-	2	0	CD72	35601807	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.848000	0.00351	-3.863000	0.00097	-3.259000	0.00049	CGC		0.433	CD72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052336.1	NM_001782	
TLN1	7094	broad.mit.edu	37	9	35712990	35712990	+	Missense_Mutation	SNP	C	C	T	rs146392528	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:35712990C>T	ENST00000314888.9	-	27	3756	c.3403G>A	c.(3403-3405)Gct>Act	p.A1135T	TLN1_ENST00000540444.1_Missense_Mutation_p.A1135T	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1135					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)	p.A1135T(1)		NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			ACTCCCCTAGCGGCCTGGGCC	0.592													C|||	4	0.000798722	0.0	0.0	5008	,	,		17694	0.0		0.0	False		,,,				2504	0.0041				p.A1135T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3403A	9						.	C	THR/ALA	2,4402	4.2+/-10.8	0,2,2200	27.0	22.0	24.0		3403	4.7	0.2	9	dbSNP_134	24	0,8600		0,0,4300	no	missense	TLN1	NM_006289.3	58	0,2,6500	TT,TC,CC		0.0,0.0454,0.0154	possibly-damaging	1135/2542	35712990	2,13002	2202	4300	6502	35702990	SO:0001583	missense	7094	exon27			AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.3403G>A	9.37:g.35712990C>T	ENSP00000316029:p.Ala1135Thr	Somatic		Capture	Illumina HiSeq	Phase_I	35702990	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168293	0.78339	4.54E-4	0.0	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.16897	2.31;2.31	5.62	4.71	0.59529	.	0.153604	0.64402	D	0.000017	T	0.21062	0.0507	L	0.52573	1.65	0.58432	D	0.999998	D	0.53462	0.96	B	0.43623	0.425	T	0.02179	-1.1200	10	0.59425	D	0.04	-11.2684	16.1011	0.81172	0.1351:0.8649:0.0:0.0	.	1135	Q9Y490	TLN1_HUMAN	T	1135	ENSP00000316029:A1135T;ENSP00000442981:A1135T	ENSP00000316029:A1135T	A	-	1	0	TLN1	35702990	1.000000	0.71417	0.242000	0.24170	0.701000	0.40568	5.855000	0.69510	1.472000	0.48140	0.655000	0.94253	GCT		0.592	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
TLN1	7094	broad.mit.edu	37	9	35733041	35733041	+	5'Flank	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:35733041delC	ENST00000314888.9	-	0	0				CREB3_ENST00000486056.1_3'UTR|TLN1_ENST00000540444.1_5'Flank|CREB3_ENST00000353704.2_Frame_Shift_Del_p.P61fs	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)	p.P61fs*4(1)		NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CCTGCTGAGTCCCCCAGCGTC	0.552																																					p.P60fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.178delC	9						.						158.0	160.0	159.0					9																	35733041		2203	4300	6503	35723041	SO:0001631	upstream_gene_variant	10488	exon2			AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874		9.37:g.35733041delC	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	35723041	NM_006368	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Frame_Shift_Del	DEL	ENST00000314888.9	37	CCDS35009.1																																																																																				0.552	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
CCIN	881	broad.mit.edu	37	9	36171259	36171259	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:36171259G>T	ENST00000335119.2	+	1	1871	c.1760G>T	c.(1759-1761)aGg>aTg	p.R587M		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	587					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.R587M(1)		breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			ATTCTTCAAAGGATTTAAACA	0.433																																					p.R587M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1760T	9						.						30.0	32.0	31.0					9																	36171259		2186	4265	6451	36161259	SO:0001583	missense	881	exon1			Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"""BTB/POZ domain containing"""	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.1760G>T	9.37:g.36171259G>T	ENSP00000334996:p.Arg587Met	Somatic		Capture	Illumina HiSeq	Phase_I	36161259	NM_005893	Q9BXG7	Missense_Mutation	SNP	ENST00000335119.2	37	CCDS6599.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.556651	0.45487	.	.	ENSG00000185972	ENST00000335119	T	0.68181	-0.31	5.85	4.95	0.65309	.	0.096640	0.45867	D	0.000328	T	0.59649	0.2209	N	0.24115	0.695	0.35506	D	0.800204	P	0.50943	0.94	P	0.50231	0.635	T	0.70029	-0.4984	10	0.87932	D	0	-24.2339	9.8844	0.41253	0.0903:0.0:0.9097:0.0	.	587	Q13939	CALI_HUMAN	M	587	ENSP00000334996:R587M	ENSP00000334996:R587M	R	+	2	0	CCIN	36161259	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.703000	0.47110	2.757000	0.94681	0.655000	0.94253	AGG		0.433	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893	
GNE	10020	broad.mit.edu	37	9	36217509	36217509	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:36217509G>A	ENST00000539815.1	-	11	2062	c.2022C>T	c.(2020-2022)caC>caT	p.H674H	GNE_ENST00000396594.3_Silent_p.H705H|GNE_ENST00000543356.2_Silent_p.H669H|GNE_ENST00000447283.2_Silent_p.H600H|GNE_ENST00000377902.5_Silent_p.H674H|GNE_ENST00000539208.1_Silent_p.H564H			Q9Y223	GLCNE_HUMAN	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	674	N-acetylmannosamine kinase.				carbohydrate phosphorylation (GO:0046835)|cell adhesion (GO:0007155)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate metabolic process (GO:0006054)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|metal ion binding (GO:0046872)|N-acylmannosamine kinase activity (GO:0009384)|UDP-N-acetylglucosamine 2-epimerase activity (GO:0008761)	p.H674H(1)		endometrium(8)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			STAD - Stomach adenocarcinoma(86;0.228)			TGTGGATATAGTGACTGGCCA	0.552																																					p.H705H	GBM(184;106 2118 20004 35750 50727)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2115T	9						.						119.0	91.0	100.0					9																	36217509		2203	4300	6503	36207509	SO:0001819	synonymous_variant	10020	exon12			AF051852	CCDS6602.1, CCDS47965.1, CCDS55308.1, CCDS55309.1, CCDS55310.1	9p13.1	2008-02-05	2003-12-01		ENSG00000159921	ENSG00000159921			23657	protein-coding gene	gene with protein product		603824	"""UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase"""	IBM2		9305887, 9305888	Standard	NM_005476		Approved	Uae1	uc010mli.3	Q9Y223	OTTHUMG00000019899	ENST00000539815.1:c.2022C>T	9.37:g.36217509G>A		Somatic		Capture	Illumina HiSeq	Phase_I	36207509	NM_001128227	A6PZH2|A6PZH3|A7UNU7|B2R6E1|B7Z372|B7Z428|D3DRP7|F5H499|H0YFA7|Q0VA94	Silent	SNP	ENST00000539815.1	37	CCDS6602.1																																																																																				0.552	GNE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052412.4	NM_005476	
FBXO10	26267	broad.mit.edu	37	9	37537870	37537870	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:37537870C>T	ENST00000432825.2	-	3	704	c.656G>A	c.(655-657)gGt>gAt	p.G219D	FBXO10_ENST00000541829.1_Intron|RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000543968.1_5'Flank	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	219					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.G219D(1)		breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		TTGGCAAGTACCCGGGCCATG	0.488																																					p.G219D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G656A	9						.						86.0	88.0	87.0					9																	37537870		1956	4131	6087	37527870	SO:0001583	missense	26267	exon3			AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"""F-boxes /  ""other"""""	13589	protein-coding gene	gene with protein product		609092	"""F-box only protein 10"""			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.656G>A	9.37:g.37537870C>T	ENSP00000403802:p.Gly219Asp	Somatic		Capture	Illumina HiSeq	Phase_I	37527870	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	37	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	C	16.28	3.078226	0.55753	.	.	ENSG00000147912	ENST00000432825	T	0.49432	0.78	5.3	5.3	0.74995	Pectin lyase fold/virulence factor (1);	0.000000	0.85682	D	0.000000	T	0.59851	0.2224	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.62854	-0.6766	10	0.87932	D	0	-13.6486	18.0885	0.89466	0.0:1.0:0.0:0.0	.	219	Q9UK96	FBX10_HUMAN	D	219	ENSP00000403802:G219D	ENSP00000276960:G219D	G	-	2	0	FBXO10	37527870	0.997000	0.39634	0.998000	0.56505	0.307000	0.27823	3.614000	0.54160	2.631000	0.89168	0.655000	0.94253	GGT		0.488	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3		
SMC5	23137	broad.mit.edu	37	9	72933847	72933847	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:72933847A>C	ENST00000361138.5	+	15	2176	c.2118A>C	c.(2116-2118)caA>caC	p.Q706H		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	706					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)	p.Q706H(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						AGAAAAGACAACTGGAACAAA	0.373																																					p.Q706H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2118C	9						.						43.0	45.0	44.0					9																	72933847		2201	4299	6500	72123667	SO:0001583	missense	23137	exon15			AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"""Structural maintenance of chromosomes proteins"""	20465	protein-coding gene	gene with protein product		609386	"""SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"""	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.2118A>C	9.37:g.72933847A>C	ENSP00000354957:p.Gln706His	Somatic		Capture	Illumina HiSeq	Phase_I	72123667	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.291697	0.40594	.	.	ENSG00000198887	ENST00000361138	T	0.20200	2.09	5.34	-1.22	0.09494	RecF/RecN/SMC (1);	0.178788	0.49916	D	0.000127	T	0.17280	0.0415	L	0.41236	1.265	0.42148	D	0.991542	P	0.34800	0.469	B	0.38954	0.286	T	0.04565	-1.0942	10	0.37606	T	0.19	-8.384	10.771	0.46323	0.4834:0.0:0.5166:0.0	.	706	Q8IY18	SMC5_HUMAN	H	706	ENSP00000354957:Q706H	ENSP00000354957:Q706H	Q	+	3	2	SMC5	72123667	0.799000	0.28903	0.981000	0.43875	0.982000	0.71751	0.395000	0.20850	-0.218000	0.10018	0.477000	0.44152	CAA		0.373	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110	
TRPM3	80036	broad.mit.edu	37	9	73233859	73233859	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:73233859G>A	ENST00000377111.2	-	16	2489	c.2246C>T	c.(2245-2247)gCg>gTg	p.A749V	TRPM3_ENST00000357533.2_Missense_Mutation_p.A753V|TRPM3_ENST00000396292.4_Missense_Mutation_p.A621V|TRPM3_ENST00000396285.1_Missense_Mutation_p.A596V|TRPM3_ENST00000396280.5_Missense_Mutation_p.A598V|TRPM3_ENST00000360823.2_Missense_Mutation_p.A611V|TRPM3_ENST00000377105.1_Missense_Mutation_p.A608V|TRPM3_ENST00000358082.3_Missense_Mutation_p.A611V|TRPM3_ENST00000377106.1_Missense_Mutation_p.A621V|TRPM3_ENST00000423814.3_Missense_Mutation_p.A776V|TRPM3_ENST00000377110.3_Missense_Mutation_p.A749V|TRPM3_ENST00000408909.2_Missense_Mutation_p.A608V	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	774					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)	p.A753V(1)|p.A621V(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						GCACGTGTGCGCGATGAAGTC	0.612																																					p.A749V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2246T	9						.						88.0	68.0	74.0					9																	73233859		2203	4300	6503	72423679	SO:0001583	missense	80036	exon16			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.2246C>T	9.37:g.73233859G>A	ENSP00000366315:p.Ala749Val	Somatic		Capture	Illumina HiSeq	Phase_I	72423679	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	37		.	.	.	.	.	.	.	.	.	.	G	36	5.890051	0.97068	.	.	ENSG00000083067	ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814	D;D;D;D;D;D;D;D;D;D;D	0.90676	-2.71;-2.71;-2.71;-2.71;-2.71;-2.71;-2.71;-2.71;-2.71;-2.71;-2.71	5.65	5.65	0.86999	.	0.055523	0.64402	D	0.000001	D	0.95999	0.8697	M	0.87682	2.9	0.80722	D	1	D;D;P;D;D;D;D;D	0.76494	0.982;0.999;0.947;0.989;0.97;0.97;0.997;0.995	P;D;P;P;P;P;D;P	0.69307	0.883;0.963;0.821;0.842;0.667;0.679;0.948;0.87	D	0.95923	0.8932	10	0.87932	D	0	-15.2304	19.9142	0.97043	0.0:0.0:1.0:0.0	.	749;749;739;753;611;608;721;596	Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.;.;.;.;.;.;.;.	V	749;749;621;611;608;753;608;596;621;611;776	ENSP00000366315:A749V;ENSP00000366314:A749V;ENSP00000366310:A621V;ENSP00000354066:A611V;ENSP00000366309:A608V;ENSP00000350140:A753V;ENSP00000386127:A608V;ENSP00000379581:A596V;ENSP00000379587:A621V;ENSP00000350791:A611V;ENSP00000389542:A776V	ENSP00000350140:A753V	A	-	2	0	TRPM3	72423679	1.000000	0.71417	0.979000	0.43373	0.996000	0.88848	9.618000	0.98365	2.941000	0.99782	0.655000	0.94253	GCG		0.612	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945	
C9orf85	138241	broad.mit.edu	37	9	74526669	74526669	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:74526669A>G	ENST00000377031.3	+	1	209	c.19A>G	c.(19-21)Aac>Gac	p.N7D	ABHD17B_ENST00000377041.2_5'Flank|ABHD17B_ENST00000333421.6_5'Flank|C9orf85_ENST00000486911.2_Missense_Mutation_p.N7D|C9orf85_ENST00000334731.2_Missense_Mutation_p.N7D			Q96MD7	CI085_HUMAN	chromosome 9 open reading frame 85	7								p.N7D(2)		kidney(2)|large_intestine(1)|lung(4)	7						CCAGAAAGGCAACGTGGCTCG	0.502																																					p.N7D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A19G	9						.						179.0	180.0	180.0					9																	74526669		2203	4300	6503	73716489	SO:0001583	missense	138241	exon1			BC010179	CCDS6639.1	9q21.2	2012-03-16			ENSG00000155621	ENSG00000155621			28784	protein-coding gene	gene with protein product						12477932	Standard	NM_182505		Approved	MGC61599	uc004ain.3	Q96MD7	OTTHUMG00000020002	ENST00000377031.3:c.19A>G	9.37:g.74526669A>G	ENSP00000366230:p.Asn7Asp	Somatic		Capture	Illumina HiSeq	Phase_I	73716489	NM_182505	Q5W0N1|Q5W0N3|Q6PJW9|Q86U95	Missense_Mutation	SNP	ENST00000377031.3	37		.	.	.	.	.	.	.	.	.	.	A	35	5.504519	0.96371	.	.	ENSG00000155621	ENST00000334731;ENST00000377031;ENST00000356065	T	0.32988	1.43	6.01	6.01	0.97437	.	0.000000	0.85682	D	0.000000	T	0.51227	0.1662	L	0.56769	1.78	0.49582	D	0.999802	D	0.89917	1.0	D	0.85130	0.997	T	0.51252	-0.8729	10	0.59425	D	0.04	-33.7882	12.9237	0.58247	1.0:0.0:0.0:0.0	.	7	Q96MD7-1	.	D	7	ENSP00000366230:N7D	ENSP00000334289:N7D	N	+	1	0	C9orf85	73716489	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.687000	0.61708	2.295000	0.77249	0.523000	0.50628	AAC		0.502	C9orf85-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052628.2	NM_182505	
C9orf41	138199	broad.mit.edu	37	9	77598699	77598699	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:77598699A>G	ENST00000376834.3	-	8	1366	c.1214T>C	c.(1213-1215)gTc>gCc	p.V405A	RP11-197P3.4_ENST00000455609.1_RNA	NM_152420.1	NP_689633.1	Q8N4J0	CI041_HUMAN	chromosome 9 open reading frame 41	405								p.V405A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|urinary_tract(2)	17						TGGCTTACGGACCACAAACAA	0.353																																					p.V405A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1214C	9						.						118.0	108.0	111.0					9																	77598699		2202	4300	6502	76788519	SO:0001583	missense	138199	exon8			AK098661	CCDS6649.1	9q21.31	2012-03-15			ENSG00000156017	ENSG00000156017			23435	protein-coding gene	gene with protein product						12477932	Standard	NM_152420		Approved	FLJ25795	uc004ajq.3	Q8N4J0	OTTHUMG00000020032	ENST00000376834.3:c.1214T>C	9.37:g.77598699A>G	ENSP00000366030:p.Val405Ala	Somatic		Capture	Illumina HiSeq	Phase_I	76788519	NM_152420	Q7Z383|Q8N7C5	Missense_Mutation	SNP	ENST00000376834.3	37	CCDS6649.1	.	.	.	.	.	.	.	.	.	.	A	4.726	0.134985	0.09032	.	.	ENSG00000156017	ENST00000376834	T	0.04119	3.7	5.68	4.51	0.55191	N2227-like (1);	0.235054	0.43747	N	0.000539	T	0.01387	0.0045	N	0.00746	-1.225	0.80722	D	1	B	0.14012	0.009	B	0.19666	0.026	T	0.39057	-0.9632	10	0.02654	T	1	-3.7765	7.3046	0.26440	0.7813:0.1465:0.0721:0.0	.	405	Q8N4J0	CI041_HUMAN	A	405	ENSP00000366030:V405A	ENSP00000366030:V405A	V	-	2	0	C9orf41	76788519	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.187000	0.50950	0.943000	0.37553	0.533000	0.62120	GTC		0.353	C9orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052703.1	NM_152420	
GCNT1	2650	broad.mit.edu	37	9	79117652	79117652	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:79117652G>A	ENST00000376730.4	+	4	838	c.355G>A	c.(355-357)Gcg>Acg	p.A119T	GCNT1_ENST00000444201.2_Missense_Mutation_p.A119T|GCNT1_ENST00000442371.1_Missense_Mutation_p.A119T|GCNT1_ENST00000536223.1_Missense_Mutation_p.A119T	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	119	Stem region. {ECO:0000250}.				cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)	p.A119T(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						TAAAGAAGAGGCGGAGTTTCC	0.418																																					p.A119T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G355A	9						.						83.0	88.0	86.0					9																	79117652		2203	4300	6503	78307472	SO:0001583	missense	2650	exon3			L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4203	protein-coding gene	gene with protein product	"""core 2 beta1,6 N-acetylglucosaminyltransferase-I"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"""	600391	"""glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.355G>A	9.37:g.79117652G>A	ENSP00000365920:p.Ala119Thr	Somatic		Capture	Illumina HiSeq	Phase_I	78307472	NM_001097635	Q6DJZ4	Missense_Mutation	SNP	ENST00000376730.4	37	CCDS6653.1	.	.	.	.	.	.	.	.	.	.	g	10.45	1.354838	0.24512	.	.	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	6.07	6.07	0.98685	.	0.430462	0.26971	N	0.021561	T	0.47967	0.1474	M	0.66939	2.045	0.31442	N	0.671795	B	0.27380	0.177	B	0.29598	0.104	T	0.52953	-0.8506	9	.	.	.	.	13.8057	0.63230	0.0695:0.0:0.9305:0.0	.	119	Q02742	GCNT1_HUMAN	T	119	ENSP00000440883:A119T;ENSP00000415454:A119T;ENSP00000390703:A119T;ENSP00000365920:A119T	.	A	+	1	0	GCNT1	78307472	0.670000	0.27512	0.920000	0.36463	0.663000	0.39108	2.387000	0.44389	2.885000	0.99019	0.655000	0.94253	GCG		0.418	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634	
GCNT1	2650	broad.mit.edu	37	9	79117891	79117891	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:79117891C>A	ENST00000376730.4	+	4	1077	c.594C>A	c.(592-594)aaC>aaA	p.N198K	GCNT1_ENST00000444201.2_Missense_Mutation_p.N198K|GCNT1_ENST00000442371.1_Missense_Mutation_p.N198K|GCNT1_ENST00000536223.1_Missense_Mutation_p.N198K	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	198	Catalytic. {ECO:0000250}.				cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)	p.N198K(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						CTGACCTCAACTGCATGAAGG	0.448																																					p.N198K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C594A	9						.						80.0	79.0	79.0					9																	79117891		2203	4300	6503	78307711	SO:0001583	missense	2650	exon3			L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4203	protein-coding gene	gene with protein product	"""core 2 beta1,6 N-acetylglucosaminyltransferase-I"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"""	600391	"""glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.594C>A	9.37:g.79117891C>A	ENSP00000365920:p.Asn198Lys	Somatic		Capture	Illumina HiSeq	Phase_I	78307711	NM_001097635	Q6DJZ4	Missense_Mutation	SNP	ENST00000376730.4	37	CCDS6653.1	.	.	.	.	.	.	.	.	.	.	c	20.5	3.994679	0.74703	.	.	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	T;T;T;T	0.11277	2.79;2.79;2.79;2.79	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.36026	0.0952	M	0.86097	2.795	0.49915	D	0.999838	D	0.89917	1.0	D	0.97110	1.0	T	0.07616	-1.0763	9	.	.	.	.	11.8716	0.52523	0.0:0.866:0.0:0.134	.	198	Q02742	GCNT1_HUMAN	K	198	ENSP00000440883:N198K;ENSP00000415454:N198K;ENSP00000390703:N198K;ENSP00000365920:N198K	.	N	+	3	2	GCNT1	78307711	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.185000	0.42584	2.885000	0.99019	0.655000	0.94253	AAC		0.448	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634	
PRUNE2	158471	broad.mit.edu	37	9	79259675	79259675	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:79259675C>A	ENST00000376718.3	-	12	8831	c.8708G>T	c.(8707-8709)aGg>aTg	p.R2903M	PRUNE2_ENST00000223609.6_Missense_Mutation_p.R168M|PRUNE2_ENST00000466266.2_5'UTR|PRUNE2_ENST00000428286.1_Missense_Mutation_p.R2545M|PRUNE2_ENST00000443509.2_Missense_Mutation_p.R152M	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2903	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.R2903M(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AATGACTCTCCTGTAGGGCTC	0.498																																					p.R2903M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8708T	9						.						120.0	103.0	108.0					9																	79259675		1568	3582	5150	78449495	SO:0001583	missense	158471	exon12			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.8708G>T	9.37:g.79259675C>A	ENSP00000365908:p.Arg2903Met	Somatic		Capture	Illumina HiSeq	Phase_I	78449495	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.97|15.97	2.989984|2.989984	0.54041|0.54041	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000426088|ENST00000376717;ENST00000376718;ENST00000428286;ENST00000441554;ENST00000443509;ENST00000424866;ENST00000223609;ENST00000422033	.|T;T;T;T;T;T	.|0.55234	.|0.95;0.91;0.9;0.96;0.53;0.95	6.06|6.06	5.07|5.07	0.68467|0.68467	.|Cellular retinaldehyde-binding/triple function, C-terminal (3);	.|0.133192	.|0.64402	.|D	.|0.000004	T|T	0.31979|0.31979	0.0814|0.0814	N|N	0.02539|0.02539	-0.55|-0.55	0.43444|0.43444	D|D	0.995623|0.995623	.|B;B;B;P;P	.|0.51537	.|0.013;0.001;0.002;0.724;0.946	.|B;B;B;B;P	.|0.53593	.|0.026;0.009;0.003;0.335;0.73	T|T	0.15292|0.15292	-1.0442|-1.0442	5|10	.|0.23891	.|T	.|0.37	-15.644|-15.644	4.055|4.055	0.09813|0.09813	0.0:0.6945:0.0:0.3055|0.0:0.6945:0.0:0.3055	.|.	.|168;167;152;2904;2903	.|B4DSQ3;Q8WUY3-5;B4DJW7;Q8WUY3-3;Q8WUY3	.|.;.;.;.;PRUN2_HUMAN	H|M	2224|168;2903;2545;121;152;73;168;2903	.|ENSP00000365907:R168M;ENSP00000365908:R2903M;ENSP00000397425:R2545M;ENSP00000393843:R152M;ENSP00000393657:R73M;ENSP00000223609:R168M	.|ENSP00000223609:R168M	Q|R	-|-	3|2	2|0	PRUNE2|PRUNE2	78449495|78449495	0.992000|0.992000	0.36948|0.36948	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	1.589000|1.589000	0.36644|0.36644	2.879000|2.879000	0.98667|0.98667	0.650000|0.650000	0.86243|0.86243	CAG|AGG		0.498	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
PRUNE2	158471	broad.mit.edu	37	9	79320025	79320025	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:79320025G>T	ENST00000376718.3	-	8	7288	c.7165C>A	c.(7165-7167)Ctg>Atg	p.L2389M	PRUNE2_ENST00000428286.1_Missense_Mutation_p.L2030M	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2389					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.L2389M(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TACGGTGCCAGCGACTGCTTC	0.483																																					p.L2389M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C7165A	9						.						104.0	97.0	99.0					9																	79320025		1568	3582	5150	78509845	SO:0001583	missense	158471	exon8			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.7165C>A	9.37:g.79320025G>T	ENSP00000365908:p.Leu2389Met	Somatic		Capture	Illumina HiSeq	Phase_I	78509845	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.432|9.432	1.085722|1.085722	0.20390|0.20390	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000426088|ENST00000376718;ENST00000428286;ENST00000422033	.|T;T	.|0.56776	.|0.44;0.46	5.93|5.93	3.01|3.01	0.34805|0.34805	.|.	.|0.306317	.|0.23750	.|N	.|0.044925	T|T	0.60573|0.60573	0.2279|0.2279	M|M	0.66939|0.66939	2.045|2.045	0.20563|0.20563	N|N	0.999883|0.999883	.|D	.|0.57899	.|0.981	.|P	.|0.54965	.|0.765	T|T	0.53165|0.53165	-0.8477|-0.8477	5|10	.|0.48119	.|T	.|0.1	-0.4188|-0.4188	9.8298|9.8298	0.40934|0.40934	0.0695:0.2636:0.6669:0.0|0.0695:0.2636:0.6669:0.0	.|.	.|2389	.|Q8WUY3	.|PRUN2_HUMAN	D|M	1710|2389;2030;2388	.|ENSP00000365908:L2389M;ENSP00000397425:L2030M	.|ENSP00000365908:L2389M	A|L	-|-	2|1	0|2	PRUNE2|PRUNE2	78509845|78509845	0.791000|0.791000	0.28800|0.28800	0.314000|0.314000	0.25224|0.25224	0.032000|0.032000	0.12392|0.12392	2.572000|2.572000	0.45999|0.45999	0.369000|0.369000	0.24510|0.24510	0.655000|0.655000	0.94253|0.94253	GCT|CTG		0.483	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
PSAT1	29968	broad.mit.edu	37	9	80923337	80923337	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:80923337T>C	ENST00000376588.3	+	6	646	c.578T>C	c.(577-579)gTg>gCg	p.V193A	PSAT1_ENST00000347159.2_Missense_Mutation_p.V193A	NM_058179.2	NP_478059.1	Q9Y617	SERC_HUMAN	phosphoserine aminotransferase 1	193					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-serine biosynthetic process (GO:0006564)|pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	O-phospho-L-serine:2-oxoglutarate aminotransferase activity (GO:0004648)|pyridoxal phosphate binding (GO:0030170)	p.V193A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	20						AAGTTTGGTGTGATTTTTGCT	0.478																																					p.V193A	Colon(34;187 791 10662 18313 37609)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T578C	9						.						113.0	104.0	107.0					9																	80923337		2203	4300	6503	80113157	SO:0001583	missense	29968	exon6			BC004863	CCDS6659.1, CCDS6660.1	9q21.2	2008-08-11			ENSG00000135069	ENSG00000135069			19129	protein-coding gene	gene with protein product		610936				12633500, 3651428	Standard	NM_058179		Approved	PSA	uc004ala.3	Q9Y617	OTTHUMG00000020066	ENST00000376588.3:c.578T>C	9.37:g.80923337T>C	ENSP00000365773:p.Val193Ala	Somatic		Capture	Illumina HiSeq	Phase_I	80113157	NM_058179	Q5T7G5|Q5T7G6|Q96AW2|Q9BQ12	Missense_Mutation	SNP	ENST00000376588.3	37	CCDS6660.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.382987	0.61845	.	.	ENSG00000135069	ENST00000421149;ENST00000347159;ENST00000376588	D;D	0.88046	-2.33;-2.33	5.74	4.59	0.56863	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.063315	0.64402	D	0.000005	D	0.83138	0.5189	L	0.38733	1.17	0.58432	D	0.99999	B;B	0.29136	0.035;0.234	B;B	0.35931	0.014;0.214	T	0.80207	-0.1478	10	0.54805	T	0.06	-16.2461	11.873	0.52531	0.0:0.0684:0.0:0.9316	.	193;193	Q9Y617-2;Q9Y617	.;SERC_HUMAN	A	17;193;193	ENSP00000317606:V193A;ENSP00000365773:V193A	ENSP00000317606:V193A	V	+	2	0	PSAT1	80113157	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.927000	0.70080	0.994000	0.38892	0.455000	0.32223	GTG		0.478	PSAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052777.1	NM_021154	
UBQLN1	29979	broad.mit.edu	37	9	86292718	86292718	+	Silent	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:86292718A>G	ENST00000376395.4	-	6	1552	c.1029T>C	c.(1027-1029)ggT>ggC	p.G343G	UBQLN1_ENST00000257468.7_Silent_p.G343G	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1	343					cellular response to hypoxia (GO:0071456)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|regulation of protein ubiquitination (GO:0031396)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|protein complex (GO:0043234)	kinase binding (GO:0019900)	p.G343G(1)		breast(4)|endometrium(2)|kidney(4)|large_intestine(6)|lung(10)|prostate(1)	27						CAGTAGTGCCACCCACAGTGC	0.522																																					p.G343G	Melanoma(186;1284 2073 12755 14558 18426)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1029C	9						.						80.0	73.0	75.0					9																	86292718		2203	4300	6503	85482538	SO:0001819	synonymous_variant	29979	exon6			AF176069	CCDS6663.1, CCDS6664.1	9q22	2013-02-12			ENSG00000135018	ENSG00000135018		"""Ubiquilin family"""	12508	protein-coding gene	gene with protein product		605046				9303440, 10807547	Standard	NM_013438		Approved	DSK2, PLIC-1, XDRP1, DA41	uc004amv.3	Q9UMX0	OTTHUMG00000020104	ENST00000376395.4:c.1029T>C	9.37:g.86292718A>G		Somatic		Capture	Illumina HiSeq	Phase_I	85482538	NM_053067	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Silent	SNP	ENST00000376395.4	37	CCDS6663.1																																																																																				0.522	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1	NM_013438	
C9orf64	84267	broad.mit.edu	37	9	86570383	86570383	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:86570383G>A	ENST00000376344.3	-	2	726	c.510C>T	c.(508-510)tgC>tgT	p.C170C	C9orf64_ENST00000376340.2_Silent_p.C29C|C9orf64_ENST00000314700.1_Silent_p.C29C	NM_032307.3	NP_115683.3	Q5T6V5	CI064_HUMAN	chromosome 9 open reading frame 64	170								p.C170C(1)		central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						TTTCTCGGACGCAGTTGAGAA	0.448																																					p.C170C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C510T	9						.						76.0	74.0	75.0					9																	86570383		2203	4300	6503	85760203	SO:0001819	synonymous_variant	84267	exon2			AK090882	CCDS6666.2	9q22.1	2014-06-11			ENSG00000165118	ENSG00000165118			28144	protein-coding gene	gene with protein product		611342				24911101	Standard	NM_032307		Approved	MGC10999	uc004anb.3	Q5T6V5	OTTHUMG00000020111	ENST00000376344.3:c.510C>T	9.37:g.86570383G>A		Somatic		Capture	Illumina HiSeq	Phase_I	85760203	NM_032307	B2RPI6|Q8N2B1|Q9BT18	Silent	SNP	ENST00000376344.3	37	CCDS6666.2																																																																																				0.448	C9orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052865.1	NM_032307	
DAPK1	1612	broad.mit.edu	37	9	90264887	90264887	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:90264887G>A	ENST00000408954.3	+	16	1815	c.1480G>A	c.(1480-1482)Gcc>Acc	p.A494T	DAPK1_ENST00000491893.1_Missense_Mutation_p.A494T|DAPK1_ENST00000472284.1_Missense_Mutation_p.A494T|DAPK1_ENST00000469640.2_Missense_Mutation_p.A494T|DAPK1_ENST00000358077.5_Missense_Mutation_p.A494T	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	494					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.A494T(1)|p.A495T(1)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						TTACTCTGTGGCCAAAGCCCT	0.547									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.A494T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1480A	9						.						62.0	67.0	65.0					9																	90264887		1938	4139	6077	89454707	SO:0001583	missense	1612	exon16	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.1480G>A	9.37:g.90264887G>A	ENSP00000386135:p.Ala494Thr	Somatic		Capture	Illumina HiSeq	Phase_I	89454707	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	G	17.12	3.308490	0.60305	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.67523	-0.27;-0.27;-0.21;-0.27;-0.21	5.63	5.63	0.86233	Ankyrin repeat-containing domain (4);	0.000000	0.51477	D	0.000087	T	0.53029	0.1771	N	0.17674	0.51	0.80722	D	1	B;B;B;B	0.22746	0.061;0.057;0.074;0.01	B;B;B;B	0.27887	0.056;0.084;0.047;0.019	T	0.47497	-0.9113	10	0.30854	T	0.27	.	13.939	0.64043	0.0735:0.0:0.9265:0.0	.	494;48;494;494	B7ZLE7;P53355-2;B7Z454;P53355	.;.;.;DAPK1_HUMAN	T	494	ENSP00000350785:A494T;ENSP00000417076:A494T;ENSP00000418885:A494T;ENSP00000386135:A494T;ENSP00000419026:A494T	ENSP00000350785:A494T	A	+	1	0	DAPK1	89454707	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.547000	0.73892	2.826000	0.97356	0.655000	0.94253	GCC		0.547	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
SPATA31E1	286234	broad.mit.edu	37	9	90503014	90503014	+	Silent	SNP	C	C	T	rs534668152		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:90503014C>T	ENST00000325643.5	+	4	3678	c.3612C>T	c.(3610-3612)ggC>ggT	p.G1204G		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	1204					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.G1204G(1)									CGGACAAGGGCGAGGCCCACA	0.652													.|||	1	0.000199681	0.0	0.0	5008	,	,		17693	0.0		0.0	False		,,,				2504	0.001				p.G1204G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3612T	9						.						11.0	11.0	11.0					9																	90503014		2192	4281	6473	89692834	SO:0001819	synonymous_variant	286234	exon4			AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.3612C>T	9.37:g.90503014C>T		Somatic		Capture	Illumina HiSeq	Phase_I	89692834	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Silent	SNP	ENST00000325643.5	37	CCDS6676.1																																																																																				0.652	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
SEMA4D	10507	broad.mit.edu	37	9	91978853	91978853	+	Missense_Mutation	SNP	A	A	G	rs145328499		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:91978853A>G	ENST00000420987.1	-	18	2341	c.1895T>C	c.(1894-1896)aTt>aCt	p.I632T	SEMA4D_ENST00000343780.4_Missense_Mutation_p.I632T|SEMA4D_ENST00000455551.2_Missense_Mutation_p.I632T|SEMA4D_ENST00000420101.2_Missense_Mutation_p.I17T|SEMA4D_ENST00000469653.1_5'UTR|SEMA4D_ENST00000339861.4_Missense_Mutation_p.I632T	NM_001142287.1	NP_001135759.1	Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	0	Ig-like C2-type.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)	p.I17T(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						GACAAAGCGAATGTCTGCAGG	0.597																																					p.I632T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1895C	9						.	A	THR/ILE	0,4406		0,0,2203	85.0	82.0	83.0		1895	5.1	0.0	9	dbSNP_134	83	1,8599	1.2+/-3.3	0,1,4299	no	missense	SEMA4D	NM_001142287.1	89	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		632/739	91978853	1,13005	2203	4300	6503	91168673	SO:0001583	missense	10507	exon19			U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000420987.1:c.1895T>C	9.37:g.91978853A>G	ENSP00000391733:p.Ile632Thr	Somatic		Capture	Illumina HiSeq	Phase_I	91168673	NM_001142287	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000420987.1	37	CCDS47991.1	.	.	.	.	.	.	.	.	.	.	A	10.12	1.261882	0.23051	0.0	1.16E-4	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000420101;ENST00000455551;ENST00000343780	T;T;T;T	0.11712	2.75;2.75;2.75;2.75	5.05	5.05	0.67936	.	0.856685	0.10063	N	0.720717	T	0.08403	0.0209	.	.	.	0.29898	N	0.824612	B	0.19200	0.034	B	0.21917	0.037	T	0.13361	-1.0512	9	0.38643	T	0.18	.	5.0185	0.14349	0.7786:0.0:0.2214:0.0	.	632	Q92854-2	.	T	632;632;17;632;632	ENSP00000344923:I632T;ENSP00000391733:I632T;ENSP00000411981:I632T;ENSP00000343418:I632T	ENSP00000344923:I632T	I	-	2	0	SEMA4D	91168673	0.017000	0.18338	0.015000	0.15790	0.647000	0.38526	1.834000	0.39171	2.129000	0.65627	0.379000	0.24179	ATT		0.597	SEMA4D-203	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402418.2	NM_006378	
NFIL3	4783	broad.mit.edu	37	9	94172745	94172745	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:94172745C>T	ENST00000297689.3	-	2	666	c.272G>A	c.(271-273)cGt>cAt	p.R91H		NM_005384.2	NP_005375.2	Q16649	NFIL3_HUMAN	nuclear factor, interleukin 3 regulated	91	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				cellular response to interleukin-4 (GO:0071353)|circadian rhythm (GO:0007623)|immune response (GO:0006955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.R91H(1)		endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	16						ACGCTTCTCACGAGATCTTTT	0.403																																					p.R91H	Esophageal Squamous(152;732 1832 10053 26981 51762)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G272A	9						.						228.0	233.0	232.0					9																	94172745		2203	4300	6503	93212566	SO:0001583	missense	4783	exon2			X64318	CCDS6690.1	9q22	2013-01-10			ENSG00000165030	ENSG00000165030		"""basic leucine zipper proteins"""	7787	protein-coding gene	gene with protein product		605327		IL3BP1		7565758, 1620116	Standard	NM_005384		Approved	E4BP4, NFIL3A, NF-IL3A	uc004arh.3	Q16649	OTTHUMG00000020209	ENST00000297689.3:c.272G>A	9.37:g.94172745C>T	ENSP00000297689:p.Arg91His	Somatic		Capture	Illumina HiSeq	Phase_I	93212566	NM_005384	B2R9Y8|Q14211|Q6FGQ8|Q96HS0	Missense_Mutation	SNP	ENST00000297689.3	37	CCDS6690.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.825388	0.90955	.	.	ENSG00000165030	ENST00000375724;ENST00000297689	T	0.72167	-0.63	4.89	4.89	0.63831	Basic-leucine zipper (bZIP) transcription factor (3);Basic leucine zipper (1);	0.166821	0.34959	N	0.003548	D	0.89518	0.6738	H	0.95950	3.745	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92633	0.6118	10	0.87932	D	0	-11.4372	18.5923	0.91218	0.0:1.0:0.0:0.0	.	91	Q16649	NFIL3_HUMAN	H	91	ENSP00000297689:R91H	ENSP00000297689:R91H	R	-	2	0	NFIL3	93212566	0.998000	0.40836	0.486000	0.27416	0.997000	0.91878	7.171000	0.77595	2.698000	0.92095	0.561000	0.74099	CGT		0.403	NFIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053038.2	NM_005384	
OGN	4969	broad.mit.edu	37	9	95165647	95165647	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:95165647G>A	ENST00000262551.4	-	2	463	c.43C>T	c.(43-45)Cct>Tct	p.P15S	CENPP_ENST00000375587.3_Intron|OGN_ENST00000375561.5_Missense_Mutation_p.P15S	NM_033014.2	NP_148935.1	P20774	MIME_HUMAN	osteoglycin	15					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|negative regulation of smooth muscle cell proliferation (GO:0048662)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)		p.P15S(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	13						TTTATCAGAGGCACAAGCAGT	0.413																																					p.P15S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C43T	9						.						96.0	96.0	96.0					9																	95165647		2203	4300	6503	94205468	SO:0001583	missense	4969	exon2			AI424992	CCDS6695.1	9q22	2008-02-05	2007-02-16		ENSG00000106809	ENSG00000106809		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	8126	protein-coding gene	gene with protein product	"""mimecan proteoglycan"""	602383	"""osteoglycin (osteoinductive factor)"""			2372374	Standard	NM_033014		Approved	mimecan, OIF, SLRR3A	uc004asa.3	P20774	OTTHUMG00000020224	ENST00000262551.4:c.43C>T	9.37:g.95165647G>A	ENSP00000262551:p.Pro15Ser	Somatic		Capture	Illumina HiSeq	Phase_I	94205468	NM_014057	Q6FIB0|Q9UF90|Q9UNK5	Missense_Mutation	SNP	ENST00000262551.4	37	CCDS6695.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.847214	0.71603	.	.	ENSG00000106809	ENST00000262551;ENST00000375561;ENST00000447356	T;T;T	0.67171	-0.12;-0.12;-0.25	5.42	5.42	0.78866	.	0.137031	0.49916	D	0.000140	T	0.62950	0.2470	L	0.29908	0.895	0.46437	D	0.999044	D;D	0.58268	0.982;0.982	P;P	0.52793	0.709;0.709	T	0.56420	-0.7982	10	0.07644	T	0.81	.	16.7451	0.85470	0.0:0.0:1.0:0.0	.	73;15	B4DI63;P20774	.;MIME_HUMAN	S	15;15;73	ENSP00000262551:P15S;ENSP00000364711:P15S;ENSP00000396709:P73S	ENSP00000262551:P15S	P	-	1	0	OGN	94205468	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.168000	0.50801	2.720000	0.93068	0.561000	0.74099	CCT		0.413	OGN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053087.1	NM_024416	
WNK2	65268	broad.mit.edu	37	9	96051706	96051706	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:96051706G>A	ENST00000297954.4	+	20	4781	c.4781G>A	c.(4780-4782)cGg>cAg	p.R1594Q	WNK2_ENST00000349097.3_Missense_Mutation_p.R1206Q|WNK2_ENST00000427277.2_Missense_Mutation_p.R1169Q|WNK2_ENST00000395477.2_Missense_Mutation_p.R1557Q|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000356055.3_5'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1594					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R1543Q(1)|p.R1594Q(1)		breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						GAGAAGCTGCGGACTCTGCTC	0.677																																					p.R1557Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4670A	9						.						32.0	37.0	35.0					9																	96051706		2203	4300	6503	95091527	SO:0001583	missense	65268	exon19			AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.4781G>A	9.37:g.96051706G>A	ENSP00000297954:p.Arg1594Gln	Somatic		Capture	Illumina HiSeq	Phase_I	95091527	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.624756|5.624756	0.96660|0.96660	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000432730;ENST00000448251;ENST00000453718|ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277	.|T;T;T;T	.|0.26223	.|1.75;1.75;1.75;1.75	5.32|5.32	5.32|5.32	0.75619|0.75619	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.52058|0.52058	0.1711|0.1711	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;0.999;1.0;1.0;0.999	.|D;D;D;D;D	.|0.91635	.|0.999;0.986;0.998;0.999;0.978	T|T	0.53322|0.53322	-0.8455|-0.8455	5|10	.|0.66056	.|D	.|0.02	.|.	18.9905|18.9905	0.92789|0.92789	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1557;1552;1160;1557;1594	.|Q9Y3S1-2;A6PVR3;A6PVR4;F8W9F9;Q9Y3S1	.|.;.;.;.;WNK2_HUMAN	R|Q	1553;354;80|1594;1557;1206;1169	.|ENSP00000297954:R1594Q;ENSP00000378860:R1557Q;ENSP00000297876:R1206Q;ENSP00000411181:R1169Q	.|ENSP00000297954:R1594Q	G|R	+|+	1|2	0|0	WNK2|WNK2	95091527|95091527	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.995000|0.995000	0.86356|0.86356	9.291000|9.291000	0.96070|0.96070	2.489000|2.489000	0.83994|0.83994	0.561000|0.561000	0.74099|0.74099	GGA|CGG		0.677	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
PTPDC1	138639	broad.mit.edu	37	9	96846997	96846997	+	Intron	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:96846997C>T	ENST00000375360.3	+	3	422				PTPDC1_ENST00000288976.3_Missense_Mutation_p.A62V	NM_001253830.1|NM_177995.2	NP_001240759.1|NP_818931.1	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1						cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.A62V(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	32						GTGATGGTGGCTGTTTCCTCA	0.547																																					p.A62V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C185T	9						.						69.0	65.0	66.0					9																	96846997		2203	4299	6502	95886818	SO:0001627	intron_variant	138639	exon1			BC051654	CCDS6707.1, CCDS6708.1, CCDS75860.1	9q22.32	2011-06-09			ENSG00000158079	ENSG00000158079		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	30184	protein-coding gene	gene with protein product	"""protein tyrosine phosphatase PTP9Q22"""					14702039	Standard	NM_152422		Approved	PTP9Q22, FLJ37312	uc010mrj.2	A2A3K4	OTTHUMG00000020258	ENST00000375360.3:c.83-536C>T	9.37:g.96846997C>T		Somatic		Capture	Illumina HiSeq	Phase_I	95886818	NM_152422	Q5T3M4|Q6NXE8|Q8IWM1|Q8N1X4|Q8N9F5	Missense_Mutation	SNP	ENST00000375360.3	37	CCDS6707.1	.	.	.	.	.	.	.	.	.	.	.	21.1	4.101886	0.76983	.	.	ENSG00000158079	ENST00000288976	T	0.17213	2.29	5.97	5.97	0.96955	.	0.146503	0.32002	N	0.006733	T	0.35770	0.0943	L	0.36672	1.1	0.41180	D	0.986228	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.02244	-1.1189	10	0.72032	D	0.01	-6.7666	19.4017	0.94632	0.0:1.0:0.0:0.0	.	62;62	E7EN59;A2A3K4-2	.;.	V	62	ENSP00000288976:A62V	ENSP00000288976:A62V	A	+	2	0	PTPDC1	95886818	1.000000	0.71417	0.972000	0.41901	0.267000	0.26476	5.872000	0.69636	2.835000	0.97688	0.591000	0.81541	GCT		0.547	PTPDC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215007.1	NM_177995, NM_152422	
CORO2A	7464	broad.mit.edu	37	9	100897160	100897160	+	Silent	SNP	C	C	T	rs147316581		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:100897160C>T	ENST00000343933.5	-	4	653	c.396G>A	c.(394-396)gcG>gcA	p.A132A	CORO2A_ENST00000375077.4_Silent_p.A132A	NM_003389.3	NP_003380.3	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A	132					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	actin cytoskeleton (GO:0015629)|transcriptional repressor complex (GO:0017053)	actin filament binding (GO:0051015)	p.A132A(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|skin(4)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				CTACTCTGCGCGCGTGGCCCA	0.602													C|||	1	0.000199681	0.0	0.0	5008	,	,		19472	0.0		0.001	False		,,,				2504	0.0				p.A132A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G396A	9						.	C	,	1,4405	2.1+/-5.4	0,1,2202	74.0	64.0	68.0		396,396	-10.7	0.0	9	dbSNP_134	68	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CORO2A	NM_003389.3,NM_052820.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	132/526,132/526	100897160	1,13005	2203	4300	6503	99936981	SO:0001819	synonymous_variant	7464	exon4			U57057	CCDS6735.1	9q22.3	2013-01-10	2001-11-28		ENSG00000106789	ENSG00000106789		"""Coronins"", ""WD repeat domain containing"""	2255	protein-coding gene	gene with protein product	"""coronin 2A"", ""coronin-like protein B"", ""WD protein IR10"", ""WD-repeat protein 2"""	602159	"""coronin, actin-binding protein, 2A"""			8985118	Standard	NM_052820		Approved	IR10, WDR2	uc004aym.3	Q92828	OTTHUMG00000020340	ENST00000343933.5:c.396G>A	9.37:g.100897160C>T		Somatic		Capture	Illumina HiSeq	Phase_I	99936981	NM_003389	Q5TBR5|Q92829|Q9BWS5	Silent	SNP	ENST00000343933.5	37	CCDS6735.1																																																																																				0.602	CORO2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053357.1	NM_003389	
OR1J4	26219	broad.mit.edu	37	9	125281725	125281725	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:125281725delT	ENST00000340750.1	+	1	306	c.306delT	c.(304-306)tatfs	p.Y102fs		NM_001004452.1	NP_001004452.1	Q8NGS1	OR1J4_HUMAN	olfactory receptor, family 1, subfamily J, member 4	102						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F104fs*7(1)		large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(1)	20						CTCAGATGTATTTTTTCATAT	0.418																																					p.Y102fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.306delT	9						.						177.0	168.0	171.0					9																	125281725		2203	4300	6503	124321546	SO:0001589	frameshift_variant	26219	exon1			X64979	CCDS35122.1	9q33.2	2013-09-20			ENSG00000239590	ENSG00000239590		"""GPCR / Class A : Olfactory receptors"""	8211	protein-coding gene	gene with protein product						1370859	Standard	NM_001004452		Approved	HTPCRX01, HSHTPCRX01	uc011lyw.2	Q8NGS1	OTTHUMG00000020606	ENST00000340750.1:c.306delT	9.37:g.125281725delT	ENSP00000343521:p.Tyr102fs	Somatic		Capture	Illumina HiSeq	Phase_I	124321546	NM_001004452	A3KFM0|Q6IEZ3|Q96R89	Frame_Shift_Del	DEL	ENST00000340750.1	37	CCDS35122.1																																																																																				0.418	OR1J4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053936.1		
EHMT1	79813	broad.mit.edu	37	9	140712582	140712582	+	Missense_Mutation	SNP	G	G	A	rs371824384		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chr9:140712582G>A	ENST00000460843.1	+	25	3559	c.3532G>A	c.(3532-3534)Gac>Aac	p.D1178N		NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	1178	Interaction with histone H3.|SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)	p.D1147N(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		CTTTGATCTCGACAATAAGGT	0.502																																					p.D1178N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3532A	9						.	G	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	161.0	147.0	152.0		3532	5.3	1.0	9		152	0,8600		0,0,4300	no	missense	EHMT1	NM_024757.4	23	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1178/1299	140712582	1,13005	2203	4300	6503	139832403	SO:0001583	missense	79813	exon25			AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.3532G>A	9.37:g.140712582G>A	ENSP00000417980:p.Asp1178Asn	Somatic		Capture	Illumina HiSeq	Phase_I	139832403	NM_024757	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	37	CCDS7050.2	.	.	.	.	.	.	.	.	.	.	G	26.5	4.745519	0.89663	2.27E-4	0.0	ENSG00000181090	ENST00000371400;ENST00000460843	D	0.90261	-2.64	5.26	5.26	0.73747	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.93363	0.7884	L	0.53780	1.695	0.80722	D	1	D	0.63880	0.993	P	0.59546	0.859	D	0.93795	0.7096	10	0.72032	D	0.01	.	18.832	0.92144	0.0:0.0:1.0:0.0	.	1178	Q9H9B1	EHMT1_HUMAN	N	1147;1178	ENSP00000417980:D1178N	ENSP00000360453:D1147N	D	+	1	0	EHMT1	139832403	1.000000	0.71417	1.000000	0.80357	0.503000	0.33858	9.101000	0.94219	2.631000	0.89168	0.462000	0.41574	GAC		0.502	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
CDKL5	6792	broad.mit.edu	37	X	18668537	18668538	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:18668537_18668538insT	ENST00000379989.3	+	21	3090_3091	c.2805_2806insT	c.(2806-2808)ttcfs	p.F936fs	RS1_ENST00000476595.1_5'UTR|RS1_ENST00000379984.3_Intron|CDKL5_ENST00000379996.3_Frame_Shift_Ins_p.F936fs	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	936					neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)	p.C937fs*4(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					CAGGAGAATACTTCTGCTGTGG	0.564																																					p.Y935fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2805_2806insT	X						.																																			18578459	SO:0001589	frameshift_variant	6792	exon20			Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"""Cyclin-dependent kinases"""	11411	protein-coding gene	gene with protein product		300203	"""serine/threonine kinase 9"""	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.2807dupT	X.37:g.18668539_18668539dupT	ENSP00000369325:p.Phe936fs	Somatic		Capture	Illumina HiSeq	Phase_I	18578458	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Frame_Shift_Ins	INS	ENST00000379989.3	37	CCDS14186.1																																																																																				0.564	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159	
ACRC	93953	broad.mit.edu	37	X	70830584	70830585	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:70830584_70830585insT	ENST00000373695.1	+	10	2202_2203	c.1665_1666insT	c.(1666-1668)ttafs	p.L556fs	ACRC_ENST00000471950.1_3'UTR|ACRC_ENST00000373696.3_Frame_Shift_Ins_p.L556fs			Q96QF7	ACRC_HUMAN	acidic repeat containing	556	SprT-like.					nucleus (GO:0005634)		p.L556fs*6(1)		autonomic_ganglia(1)|breast(1)|endometrium(15)|kidney(4)|large_intestine(4)|lung(20)|ovary(5)|prostate(1)|skin(2)|stomach(1)	54	Renal(35;0.156)					AAACTGCTGGCTTATGCAGCAC	0.485																																					p.G555fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1665_1666insT	X						.																																			70747310	SO:0001589	frameshift_variant	93953	exon11			AJ311392	CCDS35326.1	Xq13.1	2010-08-05			ENSG00000147174	ENSG00000147174			15805	protein-coding gene	gene with protein product		300369					Standard	NM_052957		Approved		uc004eae.2	Q96QF7	OTTHUMG00000033327	ENST00000373695.1:c.1667dupT	X.37:g.70830586_70830586dupT	ENSP00000362799:p.Leu556fs	Somatic		Capture	Illumina HiSeq	Phase_I	70747309	NM_052957	B9EG62	Frame_Shift_Ins	INS	ENST00000373695.1	37	CCDS35326.1																																																																																				0.485	ACRC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081856.1		
ZMAT1	84460	broad.mit.edu	37	X	101138887	101138887	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:101138887T>G	ENST00000372782.3	-	7	1559	c.1512A>C	c.(1510-1512)caA>caC	p.Q504H	ZMAT1_ENST00000540921.1_Missense_Mutation_p.Q504H|ZMAT1_ENST00000458570.1_Missense_Mutation_p.Q333H|ZMAT1_ENST00000494068.1_5'UTR	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	504						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.Q333H(1)|p.Q504H(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						AGTTATTTTCTTGCTGATTAA	0.408																																					p.Q504H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A1512C	X						.						115.0	98.0	104.0					X																	101138887		2202	4300	6502	101025543	SO:0001583	missense	84460	exon7			Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"""Zinc fingers, matrin-type"""	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.1512A>C	X.37:g.101138887T>G	ENSP00000361868:p.Gln504His	Somatic		Capture	Illumina HiSeq	Phase_I	101025543	NM_001011657	Q8NDS3|Q96JN6	Missense_Mutation	SNP	ENST00000372782.3	37	CCDS35348.1	.	.	.	.	.	.	.	.	.	.	T	10.38	1.333457	0.24167	.	.	ENSG00000166432	ENST00000372782;ENST00000540921;ENST00000458570	T;T;T	0.26373	2.3;2.3;1.74	4.37	-2.35	0.06684	.	0.553031	0.18224	N	0.147800	T	0.17152	0.0412	L	0.48986	1.54	0.09310	N	1	B	0.26195	0.144	B	0.21708	0.036	T	0.11518	-1.0584	10	0.46703	T	0.11	-3.6233	4.238	0.10635	0.3091:0.4227:0.0:0.2682	.	504	Q5H9K5	ZMAT1_HUMAN	H	504;504;333	ENSP00000361868:Q504H;ENSP00000437529:Q504H;ENSP00000413044:Q333H	ENSP00000361868:Q504H	Q	-	3	2	ZMAT1	101025543	0.542000	0.26426	0.001000	0.08648	0.987000	0.75469	-0.029000	0.12329	-0.611000	0.05709	0.486000	0.48141	CAA		0.408	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1		
CLCN4	1183	broad.mit.edu	37	X	10181808	10181808	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:10181808C>T	ENST00000380833.4	+	11	2055	c.1664C>T	c.(1663-1665)gCg>gTg	p.A555V	CLCN4_ENST00000380829.1_Missense_Mutation_p.A524V|AC003666.1_ENST00000410201.1_RNA|CLCN4_ENST00000421085.2_Missense_Mutation_p.A461V	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	555					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.A555V(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CTGATGGCGGCGGCTGTGACC	0.537																																					p.A555V	Melanoma(74;1050 1296 1576 30544 38374)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1664T	X						.						96.0	83.0	87.0					X																	10181808		2203	4300	6503	10141808	SO:0001583	missense	1183	exon11			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"""Ion channels / Chloride channels : Voltage-sensitive"""	2022	protein-coding gene	gene with protein product		302910	"""chloride channel 4"""			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.1664C>T	X.37:g.10181808C>T	ENSP00000370213:p.Ala555Val	Somatic		Capture	Illumina HiSeq	Phase_I	10141808	NM_001830	A1L3U1|B7Z5Z4|Q9UBU1	Missense_Mutation	SNP	ENST00000380833.4	37	CCDS14137.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.201997	0.58234	.	.	ENSG00000073464	ENST00000380833;ENST00000380829;ENST00000421085	D;D;D	0.95171	-3.63;-3.63;-3.63	5.52	5.52	0.82312	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.94984	0.8377	L	0.60845	1.875	0.80722	D	1	D	0.54207	0.965	P	0.49953	0.627	D	0.95159	0.8280	10	0.59425	D	0.04	-21.4057	18.5475	0.91053	0.0:1.0:0.0:0.0	.	555	P51793	CLCN4_HUMAN	V	555;524;461	ENSP00000370213:A555V;ENSP00000370209:A524V;ENSP00000405754:A461V	ENSP00000370209:A524V	A	+	2	0	CLCN4	10141808	1.000000	0.71417	0.334000	0.25495	0.031000	0.12232	5.910000	0.69931	2.324000	0.78689	0.600000	0.82982	GCG		0.537	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1		
CLCN4	1183	broad.mit.edu	37	X	10181921	10181921	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:10181921C>T	ENST00000380833.4	+	11	2168	c.1777C>T	c.(1777-1779)Cgc>Tgc	p.R593C	CLCN4_ENST00000380829.1_Missense_Mutation_p.R562C|AC003666.1_ENST00000410201.1_RNA|CLCN4_ENST00000421085.2_Missense_Mutation_p.R499C	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	593					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.R593C(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						GTTTACTCACCGCACACTGGC	0.587																																					p.R593C	Melanoma(74;1050 1296 1576 30544 38374)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1777T	X						.						93.0	61.0	72.0					X																	10181921		2203	4300	6503	10141921	SO:0001583	missense	1183	exon11			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"""Ion channels / Chloride channels : Voltage-sensitive"""	2022	protein-coding gene	gene with protein product		302910	"""chloride channel 4"""			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.1777C>T	X.37:g.10181921C>T	ENSP00000370213:p.Arg593Cys	Somatic		Capture	Illumina HiSeq	Phase_I	10141921	NM_001830	A1L3U1|B7Z5Z4|Q9UBU1	Missense_Mutation	SNP	ENST00000380833.4	37	CCDS14137.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.649882	0.47362	.	.	ENSG00000073464	ENST00000380833;ENST00000380829;ENST00000421085	D;D;D	0.88277	-2.36;-2.36;-2.36	5.52	4.57	0.56435	.	0.048882	0.85682	D	0.000000	D	0.83825	0.5338	N	0.22421	0.69	0.80722	D	1	P	0.52692	0.955	P	0.46339	0.513	D	0.86073	0.1539	10	0.72032	D	0.01	-33.4445	12.4946	0.55921	0.3065:0.6935:0.0:0.0	.	593	P51793	CLCN4_HUMAN	C	593;562;499	ENSP00000370213:R593C;ENSP00000370209:R562C;ENSP00000405754:R499C	ENSP00000370209:R562C	R	+	1	0	CLCN4	10141921	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	1.039000	0.30266	2.324000	0.78689	0.600000	0.82982	CGC		0.587	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1		
ZMAT1	84460	broad.mit.edu	37	X	101139327	101139327	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:101139327G>A	ENST00000372782.3	-	7	1119	c.1072C>T	c.(1072-1074)Cat>Tat	p.H358Y	ZMAT1_ENST00000540921.1_Missense_Mutation_p.H358Y|ZMAT1_ENST00000458570.1_Missense_Mutation_p.H187Y|ZMAT1_ENST00000494068.1_5'UTR	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	358						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.H358Y(1)|p.H187Y(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						GAAGCCTCATGTGAAAATCTT	0.438																																					p.H358Y												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1072T	X						.						147.0	132.0	137.0					X																	101139327		2203	4300	6503	101025983	SO:0001583	missense	84460	exon7			Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"""Zinc fingers, matrin-type"""	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.1072C>T	X.37:g.101139327G>A	ENSP00000361868:p.His358Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	101025983	NM_001011657	Q8NDS3|Q96JN6	Missense_Mutation	SNP	ENST00000372782.3	37	CCDS35348.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.246647	0.00022	.	.	ENSG00000166432	ENST00000372782;ENST00000540921;ENST00000458570	T;T;T	0.21543	2.58;2.58;2.0	4.17	-2.32	0.06745	.	1.545970	0.03412	N	0.204918	T	0.08670	0.0215	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.26087	-1.0113	10	0.02654	T	1	0.9092	5.4367	0.16486	0.3292:0.2056:0.4652:0.0	.	358	Q5H9K5	ZMAT1_HUMAN	Y	358;358;187	ENSP00000361868:H358Y;ENSP00000437529:H358Y;ENSP00000413044:H187Y	ENSP00000361868:H358Y	H	-	1	0	ZMAT1	101025983	0.014000	0.17966	0.000000	0.03702	0.009000	0.06853	0.066000	0.14489	-0.617000	0.05664	-0.444000	0.05651	CAT		0.438	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1		
IL1RAPL2	26280	broad.mit.edu	37	X	104440255	104440255	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:104440255C>T	ENST00000372582.1	+	3	937	c.181C>T	c.(181-183)Cgt>Tgt	p.R61C	IL1RAPL2_ENST00000344799.4_Missense_Mutation_p.R61C	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	61	Ig-like C2-type 1.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.R61C(1)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CAGTTATATTCGTACCAACTA	0.473																																					p.R61C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C181T	X						.						146.0	117.0	127.0					X																	104440255		2203	4300	6503	104326911	SO:0001583	missense	26280	exon3			AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.181C>T	X.37:g.104440255C>T	ENSP00000361663:p.Arg61Cys	Somatic		Capture	Illumina HiSeq	Phase_I	104326911	NM_017416	Q2M3U3|Q9NZN0	Missense_Mutation	SNP	ENST00000372582.1	37	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.465437	0.63513	.	.	ENSG00000189108	ENST00000372582;ENST00000344799	T;T	0.77750	-1.12;-1.12	5.59	4.68	0.58851	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.225848	0.27912	N	0.017346	D	0.85813	0.5784	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.85526	0.1206	10	0.46703	T	0.11	.	10.5317	0.44981	0.3661:0.6339:0.0:0.0	.	61	Q9NP60	IRPL2_HUMAN	C	61	ENSP00000361663:R61C;ENSP00000344976:R61C	ENSP00000344976:R61C	R	+	1	0	IL1RAPL2	104326911	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.172000	0.42463	2.350000	0.79820	0.600000	0.82982	CGT		0.473	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416	
TEX13A	56157	broad.mit.edu	37	X	104464397	104464397	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:104464397C>T	ENST00000413579.1	-	3	592	c.481G>A	c.(481-483)Ggc>Agc	p.G161S	IL1RAPL2_ENST00000344799.4_Intron|IL1RAPL2_ENST00000372582.1_Intron|TEX13A_ENST00000372578.3_Missense_Mutation_p.G161S|TEX13A_ENST00000372575.1_Missense_Mutation_p.G161S			Q9BXU3	TX13A_HUMAN	testis expressed 13A	161							zinc ion binding (GO:0008270)	p.G161S(1)		large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						GTGGCCAGGCCTGGCCACCCT	0.652																																					p.G161S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G481A	X						.						19.0	22.0	21.0					X																	104464397		2041	4070	6111	104351053	SO:0001583	missense	56157	exon3			AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"""testis expressed sequence 13A"""			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.481G>A	X.37:g.104464397C>T	ENSP00000399753:p.Gly161Ser	Somatic		Capture	Illumina HiSeq	Phase_I	104351053	NM_031274	B1B1G8|Q32NB6	Missense_Mutation	SNP	ENST00000413579.1	37		.	.	.	.	.	.	.	.	.	.	C	5.470	0.271801	0.10349	.	.	ENSG00000133149	ENST00000372578;ENST00000372575;ENST00000413579	.	.	.	2.65	0.828	0.18841	.	1.798430	0.03544	N	0.224476	T	0.57562	0.2062	.	.	.	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.75484	0.986;0.986	T	0.26849	-1.0091	8	0.40728	T	0.16	.	4.4667	0.11692	0.0:0.6501:0.0:0.3499	.	161;161	C9JWK0;Q9BXU3	.;TX13A_HUMAN	S	161	.	ENSP00000361656:G161S	G	-	1	0	TEX13A	104351053	0.001000	0.12720	0.002000	0.10522	0.008000	0.06430	0.069000	0.14552	0.098000	0.17522	0.422000	0.28245	GGC		0.652	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274	
COL4A6	1288	broad.mit.edu	37	X	107431842	107431842	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:107431842G>A	ENST00000372216.4	-	21	1595	c.1495C>T	c.(1495-1497)Cca>Tca	p.P499S	COL4A6_ENST00000545689.1_Missense_Mutation_p.P498S|COL4A6_ENST00000394872.2_Missense_Mutation_p.P499S|COL4A6_ENST00000334504.7_Missense_Mutation_p.P498S|COL4A6_ENST00000538570.1_Missense_Mutation_p.P498S	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	499	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)	p.P498S(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						GGACCAGGTGGGCCTGGTTCC	0.592									Alport syndrome with Diffuse Leiomyomatosis																												p.P498S	Melanoma(87;1895 1945 2589 7165)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1492T	X						.						42.0	42.0	42.0					X																	107431842		2203	4300	6503	107318498	SO:0001583	missense	1288	exon21	Familial Cancer Database		U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"""Collagens"""	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.1495C>T	X.37:g.107431842G>A	ENSP00000361290:p.Pro499Ser	Somatic		Capture	Illumina HiSeq	Phase_I	107318498	NM_033641	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Missense_Mutation	SNP	ENST00000372216.4	37	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	G	12.82	2.051303	0.36181	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000394872;ENST00000541389;ENST00000545689;ENST00000538570	D;D;D;D;D	0.96587	-4.06;-4.06;-4.06;-4.06;-4.06	4.12	3.24	0.37175	.	1.236440	0.06261	N	0.693943	D	0.94420	0.8205	M	0.70787	2.145	0.23010	N	0.998433	B;B;B;B	0.10296	0.003;0.003;0.003;0.003	B;B;B;B	0.14023	0.006;0.006;0.01;0.006	T	0.82694	-0.0330	10	0.09843	T	0.71	.	7.7965	0.29150	0.0894:0.0:0.7457:0.1649	.	498;498;499;498	F5H851;F5H3Q5;Q14031;Q14031-2	.;.;CO4A6_HUMAN;.	S	499;498;499;498;498;498	ENSP00000361290:P499S;ENSP00000334733:P498S;ENSP00000378340:P499S;ENSP00000443707:P498S;ENSP00000445236:P498S	ENSP00000334733:P498S	P	-	1	0	COL4A6	107318498	0.999000	0.42202	0.983000	0.44433	0.813000	0.45954	2.554000	0.45845	1.061000	0.40601	0.600000	0.82982	CCA		0.592	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2		
COL4A6	1288	broad.mit.edu	37	X	107438317	107438317	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:107438317G>A	ENST00000372216.4	-	15	1046	c.946C>T	c.(946-948)Caa>Taa	p.Q316*	COL4A6_ENST00000545689.1_Nonsense_Mutation_p.Q315*|COL4A6_ENST00000394872.2_Intron|COL4A6_ENST00000334504.7_Nonsense_Mutation_p.Q315*|COL4A6_ENST00000538570.1_Nonsense_Mutation_p.Q315*	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	316	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)	p.Q315*(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						AATACCTGTTGCCCTGGAGGG	0.428									Alport syndrome with Diffuse Leiomyomatosis																												p.Q315X	Melanoma(87;1895 1945 2589 7165)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C943T	X						.						128.0	135.0	132.0					X																	107438317		2203	4300	6503	107324973	SO:0001587	stop_gained	1288	exon15	Familial Cancer Database		U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"""Collagens"""	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.946C>T	X.37:g.107438317G>A	ENSP00000361290:p.Gln316*	Somatic		Capture	Illumina HiSeq	Phase_I	107324973	NM_033641	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Nonsense_Mutation	SNP	ENST00000372216.4	37	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	G	36	5.631766	0.96682	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000541389;ENST00000545689;ENST00000538570	.	.	.	5.23	-0.155	0.13395	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	4.5293	0.11997	0.0:0.1845:0.3233:0.4922	.	.	.	.	X	316;315;315;315;315	.	ENSP00000334733:Q315X	Q	-	1	0	COL4A6	107324973	0.006000	0.16342	0.001000	0.08648	0.795000	0.44927	0.550000	0.23345	-0.204000	0.10235	-0.328000	0.08392	CAA		0.428	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2		
DCX	1641	broad.mit.edu	37	X	110555904	110555904	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:110555904G>A	ENST00000338081.3	-	6	1406	c.1235C>T	c.(1234-1236)aCg>aTg	p.T412M	DCX_ENST00000356220.3_Missense_Mutation_p.T336M|DCX_ENST00000371993.2_Missense_Mutation_p.T331M|DCX_ENST00000356915.2_Missense_Mutation_p.T336M|DCX_ENST00000488120.1_Missense_Mutation_p.T331M	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin	412	Pro/Ser-rich.				axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)	p.T412M(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						ACTGGTGGGCGTAGAGATGGG	0.493																																					p.T331M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C992T	X						.						150.0	109.0	123.0					X																	110555904		2203	4300	6503	110442560	SO:0001583	missense	1641	exon6			AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279			2714	protein-coding gene	gene with protein product	"""doublecortex"""	300121	"""doublecortex; lissencephaly, X-linked (doublecortin)"""			9489699, 9489700	Standard	NM_178151		Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000338081.3:c.1235C>T	X.37:g.110555904G>A	ENSP00000337697:p.Thr412Met	Somatic		Capture	Illumina HiSeq	Phase_I	110442560	NM_178153	A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	Missense_Mutation	SNP	ENST00000338081.3	37	CCDS14556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.6|25.6	4.651148|4.651148	0.88056|0.88056	.|.	.|.	ENSG00000077279|ENSG00000077279	ENST00000358070|ENST00000356915;ENST00000371993;ENST00000338081;ENST00000356220;ENST00000488120	.|T;T;T;T;T	.|0.24538	.|1.89;1.89;1.85;1.89;1.89	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	.|0.329120	.|0.31721	.|N	.|0.007168	T|T	0.36552|0.36552	0.0971|0.0971	N|N	0.22421|0.22421	0.69|0.69	0.54753|0.54753	D|D	0.999987|0.999987	.|D;D	.|0.71674	.|0.998;0.998	.|P;P	.|0.62184	.|0.815;0.899	T|T	0.12344|0.12344	-1.0551|-1.0551	5|10	.|0.46703	.|T	.|0.11	.|.	18.6926|18.6926	0.91589|0.91589	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|405;412	.|B4DM53;O43602	.|.;DCX_HUMAN	C|M	409|336;331;412;336;331	.|ENSP00000349385:T336M;ENSP00000361061:T331M;ENSP00000337697:T412M;ENSP00000348553:T336M;ENSP00000419861:T331M	.|ENSP00000337697:T412M	R|T	-|-	1|2	0|0	DCX|DCX	110442560|110442560	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.539000|7.539000	0.82063|0.82063	2.359000|2.359000	0.80004|0.80004	0.600000|0.600000	0.82982|0.82982	CGC|ACG		0.493	DCX-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357058.1	NM_178153	
DCX	1641	broad.mit.edu	37	X	110653528	110653528	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:110653528G>T	ENST00000338081.3	-	2	513	c.342C>A	c.(340-342)gcC>gcA	p.A114A	DCX_ENST00000356220.3_Silent_p.A33A|DCX_ENST00000496551.1_5'UTR|DCX_ENST00000371993.2_Silent_p.A33A|DCX_ENST00000356915.2_Silent_p.A33A|DCX_ENST00000488120.1_Silent_p.A33A	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin	114					axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)	p.A114A(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						AGCTACAGTGGGCGCTGTGAG	0.502																																					p.A33A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C99A	X						.						199.0	164.0	176.0					X																	110653528		2203	4300	6503	110540184	SO:0001819	synonymous_variant	1641	exon2			AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279			2714	protein-coding gene	gene with protein product	"""doublecortex"""	300121	"""doublecortex; lissencephaly, X-linked (doublecortin)"""			9489699, 9489700	Standard	NM_178151		Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000338081.3:c.342C>A	X.37:g.110653528G>T		Somatic		Capture	Illumina HiSeq	Phase_I	110540184	NM_178153	A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	Silent	SNP	ENST00000338081.3	37	CCDS14556.1	.	.	.	.	.	.	.	.	.	.	G	9.460	1.092730	0.20471	.	.	ENSG00000077279	ENST00000358070	.	.	.	5.37	2.25	0.28309	.	.	.	.	.	T	0.53883	0.1824	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40831	-0.9542	4	.	.	.	.	5.948	0.19229	0.2907:0.1323:0.577:0.0	.	.	.	.	H	106	.	.	P	-	2	0	DCX	110540184	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.565000	0.36386	0.105000	0.17753	0.513000	0.50165	CCC		0.502	DCX-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357058.1	NM_178153	
DCX	1641	broad.mit.edu	37	X	110654060	110654060	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:110654060T>C	ENST00000338081.3	-	1	314	c.143A>G	c.(142-144)cAt>cGt	p.H48R	DCX_ENST00000356220.3_Intron|DCX_ENST00000496551.1_Intron|DCX_ENST00000371993.2_Intron|DCX_ENST00000356915.2_Intron|DCX_ENST00000488120.1_Intron	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin	48					axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)	p.H48R(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						CATGCCCACATGACTAACAGT	0.433																																					p.H48R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A143G	X						.						211.0	185.0	194.0					X																	110654060		2203	4300	6503	110540716	SO:0001583	missense	1641	exon1			AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279			2714	protein-coding gene	gene with protein product	"""doublecortex"""	300121	"""doublecortex; lissencephaly, X-linked (doublecortin)"""			9489699, 9489700	Standard	NM_178151		Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000338081.3:c.143A>G	X.37:g.110654060T>C	ENSP00000337697:p.His48Arg	Somatic		Capture	Illumina HiSeq	Phase_I	110540716	NM_000555	A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	Missense_Mutation	SNP	ENST00000338081.3	37	CCDS14556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	11.07|11.07	1.531138|1.531138	0.27387|0.27387	.|.	.|.	ENSG00000077279|ENSG00000077279	ENST00000338081|ENST00000358070	T|.	0.26223|.	1.75|.	4.4|4.4	3.24|3.24	0.37175|0.37175	.|.	0.170580|.	0.28425|.	N|.	0.015388|.	T|T	0.31796|0.31796	0.0808|0.0808	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.05084|0.05084	-1.0907|-1.0907	10|5	0.87932|.	D|.	0|.	.|.	8.1903|8.1903	0.31363|0.31363	0.0:0.0944:0.0:0.9056|0.0:0.0944:0.0:0.9056	.|.	36;48|.	B4DM53;O43602|.	.;DCX_HUMAN|.	R|V	48|40	ENSP00000337697:H48R|.	ENSP00000337697:H48R|.	H|M	-|-	2|1	0|0	DCX|DCX	110540716|110540716	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.024000|2.024000	0.41049|0.41049	0.822000|0.822000	0.34565|0.34565	0.411000|0.411000	0.27672|0.27672	CAT|ATG		0.433	DCX-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357058.1	NM_178153	
LHFPL1	340596	broad.mit.edu	37	X	111914528	111914528	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:111914528A>G	ENST00000371968.3	-	2	330	c.91T>C	c.(91-93)Tac>Cac	p.Y31H	LHFPL1_ENST00000478229.1_Intron|LHFPL1_ENST00000536453.1_Missense_Mutation_p.Y31H	NM_178175.3	NP_835469.1	Q86WI0	LHPL1_HUMAN	lipoma HMGIC fusion partner-like 1	31						integral component of membrane (GO:0016021)		p.Y31H(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)	13						AAGAGCCAGTAAGGTAGGAAG	0.552																																					p.Y31H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T91C	X						.						159.0	149.0	153.0					X																	111914528		2203	4300	6503	111801184	SO:0001583	missense	340596	exon2			AY217350	CCDS14562.1	Xq23	2008-02-05			ENSG00000182508	ENSG00000182508			6587	protein-coding gene	gene with protein product		300566				10329012	Standard	NM_178175		Approved		uc004epq.3	Q86WI0	OTTHUMG00000022214	ENST00000371968.3:c.91T>C	X.37:g.111914528A>G	ENSP00000361036:p.Tyr31His	Somatic		Capture	Illumina HiSeq	Phase_I	111801184	NM_178175	A8K1N1|Q496M9|Q496N0|Q6UXU2	Missense_Mutation	SNP	ENST00000371968.3	37	CCDS14562.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.110848	0.77210	.	.	ENSG00000182508	ENST00000371968;ENST00000536453	T;T	0.72394	-0.65;-0.65	5.44	5.44	0.79542	.	0.057470	0.64402	D	0.000001	T	0.80879	0.4708	M	0.73217	2.22	0.58432	D	0.999996	D;D	0.76494	0.999;0.999	D;D	0.85130	0.994;0.997	T	0.78076	-0.2345	10	0.19590	T	0.45	-37.9188	12.2174	0.54414	1.0:0.0:0.0:0.0	.	31;31	Q86WI0-2;Q86WI0	.;LHPL1_HUMAN	H	31	ENSP00000361036:Y31H;ENSP00000444573:Y31H	ENSP00000361036:Y31H	Y	-	1	0	LHFPL1	111801184	1.000000	0.71417	0.999000	0.59377	0.965000	0.64279	8.761000	0.91691	2.015000	0.59207	0.486000	0.48141	TAC		0.552	LHFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057947.1	NM_178175	
LONRF3	79836	broad.mit.edu	37	X	118151531	118151531	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:118151531A>T	ENST00000371628.3	+	11	2189	c.2158A>T	c.(2158-2160)Atg>Ttg	p.M720L	LONRF3_ENST00000304778.7_Missense_Mutation_p.M679L|LONRF3_ENST00000472173.1_3'UTR|LONRF3_ENST00000422289.2_Missense_Mutation_p.M464L	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	720	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)	p.M679L(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						GTGCTGGTGGATGTTAGCAGT	0.507																																					p.M679L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2035T	X						.						153.0	129.0	137.0					X																	118151531		2203	4300	6503	118035559	SO:0001583	missense	79836	exon10			AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"""RING-type (C3HC4) zinc fingers"""	21152	protein-coding gene	gene with protein product			"""ring finger protein 127"""	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.2158A>T	X.37:g.118151531A>T	ENSP00000360690:p.Met720Leu	Somatic		Capture	Illumina HiSeq	Phase_I	118035559	NM_024778	Q5JPN6|Q8NB00|Q9H647	Missense_Mutation	SNP	ENST00000371628.3	37	CCDS35374.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	2.252|2.252	-0.371389|-0.371389	0.05034|0.05034	.|.	.|.	ENSG00000175556|ENSG00000175556	ENST00000439603|ENST00000365713;ENST00000304778;ENST00000371628;ENST00000422289	.|T;T;T;T	.|0.38240	.|1.15;1.15;1.15;1.15	5.62|5.62	3.19|3.19	0.36642|0.36642	.|Peptidase S16, lon N-terminal (1);PUA-like domain (1);	.|0.821552	.|0.11289	.|N	.|0.579488	T|T	0.09730|0.09730	0.0239|0.0239	N|N	0.01081|0.01081	-1.03|-1.03	0.21499|0.21499	N|N	0.999667|0.999667	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.04013	.|0.001;0.0;0.0	T|T	0.35822|0.35822	-0.9773|-0.9773	5|10	.|0.05436	.|T	.|0.98	-27.0846|-27.0846	4.3729|4.3729	0.11256|0.11256	0.6586:0.1832:0.1582:0.0|0.6586:0.1832:0.1582:0.0	.|.	.|464;679;720	.|B3KUN7;Q496Y0-2;Q496Y0	.|.;.;LONF3_HUMAN	V|L	485|679;679;720;464	.|ENSP00000360691:M679L;ENSP00000307732:M679L;ENSP00000360690:M720L;ENSP00000408894:M464L	.|ENSP00000307732:M679L	D|M	+|+	2|1	0|0	LONRF3|LONRF3	118035559|118035559	0.989000|0.989000	0.36119|0.36119	0.733000|0.733000	0.30861|0.30861	0.974000|0.974000	0.67602|0.67602	0.963000|0.963000	0.29293|0.29293	0.730000|0.730000	0.32425|0.32425	0.483000|0.483000	0.47432|0.47432	GAT|ATG		0.507	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778	
NKRF	55922	broad.mit.edu	37	X	118724904	118724904	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:118724904A>T	ENST00000371527.1	-	2	1136	c.484T>A	c.(484-486)Ttt>Att	p.F162I	NKRF_ENST00000304449.5_Missense_Mutation_p.F162I|NKRF_ENST00000487600.1_Intron|NKRF_ENST00000542113.1_Missense_Mutation_p.F177I	NM_001173488.1	NP_001166959.1	O15226	NKRF_HUMAN	NFKB repressing factor	162	Active repression domain.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.F162I(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	30						GACTCGGGAAATGTCTGTGAT	0.458																																					p.F177I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T529A	X						.						105.0	92.0	97.0					X																	118724904		2203	4300	6503	118608932	SO:0001583	missense	55922	exon4			AJ011812	CCDS35375.1, CCDS55486.1	Xq24	2013-01-28	2008-03-26		ENSG00000186416	ENSG00000186416		"""G patch domain containing"""	19374	protein-coding gene	gene with protein product		300440	"""NF-kappaB repressing factor"""			10562553	Standard	NM_017544		Approved	ITBA4, NRF	uc022cdk.1	O15226	OTTHUMG00000022277	ENST00000371527.1:c.484T>A	X.37:g.118724904A>T	ENSP00000360582:p.Phe162Ile	Somatic		Capture	Illumina HiSeq	Phase_I	118608932	NM_001173487	G3V1N1|Q4VC41|Q9UJ91	Missense_Mutation	SNP	ENST00000371527.1	37	CCDS35375.1	.	.	.	.	.	.	.	.	.	.	A	11.38	1.620928	0.28889	.	.	ENSG00000186416	ENST00000371527;ENST00000304449;ENST00000542113	T;T;T	0.42900	0.96;0.96;0.96	5.69	5.69	0.88448	.	0.390603	0.26635	N	0.023297	T	0.28830	0.0715	N	0.24115	0.695	0.28772	N	0.900322	B	0.11235	0.004	B	0.08055	0.003	T	0.16158	-1.0412	10	0.46703	T	0.11	-5.7869	9.4721	0.38849	0.8402:0.0:0.0:0.1598	.	162	O15226	NKRF_HUMAN	I	162;162;177	ENSP00000360582:F162I;ENSP00000304803:F162I;ENSP00000442308:F177I	ENSP00000304803:F162I	F	-	1	0	NKRF	118608932	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	4.574000	0.60900	1.910000	0.55303	0.481000	0.45027	TTT		0.458	NKRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058044.1	NM_017544	
CUL4B	8450	broad.mit.edu	37	X	119674340	119674340	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:119674340C>A	ENST00000404115.3	-	13	1976	c.1575G>T	c.(1573-1575)aaG>aaT	p.K525N	CUL4B_ENST00000336592.6_Missense_Mutation_p.K512N|CUL4B_ENST00000371322.5_Missense_Mutation_p.K507N	NM_003588.3	NP_003579.3	Q13620	CUL4B_HUMAN	cullin 4B	525					cell cycle (GO:0007049)|histone H2A monoubiquitination (GO:0035518)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of protein catabolic process (GO:0045732)|ubiquitin-dependent protein catabolic process (GO:0006511)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.K507N(1)|p.K525N(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TATGGTCAACCTTATCTTTAA	0.299																																					p.K507N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1521T	X						.						105.0	94.0	98.0					X																	119674340		2201	4295	6496	119558368	SO:0001583	missense	8450	exon11			U58091	CCDS35379.1, CCDS43987.1	Xq23	2011-05-24			ENSG00000158290	ENSG00000158290			2555	protein-coding gene	gene with protein product		300304				8681378	Standard	NM_003588		Approved		uc004esw.3	Q13620	OTTHUMG00000022302	ENST00000404115.3:c.1575G>T	X.37:g.119674340C>A	ENSP00000384109:p.Lys525Asn	Somatic		Capture	Illumina HiSeq	Phase_I	119558368	NM_001079872	B1APK5|B3KVX4|B7Z5K8|Q6PIE4|Q6UP07|Q7Z673|Q9BY37|Q9UEB7|Q9UED7	Missense_Mutation	SNP	ENST00000404115.3	37	CCDS35379.1	.	.	.	.	.	.	.	.	.	.	C	8.447	0.852219	0.17106	.	.	ENSG00000158290	ENST00000371322;ENST00000336592;ENST00000404115	T;T;T	0.79653	-1.29;-1.29;-1.29	5.6	0.146	0.14833	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.78233	0.4251	M	0.75615	2.305	0.80722	D	1	B;P;P	0.37466	0.146;0.596;0.541	B;B;B	0.40444	0.161;0.329;0.221	T	0.72401	-0.4305	9	.	.	.	-12.675	10.0995	0.42495	0.0:0.3279:0.0:0.6721	.	329;525;507	Q13620-3;Q13620;Q13620-1	.;CUL4B_HUMAN;.	N	507;512;525	ENSP00000360373:K507N;ENSP00000338919:K512N;ENSP00000384109:K525N	.	K	-	3	2	CUL4B	119558368	0.661000	0.27430	0.999000	0.59377	0.034000	0.12701	-0.122000	0.10627	-0.012000	0.14223	-0.297000	0.09499	AAG		0.299	CUL4B-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058103.1	NM_003588	
MCTS1	28985	broad.mit.edu	37	X	119746061	119746061	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:119746061G>A	ENST00000371317.5	+	6	745	c.488G>A	c.(487-489)gGc>gAc	p.G163D	MCTS1_ENST00000371315.3_Missense_Mutation_p.G164D|MCTS1_ENST00000487133.1_3'UTR	NM_014060.2	NP_054779.1	Q9ULC4	MCTS1_HUMAN	malignant T cell amplified sequence 1	163	PUA. {ECO:0000255|PROSITE- ProRule:PRU00161}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|formation of translation preinitiation complex (GO:0001731)|IRES-dependent translational initiation (GO:0002192)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|ribosome disassembly (GO:0032790)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	translation initiation factor activity (GO:0003743)	p.G163D(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|stomach(1)|urinary_tract(1)	10						AAAGGAATTGGCATTGAAAAT	0.318																																					p.G164D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G491A	X						.						110.0	112.0	111.0					X																	119746061		2203	4300	6503	119630089	SO:0001583	missense	28985	exon6			AB034206	CCDS14601.1, CCDS48160.1	Xq24	2008-05-14			ENSG00000232119	ENSG00000232119			23357	protein-coding gene	gene with protein product		300587				9766643	Standard	NM_014060		Approved	MCT-1	uc011mub.2	Q9ULC4	OTTHUMG00000022303	ENST00000371317.5:c.488G>A	X.37:g.119746061G>A	ENSP00000360367:p.Gly163Asp	Somatic		Capture	Illumina HiSeq	Phase_I	119630089	NM_001137554	B4DGY2|Q502X6	Missense_Mutation	SNP	ENST00000371317.5	37	CCDS14601.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.171244	0.78452	.	.	ENSG00000232119	ENST00000371317;ENST00000371315	D;D	0.91068	-2.78;-2.78	5.55	5.55	0.83447	Uncharacterised domain CHP00451 (1);Pseudouridine synthase/archaeosine transglycosylase (3);PUA-like domain (1);	0.000000	0.85682	D	0.000000	D	0.94545	0.8243	H	0.95079	3.62	0.80722	D	1	P;P	0.40230	0.66;0.708	B;B	0.42738	0.275;0.396	D	0.95410	0.8497	9	.	.	.	-1.813	17.3822	0.87408	0.0:0.0:1.0:0.0	.	164;163	Q9ULC4-3;Q9ULC4	.;MCTS1_HUMAN	D	163;164	ENSP00000360367:G163D;ENSP00000360365:G164D	.	G	+	2	0	MCTS1	119630089	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.793000	0.99091	2.317000	0.78254	0.600000	0.82982	GGC		0.318	MCTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058110.1	NM_014060	
TLR7	51284	broad.mit.edu	37	X	12905356	12905356	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:12905356A>C	ENST00000380659.3	+	3	1868	c.1729A>C	c.(1729-1731)Agc>Cgc	p.S577R		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	577					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)	p.S577R(1)		NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	AAGCAGTAATAGCCATTATTT	0.378																																					p.S577R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1729C	X						.						124.0	133.0	130.0					X																	12905356		2203	4300	6503	12815277	SO:0001583	missense	51284	exon3			AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.1729A>C	X.37:g.12905356A>C	ENSP00000370034:p.Ser577Arg	Somatic		Capture	Illumina HiSeq	Phase_I	12815277	NM_016562	D1CS69|Q9NR98	Missense_Mutation	SNP	ENST00000380659.3	37	CCDS14151.1	.	.	.	.	.	.	.	.	.	.	A	15.31	2.796449	0.50208	.	.	ENSG00000196664	ENST00000380659	T	0.79247	-1.25	5.84	4.54	0.55810	.	0.425737	0.26187	N	0.025839	T	0.76579	0.4007	L	0.41961	1.31	0.36957	D	0.893168	P	0.42248	0.774	P	0.49597	0.616	T	0.78879	-0.2030	10	0.72032	D	0.01	.	8.4305	0.32755	0.8369:0.0:0.1631:0.0	.	577	Q9NYK1	TLR7_HUMAN	R	577	ENSP00000370034:S577R	ENSP00000370034:S577R	S	+	1	0	TLR7	12815277	0.999000	0.42202	0.996000	0.52242	0.959000	0.62525	3.161000	0.50747	0.701000	0.31803	0.486000	0.48141	AGC		0.378	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562	
XIAP	331	broad.mit.edu	37	X	123019982	123019982	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:123019982A>G	ENST00000371199.3	+	2	769	c.470A>G	c.(469-471)aAc>aGc	p.N157S	XIAP_ENST00000434753.3_Missense_Mutation_p.N157S|XIAP_ENST00000355640.3_Missense_Mutation_p.N157S|XIAP_ENST00000468691.1_Intron	NM_001167.3	NP_001158.2	P98170	XIAP_HUMAN	X-linked inhibitor of apoptosis	157					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|copper ion homeostasis (GO:0055070)|inhibition of cysteine-type endopeptidase activity involved in apoptotic process (GO:1990001)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of protein ubiquitination (GO:0031398)|protein ubiquitination (GO:0016567)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N157S(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)	25						TACCCGAGGAACCCTGCCATG	0.453									X-linked Lymphoproliferative syndrome																												p.N157S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A470G	X						.						92.0	87.0	89.0					X																	123019982		2203	4300	6503	122847663	SO:0001583	missense	331	exon2	Familial Cancer Database	XLP, Duncan syndrome, Familial Fatal Epstein-Barr Infection, incl. XLP2	U45880	CCDS14606.1	Xq25	2014-09-17	2008-03-04	2008-03-04	ENSG00000101966	ENSG00000101966		"""Baculoviral IAP repeat containing"""	592	protein-coding gene	gene with protein product		300079	"""baculoviral IAP repeat-containing 4"""	API3, BIRC4		8552191, 8654366	Standard	NM_001167		Approved	hILP	uc010nqu.3	P98170	OTTHUMG00000022336	ENST00000371199.3:c.470A>G	X.37:g.123019982A>G	ENSP00000360242:p.Asn157Ser	Somatic		Capture	Illumina HiSeq	Phase_I	122847663	NM_001167	D3DTF2|Q9NQ14	Missense_Mutation	SNP	ENST00000371199.3	37	CCDS14606.1	.	.	.	.	.	.	.	.	.	.	A	7.390	0.630488	0.14322	.	.	ENSG00000101966	ENST00000434753;ENST00000371199;ENST00000355640	T;T;T	0.72615	-0.67;-0.67;-0.67	5.74	4.56	0.56223	Baculoviral inhibition of apoptosis protein repeat (1);	0.136918	0.50627	D	0.000120	T	0.65616	0.2708	M	0.64997	1.995	0.26686	N	0.971445	B	0.23377	0.084	B	0.14023	0.01	T	0.54569	-0.8274	9	.	.	.	-3.8698	12.1804	0.54208	0.8591:0.1409:0.0:0.0	.	157	P98170	XIAP_HUMAN	S	157	ENSP00000395230:N157S;ENSP00000360242:N157S;ENSP00000347858:N157S	.	N	+	2	0	XIAP	122847663	0.640000	0.27243	0.997000	0.53966	0.985000	0.73830	1.084000	0.30828	0.785000	0.33685	0.413000	0.27773	AAC		0.453	XIAP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058165.5	NM_001167	
GPC4	2239	broad.mit.edu	37	X	132437023	132437023	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:132437023C>T	ENST00000370828.3	-	9	2067	c.1543G>A	c.(1543-1545)Gcc>Acc	p.A515T	GPC4_ENST00000535467.1_Missense_Mutation_p.A445T	NM_001448.2	NP_001439.2	O75487	GPC4_HUMAN	glypican 4	515					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.A515T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;0.000127)					TGGTCAGTGGCATTGTAGTCA	0.483																																					p.A515T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1543A	X						.						259.0	222.0	234.0					X																	132437023		2203	4300	6503	132264689	SO:0001583	missense	2239	exon9			AF030186	CCDS14637.1	Xq26.1	2008-02-05			ENSG00000076716	ENSG00000076716		"""Proteoglycans / Cell Surface : Glypicans"""	4452	protein-coding gene	gene with protein product	"""glypican proteoglycan 4"""	300168				9787072	Standard	NM_001448		Approved	K-glypican	uc004exc.1	O75487	OTTHUMG00000022434	ENST00000370828.3:c.1543G>A	X.37:g.132437023C>T	ENSP00000359864:p.Ala515Thr	Somatic		Capture	Illumina HiSeq	Phase_I	132264689	NM_001448	B2R6J7|B4E2C0|Q6ZMA6|Q96L43|Q9NU08|Q9UJN1|Q9UPD9	Missense_Mutation	SNP	ENST00000370828.3	37	CCDS14637.1	.	.	.	.	.	.	.	.	.	.	c	0.084	-1.178454	0.01633	.	.	ENSG00000076716	ENST00000370828;ENST00000536418;ENST00000535467	T;T	0.49432	0.78;0.78	5.63	4.77	0.60923	.	0.680336	0.16186	N	0.225623	T	0.20007	0.0481	N	0.02539	-0.55	0.18873	N	0.999989	B	0.02656	0.0	B	0.04013	0.001	T	0.20042	-1.0287	10	0.09590	T	0.72	-18.0128	9.1826	0.37152	0.0:0.8322:0.0:0.1678	.	515	O75487	GPC4_HUMAN	T	515;509;445	ENSP00000359864:A515T;ENSP00000444959:A445T	ENSP00000359864:A515T	A	-	1	0	GPC4	132264689	0.010000	0.17322	0.709000	0.30452	0.170000	0.22686	2.403000	0.44530	1.137000	0.42214	0.597000	0.82753	GCC		0.483	GPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058338.1	NM_001448	
CCDC160	347475	broad.mit.edu	37	X	133379644	133379644	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:133379644G>A	ENST00000517294.1	+	3	1197	c.814G>A	c.(814-816)Gca>Aca	p.A272T	CCDC160_ENST00000370809.4_Missense_Mutation_p.A272T			A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	272								p.A272T(1)		endometrium(1)|kidney(2)|large_intestine(10)|lung(2)|prostate(1)|skin(1)	17						ATTAGAAATGGCAAAGATCCG	0.378																																					p.A272T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G814A	X						.						37.0	34.0	35.0					X																	133379644		1830	4070	5900	133207310	SO:0001583	missense	347475	exon2			BC017958	CCDS48171.1	Xq26.2	2010-02-17			ENSG00000203952	ENSG00000203952			37286	protein-coding gene	gene with protein product							Standard	NM_001101357		Approved		uc011mvj.2	A6NGH7	OTTHUMG00000164183	ENST00000517294.1:c.814G>A	X.37:g.133379644G>A	ENSP00000427951:p.Ala272Thr	Somatic		Capture	Illumina HiSeq	Phase_I	133207310	NM_001101357		Missense_Mutation	SNP	ENST00000517294.1	37	CCDS48171.1	.	.	.	.	.	.	.	.	.	.	G	7.060	0.566194	0.13560	.	.	ENSG00000203952	ENST00000517294;ENST00000370809	D;D	0.90504	-2.68;-2.68	5.29	4.18	0.49190	.	0.611359	0.14640	N	0.307251	T	0.75852	0.3906	N	0.08118	0	0.09310	N	1	B	0.32160	0.358	B	0.29716	0.106	T	0.63488	-0.6626	10	0.21540	T	0.41	-11.6255	4.0512	0.09796	0.3432:0.0:0.6568:0.0	.	272	A6NGH7	CC160_HUMAN	T	272	ENSP00000427951:A272T;ENSP00000359845:A272T	ENSP00000359845:A272T	A	+	1	0	CCDC160	133207310	0.603000	0.26924	0.115000	0.21578	0.079000	0.17450	1.097000	0.30988	2.334000	0.79466	0.513000	0.50165	GCA		0.378	CCDC160-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377679.1	NM_001101357	
MOSPD1	56180	broad.mit.edu	37	X	134023214	134023214	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:134023214T>C	ENST00000370783.3	-	6	805	c.619A>G	c.(619-621)Aca>Gca	p.T207A	MOSPD1_ENST00000491609.1_5'UTR|MOSPD1_ENST00000370777.1_Missense_Mutation_p.T208A|MOSPD1_ENST00000370779.4_Missense_Mutation_p.T153A	NM_019556.1	NP_062456.1	Q9UJG1	MSPD1_HUMAN	motile sperm domain containing 1	207					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)	p.T207A(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(1)|ovary(1)	9	Acute lymphoblastic leukemia(192;0.000127)					ATGGCCATTGTGATAAGACCT	0.338																																					p.T207A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A619G	X						.						129.0	107.0	115.0					X																	134023214		2203	4300	6503	133850880	SO:0001583	missense	56180	exon6			Z83826	CCDS14645.1	Xq26.3	2008-02-05			ENSG00000101928	ENSG00000101928			25235	protein-coding gene	gene with protein product		300674				15533722	Standard	XM_005262446		Approved	dJ473B4	uc004eyb.3	Q9UJG1	OTTHUMG00000035315	ENST00000370783.3:c.619A>G	X.37:g.134023214T>C	ENSP00000359819:p.Thr207Ala	Somatic		Capture	Illumina HiSeq	Phase_I	133850880	NM_019556	B2RE62|D3DTG5|Q5H9C5|Q5H9C7	Missense_Mutation	SNP	ENST00000370783.3	37	CCDS14645.1	.	.	.	.	.	.	.	.	.	.	T	3.854	-0.031283	0.07543	.	.	ENSG00000101928	ENST00000370783;ENST00000370779;ENST00000370777	.	.	.	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.76821	0.4041	M	0.66297	2.02	0.80722	D	1	D;D	0.63880	0.993;0.99	P;D	0.70935	0.706;0.971	T	0.78186	-0.2302	9	0.54805	T	0.06	-7.1472	14.5798	0.68278	0.0:0.0:0.0:1.0	.	207;153	Q9UJG1;Q9UJG1-2	MSPD1_HUMAN;.	A	207;153;208	.	ENSP00000359813:T208A	T	-	1	0	MOSPD1	133850880	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	6.562000	0.73960	2.043000	0.60533	0.481000	0.45027	ACA		0.338	MOSPD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000085439.1	NM_019556	
ZNF75D	7626	broad.mit.edu	37	X	134424935	134424935	+	Splice_Site	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:134424935C>A	ENST00000370766.3	-	6	3532	c.823G>T	c.(823-825)Ggg>Tgg	p.G275W	ZNF75D_ENST00000494295.1_Intron|ZNF75D_ENST00000370764.1_Splice_Site_p.G180W	NM_007131.3	NP_009062.2	P51815	ZN75D_HUMAN	zinc finger protein 75D	275	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G275W(1)		autonomic_ganglia(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(14)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						GAATCTTTACCTAGAGAGATG	0.383																																					p.G275W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G823T	X						.						127.0	122.0	124.0					X																	134424935		2203	4300	6503	134252601	SO:0001630	splice_region_variant	7626	exon5			S43109	CCDS14648.1, CCDS55503.1	Xq26	2013-01-09	2008-06-11	2008-06-11	ENSG00000186376	ENSG00000186376		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13145	protein-coding gene	gene with protein product		314997	"""zinc finger protein 75 (D8C6)"""	ZNF82, ZNF75		1505955	Standard	XM_005262469		Approved	ZKSCAN24, D8C6, ZSCAN28	uc004eyo.3	P51815	OTTHUMG00000022482	ENST00000370766.3:c.823+1G>T	X.37:g.134424935C>A		Somatic		Capture	Illumina HiSeq	Phase_I	134252601	NM_007131	A6NK62|B3KRI7|Q5JPG0|Q6LDE0	Missense_Mutation	SNP	ENST00000370766.3	37	CCDS14648.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.292197	0.40594	.	.	ENSG00000186376	ENST00000370766;ENST00000370764	T;T	0.03004	4.08;4.08	2.78	2.78	0.32641	Krueppel-associated box (4);	.	.	.	.	T	0.22360	0.0539	M	0.93808	3.46	0.22317	N	0.999201	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.03374	-1.1043	8	.	.	.	.	8.277	0.31879	0.0:1.0:0.0:0.0	.	275;180	P51815;A6NK62	ZN75D_HUMAN;.	W	275;180	ENSP00000359802:G275W;ENSP00000359800:G180W	.	G	-	1	0	ZNF75D	134252601	1.000000	0.71417	0.518000	0.27811	0.049000	0.14656	3.839000	0.55835	1.668000	0.50843	0.513000	0.50165	GGG		0.383	ZNF75D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058415.1	NM_007131	Missense_Mutation
DDX26B	203522	broad.mit.edu	37	X	134713720	134713720	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:134713720T>C	ENST00000370752.4	+	15	2350	c.2016T>C	c.(2014-2016)acT>acC	p.T672T	DDX26B_ENST00000481908.1_3'UTR	NM_182540.4	NP_872346.3	Q5JSJ4	DX26B_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26B	672								p.T672T(1)		large_intestine(1)|lung(8)	9	Acute lymphoblastic leukemia(192;6.56e-05)					CAGATGCTACTATCATTCACG	0.423																																					p.T672T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2016C	X						.						78.0	74.0	75.0					X																	134713720		2203	4300	6503	134541386	SO:0001819	synonymous_variant	203522	exon15			AK096544	CCDS35401.1	Xq26	2008-02-05			ENSG00000165359	ENSG00000165359		"""DEAD-boxes"""	27334	protein-coding gene	gene with protein product							Standard	NM_182540		Approved	FLJ41215	uc004eyw.4	Q5JSJ4	OTTHUMG00000022484	ENST00000370752.4:c.2016T>C	X.37:g.134713720T>C		Somatic		Capture	Illumina HiSeq	Phase_I	134541386	NM_182540	Q5CZA2|Q6IPS3|Q6ZTU5|Q6ZWE4	Silent	SNP	ENST00000370752.4	37	CCDS35401.1																																																																																				0.423	DDX26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058420.1	NM_182540	
EGFL6	25975	broad.mit.edu	37	X	13636106	13636106	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:13636106G>T	ENST00000361306.1	+	8	1293	c.1036G>T	c.(1036-1038)Gag>Tag	p.E346*	EGFL6_ENST00000380602.3_Nonsense_Mutation_p.E346*	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	346					cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)	p.E346*(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						GCTTGAGGATGAGAAAAGAGA	0.408																																					p.E346X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1036T	X						.						52.0	55.0	54.0					X																	13636106		2203	4300	6503	13546027	SO:0001587	stop_gained	25975	exon8			AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"""MAM and EGF domain containing"""	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.1036G>T	X.37:g.13636106G>T	ENSP00000355126:p.Glu346*	Somatic		Capture	Illumina HiSeq	Phase_I	13546027	NM_001167890	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Nonsense_Mutation	SNP	ENST00000361306.1	37	CCDS14155.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.453493	0.84209	.	.	ENSG00000198759	ENST00000361306;ENST00000380602	.	.	.	5.49	3.74	0.42951	.	0.686478	0.15092	N	0.281019	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	.	11.6774	0.51438	0.148:0.0:0.852:0.0	.	.	.	.	X	346	.	ENSP00000355126:E346X	E	+	1	0	EGFL6	13546027	1.000000	0.71417	0.011000	0.14972	0.007000	0.05969	3.718000	0.54919	0.518000	0.28383	-0.204000	0.12730	GAG		0.408	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	NM_015507	
SLC9A6	10479	broad.mit.edu	37	X	135067766	135067766	+	Silent	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:135067766C>T	ENST00000370698.3	+	1	140	c.105C>T	c.(103-105)ggC>ggT	p.G35G	SLC9A6_ENST00000370701.1_5'UTR|SLC9A6_ENST00000370695.4_Silent_p.G35G	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6	35					axon extension (GO:0048675)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|dendrite extension (GO:0097484)|dendritic spine development (GO:0060996)|ion transport (GO:0006811)|neuron projection morphogenesis (GO:0048812)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon terminus (GO:0043679)|axonal spine (GO:0044308)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)	sodium:proton antiporter activity (GO:0015385)	p.G35G(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(18)|ovary(2)|upper_aerodigestive_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					TCGCAGTGGGCGTCTTTGACT	0.721																																					p.G35G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C105T	X						.						31.0	35.0	33.0					X																	135067766		2203	4299	6502	134895432	SO:0001819	synonymous_variant	10479	exon1			AF030409	CCDS14654.1, CCDS44003.1, CCDS55504.1	Xq26.3	2013-05-22	2012-03-22		ENSG00000198689	ENSG00000198689		"""Solute carriers"""	11079	protein-coding gene	gene with protein product		300231	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 6"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 6"""			9507001	Standard	NM_001042537		Approved	NHE6, KIAA0267	uc004ezk.3	Q92581	OTTHUMG00000022498	ENST00000370698.3:c.105C>T	X.37:g.135067766C>T		Somatic		Capture	Illumina HiSeq	Phase_I	134895432	NM_006359	A6NIQ9|A8K160|B4DU30|B7ZAE0|Q3ZCW7|Q5JPP8|Q5JPP9|Q86VS0	Silent	SNP	ENST00000370698.3	37	CCDS14654.1																																																																																				0.721	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058450.1	NM_006359	
TCEANC	170082	broad.mit.edu	37	X	13681448	13681448	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:13681448C>T	ENST00000380600.1	+	2	908	c.821C>T	c.(820-822)aCg>aTg	p.T274M	TCEANC_ENST00000545566.1_Missense_Mutation_p.T274M|TCEANC_ENST00000490617.1_3'UTR|TCEANC_ENST00000544987.1_Missense_Mutation_p.T274M|TCEANC_ENST00000314720.4_Missense_Mutation_p.T304M			Q8N8B7	TEANC_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing	274	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T274M(2)		central_nervous_system(1)|large_intestine(5)|lung(2)|pancreas(1)	9						GCCTCCTACACGGAATCTTGT	0.428																																					p.T304M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C911T	X						.						24.0	22.0	23.0					X																	13681448		1893	4098	5991	13591369	SO:0001583	missense	170082	exon4				CCDS48081.1, CCDS75954.1	Xp22.2	2009-01-30			ENSG00000176896	ENSG00000176896			28277	protein-coding gene	gene with protein product						12477932	Standard	XM_005274454		Approved	MGC17403	uc010neg.1	Q8N8B7	OTTHUMG00000021154	ENST00000380600.1:c.821C>T	X.37:g.13681448C>T	ENSP00000369974:p.Thr274Met	Somatic		Capture	Illumina HiSeq	Phase_I	13591369	NM_152634	A6NI06|B2RDM3	Missense_Mutation	SNP	ENST00000380600.1	37		.	.	.	.	.	.	.	.	.	.	C	15.96	2.986497	0.53934	.	.	ENSG00000176896	ENST00000545566;ENST00000544987;ENST00000314720;ENST00000380600	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.41	3.63	0.41609	Transcription elongation factor S-II, central domain (2);	0.143817	0.44285	N	0.000463	T	0.54838	0.1883	M	0.89840	3.065	0.37933	D	0.932076	D;D	0.58268	0.982;0.96	B;B	0.42188	0.379;0.375	T	0.66085	-0.6011	10	0.49607	T	0.09	.	11.6807	0.51455	0.0:0.8506:0.0:0.1494	.	304;274	Q8N8B7-2;Q8N8B7	.;TEANC_HUMAN	M	274;274;304;274	ENSP00000438952:T274M;ENSP00000440038:T274M;ENSP00000313886:T304M;ENSP00000369974:T274M	ENSP00000313886:T304M	T	+	2	0	TCEANC	13591369	0.997000	0.39634	0.419000	0.26584	0.965000	0.64279	3.565000	0.53798	0.476000	0.27440	0.600000	0.82982	ACG		0.428	TCEANC-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000055796.1	NM_152634	
ARHGEF6	9459	broad.mit.edu	37	X	135757208	135757208	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:135757208C>T	ENST00000250617.6	-	19	3198	c.1993G>A	c.(1993-1995)Gcc>Acc	p.A665T	ARHGEF6_ENST00000370622.1_Missense_Mutation_p.A511T|ARHGEF6_ENST00000370620.1_Missense_Mutation_p.A511T|ARHGEF6_ENST00000535227.1_Missense_Mutation_p.A538T	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	665					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A665T(1)		cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					GTGCAGTAGGCTTCGATCACT	0.423																																					p.A665T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1993A	X						.						165.0	140.0	148.0					X																	135757208		2203	4300	6503	135584874	SO:0001583	missense	9459	exon19			D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	685	protein-coding gene	gene with protein product	"""Rac/Cdc42 guanine exchange factor (GEF) 6"", ""PAK-interacting exchange factor, alpha"", ""rho guanine nucleotide exchange factor 6"""	300267	"""mental retardation, X-linked 46"""	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.1993G>A	X.37:g.135757208C>T	ENSP00000250617:p.Ala665Thr	Somatic		Capture	Illumina HiSeq	Phase_I	135584874	NM_004840	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Missense_Mutation	SNP	ENST00000250617.6	37	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.064044	0.76187	.	.	ENSG00000129675	ENST00000250617;ENST00000370620;ENST00000370622;ENST00000535736;ENST00000535227	T;T;T;T	0.60040	0.25;0.36;0.36;0.22	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.78648	0.4316	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.81395	-0.0952	10	0.72032	D	0.01	.	18.6464	0.91411	0.0:1.0:0.0:0.0	.	538;665	B7Z3C7;Q15052	.;ARHG6_HUMAN	T	665;511;511;511;538	ENSP00000250617:A665T;ENSP00000359654:A511T;ENSP00000359656:A511T;ENSP00000439483:A538T	ENSP00000250617:A665T	A	-	1	0	ARHGEF6	135584874	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	7.153000	0.77428	2.347000	0.79759	0.600000	0.82982	GCC		0.423	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840	
ZIC3	7547	broad.mit.edu	37	X	136649490	136649490	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:136649490G>A	ENST00000287538.5	+	1	1190	c.640G>A	c.(640-642)Gct>Act	p.A214T	ZIC3_ENST00000370606.3_Missense_Mutation_p.A214T|RP1-137H15.2_ENST00000442841.1_RNA	NM_003413.3	NP_003404.1	O60481	ZIC3_HUMAN	Zic family member 3	214					anterior/posterior pattern specification (GO:0009952)|cell differentiation (GO:0030154)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of left/right asymmetry in nervous system (GO:0035545)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|heart looping (GO:0001947)|lung development (GO:0030324)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A214T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|soft_tissue(2)|urinary_tract(1)	37	Acute lymphoblastic leukemia(192;0.000127)					CGCGGCCGGCGCTCAGTTTCC	0.657																																					p.A214T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G640A	X						.						22.0	25.0	24.0					X																	136649490		2171	4234	6405	136477156	SO:0001583	missense	7547	exon1			AF028706	CCDS14663.1	Xq24-q27.1	2013-01-08	2011-05-19		ENSG00000156925	ENSG00000156925		"""Zinc fingers, C2H2-type"""	12874	protein-coding gene	gene with protein product		300265	"""heterotaxy 1"", ""Zic family member 3 (odd-paired homolog, Drosophila)"""	HTX1		8298651, 7747776	Standard	NM_003413		Approved	HTX, ZNF203	uc004fak.3	O60481	OTTHUMG00000022525	ENST00000287538.5:c.640G>A	X.37:g.136649490G>A	ENSP00000287538:p.Ala214Thr	Somatic		Capture	Illumina HiSeq	Phase_I	136477156	NM_003413	B2CNW4|Q14DE5|Q5JY75	Missense_Mutation	SNP	ENST00000287538.5	37	CCDS14663.1	.	.	.	.	.	.	.	.	.	.	g	8.789	0.930123	0.18131	.	.	ENSG00000156925	ENST00000287538;ENST00000370606	T;T	0.35236	1.32;1.32	4.58	4.58	0.56647	.	0.000000	0.64402	D	0.000001	T	0.25044	0.0608	L	0.35487	1.065	0.58432	D	0.999994	D	0.60575	0.988	B	0.42138	0.377	T	0.10451	-1.0629	10	0.05351	T	0.99	.	15.0189	0.71613	0.0:0.0:1.0:0.0	.	214	O60481	ZIC3_HUMAN	T	214	ENSP00000287538:A214T;ENSP00000359638:A214T	ENSP00000287538:A214T	A	+	1	0	ZIC3	136477156	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.044000	0.49830	2.100000	0.63781	0.597000	0.82753	GCT		0.657	ZIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058526.1		
MCF2	4168	broad.mit.edu	37	X	138713628	138713628	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:138713628C>T	ENST00000370576.4	-	3	423	c.214G>A	c.(214-216)Gat>Aat	p.D72N	MCF2_ENST00000519895.1_Missense_Mutation_p.D132N|MCF2_ENST00000370573.4_Missense_Mutation_p.D72N|MCF2_ENST00000520602.1_Missense_Mutation_p.D132N|MCF2_ENST00000338585.6_Missense_Mutation_p.D72N|MCF2_ENST00000536274.1_Intron|MCF2_ENST00000414978.1_Missense_Mutation_p.D132N|MCF2_ENST00000370578.4_Missense_Mutation_p.D217N	NM_001171879.1|NM_005369.4	NP_001165350.1|NP_005360.3	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	72	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.D132N(1)|p.D72N(1)		NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					TGCTTGTCATCAATGTATGTC	0.408																																					p.D132N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G394A	X						.						174.0	136.0	149.0					X																	138713628		2203	4300	6503	138541294	SO:0001583	missense	4168	exon6				CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"""Rho guanine nucleotide exchange factors"""	6940	protein-coding gene	gene with protein product	"""Oncogene MCF2 (oncogene DBL)"""	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000370576.4:c.214G>A	X.37:g.138713628C>T	ENSP00000359608:p.Asp72Asn	Somatic		Capture	Illumina HiSeq	Phase_I	138541294	NM_001099855	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Missense_Mutation	SNP	ENST00000370576.4	37	CCDS14667.1	.	.	.	.	.	.	.	.	.	.	C	33	5.206266	0.95033	.	.	ENSG00000101977	ENST00000520602;ENST00000370576;ENST00000370578;ENST00000414978;ENST00000519895;ENST00000370573;ENST00000338585	T;T;T;T;T;T;T	0.63255	1.55;-0.03;1.55;1.55;1.55;-0.03;-0.03	5.91	5.91	0.95273	Cellular retinaldehyde-binding/triple function, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79263	0.4416	M	0.72894	2.215	0.49051	D	0.99974	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	0.998;1.0;0.996;0.999;1.0;0.998	T	0.80549	-0.1333	10	0.66056	D	0.02	.	17.6429	0.88141	0.0:1.0:0.0:0.0	.	132;217;72;217;72;72	E9PH77;B7Z3Z2;P10911-2;Q5JYJ7;P10911-4;P10911	.;.;.;.;.;MCF2_HUMAN	N	132;72;217;132;132;72;72	ENSP00000427745:D132N;ENSP00000359608:D72N;ENSP00000359610:D217N;ENSP00000397055:D132N;ENSP00000430276:D132N;ENSP00000359605:D72N;ENSP00000342204:D72N	ENSP00000342204:D72N	D	-	1	0	MCF2	138541294	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.188000	0.77739	2.488000	0.83962	0.594000	0.82650	GAT		0.408	MCF2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058560.1	NM_005369	
MAGEC3	139081	broad.mit.edu	37	X	140984572	140984572	+	Intron	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:140984572C>T	ENST00000298296.1	+	7	1123				MAGEC3_ENST00000443323.2_Intron|MAGEC3_ENST00000536088.1_Missense_Mutation_p.S45F|MAGEC3_ENST00000409007.1_Missense_Mutation_p.S45F|MAGEC3_ENST00000544766.1_Missense_Mutation_p.S45F|MAGEC3_ENST00000483584.1_3'UTR	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3									p.S45F(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					acttcctcttcctctttccac	0.502																																					p.S45F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C134T	X						.						133.0	88.0	103.0					X																	140984572		2203	4300	6503	140812238	SO:0001627	intron_variant	139081	exon5			AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.1124-96C>T	X.37:g.140984572C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140812238	NM_177456	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	c	6.141	0.394296	0.11638	.	.	ENSG00000165509	ENST00000536088;ENST00000544766;ENST00000409007	T;T;T	0.04156	3.69;3.69;3.69	1.32	-0.914	0.10497	.	.	.	.	.	T	0.02012	0.0063	.	.	.	0.09310	N	1	B	0.16802	0.019	B	0.11329	0.006	T	0.48293	-0.9048	8	0.10377	T	0.69	.	2.4208	0.04447	0.0:0.423:0.3243:0.2528	.	45	Q3SYA7	.	F	45	ENSP00000441107:S45F;ENSP00000440444:S45F;ENSP00000386566:S45F	ENSP00000386566:S45F	S	+	2	0	MAGEC3	140812238	0.009000	0.17119	0.005000	0.12908	0.013000	0.08279	0.249000	0.18216	-0.423000	0.07394	0.363000	0.22086	TCC		0.502	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
SLITRK4	139065	broad.mit.edu	37	X	142717671	142717671	+	Silent	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:142717671T>A	ENST00000381779.4	-	2	1479	c.1254A>T	c.(1252-1254)ggA>ggT	p.G418G	SLITRK4_ENST00000338017.4_Silent_p.G418G|SLITRK4_ENST00000356928.1_Silent_p.G418G	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	418						integral component of membrane (GO:0016021)		p.G418G(1)		autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					GAAATACGTCTCCCTTAATCA	0.388																																					p.G418G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1254T	X						.						130.0	111.0	117.0					X																	142717671		2203	4300	6503	142545337	SO:0001819	synonymous_variant	139065	exon2			BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.1254A>T	X.37:g.142717671T>A		Somatic		Capture	Illumina HiSeq	Phase_I	142545337	NM_173078	Q5JXG3|Q8TCM8|Q96DL3	Silent	SNP	ENST00000381779.4	37	CCDS14679.1																																																																																				0.388	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078	
UBE2NL	389898	broad.mit.edu	37	X	142967366	142967366	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:142967366G>A	ENST00000370494.1	+	1	194	c.164G>A	c.(163-165)cGt>cAt	p.R55H		NM_001012989.1	NP_001013007.1	Q5JXB2	UE2NL_HUMAN	ubiquitin-conjugating enzyme E2N-like (gene/pseudogene)	55						extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)	p.R55H(1)		breast(1)|endometrium(1)|large_intestine(8)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(192;6.56e-05)					ACTTTTAAACGTGAACTATTA	0.418																																					p.R55H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G164A	X						.						100.0	98.0	99.0					X																	142967366		2203	4300	6503	142795032	SO:0001583	missense	389898	exon1					Xq27.3	2014-06-11	2014-06-11		ENSG00000102069			"""Ubiquitin-conjugating enzymes E2"""	31710	protein-coding gene	gene with protein product			"""ubiquitin-conjugating enzyme E2N-like"""			20736409	Standard	NM_001012989		Approved		uc004fca.3	Q5JXB2	OTTHUMG00000022586	ENST00000370494.1:c.164G>A	X.37:g.142967366G>A	ENSP00000359525:p.Arg55His	Somatic		Capture	Illumina HiSeq	Phase_I	142795032	NM_001012989	E9KL27	Missense_Mutation	SNP	ENST00000370494.1	37	CCDS35420.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.998892	0.35226	.	.	ENSG00000102069	ENST00000370494	T	0.71817	-0.6	1.1	-0.209	0.13180	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.164354	0.24606	U	0.037096	T	0.42223	0.1193	N	0.08118	0	0.22001	N	0.999425	B	0.28636	0.218	B	0.19946	0.027	T	0.32955	-0.9887	10	0.87932	D	0	1.8896	5.1191	0.14851	0.0:0.0:0.3014:0.6986	.	55	Q5JXB2	UE2NL_HUMAN	H	55	ENSP00000359525:R55H	ENSP00000359525:R55H	R	+	2	0	UBE2NL	142795032	1.000000	0.71417	0.998000	0.56505	0.125000	0.20455	3.918000	0.56432	-0.104000	0.12154	-1.385000	0.01166	CGT		0.418	UBE2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058624.1	NM_001012989	
SLITRK2	84631	broad.mit.edu	37	X	144904848	144904848	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:144904848G>A	ENST00000370490.1	+	1	5160	c.905G>A	c.(904-906)aGc>aAc	p.S302N	SLITRK2_ENST00000428560.2_Missense_Mutation_p.S302N|SLITRK2_ENST00000413937.2_Missense_Mutation_p.S302N|SLITRK2_ENST00000434188.2_Missense_Mutation_p.S302N|SLITRK2_ENST00000447897.2_Missense_Mutation_p.S302N			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	302					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.S302N(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					CCGAAAGCCAGCCGGCCGCCC	0.542																																					p.S302N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G905A	X						.						61.0	56.0	58.0					X																	144904848		2203	4300	6503	144712540	SO:0001583	missense	84631	exon3			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"""slit-like 1 (Drosophila)"""	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.905G>A	X.37:g.144904848G>A	ENSP00000359521:p.Ser302Asn	Somatic		Capture	Illumina HiSeq	Phase_I	144712540	NM_001144006	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.686184	0.68157	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.52295	0.72;0.67;0.67;0.67;0.67;0.67	5.67	5.67	0.87782	.	0.104807	0.64402	D	0.000004	T	0.49949	0.1587	L	0.51422	1.61	0.48511	D	0.99966	D	0.55605	0.972	P	0.50136	0.632	T	0.39800	-0.9596	10	0.12766	T	0.61	-11.6693	15.945	0.79787	0.0:0.0:1.0:0.0	.	302	Q9H156	SLIK2_HUMAN	N	302	ENSP00000334374:S302N;ENSP00000411681:S302N;ENSP00000359521:S302N;ENSP00000397015:S302N;ENSP00000407347:S302N;ENSP00000412010:S302N	ENSP00000334374:S302N	S	+	2	0	SLITRK2	144712540	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.474000	0.66781	2.365000	0.80145	0.600000	0.82982	AGC		0.542	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
SLITRK2	84631	broad.mit.edu	37	X	144905471	144905471	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:144905471C>T	ENST00000370490.1	+	1	5783	c.1528C>T	c.(1528-1530)Ccc>Tcc	p.P510S	SLITRK2_ENST00000428560.2_Missense_Mutation_p.P510S|SLITRK2_ENST00000413937.2_Missense_Mutation_p.P510S|SLITRK2_ENST00000434188.2_Missense_Mutation_p.P510S|SLITRK2_ENST00000447897.2_Missense_Mutation_p.P510S			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	510					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.P510S(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					TTCTCACCTGCCCGTGAAAGG	0.502																																					p.P510S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1528T	X						.						77.0	81.0	80.0					X																	144905471		2203	4300	6503	144713163	SO:0001583	missense	84631	exon3			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"""slit-like 1 (Drosophila)"""	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.1528C>T	X.37:g.144905471C>T	ENSP00000359521:p.Pro510Ser	Somatic		Capture	Illumina HiSeq	Phase_I	144713163	NM_001144006	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	C	16.77	3.214022	0.58452	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3	5.84	5.84	0.93424	.	0.057023	0.64402	D	0.000001	T	0.69958	0.3169	L	0.53780	1.695	0.58432	D	0.999999	P	0.51791	0.948	P	0.60415	0.874	T	0.71941	-0.4440	10	0.72032	D	0.01	-5.7454	16.2774	0.82651	0.0:1.0:0.0:0.0	.	510	Q9H156	SLIK2_HUMAN	S	510	ENSP00000334374:P510S;ENSP00000411681:P510S;ENSP00000359521:P510S;ENSP00000397015:P510S;ENSP00000407347:P510S;ENSP00000412010:P510S	ENSP00000334374:P510S	P	+	1	0	SLITRK2	144713163	1.000000	0.71417	1.000000	0.80357	0.605000	0.37080	6.056000	0.71111	2.448000	0.82819	0.600000	0.82982	CCC		0.502	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
FMR1	2332	broad.mit.edu	37	X	147024667	147024667	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:147024667G>A	ENST00000370475.4	+	14	1420	c.1292G>A	c.(1291-1293)cGt>cAt	p.R431H	FMR1_ENST00000492846.1_3'UTR|FMR1_ENST00000370471.3_Intron|FMR1_ENST00000439526.2_Missense_Mutation_p.R408H|FMR1_ENST00000370470.1_Missense_Mutation_p.R431H|FMR1_ENST00000370477.1_Missense_Mutation_p.R410H|FMR1_ENST00000440235.2_Missense_Mutation_p.R78H|FMR1_ENST00000218200.8_Missense_Mutation_p.R410H	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	431	Interaction with RANBP9.				central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R431H(1)		NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					GACCAGTTGCGTTTGGAGAGA	0.323									Fragile X syndrome																												p.R410H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1229A	X						.						125.0	115.0	118.0					X																	147024667		2203	4300	6503	146832359	SO:0001583	missense	2332	exon13	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"""premature ovarian failure 1"""	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.1292G>A	X.37:g.147024667G>A	ENSP00000359506:p.Arg431His	Somatic		Capture	Illumina HiSeq	Phase_I	146832359	NM_001185082	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Missense_Mutation	SNP	ENST00000370475.4	37	CCDS14682.1	.	.	.	.	.	.	.	.	.	.	G	17.40	3.380984	0.61845	.	.	ENSG00000102081	ENST00000218200;ENST00000370477;ENST00000370475;ENST00000439526;ENST00000370470;ENST00000440235	T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01	5.73	5.73	0.89815	.	0.103776	0.64402	D	0.000003	T	0.60843	0.2300	L	0.51422	1.61	0.58432	D	0.999999	D;B;D;P;P	0.89917	1.0;0.428;0.968;0.661;0.471	D;B;P;B;B	0.83275	0.996;0.394;0.749;0.222;0.156	T	0.60964	-0.7158	10	0.56958	D	0.05	-20.9072	17.7241	0.88360	0.0:0.0:1.0:0.0	.	78;431;326;410;408	F8W871;Q06787;Q59GC1;Q06787-8;G3V0J0	.;FMR1_HUMAN;.;.;.	H	410;410;431;408;431;78	ENSP00000218200:R410H;ENSP00000359508:R410H;ENSP00000359506:R431H;ENSP00000395923:R408H;ENSP00000359501:R431H;ENSP00000413764:R78H	ENSP00000218200:R410H	R	+	2	0	FMR1	146832359	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.058000	0.76676	2.404000	0.81709	0.600000	0.82982	CGT		0.323	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024	
MTM1	4534	broad.mit.edu	37	X	149807467	149807467	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:149807467G>A	ENST00000370396.2	+	7	550	c.496G>A	c.(496-498)Gtt>Att	p.V166I	MTM1_ENST00000542741.1_Missense_Mutation_p.V71I|MTM1_ENST00000306167.7_3'UTR|MTM1_ENST00000413012.2_Missense_Mutation_p.V129I|MTM1_ENST00000543350.1_Missense_Mutation_p.V51I	NM_000252.2	NP_000243.1	Q13496	MTM1_HUMAN	myotubularin 1	166	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				endosome to lysosome transport (GO:0008333)|intermediate filament organization (GO:0045109)|mitochondrion distribution (GO:0048311)|mitochondrion morphogenesis (GO:0070584)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|protein transport (GO:0015031)|regulation of vacuole organization (GO:0044088)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	intermediate filament binding (GO:0019215)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)	p.V166I(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Acute lymphoblastic leukemia(192;6.56e-05)					TGGATGGACAGTTTACAATCC	0.363																																					p.V166I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G496A	X						.						203.0	178.0	187.0					X																	149807467		2203	4300	6503	149558125	SO:0001583	missense	4534	exon7			U46024	CCDS14694.1	Xq27.3-q28	2014-09-17			ENSG00000171100	ENSG00000171100		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7448	protein-coding gene	gene with protein product		300415	"""myotubular myopathy 1"""				Standard	NM_000252		Approved		uc004fef.4	Q13496	OTTHUMG00000024158	ENST00000370396.2:c.496G>A	X.37:g.149807467G>A	ENSP00000359423:p.Val166Ile	Somatic		Capture	Illumina HiSeq	Phase_I	149558125	NM_000252	A6NDB1|B7Z491|F2Z330|Q8NEL1	Missense_Mutation	SNP	ENST00000370396.2	37	CCDS14694.1	.	.	.	.	.	.	.	.	.	.	G	12.44	1.939098	0.34189	.	.	ENSG00000171100	ENST00000370396;ENST00000542741;ENST00000543350;ENST00000424519;ENST00000413012	D;D;D;D;D	0.95554	-2.55;-2.55;-2.55;-3.74;-2.55	5.27	5.27	0.74061	Myotubularin phosphatase domain (1);	0.120992	0.56097	N	0.000034	D	0.90270	0.6957	N	0.12887	0.27	0.43890	D	0.996519	B;B	0.12013	0.002;0.005	B;B	0.14578	0.011;0.011	D	0.85799	0.1372	10	0.29301	T	0.29	.	18.1936	0.89814	0.0:0.0:1.0:0.0	.	129;166	B7Z491;Q13496	.;MTM1_HUMAN	I	166;71;51;95;129	ENSP00000359423:V166I;ENSP00000444015:V71I;ENSP00000439784:V51I;ENSP00000400699:V95I;ENSP00000389157:V129I	ENSP00000359423:V166I	V	+	1	0	MTM1	149558125	1.000000	0.71417	0.935000	0.37517	0.977000	0.68977	3.571000	0.53841	2.321000	0.78463	0.594000	0.82650	GTT		0.363	MTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060847.3	NM_000252	
GPR50	9248	broad.mit.edu	37	X	150348621	150348621	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:150348621C>G	ENST00000218316.3	+	2	635	c.566C>G	c.(565-567)aCt>aGt	p.T189S	AF003625.3_ENST00000602313.1_lincRNA|GPR50-AS1_ENST00000454196.1_RNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	189					cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)	p.T189S(2)		breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					CCTGTCTTCACTGTTACCATC	0.552																																					p.T189S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C566G	X						.						256.0	230.0	239.0					X																	150348621		2174	4245	6419	150099279	SO:0001583	missense	9248	exon2			U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.566C>G	X.37:g.150348621C>G	ENSP00000218316:p.Thr189Ser	Somatic		Capture	Illumina HiSeq	Phase_I	150099279	NM_004224	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	37	CCDS44012.1	.	.	.	.	.	.	.	.	.	.	C	10.71	1.427453	0.25726	.	.	ENSG00000102195	ENST00000535473;ENST00000218316	T	0.37752	1.18	4.32	3.39	0.38822	GPCR, rhodopsin-like superfamily (1);	0.163600	0.53938	D	0.000051	T	0.57198	0.2037	H	0.94423	3.535	0.28165	N	0.928811	B;B	0.25521	0.128;0.064	B;B	0.40901	0.343;0.155	T	0.57458	-0.7808	10	0.38643	T	0.18	-10.6688	11.7072	0.51603	0.0:0.8236:0.1764:0.0	.	142;189	F5H1S3;Q13585	.;MTR1L_HUMAN	S	142;189	ENSP00000218316:T189S	ENSP00000218316:T189S	T	+	2	0	GPR50	150099279	0.991000	0.36638	0.031000	0.17742	0.378000	0.30076	4.000000	0.57039	1.898000	0.54952	0.523000	0.50628	ACT		0.552	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224	
VMA21	203547	broad.mit.edu	37	X	150573501	150573501	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:150573501C>T	ENST00000330374.6	+	3	382	c.277C>T	c.(277-279)Cga>Tga	p.R93*	VMA21_ENST00000477649.1_3'UTR|VMA21_ENST00000370361.1_Nonsense_Mutation_p.R148*	NM_001017980.3	NP_001017980.1			VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)									p.R93*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	7						TGAAGGCTCACGACAGTGGCG	0.448																																					p.R93X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C277T	X						.						141.0	112.0	122.0					X																	150573501		2203	4300	6503	150324159	SO:0001587	stop_gained	203547	exon3			AK096835	CCDS35430.1	Xq28	2014-09-17			ENSG00000160131	ENSG00000160131			22082	protein-coding gene	gene with protein product		300913	"""myopathy with excessive autophagy"""	MEAX		2892402, 10757644, 19379691	Standard	NM_001017980		Approved	XMEA	uc004feu.3	Q3ZAQ7	OTTHUMG00000024168	ENST00000330374.6:c.277C>T	X.37:g.150573501C>T	ENSP00000333255:p.Arg93*	Somatic		Capture	Illumina HiSeq	Phase_I	150324159	NM_001017980		Nonsense_Mutation	SNP	ENST00000330374.6	37	CCDS35430.1	.	.	.	.	.	.	.	.	.	.	.	32	5.178347	0.94846	.	.	ENSG00000160131	ENST00000370361;ENST00000330374	.	.	.	5.8	4.01	0.46588	.	0.071302	0.64402	D	0.000017	.	.	.	.	.	.	0.44454	D	0.997387	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.6806	12.4706	0.55785	0.3024:0.6976:0.0:0.0	.	.	.	.	X	148;93	.	ENSP00000333255:R93X	R	+	1	2	VMA21	150324159	0.995000	0.38212	0.975000	0.42487	0.993000	0.82548	1.525000	0.35953	0.576000	0.29452	0.600000	0.82982	CGA		0.448	VMA21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060876.1	NM_001017980	
PNMA5	114824	broad.mit.edu	37	X	152160130	152160130	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:152160130G>A	ENST00000439251.1	-	2	451	c.13C>T	c.(13-15)Ctg>Ttg	p.L5L	PNMA5_ENST00000452693.1_Silent_p.L5L|PNMA5_ENST00000535214.1_Silent_p.L5L|PNMA5_ENST00000361887.5_Silent_p.L5L	NM_001103150.1	NP_001096620.1	Q96PV4	PNMA5_HUMAN	paraneoplastic Ma antigen family member 5	5					positive regulation of apoptotic process (GO:0043065)			p.L5L(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					tcctctagcagtgtcagtgcc	0.512																																					p.L5L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C13T	X						.						207.0	165.0	179.0					X																	152160130		2203	4299	6502	151910786	SO:0001819	synonymous_variant	114824	exon2			AB067521	CCDS14718.1	Xq28	2012-02-09	2012-02-09		ENSG00000198883	ENSG00000198883		"""Paraneoplastic Ma antigens"""	18743	protein-coding gene	gene with protein product	"""paraneoplastic antigen family 5"""	300916	"""paraneoplastic antigen like 5"""			16214224	Standard	NM_052926		Approved	KIAA1934	uc004fgy.4	Q96PV4	OTTHUMG00000024184	ENST00000439251.1:c.13C>T	X.37:g.152160130G>A		Somatic		Capture	Illumina HiSeq	Phase_I	151910786	NM_001103150	B4DI72|B7Z9Y9|Q495L5|Q8NET3	Silent	SNP	ENST00000439251.1	37	CCDS14718.1																																																																																				0.512	PNMA5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060925.1	NM_052926	
AVPR2	554	broad.mit.edu	37	X	153172027	153172027	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:153172027A>G	ENST00000358927.2	+	4	1170	c.961A>G	c.(961-963)Aac>Gac	p.N321D	AVPR2_ENST00000337474.5_Missense_Mutation_p.N321D|AVPR2_ENST00000370049.1_3'UTR|ARHGAP4_ENST00000467421.1_5'Flank			P30518	V2R_HUMAN	arginine vasopressin receptor 2	321			N -> D (in XNDI).|N -> K (in XNDI).|N -> Y (in XNDI).		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|excretion (GO:0007588)|hemostasis (GO:0007599)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-gamma production (GO:0032609)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of systemic arterial blood pressure (GO:0003084)|response to cytokine (GO:0034097)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	vasopressin receptor activity (GO:0005000)	p.N321D(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	26	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Conivaptan(DB00872)|Desmopressin(DB00035)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	CAGCTGCACCAACCCCTGGAT	0.622																																					p.N321D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A961G	X	GRCh37	CM001640|CM983533	AVPR2	M		.						156.0	134.0	142.0					X																	153172027		2203	4300	6503	152825221	SO:0001583	missense	554	exon3			Z11687	CCDS14735.1, CCDS55539.1	Xq28	2014-09-17	2008-08-01		ENSG00000126895	ENSG00000126895		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	897	protein-coding gene	gene with protein product	"""nephrogenic diabetes insipidus"""	300538		DIR3, DIR		1324225	Standard	NM_000054		Approved	V2R	uc004fjh.4	P30518	OTTHUMG00000024227	ENST00000358927.2:c.961A>G	X.37:g.153172027A>G	ENSP00000351805:p.Asn321Asp	Somatic		Capture	Illumina HiSeq	Phase_I	152825221	NM_000054	C5HF20|O43192|Q3MJD3|Q9UCV9	Missense_Mutation	SNP	ENST00000358927.2	37	CCDS14735.1	.	.	.	.	.	.	.	.	.	.	a	20.9	4.061028	0.76074	.	.	ENSG00000126895	ENST00000358927;ENST00000337474	D;D	0.83992	-1.79;-1.79	4.3	4.3	0.51218	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.91536	0.7327	M	0.88105	2.93	0.54753	D	0.999988	D	0.89917	1.0	D	0.97110	1.0	D	0.92643	0.6126	10	0.87932	D	0	.	11.9169	0.52771	1.0:0.0:0.0:0.0	.	321	P30518	V2R_HUMAN	D	321	ENSP00000351805:N321D;ENSP00000338072:N321D	ENSP00000338072:N321D	N	+	1	0	AVPR2	152825221	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.344000	0.79328	1.512000	0.48834	0.342000	0.21767	AAC		0.622	AVPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061127.2		
GYG2	8908	broad.mit.edu	37	X	2778030	2778030	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:2778030C>T	ENST00000381163.3	+	8	1136	c.854C>T	c.(853-855)aCg>aTg	p.T285M	GYG2_ENST00000542787.1_Missense_Mutation_p.T285M|GYG2_ENST00000398806.3_Missense_Mutation_p.T254M|GYG2_ENST00000338623.5_Missense_Mutation_p.T285M|GYG2_ENST00000381161.1_3'UTR	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	285					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)	p.T285M(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CTCTGGTGGACGGTCTACCAG	0.562																																					p.T285M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C854T	X						.						47.0	44.0	45.0					X																	2778030		2203	4297	6500	2788030	SO:0001583	missense	8908	exon8			U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4700	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.854C>T	X.37:g.2778030C>T	ENSP00000370555:p.Thr285Met	Somatic		Capture	Illumina HiSeq	Phase_I	2788030	NM_001184703	B7WNN6|O15485|O15486|O15487|O15489|O15490	Missense_Mutation	SNP	ENST00000381163.3	37	CCDS14121.1	.	.	.	.	.	.	.	.	.	.	C	7.816	0.716676	0.15306	.	.	ENSG00000056998	ENST00000398806;ENST00000381163;ENST00000338623;ENST00000542787	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	3.74	-7.48	0.01360	.	4.089360	0.01085	N	0.005066	T	0.47581	0.1453	N	0.14661	0.345	0.09310	N	1	D;B;P;P;B;B	0.56521	0.976;0.121;0.924;0.837;0.018;0.026	P;B;B;B;B;B	0.47470	0.548;0.04;0.255;0.243;0.028;0.02	T	0.60900	-0.7171	10	0.51188	T	0.08	.	8.1293	0.31018	0.4377:0.384:0.1783:0.0	.	285;285;245;254;254;285	O15488-6;O15488-4;O15488-3;A8K8Y1;O15488-2;O15488	.;.;.;.;.;GLYG2_HUMAN	M	254;285;285;285	ENSP00000381786:T254M;ENSP00000370555:T285M;ENSP00000341273:T285M;ENSP00000446092:T285M	ENSP00000341273:T285M	T	+	2	0	GYG2	2788030	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.063000	0.11655	-2.573000	0.00466	-1.711000	0.00714	ACG		0.562	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055645.1	NM_003918	
MXRA5	25878	broad.mit.edu	37	X	3235604	3235604	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:3235604G>A	ENST00000217939.6	-	6	6272	c.6118C>T	c.(6118-6120)Ctg>Ttg	p.L2040L		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2040	Ig-like C2-type 4.					extracellular vesicular exosome (GO:0070062)		p.L2040L(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GCCACGTGCAGGCGGATGGCC	0.627																																					p.L2040L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C6118T	X						.						27.0	22.0	24.0					X																	3235604		2203	4298	6501	3245604	SO:0001819	synonymous_variant	25878	exon6			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.6118C>T	X.37:g.3235604G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3245604	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																				0.627	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
STS	412	broad.mit.edu	37	X	7175329	7175329	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:7175329C>T	ENST00000217961.4	+	3	419	c.199C>T	c.(199-201)Cag>Tag	p.Q67*		NM_000351.4	NP_000342.2	P08842	STS_HUMAN	steroid sulfatase (microsomal), isozyme S	67					cellular protein metabolic process (GO:0044267)|epidermis development (GO:0008544)|female pregnancy (GO:0007565)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|steroid catabolic process (GO:0006706)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|steryl-sulfatase activity (GO:0004773)|sulfuric ester hydrolase activity (GO:0008484)	p.Q67*(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(1)	27		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Norelgestromin(DB06713)	GAAACTCACTCAGCACCTGGC	0.507									Ichthyosis																												p.Q67X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C199T	X						.						72.0	50.0	57.0					X																	7175329		2203	4299	6502	7185329	SO:0001587	stop_gained	412	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	M16505	CCDS14127.1	Xp22.32	2013-06-10	2007-07-19		ENSG00000101846	ENSG00000101846	3.1.6.2	"""Arylsulfatase family"""	11425	protein-coding gene	gene with protein product	"""arylsulfatase C"""	300747	"""steroid sulfatase (microsomal), arylsulfatase C, isozyme S"""	ARSC1			Standard	NM_000351		Approved	ARSC	uc004cry.4	P08842	OTTHUMG00000021102	ENST00000217961.4:c.199C>T	X.37:g.7175329C>T	ENSP00000217961:p.Gln67*	Somatic		Capture	Illumina HiSeq	Phase_I	7185329	NM_000351	B2RA47	Nonsense_Mutation	SNP	ENST00000217961.4	37	CCDS14127.1	.	.	.	.	.	.	.	.	.	.	C	36	5.810361	0.96975	.	.	ENSG00000101846	ENST00000217961	.	.	.	3.86	3.86	0.44501	.	0.177548	0.51477	D	0.000092	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	13.9416	0.64059	0.0:1.0:0.0:0.0	.	.	.	.	X	67	.	ENSP00000217961:Q67X	Q	+	1	0	STS	7185329	1.000000	0.71417	0.914000	0.36105	0.549000	0.35272	6.707000	0.74654	1.546000	0.49388	0.600000	0.82982	CAG		0.507	STS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055686.1	NM_000351	
PNPLA4	8228	broad.mit.edu	37	X	7890117	7890117	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:7890117T>A	ENST00000381042.4	-	3	373	c.203A>T	c.(202-204)aAg>aTg	p.K68M	PNPLA4_ENST00000444736.1_Missense_Mutation_p.K68M|PNPLA4_ENST00000537427.1_De_novo_Start_InFrame	NM_004650.2	NP_004641.1	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	68	Patatin.				lipid catabolic process (GO:0016042)		triglyceride lipase activity (GO:0004806)	p.K68M(1)		kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				TTCGGCAAACTTGTAGGTAAA	0.393																																					p.K68M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A203T	X						.						70.0	62.0	65.0					X																	7890117		2203	4299	6502	7850117	SO:0001583	missense	8228	exon3			U03886	CCDS14129.1, CCDS55368.1	Xp22.3	2014-03-14			ENSG00000006757	ENSG00000006757	3.1.1.3	"""Patatin-like phospholipase domain containing"""	24887	protein-coding gene	gene with protein product		300102				7806223, 16799181, 19029121	Standard	NM_004650		Approved	DXS1283E, GS2, iPLA2eta	uc011mhr.1	P41247	OTTHUMG00000021103	ENST00000381042.4:c.203A>T	X.37:g.7890117T>A	ENSP00000370430:p.Lys68Met	Somatic		Capture	Illumina HiSeq	Phase_I	7850117	NM_004650	A8K1H3|B4E362|Q8WW83	Missense_Mutation	SNP	ENST00000381042.4	37	CCDS14129.1	.	.	.	.	.	.	.	.	.	.	T	11.92	1.783319	0.31593	.	.	ENSG00000006757	ENST00000381042;ENST00000444736;ENST00000442940	T;T;T	0.78003	-1.14;-1.14;-1.14	4.59	-1.45	0.08828	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	1.293080	0.04758	N	0.425856	T	0.77075	0.4077	L	0.29908	0.895	0.09310	N	0.999998	D	0.55172	0.97	P	0.56474	0.799	T	0.65869	-0.6063	10	0.54805	T	0.06	-0.2158	8.4089	0.32632	0.0:0.0839:0.5603:0.3558	.	68	P41247	PLPL4_HUMAN	M	68	ENSP00000370430:K68M;ENSP00000415245:K68M;ENSP00000406698:K68M	ENSP00000370430:K68M	K	-	2	0	PNPLA4	7850117	0.049000	0.20398	0.000000	0.03702	0.322000	0.28314	0.577000	0.23758	-0.702000	0.05056	-0.378000	0.06908	AAG		0.393	PNPLA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055687.1	NM_004650	
SHROOM2	357	broad.mit.edu	37	X	9863199	9863199	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:9863199G>A	ENST00000380913.3	+	4	1341	c.1251G>A	c.(1249-1251)gtG>gtA	p.V417V		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	417					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)	p.V417V(1)		breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				GCTCAGATGTGCGCTTCCCTC	0.672																																					p.V417V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1251A	X						.						47.0	40.0	43.0					X																	9863199		2203	4300	6503	9823199	SO:0001819	synonymous_variant	357	exon4			X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"""apical protein, Xenopus laevis-like"", ""apical protein-like (Xenopus laevis)"""	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.1251G>A	X.37:g.9863199G>A		Somatic		Capture	Illumina HiSeq	Phase_I	9823199	NM_001649	B9EIQ7	Silent	SNP	ENST00000380913.3	37	CCDS14135.1																																																																																				0.672	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649	
NHS	4810	broad.mit.edu	37	X	17750487	17750487	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:17750487G>A	ENST00000380060.3	+	8	5134	c.4796G>A	c.(4795-4797)cGg>cAg	p.R1599Q	NHS_ENST00000398097.3_Missense_Mutation_p.R1443Q	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1620					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.R1599Q(2)|p.R1443Q(2)		breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					GTCCGCTGCCGGCTGTACAAT	0.587																																					p.R1443Q												.	.	4	Substitution - Missense(4)	large_intestine(2)|endometrium(2)	c.G4328A	X						.						55.0	56.0	56.0					X																	17750487		2203	4300	6503	17660408	SO:0001583	missense	4810	exon9				CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.4796G>A	X.37:g.17750487G>A	ENSP00000369400:p.Arg1599Gln	Somatic		Capture	Illumina HiSeq	Phase_I	17660408	NM_001136024	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	37	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	G	36	5.849198	0.97023	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.74315	-0.83;-0.83	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.86414	0.5927	M	0.70275	2.135	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.998	D	0.86910	0.2060	10	0.72032	D	0.01	-14.7747	19.3889	0.94570	0.0:0.0:1.0:0.0	.	1620;1441;1443;1599	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	Q	1599;1443;1441	ENSP00000369400:R1599Q;ENSP00000381170:R1443Q	ENSP00000369397:R1441Q	R	+	2	0	NHS	17660408	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.412000	0.97347	2.618000	0.88619	0.600000	0.82982	CGG		0.587	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270	
RAI2	10742	broad.mit.edu	37	X	17818711	17818711	+	Missense_Mutation	SNP	C	C	T	rs147416008	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:17818711C>T	ENST00000545871.1	-	3	1880	c.1420G>A	c.(1420-1422)Gtg>Atg	p.V474M	RAI2_ENST00000451717.1_Missense_Mutation_p.V474M|RAI2_ENST00000415486.3_Missense_Mutation_p.V424M|RAI2_ENST00000360011.1_Missense_Mutation_p.V474M|RAI2_ENST00000331511.1_Missense_Mutation_p.V474M	NM_001172739.1|NM_001172743.1	NP_001166210|NP_001166214	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	474					embryo development (GO:0009790)			p.V474M(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	22	Hepatocellular(33;0.183)					CCCTGAAGCACGGAGTCTTCT	0.478													C|||	3	0.000794702	0.0015	0.0	3775	,	,		11839	0.001		0.0	False		,,,				2504	0.0				p.V474M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1420A	X						.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL	6,3829		0,5,1,1627,570	230.0	234.0	233.0		1270,1420,1420,1420	1.5	1.0	X	dbSNP_134	233	0,6728		0,0,0,2428,1872	yes	missense,missense,missense,missense	RAI2	NM_001172732.1,NM_001172739.1,NM_001172743.1,NM_021785.4	21,21,21,21	0,5,1,4055,2442	TT,TC,T,CC,C		0.0,0.1565,0.0568	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	424/481,474/531,474/531,474/531	17818711	6,10557	2203	4300	6503	17728632	SO:0001583	missense	10742	exon3			Z93242	CCDS14183.1, CCDS55374.1	Xp22	2008-02-05			ENSG00000131831	ENSG00000131831			9835	protein-coding gene	gene with protein product		300217				10049581, 10394933	Standard	NR_033348		Approved		uc010nfa.3	Q9Y5P3	OTTHUMG00000021209	ENST00000545871.1:c.1420G>A	X.37:g.17818711C>T	ENSP00000444210:p.Val474Met	Somatic		Capture	Illumina HiSeq	Phase_I	17728632	NM_001172739	B1B1K2|B4DQM9|E7EMN4|Q8N6X7	Missense_Mutation	SNP	ENST00000545871.1	37	CCDS14183.1	1	6.027727546714888E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	12.62	1.991458	0.35131	0.001565	0.0	ENSG00000131831	ENST00000331511;ENST00000360011;ENST00000545871;ENST00000451717;ENST00000415486	T;T;T;T;T	0.33654	1.41;1.41;1.41;1.41;1.4	5.12	1.46	0.22682	.	0.191387	0.36101	N	0.002796	T	0.21631	0.0521	N	0.17082	0.46	0.34063	D	0.657531	B;B	0.25390	0.125;0.125	B;B	0.24541	0.054;0.03	T	0.15321	-1.0441	10	0.52906	T	0.07	-7.1323	10.4494	0.44513	0.0:0.7492:0.0:0.2508	.	424;474	E7EMN4;Q9Y5P3	.;RAI2_HUMAN	M	474;474;474;474;424	ENSP00000333456:V474M;ENSP00000353106:V474M;ENSP00000444210:V474M;ENSP00000401323:V474M;ENSP00000392578:V424M	ENSP00000333456:V474M	V	-	1	0	RAI2	17728632	0.828000	0.29307	0.996000	0.52242	0.993000	0.82548	0.536000	0.23129	-0.022000	0.13986	-0.191000	0.12829	GTG		0.478	RAI2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055937.1	NM_021785	
CDKL5	6792	broad.mit.edu	37	X	18622115	18622115	+	Silent	SNP	C	C	T	rs144204039		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:18622115C>T	ENST00000379989.3	+	13	1356	c.1071C>T	c.(1069-1071)gaC>gaT	p.D357D	CDKL5_ENST00000463994.1_3'UTR|CDKL5_ENST00000379996.3_Silent_p.D357D	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	357					neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)	p.D357D(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					CCCGGGCTGACGAAGGTCTCC	0.517																																					p.D357D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1071T	X						.	C	,	0,3835		0,0,1632,571	138.0	141.0	140.0		1071,1071	-11.8	0.1	X	dbSNP_134	140	1,6727		0,1,2427,1872	no	coding-synonymous,coding-synonymous	CDKL5	NM_001037343.1,NM_003159.2	,	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	,	357/1031,357/1031	18622115	1,10562	2203	4300	6503	18532036	SO:0001819	synonymous_variant	6792	exon12			Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"""Cyclin-dependent kinases"""	11411	protein-coding gene	gene with protein product		300203	"""serine/threonine kinase 9"""	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.1071C>T	X.37:g.18622115C>T		Somatic		Capture	Illumina HiSeq	Phase_I	18532036	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Silent	SNP	ENST00000379989.3	37	CCDS14186.1																																																																																				0.517	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159	
GPR64	10149	broad.mit.edu	37	X	19028750	19028750	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:19028750G>A	ENST00000379869.3	-	17	1409	c.1246C>T	c.(1246-1248)Ctg>Ttg	p.L416L	GPR64_ENST00000379878.3_Silent_p.L400L|GPR64_ENST00000379873.2_Silent_p.L416L|GPR64_ENST00000357991.3_Silent_p.L413L|GPR64_ENST00000340581.3_Silent_p.L386L|GPR64_ENST00000360279.4_Silent_p.L394L|GPR64_ENST00000379876.1_Silent_p.L392L|GPR64_ENST00000357544.3_Silent_p.L386L|GPR64_ENST00000356606.4_Silent_p.L402L|GPR64_ENST00000354791.3_Silent_p.L400L	NM_001079858.2|NM_005756.3	NP_001073327.1|NP_005747.2	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64	416					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)|spermatogenesis (GO:0007283)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.L413L(1)		breast(5)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(18)|stomach(1)|urinary_tract(1)	42	Hepatocellular(33;0.183)					AGAGGGGCCAGCATGTCAGGC	0.522																																					p.L386L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1156T	X						.						169.0	137.0	148.0					X																	19028750		2203	4300	6503	18938671	SO:0001819	synonymous_variant	10149	exon15			X81892	CCDS14191.1, CCDS43921.1, CCDS43922.1, CCDS43923.1, CCDS55376.1, CCDS55377.1, CCDS55378.1, CCDS55379.1	Xp22.13	2014-08-08			ENSG00000173698	ENSG00000173698		"""-"", ""GPCR / Class B : Orphans"""	4516	protein-coding gene	gene with protein product	"""epididymal protein 6"""	300572				9739419, 9150425	Standard	NM_005756		Approved	HE6, TM7LN2, EDDM6	uc004cyx.3	Q8IZP9	OTTHUMG00000021223	ENST00000379869.3:c.1246C>T	X.37:g.19028750G>A		Somatic		Capture	Illumina HiSeq	Phase_I	18938671	NM_001184837	B1AWB3|B1AWB4|B1AWB6|B1AWB7|O00406|Q14CE0|Q8IWT2|Q8IZE4|Q8IZE5|Q8IZE6|Q8IZE7|Q8IZP3|Q8IZP4	Silent	SNP	ENST00000379869.3	37	CCDS43923.1																																																																																				0.522	GPR64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055970.2		
MAP7D2	256714	broad.mit.edu	37	X	20074902	20074902	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:20074902A>G	ENST00000379651.3	-	4	398	c.380T>C	c.(379-381)cTg>cCg	p.L127P	MAP7D2_ENST00000443379.3_Missense_Mutation_p.L127P|MAP7D2_ENST00000543767.1_5'Flank|MAP7D2_ENST00000379643.5_Missense_Mutation_p.L127P|MAP7D2_ENST00000452324.3_Missense_Mutation_p.L83P	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	127					microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)		p.L127P(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						CATCGCCTCCAGCCGTTCCTA	0.557																																					p.L127P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T380C	X						.						67.0	51.0	56.0					X																	20074902		2203	4300	6503	19984823	SO:0001583	missense	256714	exon4			BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.380T>C	X.37:g.20074902A>G	ENSP00000368972:p.Leu127Pro	Somatic		Capture	Illumina HiSeq	Phase_I	19984823	NM_001168465	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Missense_Mutation	SNP	ENST00000379651.3	37	CCDS14195.1	.	.	.	.	.	.	.	.	.	.	A	13.02	2.111435	0.37242	.	.	ENSG00000184368	ENST00000379651;ENST00000379643;ENST00000443379;ENST00000452324;ENST00000330274	T;T;T;T	0.04360	3.64;3.64;3.64;3.64	5.34	5.34	0.76211	.	0.000000	0.50627	D	0.000106	T	0.16938	0.0407	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.994;0.997;0.997;1.0;0.994	T	0.00599	-1.1651	10	0.42905	T	0.14	-12.9737	14.5228	0.67863	1.0:0.0:0.0:0.0	.	127;83;127;127;127	B7Z3S7;C9JYW0;Q96T17-2;B5ME62;Q96T17	.;.;.;.;MA7D2_HUMAN	P	127;127;127;83;127	ENSP00000368972:L127P;ENSP00000368964:L127P;ENSP00000388239:L127P;ENSP00000413301:L83P	ENSP00000332677:L127P	L	-	2	0	MAP7D2	19984823	1.000000	0.71417	1.000000	0.80357	0.428000	0.31595	5.973000	0.70456	1.878000	0.54408	0.412000	0.27726	CTG		0.557	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780	
DCAF8L1	139425	broad.mit.edu	37	X	27998990	27998990	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:27998990G>T	ENST00000441525.1	-	1	576	c.462C>A	c.(460-462)cgC>cgA	p.R154R		NM_001017930.1	NP_001017930.1	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	154								p.R154R(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(24)|ovary(3)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	56						GGACTTGCCAGCGAGATCGGG	0.572																																					p.R154R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C462A	X						.						55.0	46.0	49.0					X																	27998990		2202	4299	6501	27908911	SO:0001819	synonymous_variant	139425	exon1				CCDS35222.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17	ENSG00000226372	ENSG00000226372		"""WD repeat domain containing"""	31810	protein-coding gene	gene with protein product			"""WD repeat domain 42B"""	WDR42B			Standard	NM_001017930		Approved		uc004dbx.1	A6NGE4	OTTHUMG00000021312	ENST00000441525.1:c.462C>A	X.37:g.27998990G>T		Somatic		Capture	Illumina HiSeq	Phase_I	27908911	NM_001017930	B3KXX1	Silent	SNP	ENST00000441525.1	37	CCDS35222.1																																																																																				0.572	DCAF8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056150.2	XM_066690	
MAGEB1	4112	broad.mit.edu	37	X	30269409	30269409	+	Missense_Mutation	SNP	C	C	T	rs7062640	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:30269409C>T	ENST00000378981.3	+	4	1120	c.799C>T	c.(799-801)Cgc>Tgc	p.R267C	MAGEB1_ENST00000397550.1_Missense_Mutation_p.R267C|MAGEB1_ENST00000397548.2_Missense_Mutation_p.R267C	NM_002363.4	NP_002354.2	P43366	MAGB1_HUMAN	melanoma antigen family B, 1	267	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		R -> C (in dbSNP:rs7062640).					p.R267C(1)		NS(2)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	32						TGATCCCCCACGCTATCAATT	0.502													C|||	18	0.00476821	0.0136	0.0	3775	,	,		14801	0.0		0.0	False		,,,				2504	0.0				p.R267C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C799T	X						.	C	CYS/ARG,CYS/ARG,CYS/ARG	95,3738		0,86,9,1545,562	104.0	92.0	96.0		799,799,799	-8.0	0.0	X	dbSNP_116	96	0,6728		0,0,0,2428,1872	yes	missense,missense,missense	MAGEB1	NM_002363.4,NM_177404.2,NM_177415.2	180,180,180	0,86,9,3973,2434	TT,TC,T,CC,C		0.0,2.4785,0.8995	benign,benign,benign	267/348,267/348,267/348	30269409	95,10466	2202	4300	6502	30179330	SO:0001583	missense	4112	exon4				CCDS14222.1	Xp21.3	2009-03-17			ENSG00000214107	ENSG00000214107			6808	protein-coding gene	gene with protein product	"""DSS/AHC critical interval MAGE superfamily 10"", ""cancer/testis antigen family 3, member 1"""	300097				7761436, 9441743	Standard	NM_002363		Approved	MAGEL1, MAGE-Xp, DAM10, MGC9322, CT3.1	uc004dce.3	P43366	OTTHUMG00000021322	ENST00000378981.3:c.799C>T	X.37:g.30269409C>T	ENSP00000368264:p.Arg267Cys	Somatic		Capture	Illumina HiSeq	Phase_I	30179330	NM_002363	B2RC79|O00601|O75862|Q6FHJ0|Q96CW8	Missense_Mutation	SNP	ENST00000378981.3	37	CCDS14222.1	5	0.0030138637733574444	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	0.016	-1.536819	0.00942	0.024785	0.0	ENSG00000214107	ENST00000378981;ENST00000397550;ENST00000397548	T;T;T	0.05025	3.51;3.51;3.51	3.99	-7.97	0.01139	.	0.779445	0.11212	N	0.587598	T	0.01454	0.0047	N	0.25060	0.705	0.09310	N	1	B	0.28350	0.208	B	0.27170	0.077	T	0.18935	-1.0321	10	0.38643	T	0.18	.	4.9342	0.13932	0.1882:0.1168:0.0928:0.6023	rs7062640;rs52814259;rs7062640	267	P43366	MAGB1_HUMAN	C	267	ENSP00000368264:R267C;ENSP00000380683:R267C;ENSP00000380681:R267C	ENSP00000368264:R267C	R	+	1	0	MAGEB1	30179330	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-3.493000	0.00452	-3.569000	0.00139	-3.197000	0.00054	CGC		0.502	MAGEB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056160.1	NM_002363	
DMD	1756	broad.mit.edu	37	X	31224764	31224764	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:31224764C>T	ENST00000357033.4	-	66	9790	c.9584G>A	c.(9583-9585)cGt>cAt	p.R3195H	DMD_ENST00000361471.4_Missense_Mutation_p.R127H|DMD_ENST00000378677.2_Missense_Mutation_p.R3191H|DMD_ENST00000378723.3_Missense_Mutation_p.R127H|DMD_ENST00000343523.2_Missense_Mutation_p.R735H|DMD_ENST00000541735.1_Missense_Mutation_p.R735H|DMD_ENST00000474231.1_Missense_Mutation_p.R735H|DMD_ENST00000378702.4_Missense_Mutation_p.R127H|DMD_ENST00000359836.1_Missense_Mutation_p.R735H|DMD_ENST00000378707.3_Missense_Mutation_p.R735H|DMD_ENST00000378680.2_Missense_Mutation_p.R127H	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3195	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.R3190H(2)|p.R735H(2)|p.R1854H(1)|p.R3191P(1)|p.R3195P(1)|p.R127P(1)|p.R1854P(1)|p.R3190P(1)|p.R735P(1)|p.R3191H(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AGACAGGACACGGATCCTCCC	0.373																																					p.R127H												.	.	12	Substitution - Missense(12)	large_intestine(6)|endometrium(6)	c.G380A	X						.						97.0	81.0	87.0					X																	31224764		2202	4300	6502	31134685	SO:0001583	missense	1756	exon5			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.9584G>A	X.37:g.31224764C>T	ENSP00000354923:p.Arg3195His	Somatic		Capture	Illumina HiSeq	Phase_I	31134685	NM_004015	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888553	0.91814	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378723;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000378702;ENST00000474231;ENST00000361471;ENST00000378680	T;T;T;T;T;T;T;T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23	5.21	5.21	0.72293	EF-hand domain, type 1 (1);	0.000000	0.37053	U	0.002276	D	0.86314	0.5903	M	0.92219	3.285	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.998;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.83275	0.965;0.979;0.996;0.996;0.996;0.996;0.984;0.963;0.973;0.996;0.993;0.99;0.972;0.973;0.953;0.991	D	0.89765	0.3950	10	0.87932	D	0	.	17.8941	0.88881	0.0:1.0:0.0:0.0	.	127;3187;3195;3191;1854;1851;735;735;735;735;735;3072;127;127;127;127	B4DSV7;P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3;P11532-5;Q8N754;Q6NSJ9;E9PDN1	.;.;DMD_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.	H	3187;1854;1851;127;891;3191;3195;735;735;3195;3072;735;735;127;735;127;127	ENSP00000367997:R127H;ENSP00000350765:R891H;ENSP00000367948:R3191H;ENSP00000354923:R3195H;ENSP00000352894:R735H;ENSP00000340057:R735H;ENSP00000367979:R735H;ENSP00000444119:R735H;ENSP00000367974:R127H;ENSP00000417123:R735H;ENSP00000354464:R127H;ENSP00000367951:R127H	ENSP00000340057:R735H	R	-	2	0	DMD	31134685	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.458000	0.80787	2.415000	0.81967	0.600000	0.82982	CGT		0.373	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
DMD	1756	broad.mit.edu	37	X	31893417	31893417	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:31893417delT	ENST00000357033.4	-	48	7192	c.6986delA	c.(6985-6987)aagfs	p.K2329fs	DMD_ENST00000378677.2_Frame_Shift_Del_p.K2325fs|DMD_ENST00000359836.1_5'UTR|DMD_ENST00000474231.1_5'UTR|DMD_ENST00000343523.2_5'UTR|DMD_ENST00000378707.3_5'UTR|DMD_ENST00000541735.1_5'UTR	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2329			Missing (in DMD).		cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.K2325fs*9(1)|p.K2324fs*9(1)|p.K988fs*9(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GTCTTCAAGCTTTTTTTCAAG	0.373																																					p.K988fs												.	.	3	Deletion - Frameshift(3)	large_intestine(3)	c.2963delA	X	GRCh37	CD972168	DMD	D		.						75.0	61.0	66.0					X																	31893417		2201	4300	6501	31803338	SO:0001589	frameshift_variant	1756	exon20			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.6986delA	X.37:g.31893417delT	ENSP00000354923:p.Lys2329fs	Somatic		Capture	Illumina HiSeq	Phase_I	31803338	NM_004011	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Frame_Shift_Del	DEL	ENST00000357033.4	37	CCDS14233.1																																																																																				0.373	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
SRPX	8406	broad.mit.edu	37	X	38024106	38024106	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:38024106C>T	ENST00000378533.3	-	5	675	c.569G>A	c.(568-570)cGc>cAc	p.R190H	TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000544439.1_Missense_Mutation_p.R170H|SRPX_ENST00000343800.6_Missense_Mutation_p.R177H|SRPX_ENST00000538295.1_Missense_Mutation_p.R190H|SRPX_ENST00000432886.2_Missense_Mutation_p.R131H	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	190	HYR. {ECO:0000255|PROSITE- ProRule:PRU00113}.				autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.R190H(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						TTCTGCAATGCGTTCCTTCAC	0.443																																					p.R190H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G569A	X						.						167.0	142.0	151.0					X																	38024106		2202	4300	6502	37909050	SO:0001583	missense	8406	exon5			U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"""sushi-repeat-containing protein, X chromosome"", ""sushi-repeat-containing protein, X-linked"""			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.569G>A	X.37:g.38024106C>T	ENSP00000367794:p.Arg190His	Somatic		Capture	Illumina HiSeq	Phase_I	37909050	NM_006307	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	Missense_Mutation	SNP	ENST00000378533.3	37	CCDS14245.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.665181	0.88251	.	.	ENSG00000101955	ENST00000544439;ENST00000432886;ENST00000538295;ENST00000378533;ENST00000343800	T;T;T;T;T	0.26067	1.76;1.76;1.76;1.76;1.76	5.79	5.79	0.91817	Hyalin (2);	0.046879	0.85682	D	0.000000	T	0.27384	0.0672	N	0.19112	0.55	0.41709	D	0.989448	D;D;D;D	0.76494	0.997;0.999;0.997;0.998	D;D;P;P	0.66847	0.947;0.919;0.754;0.841	T	0.15838	-1.0423	10	0.15066	T	0.55	-12.9387	6.7217	0.23334	0.0:0.7669:0.0:0.2331	.	190;131;170;190	F5H4D7;B4DQH5;G3V1L0;P78539	.;.;.;SRPX_HUMAN	H	170;131;190;190;177	ENSP00000440758:R170H;ENSP00000411165:R131H;ENSP00000445034:R190H;ENSP00000367794:R190H;ENSP00000339211:R177H	ENSP00000339211:R177H	R	-	2	0	SRPX	37909050	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	4.674000	0.61612	2.426000	0.82243	0.506000	0.49869	CGC		0.443	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307	
BCOR	54880	broad.mit.edu	37	X	39923642	39923642	+	Missense_Mutation	SNP	T	T	C	rs373730020		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:39923642T>C	ENST00000378444.4	-	7	3677	c.3449A>G	c.(3448-3450)gAg>gGg	p.E1150G	BCOR_ENST00000397354.3_Missense_Mutation_p.E1150G|BCOR_ENST00000342274.4_Missense_Mutation_p.E1150G|BCOR_ENST00000378455.4_Missense_Mutation_p.E1132G|BCOR_ENST00000378463.1_Missense_Mutation_p.E27G	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1150					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.E1150G(1)		breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						TGGCACCTCCTCCGCAGTGGT	0.642			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																														p.E1150G			Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3449G	X						.	T	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	0,3833		0,0,1631,571	57.0	48.0	51.0		3449,3395,3449,3449	5.5	0.0	X		51	1,6727		0,1,2427,1872	no	missense,missense,missense,missense	BCOR	NM_001123383.1,NM_001123384.1,NM_001123385.1,NM_017745.5	98,98,98,98	0,1,4058,2443	CC,CT,TT,T		0.0149,0.0,0.0095	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	1150/1722,1132/1704,1150/1756,1150/1722	39923642	1,10560	2202	4300	6502	39808586	SO:0001583	missense	54880	exon7			AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.3449A>G	X.37:g.39923642T>C	ENSP00000367705:p.Glu1150Gly	Somatic		Capture	Illumina HiSeq	Phase_I	39808586	NM_001123383	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	37	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	T	19.43	3.825912	0.71143	0.0	1.49E-4	ENSG00000183337	ENST00000413905;ENST00000378463;ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000406200	T;T;T;T;T;T;T	0.11277	2.79;2.79;2.79;2.79;2.79;2.79;2.79	5.48	5.48	0.80851	.	.	.	.	.	T	0.15349	0.0370	L	0.27053	0.805	0.21355	N	0.999716	P;P;D	0.55385	0.915;0.952;0.971	P;P;P	0.53035	0.574;0.524;0.716	T	0.09885	-1.0654	9	0.87932	D	0	-9.8683	11.9348	0.52868	0.0:0.0:0.0:1.0	.	1132;1150;1150	Q6W2J9-4;Q6W2J9;Q6W2J9-2	.;BCOR_HUMAN;.	G	54;27;1132;1150;1150;1150;1150	ENSP00000408006:E54G;ENSP00000367724:E27G;ENSP00000367716:E1132G;ENSP00000380512:E1150G;ENSP00000367705:E1150G;ENSP00000345923:E1150G;ENSP00000384485:E1150G	ENSP00000345923:E1150G	E	-	2	0	BCOR	39808586	0.991000	0.36638	0.028000	0.17463	0.945000	0.59286	4.632000	0.61311	1.842000	0.53543	0.430000	0.28490	GAG		0.642	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
BCOR	54880	broad.mit.edu	37	X	39933072	39933072	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:39933072C>A	ENST00000378444.4	-	4	1755	c.1527G>T	c.(1525-1527)tgG>tgT	p.W509C	BCOR_ENST00000397354.3_Missense_Mutation_p.W509C|BCOR_ENST00000342274.4_Missense_Mutation_p.W509C|BCOR_ENST00000378455.4_Missense_Mutation_p.W509C	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	509	Interaction with BCL6.				heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.W509C(1)		breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						CGGGCACCACCCAGGATGAGG	0.498			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																														p.W509C			Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1527T	X						.						91.0	60.0	70.0					X																	39933072		2202	4300	6502	39818016	SO:0001583	missense	54880	exon4			AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.1527G>T	X.37:g.39933072C>A	ENSP00000367705:p.Trp509Cys	Somatic		Capture	Illumina HiSeq	Phase_I	39818016	NM_001123383	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	37	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.221650	0.58560	.	.	ENSG00000183337	ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000406200	T;T;T;T;T	0.27104	1.69;1.69;1.69;1.69;1.69	5.6	5.6	0.85130	.	.	.	.	.	T	0.43389	0.1245	L	0.32530	0.975	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.998;0.999	T	0.38134	-0.9675	9	0.87932	D	0	-12.3462	18.6437	0.91404	0.0:1.0:0.0:0.0	.	509;509;509;509	Q6W2J9-3;Q6W2J9-4;Q6W2J9;Q6W2J9-2	.;.;BCOR_HUMAN;.	C	509	ENSP00000367716:W509C;ENSP00000380512:W509C;ENSP00000367705:W509C;ENSP00000345923:W509C;ENSP00000384485:W509C	ENSP00000345923:W509C	W	-	3	0	BCOR	39818016	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.445000	0.80570	2.346000	0.79739	0.600000	0.82982	TGG		0.498	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
MED14	9282	broad.mit.edu	37	X	40585998	40585998	+	Splice_Site	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:40585998C>T	ENST00000324817.1	-	3	466	c.348G>A	c.(346-348)gcG>gcA	p.A116A		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	116					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.A116A(1)		NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TTTAACTCACCGCACATTTTT	0.338																																					p.A116A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G348A	X						.						44.0	41.0	42.0					X																	40585998		2203	4300	6503	40470942	SO:0001630	splice_region_variant	9282	exon3			AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"""cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"""	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.348+1G>A	X.37:g.40585998C>T		Somatic		Capture	Illumina HiSeq	Phase_I	40470942	NM_004229	Q4KMR7|Q9UNB3	Silent	SNP	ENST00000324817.1	37	CCDS14254.1																																																																																				0.338	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229	Silent
RGN	9104	broad.mit.edu	37	X	46940593	46940593	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:46940593G>A	ENST00000352078.4	+	2	395	c.50G>A	c.(49-51)gGt>gAt	p.G17D	RGN_ENST00000336169.3_Missense_Mutation_p.G17D|RGN_ENST00000457380.1_Missense_Mutation_p.G17D|RGN_ENST00000397180.1_Missense_Mutation_p.G17D|RGN_ENST00000469346.1_3'UTR	NM_004683.4	NP_004674.1	Q15493	RGN_HUMAN	regucalcin	17					cellular calcium ion homeostasis (GO:0006874)|L-ascorbic acid biosynthetic process (GO:0019853)|positive regulation of ATPase activity (GO:0032781)|regulation of calcium-mediated signaling (GO:0050848)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|enzyme regulator activity (GO:0030234)|gluconolactonase activity (GO:0004341)|zinc ion binding (GO:0008270)	p.G17D(1)		breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	9						TGCCGGTGTGGTGAGTCTCCA	0.478																																					p.G17D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G50A	X						.						227.0	183.0	198.0					X																	46940593		2203	4300	6503	46825537	SO:0001583	missense	9104	exon3			D31815	CCDS14272.1, CCDS75968.1	Xp11.3	2014-03-14	2013-04-26		ENSG00000130988	ENSG00000130988	3.1.1.17		9989	protein-coding gene	gene with protein product	"""senescence marker protein-30"", ""gluconolactonase"""	300212	"""regucalcin (senescence marker protein-30)"""			7548213	Standard	NM_152869		Approved	SMP30, RC	uc004dha.1	Q15493	OTTHUMG00000021435	ENST00000352078.4:c.50G>A	X.37:g.46940593G>A	ENSP00000253303:p.Gly17Asp	Somatic		Capture	Illumina HiSeq	Phase_I	46825537	NM_152869	A4FTW1|A8K271|Q53FC9|Q5JRR5	De_novo_Start_OutOfFrame	SNP	ENST00000352078.4	37	CCDS14272.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.575369	0.86645	.	.	ENSG00000130988	ENST00000397180;ENST00000457380;ENST00000352078;ENST00000336169	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.45	5.45	0.79879	SMP-30/Gluconolaconase/LRE-like region (1);Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.72471	0.3464	H	0.97829	4.085	0.43222	D	0.995102	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.84338	0.0525	10	0.87932	D	0	-2.9442	18.3548	0.90353	0.0:0.0:1.0:0.0	.	17;17	Q15493-2;Q15493	.;RGN_HUMAN	D	17	ENSP00000380365:G17D;ENSP00000406568:G17D;ENSP00000253303:G17D;ENSP00000338400:G17D	ENSP00000338400:G17D	G	+	2	0	RGN	46825537	1.000000	0.71417	0.635000	0.29338	0.814000	0.46013	8.419000	0.90253	2.274000	0.75844	0.513000	0.50165	GGT		0.478	RGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056385.1	NM_004683	
RBM10	8241	broad.mit.edu	37	X	47039853	47039853	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:47039853C>T	ENST00000377604.3	+	12	1938	c.1196C>T	c.(1195-1197)gCt>gTt	p.A399V	RBM10_ENST00000329236.7_Missense_Mutation_p.A321V|RBM10_ENST00000345781.6_Missense_Mutation_p.A322V|RBM10_ENST00000478410.1_3'UTR	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	399					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)	p.A399V(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						CGCATCAGTGCTGCCTCTGTG	0.617																																					p.A399V	Melanoma(171;120 2705 19495 39241)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1196T	X						.						41.0	32.0	35.0					X																	47039853		2203	4300	6503	46924797	SO:0001583	missense	8241	exon12			U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"""Zinc fingers, RAN-binding domain containing"", ""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.1196C>T	X.37:g.47039853C>T	ENSP00000366829:p.Ala399Val	Somatic		Capture	Illumina HiSeq	Phase_I	46924797	NM_005676	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	37	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.161377	0.78226	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	T;T;T	0.20738	2.72;2.05;2.31	2.92	2.92	0.33932	.	0.151400	0.43110	D	0.000611	T	0.36799	0.0980	L	0.49126	1.545	0.49798	D	0.999822	P;P;D;D;D	0.89917	0.946;0.941;0.997;0.996;1.0	B;P;P;D;D	0.87578	0.41;0.571;0.895;0.99;0.998	T	0.11767	-1.0574	10	0.54805	T	0.06	-7.1509	11.024	0.47734	0.0:1.0:0.0:0.0	.	322;464;398;321;399	P98175-3;Q7Z3D7;P98175-2;P98175-4;P98175	.;.;.;.;RBM10_HUMAN	V	399;321;322	ENSP00000366829:A399V;ENSP00000328848:A321V;ENSP00000329659:A322V	ENSP00000328848:A321V	A	+	2	0	RBM10	46924797	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.787000	0.69013	1.724000	0.51502	0.525000	0.51046	GCT		0.617	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676	
USP11	8237	broad.mit.edu	37	X	47100031	47100031	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:47100031G>A	ENST00000218348.3	+	6	856	c.856G>A	c.(856-858)Gca>Aca	p.A286T	USP11_ENST00000377107.2_Missense_Mutation_p.A243T	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	286					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)	p.A286T(2)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						TTGGCCCAGCGCACAGCTGCA	0.522																																					p.A286T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G856A	X						.						68.0	62.0	64.0					X																	47100031		2203	4300	6503	46984975	SO:0001583	missense	8237	exon6			U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"""Ubiquitin-specific peptidases"""	12609	protein-coding gene	gene with protein product		300050	"""ubiquitin specific protease 11"""			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.856G>A	X.37:g.47100031G>A	ENSP00000218348:p.Ala286Thr	Somatic		Capture	Illumina HiSeq	Phase_I	46984975	NM_004651	B2RTX1|Q8IUG6|Q9BWE1	Missense_Mutation	SNP	ENST00000218348.3	37	CCDS14277.1	.	.	.	.	.	.	.	.	.	.	G	17.40	3.380766	0.61845	.	.	ENSG00000102226	ENST00000377107;ENST00000218348;ENST00000377078	T;T;T	0.42900	2.02;2.01;0.96	5.6	0.0622	0.14344	.	0.846335	0.10226	N	0.700276	T	0.25568	0.0622	L	0.44542	1.39	0.31428	N	0.673526	B;B	0.13594	0.002;0.008	B;B	0.09377	0.004;0.003	T	0.34054	-0.9844	10	0.13470	T	0.59	-0.8477	0.4929	0.00567	0.3011:0.1243:0.3221:0.2525	.	13;286	B3KP28;P51784	.;UBP11_HUMAN	T	243;286;13	ENSP00000366311:A243T;ENSP00000218348:A286T;ENSP00000366279:A13T	ENSP00000218348:A286T	A	+	1	0	USP11	46984975	0.521000	0.26258	0.001000	0.08648	0.762000	0.43233	1.189000	0.32114	-0.058000	0.13177	0.513000	0.50165	GCA		0.522	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651	
SSX5	6758	broad.mit.edu	37	X	48049616	48049616	+	Missense_Mutation	SNP	C	C	T	rs144094801	byFrequency	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:48049616C>T	ENST00000376923.1	-	5	418	c.419G>A	c.(418-420)cGc>cAc	p.R140H	SSX5_ENST00000311798.1_Missense_Mutation_p.R181H|SSX5_ENST00000347757.1_Missense_Mutation_p.R140H			O60225	SSX5_HUMAN	synovial sarcoma, X breakpoint 5	140					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.R181H(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|skin(1)	18						TCCTGAGGGGCGCAGCTGTTT	0.468																																					p.R140H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G419A	X						.	C	HIS/ARG,HIS/ARG	5,3830		0,5,1627,571	156.0	138.0	144.0		542,419	0.4	0.0	X	dbSNP_134	144	0,6727		0,0,2428,1871	yes	missense,missense	SSX5	NM_021015.3,NM_175723.1	29,29	0,5,4055,2442	TT,TC,CC,C		0.0,0.1304,0.0473	benign,benign	181/230,140/189	48049616	5,10557	2203	4299	6502	47934560	SO:0001583	missense	6758	exon6			BC016640	CCDS14288.1, CCDS14289.1	Xp11.23	2008-02-05			ENSG00000165583	ENSG00000165583			11339	protein-coding gene	gene with protein product		300327					Standard	NM_021015		Approved		uc004diz.1	O60225	OTTHUMG00000021471	ENST00000376923.1:c.419G>A	X.37:g.48049616C>T	ENSP00000366122:p.Arg140His	Somatic		Capture	Illumina HiSeq	Phase_I	47934560	NM_175723	Q5JQ59|Q5JQ60|Q96AW3	Missense_Mutation	SNP	ENST00000376923.1	37	CCDS14289.1	.	.	.	.	.	.	.	.	.	.	N	0.318	-0.963419	0.02249	0.001304	0.0	ENSG00000165583	ENST00000311798;ENST00000376923;ENST00000347757;ENST00000403001	T;T;T;T	0.32023	3.08;3.12;3.12;1.47	1.36	0.406	0.16366	.	1.623200	0.03986	N	0.294057	T	0.15998	0.0385	N	0.12182	0.205	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.08055	0.001;0.003	T	0.18493	-1.0335	10	0.15499	T	0.54	.	4.4085	0.11421	0.3834:0.6166:0.0:0.0	.	140;181	O60225;O60225-2	SSX5_HUMAN;.	H	181;140;140;80	ENSP00000312415:R181H;ENSP00000366122:R140H;ENSP00000290558:R140H;ENSP00000385051:R80H	ENSP00000312415:R181H	R	-	2	0	SSX5	47934560	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.617000	0.05584	0.071000	0.16664	0.171000	0.16805	CGC		0.468	SSX5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056466.1	NM_021015	
TIMM17B	10245	broad.mit.edu	37	X	48754134	48754134	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:48754134G>A	ENST00000376582.3	-	3	182	c.34C>T	c.(34-36)Cga>Tga	p.R12*	PQBP1_ENST00000376563.1_5'Flank|PQBP1_ENST00000447146.2_5'Flank|PQBP1_ENST00000218224.4_5'Flank|TIMM17B_ENST00000396779.3_Nonsense_Mutation_p.R12*|TIMM17B_ENST00000465150.2_Nonsense_Mutation_p.R12*|TIMM17B_ENST00000495490.2_5'UTR|PQBP1_ENST00000376566.4_5'Flank|PQBP1_ENST00000396763.1_5'Flank|TIMM17B_ENST00000472645.1_5'UTR|PQBP1_ENST00000247140.4_5'Flank|PQBP1_ENST00000376548.5_5'Flank	NM_005834.3	NP_005825.1	O60830	TI17B_HUMAN	translocase of inner mitochondrial membrane 17 homolog B (yeast)	12					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane presequence translocase complex (GO:0005744)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)	p.R12*(1)		kidney(1)|large_intestine(1)|lung(3)|ovary(1)	6						TCCACAATTCGCCATGGGCTG	0.562																																					p.R12X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C34T	X						.						79.0	59.0	66.0					X																	48754134		2203	4300	6503	48639078	SO:0001587	stop_gained	10245	exon3			AF034790	CCDS14308.1, CCDS55411.1	Xp11.23	2008-02-05			ENSG00000126768	ENSG00000126768			17310	protein-coding gene	gene with protein product		300249				10339406	Standard	NM_001167947		Approved	DXS9822, JM3	uc004dla.2	O60830	OTTHUMG00000034498	ENST00000376582.3:c.34C>T	X.37:g.48754134G>A	ENSP00000365766:p.Arg12*	Somatic		Capture	Illumina HiSeq	Phase_I	48639078	NM_001167947	A8K2E2|J3KPV3|Q9UJV0	Nonsense_Mutation	SNP	ENST00000376582.3	37	CCDS14308.1	.	.	.	.	.	.	.	.	.	.	G	37	6.459383	0.97585	.	.	ENSG00000126768	ENST00000376582;ENST00000396779	.	.	.	5.61	1.14	0.20703	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.4909	14.7397	0.69445	0.0:0.0:0.4352:0.5648	.	.	.	.	X	12	.	ENSP00000365766:R12X	R	-	1	2	TIMM17B	48639078	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	2.307000	0.43682	0.135000	0.18707	-0.358000	0.07595	CGA		0.562	TIMM17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083411.2	NM_005834	
OTUD5	55593	broad.mit.edu	37	X	48783167	48783167	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:48783167G>A	ENST00000156084.4	-	6	1294	c.1234C>T	c.(1234-1236)Cgg>Tgg	p.R412W	OTUD5_ENST00000376488.3_Missense_Mutation_p.R407W|OTUD5_ENST00000428668.2_Missense_Mutation_p.R190W|OTUD5_ENST00000484499.1_5'Flank|OTUD5_ENST00000396743.3_Missense_Mutation_p.R407W	NM_017602.3	NP_060072.1	Q96G74	OTUD5_HUMAN	OTU deubiquitinase 5	412					innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)	ubiquitin-specific protease activity (GO:0004843)	p.R383W(1)|p.R412W(1)		endometrium(2)|large_intestine(3)|lung(6)|pancreas(2)	13						TCCTGATCCCGCAACCACTGC	0.562																																					p.R407W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1219T	X						.						84.0	63.0	71.0					X																	48783167		2202	4300	6502	48668111	SO:0001583	missense	55593	exon6				CCDS14313.1, CCDS48104.1, CCDS48105.1	Xp11.23	2014-06-09	2014-02-24		ENSG00000068308	ENSG00000068308		"""OTU domain containing"""	25402	protein-coding gene	gene with protein product		300713	"""OTU domain containing 5"""			24143256	Standard	NM_001136157		Approved	DKFZp761A052, DUBA	uc004dlu.3	Q96G74	OTTHUMG00000024130	ENST00000156084.4:c.1234C>T	X.37:g.48783167G>A	ENSP00000156084:p.Arg412Trp	Somatic		Capture	Illumina HiSeq	Phase_I	48668111	NM_001136157	B4DGG7|G5E9D7|Q4KMN9|Q8N6T5|Q9H650|Q9H9U0|Q9NT65	Missense_Mutation	SNP	ENST00000156084.4	37	CCDS14313.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110503	0.77210	.	.	ENSG00000068308	ENST00000396743;ENST00000453548;ENST00000455452;ENST00000156084;ENST00000376488;ENST00000428668	D;T;D;D;T	0.84873	-1.91;0.89;-1.91;-1.91;0.89	5.17	0.966	0.19667	.	0.184842	0.38005	N	0.001857	D	0.89336	0.6686	L	0.57536	1.79	0.46798	D	0.999208	D;B;D	0.89917	0.999;0.214;1.0	P;B;D	0.75484	0.8;0.037;0.986	D	0.88069	0.2799	10	0.87932	D	0	-13.3359	12.7994	0.57578	0.0:0.0:0.4306:0.5694	.	190;412;407	B4DGG7;Q96G74;G5E9D7	.;OTUD5_HUMAN;.	W	407;383;285;412;407;190	ENSP00000379969:R407W;ENSP00000390767:R285W;ENSP00000156084:R412W;ENSP00000365671:R407W;ENSP00000401629:R190W	ENSP00000156084:R412W	R	-	1	2	OTUD5	48668111	0.997000	0.39634	0.991000	0.47740	0.977000	0.68977	2.792000	0.47837	-0.063000	0.13065	0.544000	0.68410	CGG		0.562	OTUD5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000060799.1	NM_017602	
PPP1R3F	89801	broad.mit.edu	37	X	49142522	49142522	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:49142522C>T	ENST00000055335.6	+	4	1386	c.1370C>T	c.(1369-1371)gCc>gTc	p.A457V	PPP1R3F_ENST00000376188.1_Missense_Mutation_p.A111V|PPP1R3F_ENST00000438316.1_Missense_Mutation_p.A128V|PPP1R3F_ENST00000495799.1_Missense_Mutation_p.A111V|PPP1R3F_ENST00000466508.1_Missense_Mutation_p.A111V	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	457					regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)	p.A457V(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					CAGGCAGAGGCCACATGGGGA	0.672																																					p.A457V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1370T	X						.						20.0	15.0	17.0					X																	49142522		2190	4281	6471	49029466	SO:0001583	missense	89801	exon4				CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14944	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3F"""			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.1370C>T	X.37:g.49142522C>T	ENSP00000055335:p.Ala457Val	Somatic		Capture	Illumina HiSeq	Phase_I	49029466	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Missense_Mutation	SNP	ENST00000055335.6	37	CCDS35254.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.849373	0.32699	.	.	ENSG00000049769	ENST00000466508;ENST00000438316;ENST00000055335;ENST00000495799;ENST00000376188	T;T;T;T;T	0.59224	0.72;0.72;0.28;0.72;0.72	5.34	4.42	0.53409	.	0.136762	0.33895	N	0.004450	T	0.48607	0.1509	L	0.27053	0.805	0.20926	N	0.999827	P;P;P	0.51057	0.705;0.869;0.941	B;P;P	0.47827	0.359;0.558;0.531	T	0.45789	-0.9237	10	0.59425	D	0.04	-6.025	9.6552	0.39921	0.2071:0.7929:0.0:0.0	.	128;142;457	F5H262;A2VDJ8;Q6ZSY5	.;.;PPR3F_HUMAN	V	111;128;457;111;111	ENSP00000420687:A111V;ENSP00000415548:A128V;ENSP00000055335:A457V;ENSP00000417535:A111V;ENSP00000365359:A111V	ENSP00000055335:A457V	A	+	2	0	PPP1R3F	49029466	0.506000	0.26139	0.771000	0.31576	0.080000	0.17528	0.654000	0.24918	2.379000	0.81126	0.529000	0.55759	GCC		0.672	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215	
NUDT10	170685	broad.mit.edu	37	X	51076060	51076060	+	Silent	SNP	C	C	T	rs183396979		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:51076060C>T	ENST00000376006.3	+	2	463	c.243C>T	c.(241-243)ggC>ggT	p.G81G	NUDT10_ENST00000356450.2_Silent_p.G81G	NM_153183.2	NP_694853.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 10	0					ADP catabolic process (GO:0046032)|IDP catabolic process (GO:0046709)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrial matrix (GO:0005759)	adenosine-diphosphatase activity (GO:0043262)|ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)	p.G81G(1)		cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(1)|prostate(3)|upper_aerodigestive_tract(1)	16	Ovarian(276;0.236)					GGCTCCTGGGCGTCTTCGAAC	0.627													C|||	2	0.000529801	0.0	0.0	3775	,	,		10832	0.002		0.0	False		,,,				2504	0.0				p.G81G	NSCLC(90;1817 2035 37909 38249)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C243T	X						.						71.0	76.0	74.0					X																	51076060		2203	4300	6503	51092800	SO:0001819	synonymous_variant	170685	exon2			AF469196	CCDS35278.1	Xp11.22-p11.1	2014-05-20			ENSG00000122824	ENSG00000122824		"""Nudix motif containing"""	17621	protein-coding gene	gene with protein product		300527				12105228	Standard	NM_153183		Approved	DIPP3a, hDIPP3alpha	uc004dph.3	Q8NFP7	OTTHUMG00000021530	ENST00000376006.3:c.243C>T	X.37:g.51076060C>T		Somatic		Capture	Illumina HiSeq	Phase_I	51092800	NM_153183	Q8NBN1|Q8NCB9|Q8NG25	Silent	SNP	ENST00000376006.3	37	CCDS35278.1																																																																																				0.627	NUDT10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056578.1	NM_153183	
MAGED1	9500	broad.mit.edu	37	X	51638272	51638272	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:51638272C>T	ENST00000375722.1	+	3	421	c.169C>T	c.(169-171)Cca>Tca	p.P57S	MAGED1_ENST00000375772.3_Missense_Mutation_p.P57S|MAGED1_ENST00000326587.7_Missense_Mutation_p.P57S|MAGED1_ENST00000375695.2_Missense_Mutation_p.P113S|MAGED1_ENST00000494718.1_3'UTR			Q9Y5V3	MAGD1_HUMAN	melanoma antigen family D, 1	57					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|circadian regulation of gene expression (GO:0032922)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of circadian rhythm (GO:0042752)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	transcription coactivator activity (GO:0003713)	p.P113S(1)		breast(1)|endometrium(4)|large_intestine(10)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	32	Ovarian(276;0.236)					TTCACAGCCCCCAACTGCCAA	0.552										Multiple Myeloma(10;0.10)																											p.P57S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C169T	X						.						47.0	40.0	42.0					X																	51638272		2203	4300	6503	51655012	SO:0001583	missense	9500	exon3			AF124440	CCDS14337.1, CCDS35279.1	Xp11.23	2008-08-01			ENSG00000179222	ENSG00000179222			6813	protein-coding gene	gene with protein product		300224				10409427	Standard	NM_006986		Approved	NRAGE, DLXIN-1	uc004dpn.3	Q9Y5V3	OTTHUMG00000021540	ENST00000375722.1:c.169C>T	X.37:g.51638272C>T	ENSP00000364874:p.Pro57Ser	Somatic		Capture	Illumina HiSeq	Phase_I	51655012	NM_006986	Q5VSH6|Q8IZ84|Q8WY92|Q9H352|Q9HBT4|Q9UF36	Missense_Mutation	SNP	ENST00000375722.1	37	CCDS14337.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.825452	0.50739	.	.	ENSG00000179222	ENST00000375772;ENST00000375722;ENST00000326587;ENST00000375695;ENST00000430189	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	3.27	3.27	0.37495	.	0.000000	0.41194	D	0.000935	T	0.60702	0.2289	L	0.43923	1.385	0.30398	N	0.780332	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.996	T	0.58918	-0.7551	10	0.56958	D	0.05	.	9.2178	0.37358	0.0:1.0:0.0:0.0	.	57;113;57	B4DQ04;Q9Y5V3-2;Q9Y5V3	.;.;MAGD1_HUMAN	S	57;57;57;113;57	ENSP00000364927:P57S;ENSP00000364874:P57S;ENSP00000325333:P57S;ENSP00000364847:P113S	ENSP00000325333:P57S	P	+	1	0	MAGED1	51655012	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	2.801000	0.47908	1.914000	0.55421	0.458000	0.33432	CCA		0.552	MAGED1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056593.1	NM_001005332	
GNL3L	54552	broad.mit.edu	37	X	54570741	54570741	+	Silent	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:54570741G>A	ENST00000336470.4	+	8	751	c.612G>A	c.(610-612)caG>caA	p.Q204Q	GNL3L_ENST00000360845.2_Silent_p.Q204Q|GNL3L_ENST00000489691.1_3'UTR	NM_019067.5	NP_061940.1	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)-like	204	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.Q204Q(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	30						CCAGTACCCAGCATCAGGTCA	0.552																																					p.Q204Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G612A	X						.						65.0	50.0	55.0					X																	54570741		2203	4300	6503	54587466	SO:0001819	synonymous_variant	54552	exon8			AK001475	CCDS14360.1	Xp11.22	2010-03-17			ENSG00000130119	ENSG00000130119			25553	protein-coding gene	gene with protein product		300873				12477932	Standard	NM_019067		Approved	FLJ10613	uc004dth.2	Q9NVN8	OTTHUMG00000021629	ENST00000336470.4:c.612G>A	X.37:g.54570741G>A		Somatic		Capture	Illumina HiSeq	Phase_I	54587466	NM_019067		Silent	SNP	ENST00000336470.4	37	CCDS14360.1																																																																																				0.552	GNL3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056805.1	NM_019067	
UBQLN2	29978	broad.mit.edu	37	X	56591232	56591232	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:56591232G>A	ENST00000338222.5	+	1	1207	c.926G>A	c.(925-927)cGc>cAc	p.R309H		NM_013444.3	NP_038472.2	Q9UHD9	UBQL2_HUMAN	ubiquilin 2	309					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R309H(1)		breast(2)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)	21						CAGCCTTCCCGCACAGAAAAT	0.572																																					p.R309H	Esophageal Squamous(104;218 1492 6022 10838 28884)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G926A	X						.						60.0	49.0	53.0					X																	56591232		2203	4300	6503	56607957	SO:0001583	missense	29978	exon1			AF189009	CCDS14374.1	Xp11.21	2014-09-17			ENSG00000188021	ENSG00000188021		"""Ubiquilin family"""	12509	protein-coding gene	gene with protein product	"""NEDD4 binding protein 4"""	300264				10675567	Standard	NM_013444		Approved	Chap1, Dsk2, RIHFB2157, LIC-2, CHAP1/DSK2, PLIC-2, N4BP4, PLIC2	uc004dus.3	Q9UHD9	OTTHUMG00000021669	ENST00000338222.5:c.926G>A	X.37:g.56591232G>A	ENSP00000345195:p.Arg309His	Somatic		Capture	Illumina HiSeq	Phase_I	56607957	NM_013444	O94798|Q5D027|Q9H3W6|Q9HAZ4	Missense_Mutation	SNP	ENST00000338222.5	37	CCDS14374.1	.	.	.	.	.	.	.	.	.	.	G	17.63	3.438300	0.62955	.	.	ENSG00000188021	ENST00000338222;ENST00000535171	T	0.80214	-1.35	4.93	4.06	0.47325	.	0.000000	0.64402	D	0.000001	D	0.87565	0.6209	M	0.80183	2.485	0.44871	D	0.99788	D;D	0.89917	0.998;1.0	D;D	0.69142	0.925;0.962	D	0.86941	0.2079	10	0.45353	T	0.12	-7.5899	9.8753	0.41200	0.1038:0.0:0.8962:0.0	.	309;309	B4DZF1;Q9UHD9	.;UBQL2_HUMAN	H	309	ENSP00000345195:R309H	ENSP00000345195:R309H	R	+	2	0	UBQLN2	56607957	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.858000	0.75461	2.440000	0.82611	0.600000	0.82982	CGC		0.572	UBQLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056891.1	NM_013444	
UBQLN2	29978	broad.mit.edu	37	X	56591874	56591874	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:56591874delC	ENST00000338222.5	+	1	1849	c.1568delC	c.(1567-1569)gccfs	p.A523fs		NM_013444.3	NP_038472.2	Q9UHD9	UBQL2_HUMAN	ubiquilin 2	523	12 X 3 AA tandem repeats of P-X-X.				cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P525fs*71(1)		breast(2)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)	21						GGCCCTGCAGCCCCCCCTGGC	0.642																																					p.A523fs	Esophageal Squamous(104;218 1492 6022 10838 28884)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1568delC	X						.						8.0	9.0	8.0					X																	56591874		2158	4239	6397	56608599	SO:0001589	frameshift_variant	29978	exon1			AF189009	CCDS14374.1	Xp11.21	2014-09-17			ENSG00000188021	ENSG00000188021		"""Ubiquilin family"""	12509	protein-coding gene	gene with protein product	"""NEDD4 binding protein 4"""	300264				10675567	Standard	NM_013444		Approved	Chap1, Dsk2, RIHFB2157, LIC-2, CHAP1/DSK2, PLIC-2, N4BP4, PLIC2	uc004dus.3	Q9UHD9	OTTHUMG00000021669	ENST00000338222.5:c.1568delC	X.37:g.56591874delC	ENSP00000345195:p.Ala523fs	Somatic		Capture	Illumina HiSeq	Phase_I	56608599	NM_013444	O94798|Q5D027|Q9H3W6|Q9HAZ4	Frame_Shift_Del	DEL	ENST00000338222.5	37	CCDS14374.1																																																																																				0.642	UBQLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056891.1	NM_013444	
EDA2R	60401	broad.mit.edu	37	X	65819341	65819341	+	Silent	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:65819341T>C	ENST00000374719.3	-	6	935	c.879A>G	c.(877-879)gaA>gaG	p.E293E	EDA2R_ENST00000450752.1_Silent_p.E314E|EDA2R_ENST00000253392.5_Silent_p.E314E|EDA2R_ENST00000456230.2_Silent_p.E293E|EDA2R_ENST00000396050.1_Silent_p.E293E|EDA2R_ENST00000451436.2_Silent_p.E169E	NM_021783.3	NP_068555	Q9HAV5	TNR27_HUMAN	ectodysplasin A2 receptor	293					cell differentiation (GO:0030154)|embryo development (GO:0009790)|epidermis development (GO:0008544)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)	p.E293E(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						GGCTGGGAACTTCAAAGGGCA	0.453																																					p.E293E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A879G	X						.						25.0	21.0	22.0					X																	65819341		2202	4294	6496	65736066	SO:0001819	synonymous_variant	60401	exon6			AF298812	CCDS14386.1, CCDS56603.1	Xq11.1	2013-05-22			ENSG00000131080	ENSG00000131080		"""Tumor necrosis factor receptor superfamily"""	17756	protein-coding gene	gene with protein product		300276				11039935	Standard	NM_021783		Approved	XEDAR, EDA-A2R, EDAA2R, TNFRSF27	uc004dwt.2	Q9HAV5	OTTHUMG00000021736	ENST00000374719.3:c.879A>G	X.37:g.65819341T>C		Somatic		Capture	Illumina HiSeq	Phase_I	65736066	NM_001199687	Q5VYX9|Q5VYY0|Q6UWM2|Q8IZA6	Silent	SNP	ENST00000374719.3	37	CCDS14386.1																																																																																				0.453	EDA2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057002.1	NM_021783	
YIPF6	286451	broad.mit.edu	37	X	67751762	67751762	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:67751762G>A	ENST00000462683.1	+	7	1376	c.632G>A	c.(631-633)cGc>cAc	p.R211H	YIPF6_ENST00000374622.2_Missense_Mutation_p.R168H	NM_173834.3	NP_776195.2	Q96EC8	YIPF6_HUMAN	Yip1 domain family, member 6	211					intestinal epithelial cell development (GO:0060576)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)		p.R211H(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(1)	7						CCTCCAAACCGCAGAGCCCTA	0.378																																					p.R168H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G503A	X						.						154.0	109.0	124.0					X																	67751762		2193	4290	6483	67668487	SO:0001583	missense	286451	exon6			BC012469	CCDS14389.1, CCDS56604.1	Xq13.1	2008-02-05			ENSG00000181704	ENSG00000181704		"""Yip1 domain family"""	28304	protein-coding gene	gene with protein product						12477932	Standard	NM_173834		Approved	MGC21416, FinGER6	uc004dwz.3	Q96EC8	OTTHUMG00000021745	ENST00000462683.1:c.632G>A	X.37:g.67751762G>A	ENSP00000417573:p.Arg211His	Somatic		Capture	Illumina HiSeq	Phase_I	67668487	NM_001195214	B4E1U7|G5E997|Q5JP08	Missense_Mutation	SNP	ENST00000462683.1	37	CCDS14389.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.683943	0.68157	.	.	ENSG00000181704	ENST00000462683;ENST00000451537;ENST00000374622	T;T;T	0.60672	0.92;0.17;0.92	5.8	4.95	0.65309	Yip1 domain (1);	0.000000	0.85682	D	0.000000	T	0.80248	0.4588	M	0.92880	3.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.995;0.998	D	0.83923	0.0302	10	0.87932	D	0	-25.1819	11.5982	0.50986	0.0877:0.0:0.9123:0.0	.	168;211	G5E997;Q96EC8	.;YIPF6_HUMAN	H	211;168;168	ENSP00000417573:R211H;ENSP00000401799:R168H;ENSP00000363751:R168H	ENSP00000363751:R168H	R	+	2	0	YIPF6	67668487	1.000000	0.71417	0.905000	0.35620	0.425000	0.31504	9.393000	0.97256	1.206000	0.43276	-0.192000	0.12808	CGC		0.378	YIPF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057016.1	NM_173834	
EFNB1	1947	broad.mit.edu	37	X	68058542	68058542	+	Missense_Mutation	SNP	C	C	T	rs367996552		TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:68058542C>T	ENST00000204961.4	+	2	991	c.211C>T	c.(211-213)Cgg>Tgg	p.R71W		NM_004429.4	NP_004420.1	P98172	EFNB1_HUMAN	ephrin-B1	71	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|embryonic pattern specification (GO:0009880)|ephrin receptor signaling pathway (GO:0048013)|neural crest cell migration (GO:0001755)|positive regulation of T cell proliferation (GO:0042102)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ephrin receptor binding (GO:0046875)	p.R71W(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	22						AGAAGCAGGGCGGCCCTATGA	0.572																																					p.R71W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C211T	X						.	C	TRP/ARG	0,3835		0,0,1632,571	58.0	45.0	50.0		211	1.1	1.0	X		50	1,6727		0,1,2427,1872	no	missense	EFNB1	NM_004429.4	101	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	probably-damaging	71/347	68058542	1,10562	2203	4300	6503	67975267	SO:0001583	missense	1947	exon2			U09303	CCDS14391.1	Xq12	2011-03-09			ENSG00000090776	ENSG00000090776		"""Ephrins"""	3226	protein-coding gene	gene with protein product		300035	"""craniofrontonasal syndrome (craniofrontonasal dysplasia)"""	EPLG2, CFNS		7774950, 16526919	Standard	NM_004429		Approved	LERK2, Elk-L	uc004dxd.4	P98172	OTTHUMG00000021751	ENST00000204961.4:c.211C>T	X.37:g.68058542C>T	ENSP00000204961:p.Arg71Trp	Somatic		Capture	Illumina HiSeq	Phase_I	67975267	NM_004429	D3DVU0	Missense_Mutation	SNP	ENST00000204961.4	37	CCDS14391.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.296787	0.60086	0.0	1.49E-4	ENSG00000090776	ENST00000204961	D	0.93426	-3.22	5.03	1.06	0.20224	Cupredoxin (2);	0.449209	0.22871	N	0.054633	D	0.93575	0.7949	L	0.50333	1.59	0.42286	D	0.992112	D	0.76494	0.999	P	0.57846	0.828	D	0.91965	0.5582	10	0.72032	D	0.01	-21.7179	12.4068	0.55445	0.565:0.435:0.0:0.0	.	71	P98172	EFNB1_HUMAN	W	71	ENSP00000204961:R71W	ENSP00000204961:R71W	R	+	1	2	EFNB1	67975267	0.902000	0.30710	0.995000	0.50966	0.944000	0.59088	0.385000	0.20685	-0.108000	0.12066	-0.763000	0.03452	CGG		0.572	EFNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057029.1	NM_004429	
KIF4A	24137	broad.mit.edu	37	X	69510346	69510346	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:69510346C>T	ENST00000374403.3	+	2	120	c.38C>T	c.(37-39)gCg>gTg	p.A13V	PDZD11_ENST00000374454.1_5'Flank|KIF4A_ENST00000485406.1_3'UTR|PDZD11_ENST00000473667.1_5'Flank|KIF4A_ENST00000374388.3_Missense_Mutation_p.A13V|PDZD11_ENST00000239666.4_5'Flank	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	13	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.A13V(2)		breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						GTAAGAGTGGCGCTGCGTTGT	0.562																																					p.A13V												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C38T	X						.						80.0	70.0	73.0					X																	69510346		2203	4300	6503	69427071	SO:0001583	missense	24137	exon2			AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"""Kinesins"""	13339	protein-coding gene	gene with protein product	"""chromokinesin"""	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.38C>T	X.37:g.69510346C>T	ENSP00000363524:p.Ala13Val	Somatic		Capture	Illumina HiSeq	Phase_I	69427071	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Missense_Mutation	SNP	ENST00000374403.3	37	CCDS14401.1	.	.	.	.	.	.	.	.	.	.	c	37	6.270632	0.97431	.	.	ENSG00000090889	ENST00000374388;ENST00000374403	T;T	0.72167	-0.63;-0.63	6.16	6.16	0.99307	Kinesin, motor domain (3);	0.000000	0.64402	D	0.000010	T	0.78123	0.4234	L	0.31476	0.935	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.75484	0.986;0.968	T	0.79097	-0.1943	10	0.59425	D	0.04	.	18.5771	0.91159	0.0:1.0:0.0:0.0	.	13;13	O95239;O95239-2	KIF4A_HUMAN;.	V	13	ENSP00000363509:A13V;ENSP00000363524:A13V	ENSP00000363509:A13V	A	+	2	0	KIF4A	69427071	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	5.515000	0.67049	2.615000	0.88500	0.597000	0.82753	GCG		0.562	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310	
TEX11	56159	broad.mit.edu	37	X	69898657	69898657	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:69898657delA	ENST00000395889.2	-	16	1439	c.1284delT	c.(1282-1284)tttfs	p.F428fs	TEX11_ENST00000374320.2_Frame_Shift_Del_p.F103fs|TEX11_ENST00000344304.3_Frame_Shift_Del_p.F428fs|TEX11_ENST00000374333.2_Frame_Shift_Del_p.F413fs	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	428					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.F413fs*17(1)		breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					CTCAAACCTCAAAACTACTGG	0.333																																					p.F428fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1284delT	X						.						109.0	95.0	99.0					X																	69898657		2203	4300	6503	69815382	SO:0001589	frameshift_variant	56159	exon16			AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"""testis expressed sequence 11"""			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.1284delT	X.37:g.69898657delA	ENSP00000379226:p.Phe428fs	Somatic		Capture	Illumina HiSeq	Phase_I	69815382	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Frame_Shift_Del	DEL	ENST00000395889.2	37	CCDS35323.1																																																																																				0.333	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1		
MED12	9968	broad.mit.edu	37	X	70351422	70351422	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:70351422G>A	ENST00000374080.3	+	29	4102	c.4070G>A	c.(4069-4071)cGc>cAc	p.R1357H	MED12_ENST00000374102.1_Missense_Mutation_p.R1357H|MED12_ENST00000333646.6_Missense_Mutation_p.R1357H			Q93074	MED12_HUMAN	mediator complex subunit 12	1357					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.R1357H(2)		breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					TGGACCATGCGCCAGTCTTCC	0.547			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.R1357H			Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4070A	X						.						129.0	123.0	125.0					X																	70351422		2093	4197	6290	70268147	SO:0001583	missense	9968	exon29			U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.4070G>A	X.37:g.70351422G>A	ENSP00000363193:p.Arg1357His	Somatic		Capture	Illumina HiSeq	Phase_I	70268147	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	37	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769276	0.90020	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072;ENST00000439750	D;D;D;D;T	0.84589	-1.87;-1.87;-1.87;-1.87;1.58	3.62	3.62	0.41486	.	0.000000	0.85682	D	0.000000	D	0.91270	0.7248	M	0.72353	2.195	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.996;0.998;0.995	D	0.92658	0.6139	10	0.87932	D	0	-12.8383	15.6611	0.77188	0.0:0.0:1.0:0.0	.	1357;1204;1357;1357	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	H	1357;1357;1357;1357;1325;102	ENSP00000333125:R1357H;ENSP00000363215:R1357H;ENSP00000363193:R1357H;ENSP00000414203:R1325H;ENSP00000408388:R102H	ENSP00000333125:R1357H	R	+	2	0	MED12	70268147	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.359000	0.97115	2.065000	0.61736	0.600000	0.82982	CGC		0.547	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
GJB1	2705	broad.mit.edu	37	X	70443559	70443559	+	Start_Codon_SNP	SNP	T	T	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:70443559T>C	ENST00000374022.3	+	2	97	c.2T>C	c.(1-3)aTg>aCg	p.M1T	GJB1_ENST00000374029.1_Start_Codon_SNP_p.M1T|GJB1_ENST00000361726.6_Start_Codon_SNP_p.M1T	NM_001097642.2	NP_001091111.1	P08034	CXB1_HUMAN	gap junction protein, beta 1, 32kDa	1					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)|purine ribonucleotide transport (GO:0015868)|transport (GO:0006810)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)	p.M1T(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(1)	10	Renal(35;0.156)					TGAGGCAGGATGAACTGGACA	0.552																																					p.M1T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2C	X						.						93.0	78.0	83.0					X																	70443559		2203	4300	6503	70360284	SO:0001582	initiator_codon_variant	2705	exon2			X04325	CCDS14408.1	Xq13.1	2014-09-17	2007-01-16		ENSG00000169562	ENSG00000169562		"""Ion channels / Gap junction proteins (connexins)"""	4283	protein-coding gene	gene with protein product	"""Charcot-Marie-Tooth neuropathy, X-linked"", ""connexin 32"""	304040	"""gap junction protein, beta 1, 32kD (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)"", ""gap junction protein, beta 1, 32kDa (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)"", ""gap junction protein, beta 1, 32kDa (connexin 32)"""	CMTX1, CMTX		1319395	Standard	NM_000166		Approved	CX32	uc004dzf.3	P08034	OTTHUMG00000021797	ENST00000374022.3:c.2T>C	X.37:g.70443559T>C	ENSP00000363134:p.Met1Thr	Somatic		Capture	Illumina HiSeq	Phase_I	70360284	NM_000166	B2R8R2|D3DVV2|Q5U0S4	Missense_Mutation	SNP	ENST00000374022.3	37	CCDS14408.1	.	.	.	.	.	.	.	.	.	.	T	15.25	2.777539	0.49786	.	.	ENSG00000169562	ENST00000374029;ENST00000374022;ENST00000447581;ENST00000361726	D;D;D;D	0.99479	-4.89;-4.89;-5.98;-4.89	4.15	4.15	0.48705	.	0.000000	0.85682	D	0.000000	D	0.99438	0.9801	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.98664	1.0685	9	0.87932	D	0	.	12.3146	0.54948	0.0:0.0:0.0:1.0	.	1	P08034	CXB1_HUMAN	T	1	ENSP00000363141:M1T;ENSP00000363134:M1T;ENSP00000407223:M1T;ENSP00000354900:M1T	ENSP00000354900:M1T	M	+	2	0	GJB1	70360284	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.844000	0.86867	1.556000	0.49512	0.424000	0.28305	ATG		0.552	GJB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057133.1	NM_000166	Missense_Mutation
PHKA1	5255	broad.mit.edu	37	X	71932665	71932665	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:71932665C>T	ENST00000373542.4	-	2	352	c.193G>A	c.(193-195)Gca>Aca	p.A65T	PHKA1_ENST00000373539.3_Missense_Mutation_p.A65T|PHKA1_ENST00000541944.1_Missense_Mutation_p.A65T|PHKA1_ENST00000339490.3_Missense_Mutation_p.A65T|PHKA1-AS1_ENST00000420998.1_RNA|PHKA1_ENST00000373545.3_Missense_Mutation_p.A65T	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	65					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.A65T(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					TCCCGGTCTGCATTCTTCCGA	0.488																																					p.A65T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G193A	X						.						61.0	52.0	55.0					X																	71932665		2203	4298	6501	71849390	SO:0001583	missense	5255	exon2				CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.193G>A	X.37:g.71932665C>T	ENSP00000362643:p.Ala65Thr	Somatic		Capture	Illumina HiSeq	Phase_I	71849390	NM_001172436	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	37	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.034652	0.93575	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.92299	-2.94;-3.01;-2.93;-2.98;-2.98	4.52	4.52	0.55395	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.050613	0.85682	D	0.000000	D	0.95695	0.8600	M	0.81802	2.56	0.80722	D	1	D;P;D	0.89917	0.998;0.928;1.0	D;P;D	0.85130	0.994;0.839;0.997	D	0.95840	0.8865	10	0.59425	D	0.04	-15.8264	13.7933	0.63155	0.0:1.0:0.0:0.0	.	65;65;65	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	T	65	ENSP00000362646:A65T;ENSP00000362643:A65T;ENSP00000441251:A65T;ENSP00000342469:A65T;ENSP00000362640:A65T	ENSP00000342469:A65T	A	-	1	0	PHKA1	71849390	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	7.521000	0.81832	2.214000	0.71695	0.600000	0.82982	GCA		0.488	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1		
MAGEE1	57692	broad.mit.edu	37	X	75649385	75649385	+	Silent	SNP	T	T	G			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:75649385T>G	ENST00000361470.2	+	1	1340	c.1062T>G	c.(1060-1062)acT>acG	p.T354T		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	354	Pro-rich.					dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)		p.T354T(2)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						GACCAAGCACTTCCGTACTGC	0.697																																					p.T354T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1062G	X						.						37.0	32.0	34.0					X																	75649385		2203	4299	6502	75565789	SO:0001819	synonymous_variant	57692	exon1			AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.1062T>G	X.37:g.75649385T>G		Somatic		Capture	Illumina HiSeq	Phase_I	75565789	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Silent	SNP	ENST00000361470.2	37	CCDS14433.1																																																																																				0.697	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932	
FAM133A	286499	broad.mit.edu	37	X	92965089	92965089	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:92965089A>C	ENST00000355813.5	+	4	1197	c.671A>C	c.(670-672)aAg>aCg	p.K224T	FAM133A_ENST00000538690.1_Missense_Mutation_p.K224T|FAM133A_ENST00000322139.4_Missense_Mutation_p.K224T|FAM133A_ENST00000332647.4_Missense_Mutation_p.K224T	NM_001171109.1|NM_173698.2	NP_001164580.1|NP_775969.1	Q8N9E0	F133A_HUMAN	family with sequence similarity 133, member A	224	Lys-rich.							p.K224T(1)		breast(2)|endometrium(2)|large_intestine(8)|lung(7)|upper_aerodigestive_tract(1)	20						AAAGTAaagaagaagaagaag	0.363																																					p.K224T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A671C	X						.						22.0	21.0	22.0					X																	92965089		2196	4291	6487	92851745	SO:0001583	missense	286499	exon5			AK094978	CCDS14466.1	Xq21.32	2010-05-04			ENSG00000179083	ENSG00000179083			26748	protein-coding gene	gene with protein product	"""cancer/testis antigen 115"""						Standard	NM_173698		Approved	RP1-32F7.2, FLJ37659, CT115	uc022bzv.1	Q8N9E0	OTTHUMG00000021975	ENST00000355813.5:c.671A>C	X.37:g.92965089A>C	ENSP00000348067:p.Lys224Thr	Somatic		Capture	Illumina HiSeq	Phase_I	92851745	NM_001171110		Missense_Mutation	SNP	ENST00000355813.5	37	CCDS14466.1	.	.	.	.	.	.	.	.	.	.	a	1.637	-0.517451	0.04171	.	.	ENSG00000179083	ENST00000538690;ENST00000355813;ENST00000322139;ENST00000332647	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	2.76	2.76	0.32466	.	1.755530	0.03541	U	0.223957	T	0.58623	0.2135	L	0.36672	1.1	0.21527	N	0.999651	D	0.76494	0.999	D	0.78314	0.991	T	0.43877	-0.9364	10	0.46703	T	0.11	.	6.5054	0.22192	1.0:0.0:0.0:0.0	.	224	Q8N9E0	F133A_HUMAN	T	224	ENSP00000441389:K224T;ENSP00000348067:K224T;ENSP00000318974:K224T;ENSP00000362169:K224T	ENSP00000318974:K224T	K	+	2	0	FAM133A	92851745	1.000000	0.71417	0.947000	0.38551	0.798000	0.45092	2.116000	0.41930	1.332000	0.45431	0.483000	0.47432	AAG		0.363	FAM133A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057452.1	NM_173698	
PCDH19	57526	broad.mit.edu	37	X	99662937	99662937	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:99662937C>T	ENST00000373034.4	-	1	2334	c.659G>A	c.(658-660)gGc>gAc	p.G220D	PCDH19_ENST00000255531.7_Missense_Mutation_p.G220D|PCDH19_ENST00000420881.2_Missense_Mutation_p.G220D	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	220	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G220D(1)		breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						GCCAACGGTGCCCAGGCGCGG	0.607																																					p.G220D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G659A	X						.						81.0	85.0	84.0					X																	99662937		2169	4246	6415	99549593	SO:0001583	missense	57526	exon1			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"""Cadherins / Protocadherins : Non-clustered"""	14270	protein-coding gene	gene with protein product		300460	"""epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"""	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.659G>A	X.37:g.99662937C>T	ENSP00000362125:p.Gly220Asp	Somatic		Capture	Illumina HiSeq	Phase_I	99549593	NM_001105243	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	37	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	C	19.83	3.899843	0.72754	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.54279	0.58;0.58;0.58	5.98	5.98	0.97165	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.75324	0.3834	M	0.79475	2.455	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.999	T	0.77574	-0.2537	10	0.87932	D	0	.	19.3431	0.94352	0.0:1.0:0.0:0.0	.	220;220;220	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	D	220	ENSP00000400327:G220D;ENSP00000362125:G220D;ENSP00000255531:G220D	ENSP00000255531:G220D	G	-	2	0	PCDH19	99549593	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	7.818000	0.86416	2.521000	0.84997	0.544000	0.68410	GGC		0.607	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766	
NRK	203447	broad.mit.edu	37	X	105156736	105156736	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:105156736delA	ENST00000243300.9	+	14	2641	c.2338delA	c.(2338-2340)aaafs	p.K781fs	NRK_ENST00000428173.2_Frame_Shift_Del_p.K782fs	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	781					activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.I783fs*66(1)|p.I782fs*66(1)		breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						TTCAAATCCTAAAAAAATTGA	0.343										HNSCC(51;0.14)																											p.K780fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.2338delA	X						.						27.0	23.0	24.0					X																	105156736		1798	4041	5839	105043392	SO:0001589	frameshift_variant	203447	exon14			BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.2338delA	X.37:g.105156736delA	ENSP00000434830:p.Lys781fs	Somatic		Capture	Illumina HiSeq	Phase_I	105043392	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Frame_Shift_Del	DEL	ENST00000243300.9	37																																																																																					0.343	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465	
CHRDL1	91851	broad.mit.edu	37	X	109924815	109924815	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:109924815delC	ENST00000372045.1	-	10	1158	c.1027delG	c.(1027-1029)gtgfs	p.V343fs	CHRDL1_ENST00000218054.4_Frame_Shift_Del_p.V349fs|CHRDL1_ENST00000372042.1_Frame_Shift_Del_p.V351fs|CHRDL1_ENST00000444321.2_Frame_Shift_Del_p.V350fs|CHRDL1_ENST00000434224.1_Frame_Shift_Del_p.V270fs|CHRDL1_ENST00000394797.4_Frame_Shift_Del_p.V349fs|CHRDL1_ENST00000482160.1_Frame_Shift_Del_p.V271fs			Q9BU40	CRDL1_HUMAN	chordin-like 1	343					BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|compound eye development (GO:0048749)|eye development (GO:0001654)|negative regulation of BMP signaling pathway (GO:0030514)|nervous system development (GO:0007399)|ossification (GO:0001503)	extracellular region (GO:0005576)		p.V349fs*16(1)		endometrium(1)|large_intestine(12)|liver(1)|lung(15)|prostate(1)|skin(1)	31						GACTCATACACAGGCATCGTT	0.458																																					p.V351fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1051delG	X						.						187.0	145.0	160.0					X																	109924815		2203	4300	6503	109811471	SO:0001589	frameshift_variant	91851	exon10			AL049176	CCDS14553.1, CCDS48148.1, CCDS48149.1, CCDS48150.1, CCDS48148.2	Xq23	2014-01-31			ENSG00000101938	ENSG00000101938			29861	protein-coding gene	gene with protein product		300350	"""megalocornea 1 (X-linked)"""	MGC1		11441185, 11118896, 22284829	Standard	NM_001143981		Approved	NRLN1, CHL	uc004eow.3	Q9BU40	OTTHUMG00000022199	ENST00000372045.1:c.1027delG	X.37:g.109924815delC	ENSP00000361115:p.Val343fs	Somatic		Capture	Illumina HiSeq	Phase_I	109811471	NM_001143981	B1AKD0|B4DMP3|D3DUY6|E9PGS5|Q539E4|Q9Y3H7	Frame_Shift_Del	DEL	ENST00000372045.1	37																																																																																					0.458	CHRDL1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057912.1	NM_145234	
MAMLD1	10046	broad.mit.edu	37	X	149638074	149638074	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:149638074delG	ENST00000370401.2	+	4	539	c.229delG	c.(229-231)gggfs	p.G78fs	MAMLD1_ENST00000455522.2_5'Flank|MAMLD1_ENST00000432680.2_Frame_Shift_Del_p.G53fs|MAMLD1_ENST00000426613.2_Frame_Shift_Del_p.G53fs|MAMLD1_ENST00000262858.5_Frame_Shift_Del_p.G78fs|MAMLD1_ENST00000468306.1_3'UTR			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	78					male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.G5fs*36(1)|p.G78fs*36(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					CATGGCTGATGGGGGCTACCC	0.493																																					p.G52fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.154delG	X						.						83.0	85.0	84.0					X																	149638074		2203	4300	6503	149388732	SO:0001589	frameshift_variant	10046	exon2			U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"""chromosome X open reading frame 6"""	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.229delG	X.37:g.149638074delG	ENSP00000359428:p.Gly78fs	Somatic		Capture	Illumina HiSeq	Phase_I	149388732	NM_001177466	B2RCQ4|B4DG93|B9EGA5	Frame_Shift_Del	DEL	ENST00000370401.2	37	CCDS14693.2																																																																																				0.493	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491	
FLNA	2316	broad.mit.edu	37	X	153590650	153590650	+	Silent	SNP	G	G	T			TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3672-01A-01W-0900-09	TCGA-AA-3672-10A-01W-0900-09	g.chrX:153590650G>T	ENST00000369850.3	-	18	2852	c.2616C>A	c.(2614-2616)gcC>gcA	p.A872A	FLNA_ENST00000344736.4_Silent_p.A872A|FLNA_ENST00000422373.1_Silent_p.A872A|FLNA_ENST00000360319.4_Silent_p.A872A	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	872					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)	p.A872A(1)		breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TCACCTTACTGGCGTCATGAG	0.657																																					p.A872A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2616A	X						.						61.0	65.0	64.0					X																	153590650		2084	4184	6268	153243844	SO:0001819	synonymous_variant	2316	exon18			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.2616C>A	X.37:g.153590650G>T		Somatic		Capture	Illumina HiSeq	Phase_I	153243844	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Silent	SNP	ENST00000369850.3	37	CCDS48194.1																																																																																				0.657	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
