#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
AKNA	80709	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	117139683	117139683	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr9:117139683T>A	ENST00000307564.4	-	3	565	c.404A>T	c.(403-405)gAg>gTg	p.E135V	AKNA_ENST00000374075.5_Missense_Mutation_p.E54V|AKNA_ENST00000223791.3_5'Flank|AKNA_ENST00000374088.3_Missense_Mutation_p.E135V|AKNA_ENST00000312033.3_Missense_Mutation_p.E135V	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	135					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.E135V(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						TCCAGCCTCCTCAACCTCCAG	0.612																																																	1	Substitution - Missense(1)	kidney(1)											40.0	38.0	39.0					9																	117139683		2203	4300	6503	SO:0001583	missense	80709			AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.404A>T	9.37:g.117139683T>A	ENSP00000303769:p.Glu135Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	T	13.55	2.270598	0.40194	.	.	ENSG00000106948	ENST00000307564;ENST00000374088;ENST00000374075;ENST00000312033;ENST00000394574	T;T;T;T	0.36878	2.46;2.46;2.46;1.23	4.58	4.58	0.56647	.	0.598725	0.13919	N	0.353681	T	0.38081	0.1027	N	0.19112	0.55	0.58432	D	0.999999	D;P;P	0.58268	0.982;0.917;0.95	P;B;P	0.56612	0.802;0.421;0.648	T	0.21690	-1.0238	10	0.72032	D	0.01	-4.3384	10.6295	0.45527	0.0:0.0:0.0:1.0	.	135;135;54	Q7Z591-6;Q7Z591;Q7Z591-2	.;AKNA_HUMAN;.	V	135;135;54;135;135	ENSP00000303769:E135V;ENSP00000363201:E135V;ENSP00000363188:E54V;ENSP00000309222:E135V	ENSP00000303769:E135V	E	-	2	0	AKNA	116179504	0.004000	0.15560	0.024000	0.17045	0.050000	0.14768	1.128000	0.31369	1.831000	0.53308	0.379000	0.24179	GAG		0.612	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2		NM_030767	
ADAMTS13	11093	broad.mit.edu;hgsc.bcm.edu	37	9	136313849	136313849	+	Splice_Site	SNP	G	G	C	rs200273776	byFrequency	TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr9:136313849G>C	ENST00000371929.3	+	22	3305	c.2861G>C	c.(2860-2862)cGg>cCg	p.R954P	ADAMTS13_ENST00000356589.2_Splice_Site_p.R923P|ADAMTS13_ENST00000355699.2_Splice_Site_p.R954P|ADAMTS13_ENST00000536611.1_3'UTR|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000371916.1_3'UTR	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	954	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R954P(1)		central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		TGCCCTGCTCGGTGAGTGAGG	0.677																																																	1	Substitution - Missense(1)	kidney(1)											44.0	42.0	43.0					9																	136313849		2203	4299	6502	SO:0001630	splice_region_variant	11093			AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.2861+1G>C	9.37:g.136313849G>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	37	CCDS6970.1	.	.	.	.	.	.	.	.	.	.	G	12.30	1.895843	0.33442	.	.	ENSG00000160323	ENST00000371929;ENST00000355699;ENST00000356589	T;T;T	0.60548	0.18;0.18;0.18	5.51	1.7	0.24286	.	.	.	.	.	T	0.60483	0.2272	M	0.71581	2.175	0.80722	D	1	D;D;D	0.65815	0.992;0.995;0.995	P;P;P	0.55345	0.599;0.774;0.774	T	0.55566	-0.8121	9	0.25751	T	0.34	.	4.309	0.10962	0.3207:0.0:0.5319:0.1474	.	954;923;954	Q76LX8;Q76LX8-3;Q76LX8-2	ATS13_HUMAN;.;.	P	954;954;923	ENSP00000360997:R954P;ENSP00000347927:R954P;ENSP00000348997:R923P	ENSP00000347927:R954P	R	+	2	0	ADAMTS13	135303670	0.933000	0.31639	0.169000	0.22859	0.465000	0.32709	1.366000	0.34193	0.051000	0.15978	-0.749000	0.03505	CGG		0.677	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1		NM_139025	Missense_Mutation
AMPH	273	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	38429478	38429478	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr7:38429478G>A	ENST00000356264.2	-	20	2122	c.1907C>T	c.(1906-1908)gCa>gTa	p.A636V	AMPH_ENST00000428293.2_Missense_Mutation_p.A594V|AMPH_ENST00000325590.5_Missense_Mutation_p.A594V|AMPH_ENST00000471913.1_5'Flank	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	636	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)	p.A636V(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						ATCAGAATTTGCTGCCTCAAA	0.413																																																	1	Substitution - Missense(1)	kidney(1)											169.0	159.0	162.0					7																	38429478		2203	4300	6503	SO:0001583	missense	273				CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1907C>T	7.37:g.38429478G>A	ENSP00000348602:p.Ala636Val	Somatic		WXS	Illumina HiSeq	Phase_I	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	37	CCDS5456.1	.	.	.	.	.	.	.	.	.	.	G	32	5.157203	0.94686	.	.	ENSG00000078053	ENST00000325590;ENST00000356264;ENST00000428293;ENST00000353242	T;T;T	0.46819	0.86;0.86;0.86	5.04	5.04	0.67666	Src homology-3 domain (3);Variant SH3 (1);	0.106861	0.64402	D	0.000006	T	0.64204	0.2577	L	0.49455	1.56	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.97110	0.999;1.0;0.987	T	0.58555	-0.7616	10	0.32370	T	0.25	-23.8179	19.2716	0.94013	0.0:0.0:1.0:0.0	.	594;636;524	P49418-2;P49418;Q8NFL4	.;AMPH_HUMAN;.	V	594;636;594;538	ENSP00000317441:A594V;ENSP00000348602:A636V;ENSP00000390734:A594V	ENSP00000317441:A594V	A	-	2	0	AMPH	38396003	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.492000	0.90471	2.733000	0.93635	0.467000	0.42956	GCA		0.413	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2		NM_001635	
ARHGAP10	79658	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	148861022	148861022	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr4:148861022G>C	ENST00000336498.3	+	14	1514	c.1275G>C	c.(1273-1275)aaG>aaC	p.K425N	ARHGAP10_ENST00000414545.2_Missense_Mutation_p.K74N	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	1190					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)	p.K425N(1)		autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		TGAGTTCAAAGGTCCAGAGAC	0.348																																																	1	Substitution - Missense(1)	kidney(1)											251.0	253.0	252.0					4																	148861022		2203	4300	6503	SO:0001583	missense	79658			BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"""Rho GTPase activating proteins"""	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.1275G>C	4.37:g.148861022G>C	ENSP00000336923:p.Lys425Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	37	CCDS34075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.1|21.1	4.094721|4.094721	0.76870|0.76870	.|.	.|.	ENSG00000071205|ENSG00000071205	ENST00000507661|ENST00000336498;ENST00000414545	.|T;T	.|0.19394	.|2.15;2.15	5.58|5.58	5.58|5.58	0.84498|0.84498	.|Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.45377|0.45377	0.1339|0.1339	L|L	0.55103|0.55103	1.725|1.725	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.87578	.|0.998;0.989	T|T	0.32613|0.32613	-0.9900|-0.9900	5|10	.|0.87932	.|D	.|0	.|.	19.5539|19.5539	0.95333|0.95333	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|74;425	.|E7EUW5;A1A4S6	.|.;RHG10_HUMAN	R|N	103|425;74	.|ENSP00000336923:K425N;ENSP00000406624:K74N	.|ENSP00000336923:K425N	G|K	+|+	1|3	0|2	ARHGAP10|ARHGAP10	149080472|149080472	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	4.634000|4.634000	0.61325|0.61325	2.630000|2.630000	0.89119|0.89119	0.655000|0.655000	0.94253|0.94253	GGT|AAG		0.348	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1		NM_024605	
ASB16	92591	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	42249679	42249679	+	Silent	SNP	G	G	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr17:42249679G>A	ENST00000293414.1	+	2	651	c.567G>A	c.(565-567)ttG>ttA	p.L189L		NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	189					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.L189L(1)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|liver(2)|lung(2)|prostate(1)	14		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CCGAGTCCTTGCAGTAGGTGC	0.572																																																	1	Substitution - coding silent(1)	kidney(1)											51.0	46.0	48.0					17																	42249679		2203	4300	6503	SO:0001819	synonymous_variant	92591			AK054727	CCDS11478.1	17q21.31	2013-01-10	2011-01-25		ENSG00000161664	ENSG00000161664		"""Ankyrin repeat domain containing"""	19768	protein-coding gene	gene with protein product		615056	"""ankyrin repeat and SOCS box-containing 16"""			12076535	Standard	NM_080863		Approved	FLJ30165	uc002ifl.1	Q96NS5	OTTHUMG00000181809	ENST00000293414.1:c.567G>A	17.37:g.42249679G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2RBC0|Q8WXK0	Silent	SNP	ENST00000293414.1	37	CCDS11478.1																																																																																				0.572	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1			
ATG2A	23130	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	64676580	64676580	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr11:64676580C>G	ENST00000377264.3	-	16	2359	c.2247G>C	c.(2245-2247)tgG>tgC	p.W749C	ATG2A_ENST00000421419.2_Missense_Mutation_p.W749C	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	749					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)		p.W749C(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						GGGCCACCTCCCACTGTGTGC	0.642																																																	1	Substitution - Missense(1)	kidney(1)											72.0	53.0	60.0					11																	64676580		2201	4297	6498	SO:0001583	missense	23130				CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.2247G>C	11.37:g.64676580C>G	ENSP00000366475:p.Trp749Cys	Somatic		WXS	Illumina HiSeq	Phase_I	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.32|18.32	3.598784|3.598784	0.66332|0.66332	.|.	.|.	ENSG00000110046|ENSG00000110046	ENST00000418259|ENST00000421419;ENST00000377264	.|T;T	.|0.06608	.|3.28;3.28	4.77|4.77	4.77|4.77	0.60923|0.60923	.|.	.|0.442134	.|0.21803	.|N	.|0.068887	T|T	0.16811|0.16811	0.0404|0.0404	L|L	0.51422|0.51422	1.61|1.61	0.80722|0.80722	D|D	1|1	.|D	.|0.69078	.|0.997	.|P	.|0.59012	.|0.85	T|T	0.00134|0.00134	-1.2008|-1.2008	5|10	.|0.62326	.|D	.|0.03	.|.	15.7078|15.7078	0.77598|0.77598	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|749	.|Q2TAZ0	.|ATG2A_HUMAN	R|C	551|749	.|ENSP00000410522:W749C;ENSP00000366475:W749C	.|ENSP00000366475:W749C	G|W	-|-	1|3	0|0	ATG2A|ATG2A	64433156|64433156	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.912000|0.912000	0.54170|0.54170	3.685000|3.685000	0.54678|0.54678	2.644000|2.644000	0.89710|0.89710	0.655000|0.655000	0.94253|0.94253	GGA|TGG		0.642	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1		NM_015104	
ATP2A2	488	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	110783864	110783864	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr12:110783864G>C	ENST00000539276.2	+	19	2909	c.2800G>C	c.(2800-2802)Ggc>Cgc	p.G934R	ATP2A2_ENST00000395494.2_Missense_Mutation_p.G907R|ATP2A2_ENST00000308664.6_Missense_Mutation_p.G934R			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	934					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)	p.G934R(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						CTGGCTCGTGGGCTCCATCTG	0.592																																																	1	Substitution - Missense(1)	kidney(1)											175.0	151.0	159.0					12																	110783864		2203	4300	6503	SO:0001583	missense	488				CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"""ATPases / P-type"""	812	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 2"", ""calcium pump 2"""	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.2800G>C	12.37:g.110783864G>C	ENSP00000440045:p.Gly934Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A6NDN7|B4DF05|P16614|Q86VJ2	Missense_Mutation	SNP	ENST00000539276.2	37	CCDS9144.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.13|19.13	3.767310|3.767310	0.69878|0.69878	.|.	.|.	ENSG00000174437|ENSG00000174437	ENST00000548169|ENST00000308664;ENST00000395494;ENST00000539276	.|D;D;D	.|0.96041	.|-3.89;-3.89;-3.89	6.17|6.17	6.17|6.17	0.99709|0.99709	.|ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.97823|0.97823	0.9285|0.9285	M|M	0.90977|0.90977	3.165|3.165	0.80722|0.80722	D|D	1|1	.|P;D;D	.|0.59357	.|0.887;0.965;0.985	.|P;P;P	.|0.57371	.|0.664;0.723;0.819	D|D	0.96405|0.96405	0.9300|0.9300	6|10	.|0.25751	.|T	.|0.34	.|.	20.8794|20.8794	0.99867|0.99867	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|907;934;934	.|P16615-4;P16615-2;P16615	.|.;.;AT2A2_HUMAN	A|R	824|934;907;934	.|ENSP00000311186:G934R;ENSP00000378872:G907R;ENSP00000440045:G934R	.|ENSP00000311186:G934R	G|G	+|+	2|1	0|0	ATP2A2|ATP2A2	109268247|109268247	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.869000|9.869000	0.99810|0.99810	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GGG|GGC		0.592	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1		NM_001681	
ATP8B2	57198	hgsc.bcm.edu	37	1	154316516	154316516	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr1:154316516G>A	ENST00000368489.3	+	18	2005	c.2005G>A	c.(2005-2007)Gtt>Att	p.V669I		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	655					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	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)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CTATGAGGAGGTTGAGAACAA	0.592																																																	0													46.0	49.0	48.0					1																	154316516		2203	4300	6503	SO:0001583	missense	57198			AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"""ATPases / P-type"""	13534	protein-coding gene	gene with protein product		605867	"""ATPase, class I, type 8B, member 2"""			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.2005G>A	1.37:g.154316516G>A	ENSP00000357475:p.Val669Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	37	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	G	0.019	-1.459915	0.01062	.	.	ENSG00000143515	ENST00000368489	T	0.57752	0.38	5.5	1.65	0.23941	.	0.133352	0.50627	D	0.000116	T	0.03477	0.0100	N	0.00162	-1.95	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.47381	-0.9122	10	0.02654	T	1	.	8.3951	0.32553	0.3763:0.0:0.6237:0.0	.	669	P98198-3	.	I	669	ENSP00000357475:V669I	ENSP00000357475:V669I	V	+	1	0	ATP8B2	152583140	1.000000	0.71417	0.633000	0.29310	0.008000	0.06430	1.881000	0.39638	0.159000	0.19401	-0.157000	0.13467	GTT		0.592	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2		NM_020452	
BRCA2	675	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	32906553	32906553	+	Missense_Mutation	SNP	C	C	A	rs397507428		TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr13:32906553C>A	ENST00000380152.3	+	10	1171	c.938C>A	c.(937-939)tCt>tAt	p.S313Y	BRCA2_ENST00000544455.1_Missense_Mutation_p.S313Y			P51587	BRCA2_HUMAN	breast cancer 2, early onset	313					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.S313Y(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TTATGTTTTTCTAAATGTAGA	0.303			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)		yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	2	Substitution - Missense(2)	kidney(2)											49.0	53.0	52.0					13																	32906553		2203	4289	6492	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.938C>A	13.37:g.32906553C>A	ENSP00000369497:p.Ser313Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	6.769	0.510876	0.12883	.	.	ENSG00000139618	ENST00000380152;ENST00000544455;ENST00000530893	T;T	0.00768	5.72;5.72	5.6	2.84	0.33178	.	1.387810	0.04415	N	0.366585	T	0.01029	0.0034	L	0.38175	1.15	0.09310	N	1	P;P	0.37398	0.593;0.593	B;B	0.37047	0.24;0.24	T	0.47873	-0.9083	10	0.62326	D	0.03	.	3.9912	0.09538	0.2606:0.4119:0.2535:0.074	.	313;313	P51587;A1YBP1	BRCA2_HUMAN;.	Y	313;313;311	ENSP00000369497:S313Y;ENSP00000439902:S313Y	ENSP00000369497:S313Y	S	+	2	0	BRCA2	31804553	0.002000	0.14202	0.036000	0.18154	0.206000	0.24218	0.349000	0.20055	0.269000	0.21961	-0.140000	0.14226	TCT		0.303	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2		NM_000059	
BRD1	23774	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	50191673	50191673	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr22:50191673C>G	ENST00000216267.8	-	5	2364	c.1878G>C	c.(1876-1878)gaG>gaC	p.E626D	BRD1_ENST00000404760.1_Missense_Mutation_p.E626D|BRD1_ENST00000542442.1_Missense_Mutation_p.E314D|BRD1_ENST00000342989.5_Missense_Mutation_p.E221D|BRD1_ENST00000457780.2_Missense_Mutation_p.E626D|BRD1_ENST00000404034.1_Missense_Mutation_p.E626D	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	626	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.E626D(1)|p.E221D(1)		endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		CCTCCTCAAACTCATGGAGGT	0.438																																																	2	Substitution - Missense(2)	kidney(2)											111.0	107.0	108.0					22																	50191673		2203	4300	6503	SO:0001583	missense	23774			AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.1878G>C	22.37:g.50191673C>G	ENSP00000216267:p.Glu626Asp	Somatic		WXS	Illumina HiSeq	Phase_I	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	37	CCDS14080.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.523816	0.27299	.	.	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000457780;ENST00000542442;ENST00000342989;ENST00000419212	T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5	5.44	2.11	0.27256	Bromodomain (6);Bromodomain, conserved site (1);	0.103153	0.64402	D	0.000004	T	0.17662	0.0424	N	0.21097	0.63	0.47407	D	0.999412	P;B;P;P	0.46578	0.88;0.003;0.658;0.854	B;B;B;B	0.43728	0.429;0.01;0.352;0.303	T	0.06698	-1.0812	10	0.12430	T	0.62	.	6.6278	0.22839	0.0:0.6146:0.1195:0.266	.	626;221;626;626	Q86X06;B7Z926;O95696;O95696-2	.;.;BRD1_HUMAN;.	D	626;626;626;626;314;221;86	ENSP00000216267:E626D;ENSP00000384076:E626D;ENSP00000385858:E626D;ENSP00000410042:E626D;ENSP00000437514:E314D;ENSP00000345886:E221D	ENSP00000216267:E626D	E	-	3	2	BRD1	48577677	0.959000	0.32827	0.997000	0.53966	0.999000	0.98932	0.136000	0.15974	0.641000	0.30601	0.655000	0.94253	GAG		0.438	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1		NM_014577	
CACNA1A	773	hgsc.bcm.edu;ucsc.edu	37	19	13566012	13566013	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr19:13566012_13566013delAT	ENST00000360228.5	-	2	306_307	c.307_308delAT	c.(307-309)atgfs	p.M103fs	CACNA1A_ENST00000573710.2_Frame_Shift_Del_p.M103fs	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	103					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GGCTAAAATCATATATTCAAAG	0.48																																																	0																																										SO:0001589	frameshift_variant	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.307_308delAT	19.37:g.13566016_13566017delAT	ENSP00000353362:p.Met103fs	Somatic		WXS	Illumina HiSeq	Phase_I	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Frame_Shift_Del	DEL	ENST00000360228.5	37	CCDS45998.1																																																																																				0.480	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2		NM_000068	
CECR1	51816	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	17672628	17672628	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr22:17672628A>C	ENST00000399839.1	-	5	1096	c.826T>G	c.(826-828)Ttt>Gtt	p.F276V	CECR1_ENST00000449907.2_Missense_Mutation_p.F234V|CECR1_ENST00000399837.2_Missense_Mutation_p.F276V|CECR1_ENST00000480276.1_5'UTR|CECR1_ENST00000262607.3_Missense_Mutation_p.F276V|CECR1_ENST00000330232.4_Missense_Mutation_p.F35V	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	276					adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)	p.F35V(1)|p.F276V(1)		endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				GTTTCCACAAACTTCTGAGCT	0.473																																																	2	Substitution - Missense(2)	kidney(2)											168.0	165.0	166.0					22																	17672628		2203	4300	6503	SO:0001583	missense	51816			AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.826T>G	22.37:g.17672628A>C	ENSP00000382733:p.Phe276Val	Somatic		WXS	Illumina HiSeq	Phase_I	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Missense_Mutation	SNP	ENST00000399839.1	37	CCDS13742.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631828	0.87660	.	.	ENSG00000093072	ENST00000399839;ENST00000330232;ENST00000262607;ENST00000449907;ENST00000399837	D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63	3.58	3.58	0.41010	Adenosine/AMP deaminase (1);	0.136815	0.52532	U	0.000064	D	0.90943	0.7153	M	0.86805	2.84	0.58432	D	0.999992	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.976	D	0.91750	0.5411	10	0.87932	D	0	.	11.0296	0.47765	1.0:0.0:0.0:0.0	.	276;35	Q9NZK5;Q9NZK5-2	CECR1_HUMAN;.	V	276;35;276;234;276	ENSP00000382733:F276V;ENSP00000332871:F35V;ENSP00000262607:F276V;ENSP00000406443:F234V;ENSP00000382731:F276V	ENSP00000262607:F276V	F	-	1	0	CECR1	16052628	1.000000	0.71417	0.020000	0.16555	0.720000	0.41350	7.195000	0.77798	1.393000	0.46605	0.260000	0.18958	TTT		0.473	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1			
COPE	11316	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	19014155	19014155	+	Silent	SNP	G	G	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr19:19014155G>A	ENST00000262812.4	-	7	705	c.657C>T	c.(655-657)ctC>ctT	p.L219L	COPE_ENST00000349893.4_Intron|COPE_ENST00000600932.1_Silent_p.L242L|COPE_ENST00000598969.1_5'UTR|COPE_ENST00000351079.4_Silent_p.L168L	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	219					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|membrane organization (GO:0061024)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.L219L(1)		breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	11						CCTGCCCATTGAGCAGCAGCA	0.647																																																	1	Substitution - coding silent(1)	kidney(1)											53.0	46.0	48.0					19																	19014155		2203	4300	6503	SO:0001819	synonymous_variant	11316			AJ131182	CCDS12387.1, CCDS12388.1, CCDS12389.1	19p13.11	2008-02-05				ENSG00000105669			2234	protein-coding gene	gene with protein product		606942				10469566	Standard	NM_007263		Approved	epsilon-COP	uc002nkk.3	O14579		ENST00000262812.4:c.657C>T	19.37:g.19014155G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6NE29|A6NKA3|O76097|Q6IBB8|Q9UGP6	Silent	SNP	ENST00000262812.4	37	CCDS12387.1																																																																																				0.647	COPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464801.1		NM_007263	
CRYGS	1427	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	186256604	186256604	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr3:186256604A>T	ENST00000392499.2	-	4	757	c.418T>A	c.(418-420)Tat>Aat	p.Y140N	CRYGS_ENST00000307944.5_Missense_Mutation_p.Y140N	NM_017541.2	NP_060011.1	P22914	CRBS_HUMAN	crystallin, gamma S	140	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|morphogenesis of an epithelium (GO:0002009)		structural constituent of eye lens (GO:0005212)	p.Y140N(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	11	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.5e-22)	GBM - Glioblastoma multiforme(93;0.0906)		GGTAGCTCATAGAAAATCCAG	0.527																																																	1	Substitution - Missense(1)	kidney(1)											91.0	84.0	87.0					3																	186256604		2203	4300	6503	SO:0001583	missense	1427				CCDS3275.1	3q27.3	2013-02-14			ENSG00000213139	ENSG00000213139			2417	protein-coding gene	gene with protein product	"""crystallin, gamma 8"""	123730		CRYG8			Standard	NM_017541		Approved		uc003fqe.3	P22914	OTTHUMG00000156615	ENST00000392499.2:c.418T>A	3.37:g.186256604A>T	ENSP00000376287:p.Tyr140Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B2RAF8	Missense_Mutation	SNP	ENST00000392499.2	37	CCDS3275.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.946092	0.73672	.	.	ENSG00000213139	ENST00000392499;ENST00000307944	D;D	0.86694	-2.16;-2.16	5.95	5.95	0.96441	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.64402	U	0.000008	D	0.95692	0.8599	H	0.96777	3.88	0.51482	D	0.999928	D	0.89917	1.0	D	0.81914	0.995	D	0.96943	0.9689	10	0.87932	D	0	.	14.368	0.66820	1.0:0.0:0.0:0.0	.	140	P22914	CRBS_HUMAN	N	140	ENSP00000376287:Y140N;ENSP00000312099:Y140N	ENSP00000312099:Y140N	Y	-	1	0	CRYGS	187739298	1.000000	0.71417	0.990000	0.47175	0.993000	0.82548	5.201000	0.65163	2.279000	0.76181	0.533000	0.62120	TAT		0.527	CRYGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344784.1		NM_017541	
DCT	1638	hgsc.bcm.edu;ucsc.edu	37	13	95092164	95092165	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr13:95092164_95092165delTG	ENST00000377028.5	-	8	1960_1961	c.1547_1548delCA	c.(1546-1548)acafs	p.T516fs	DCT_ENST00000446125.1_Frame_Shift_Del_p.T549fs	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	516					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		AGGCTTCTTCTGTGTATCTCTT	0.436																																																	0																																										SO:0001589	frameshift_variant	1638			D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"""dopachrome delta-isomerase"""	191275	"""tyrosine-related protein 2"""	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.1547_1548delCA	13.37:g.95092166_95092167delTG	ENSP00000366227:p.Thr516fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q09GT4	Frame_Shift_Del	DEL	ENST00000377028.5	37	CCDS9470.1																																																																																				0.436	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			
DOCK8	81704	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	304680	304680	+	Silent	SNP	G	G	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr9:304680G>A	ENST00000453981.1	+	5	616	c.504G>A	c.(502-504)ttG>ttA	p.L168L	DOCK8_ENST00000432829.2_Silent_p.L100L|DOCK8_ENST00000469391.1_Silent_p.L100L			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	168					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.L100L(1)|p.L168L(1)		breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CGGAAACCTTGGAGTGCAGTG	0.463																																																	2	Substitution - coding silent(2)	kidney(2)											121.0	126.0	124.0					9																	304680		2203	4300	6503	SO:0001819	synonymous_variant	81704			AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.504G>A	9.37:g.304680G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																				0.463	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5		XM_036307	
DSCAML1	57453	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	117332278	117332278	+	Silent	SNP	C	C	G			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr11:117332278C>G	ENST00000321322.6	-	18	3481	c.3480G>C	c.(3478-3480)ctG>ctC	p.L1160L	DSCAML1_ENST00000527706.1_Silent_p.L890L	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1100	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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.L1160L(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)		AAGTGATGGACAGGGCCCGGA	0.607																																																	1	Substitution - coding silent(1)	kidney(1)											60.0	63.0	62.0					11																	117332278		2201	4296	6497	SO:0001819	synonymous_variant	57453				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.3480G>C	11.37:g.117332278C>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																				0.607	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2		NM_020693	
DST	667	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	56500387	56500387	+	Splice_Site	SNP	C	C	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr6:56500387C>A	ENST00000361203.3	-	20	2560	c.2553G>T	c.(2551-2553)atG>atT	p.M851I	DST_ENST00000370788.2_Splice_Site_p.M851I|DST_ENST00000370754.5_Splice_Site_p.M1029I|DST_ENST00000446842.2_Splice_Site_p.M525I|DST_ENST00000518935.1_Splice_Site_p.M525I|DST_ENST00000312431.6_Splice_Site_p.M851I|DST_ENST00000370765.6_Splice_Site_p.M525I|DST_ENST00000244364.6_Splice_Site_p.M525I|DST_ENST00000421834.2_Splice_Site_p.M851I|DST_ENST00000370769.4_Splice_Site_p.M851I			Q03001	DYST_HUMAN	dystonin	851					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.M525I(3)|p.M851I(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)			GTATTAGTACCATTGATTCCT	0.338																																																	4	Substitution - Missense(4)	kidney(4)											109.0	98.0	102.0					6																	56500387		2203	4300	6503	SO:0001630	splice_region_variant	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.2553+1G>T	6.37:g.56500387C>A		Somatic		WXS	Illumina HiSeq	Phase_I	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	33	5.205586	0.95033	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	T;T;T;T;T;T;T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000019	T	0.58104	0.2099	M	0.80982	2.52	0.33230	D	0.555826	D;P;D;D;D;D;D;D	0.65815	0.993;0.936;0.969;0.991;0.995;0.967;0.993;0.99	D;P;D;P;D;D;D;D	0.73380	0.968;0.885;0.914;0.833;0.937;0.959;0.968;0.98	T	0.58103	-0.7695	8	.	.	.	.	19.773	0.96379	0.0:1.0:0.0:0.0	.	851;851;1029;525;525;525;851;525	Q5TBT1;E7ERU2;E9PEB9;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;DYST_HUMAN;.	I	525;1029;851;851;525;851;851;851;525;891;525;525	ENSP00000244364:M525I;ENSP00000359790:M1029I;ENSP00000359805:M851I;ENSP00000400883:M851I;ENSP00000393645:M525I;ENSP00000307959:M851I;ENSP00000359824:M851I;ENSP00000354508:M851I;ENSP00000404924:M525I;ENSP00000431030:M891I;ENSP00000359801:M525I;ENSP00000431003:M525I	.	M	-	3	0	DST	56608346	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.999000	0.70665	2.677000	0.91161	0.655000	0.94253	ATG		0.338	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3		NM_001723	Missense_Mutation
EDEM2	55741	broad.mit.edu;hgsc.bcm.edu	37	20	33703674	33703674	+	Silent	SNP	A	A	C			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr20:33703674A>C	ENST00000374492.3	-	11	1404	c.1299T>G	c.(1297-1299)acT>acG	p.T433T	EDEM2_ENST00000542871.1_Silent_p.T157T|EDEM2_ENST00000374491.3_Silent_p.T396T|EDEM2_ENST00000541621.1_Silent_p.T212T|SNORD56_ENST00000364281.1_RNA	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	433					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.T433T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			GGTATTTCACAGTCTCGGCCA	0.537																																					Esophageal Squamous(51;906 1021 24535 36410 39145)												1	Substitution - coding silent(1)	kidney(1)											71.0	68.0	69.0					20																	33703674		2203	4300	6503	SO:0001819	synonymous_variant	55741			AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"""chromosome 20 open reading frame 31"""	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.1299T>G	20.37:g.33703674A>C		Somatic		WXS	Illumina HiSeq	Phase_I	B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Silent	SNP	ENST00000374492.3	37	CCDS13247.1																																																																																				0.537	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2		NM_018217	
EWSR1	2130	broad.mit.edu;hgsc.bcm.edu	37	22	29686417	29686417	+	Intron	SNP	C	C	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr22:29686417C>A	ENST00000397938.2	+	9	1293				EWSR1_ENST00000332050.6_Intron|EWSR1_ENST00000406548.1_Intron|EWSR1_ENST00000333395.6_Missense_Mutation_p.S330R|EWSR1_ENST00000331029.7_Intron|EWSR1_ENST00000332035.6_Intron|EWSR1_ENST00000414183.2_Intron	NM_001163285.1|NM_001163286.1|NM_005243.3|NM_013986.3	NP_001156757.1|NP_001156758.1|NP_005234.1|NP_053733.2	Q01844	EWS_HUMAN	EWS RNA-binding protein 1						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.S330R(1)	EWSR1/ATF1(347)|EWSR1/POU5F1(10)|EWSR1/PBX1(3)|EWSR1/DDIT3(45)|EWSR1/FEV(11)|EWSR1/CREB1(44)|EWSR1/SMARCA5(2)|EWSR1/ETV4(6)|EWSR1/ERG(178)|EWSR1/ZNF384(4)|EWSR1/ETV1(7)|EWSR1/FLI1(2569)|EWSR1/NR4A3(146)|EWSR1/SP3(3)|EWSR1/PATZ1(2)|EWSR1/WT1(234)|EWSR1/NFATC2(9)	breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						AAAGTGAGAGCCTTGTATACA	0.388			T	"""FLI1, ERG, ZNF278, NR4A3, FEV, ATF1, ETV1, ETV4, WT1, ZNF384, CREB1, POU5F1,  PBX1"""	"""Ewing sarcoma,  desmoplastic small round cell tumor , ALL, clear cell sarcoma, sarcoma, myoepithelioma"""																																			Dom	yes		22	22q12	2130	Ewing sarcoma breakpoint region 1 (EWS)		"""L, M"""	1	Substitution - Missense(1)	kidney(1)											62.0	53.0	55.0					22																	29686417		1568	3582	5150	SO:0001627	intron_variant	2130				CCDS13851.1, CCDS13852.1, CCDS13852.2, CCDS54512.1, CCDS54513.1, CCDS54514.1	22q12.2	2013-05-24	2013-05-24		ENSG00000182944	ENSG00000182944		"""RNA binding motif (RRM) containing"""	3508	protein-coding gene	gene with protein product		133450	"""Ewing sarcoma breakpoint region 1"""			1522903	Standard	NM_005243		Approved	EWS	uc003aev.3	Q01844	OTTHUMG00000151107	ENST00000397938.2:c.975-1134C>A	22.37:g.29686417C>A		Somatic		WXS	Illumina HiSeq	Phase_I	B0QYK1|Q5THL0|Q92635|Q96FE8|Q96MN4|Q96MX4|Q9BWA2	Missense_Mutation	SNP	ENST00000397938.2	37	CCDS13851.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.334977	0.41398	.	.	ENSG00000182944	ENST00000333395	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	T	0.74382	0.3709	.	.	.	0.80722	D	1	D	0.64830	0.994	P	0.53912	0.737	T	0.77480	-0.2572	7	0.72032	D	0.01	.	19.4102	0.94670	0.0:1.0:0.0:0.0	.	330	Q9BWA2	.	R	330	.	ENSP00000327456:S330R	S	+	3	2	EWSR1	28016417	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.599000	0.87857	0.655000	0.94253	AGC		0.388	EWSR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321345.1		NM_005243	
FAM135B	51059	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	139165076	139165076	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr8:139165076C>A	ENST00000395297.1	-	13	1812	c.1642G>T	c.(1642-1644)Gcc>Tcc	p.A548S		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	548								p.A548S(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)			AGCACTGGGGCCTGTCCATCC	0.507										HNSCC(54;0.14)																																							2	Substitution - Missense(2)	kidney(2)											82.0	81.0	81.0					8																	139165076		1955	4149	6104	SO:0001583	missense	51059			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.1642G>T	8.37:g.139165076C>A	ENSP00000378710:p.Ala548Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	12.69	2.012190	0.35511	.	.	ENSG00000147724	ENST00000395297	T	0.15139	2.45	5.45	0.391	0.16282	.	1.070190	0.07132	N	0.845765	T	0.12008	0.0292	L	0.51422	1.61	0.09310	N	1	B;B;B	0.20052	0.041;0.019;0.001	B;B;B	0.17722	0.019;0.019;0.002	T	0.40117	-0.9580	10	0.08837	T	0.75	-0.2566	0.8838	0.01240	0.2413:0.3703:0.1178:0.2706	.	548;548;548	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	S	548	ENSP00000378710:A548S	ENSP00000276737:A548S	A	-	1	0	FAM135B	139234258	0.000000	0.05858	0.004000	0.12327	0.987000	0.75469	-0.552000	0.06020	-0.140000	0.11394	0.655000	0.94253	GCC		0.507	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3		NM_015912	
BRINP3	339479	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	190067930	190067930	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr1:190067930G>A	ENST00000367462.3	-	8	1750	c.1519C>T	c.(1519-1521)Cga>Tga	p.R507*	BRINP3_ENST00000534846.1_Nonsense_Mutation_p.R405*	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	507					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)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)		p.R507*(3)									ACTTCTATTCGTCTGTCCGTT	0.483																																																	3	Substitution - Nonsense(3)	large_intestine(1)|kidney(1)|endometrium(1)											159.0	152.0	154.0					1																	190067930		2203	4300	6503	SO:0001587	stop_gained	339479			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member C"""	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1519C>T	1.37:g.190067930G>A	ENSP00000356432:p.Arg507*	Somatic		WXS	Illumina HiSeq	Phase_I	B3KVP1|B7Z260|O95726|Q2M330	Nonsense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.028520	0.93518	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	.	.	.	5.75	4.77	0.60923	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.6238	0.45495	0.0:0.0:0.6879:0.3121	.	.	.	.	X	507;405	.	ENSP00000356432:R507X	R	-	1	2	FAM5C	188334553	0.819000	0.29175	0.368000	0.25939	0.962000	0.63368	1.147000	0.31602	2.712000	0.92718	0.591000	0.81541	CGA		0.483	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1		NM_199051	
FES	2242	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	91430480	91430480	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr15:91430480A>G	ENST00000328850.3	+	5	690	c.548A>G	c.(547-549)cAc>cGc	p.H183R	FES_ENST00000394302.1_Missense_Mutation_p.H125R|FES_ENST00000450438.2_Missense_Mutation_p.H125R|FES_ENST00000394300.3_Missense_Mutation_p.H125R|FES_ENST00000444422.2_Missense_Mutation_p.H183R|FES_ENST00000414248.2_Missense_Mutation_p.H125R	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	183	Important for interaction with membranes containing phosphoinositides.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of mast cell degranulation (GO:0043304)|regulation of vesicle-mediated transport (GO:0060627)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule cytoskeleton (GO:0015630)	ATP binding (GO:0005524)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol binding (GO:0035091)|protein tyrosine kinase activity (GO:0004713)	p.H183R(1)		lung(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			TTTGCTCACCACAACCGCTAT	0.617																																																	1	Substitution - Missense(1)	kidney(1)											69.0	73.0	71.0					15																	91430480		2198	4298	6496	SO:0001583	missense	2242			X52192	CCDS10365.1, CCDS45349.1, CCDS45350.1, CCDS45351.1	15q26.1	2014-06-26	2014-06-26		ENSG00000182511	ENSG00000182511	2.7.10.1	"""SH2 domain containing"""	3657	protein-coding gene	gene with protein product	"""Oncogene FES, feline sarcoma virus"", ""c-fes/fps protein"""	190030	"""feline sarcoma (Snyder-Theilen) viral (v-fes)/Fujinami avian sarcoma (PRCII) viral (v-fps) oncogene homolog"", ""feline sarcoma oncogene"""			1870997	Standard	NM_002005		Approved	FPS	uc002bpv.3	P07332	OTTHUMG00000044456	ENST00000328850.3:c.548A>G	15.37:g.91430480A>G	ENSP00000331504:p.His183Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Missense_Mutation	SNP	ENST00000328850.3	37	CCDS10365.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.356188	0.82243	.	.	ENSG00000182511	ENST00000328850;ENST00000414248;ENST00000394302;ENST00000444422;ENST00000394300;ENST00000450438	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76;2.76	4.81	3.66	0.41972	.	0.000000	0.85682	D	0.000000	T	0.31167	0.0788	M	0.74647	2.275	0.51012	D	0.999902	D;D;D;D;D;D	0.89917	1.0;0.984;0.973;1.0;0.994;1.0	D;D;D;D;D;D	0.91635	0.997;0.964;0.921;0.999;0.983;0.997	T	0.02404	-1.1164	10	0.87932	D	0	-38.8097	11.656	0.51318	0.8511:0.1489:0.0:0.0	.	165;125;125;125;183;183	B4DUD9;P07332-2;E7ENM8;P07332-3;P07332-4;P07332	.;.;.;.;.;FES_HUMAN	R	183;125;125;183;125;125	ENSP00000331504:H183R;ENSP00000414629:H125R;ENSP00000377839:H125R;ENSP00000400868:H183R;ENSP00000377837:H125R;ENSP00000409915:H125R	ENSP00000331504:H183R	H	+	2	0	FES	89231484	1.000000	0.71417	0.988000	0.46212	0.988000	0.76386	6.978000	0.76147	0.699000	0.31761	0.454000	0.30748	CAC		0.617	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1		NM_002005	
FHL5	9457	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	97063550	97063550	+	Missense_Mutation	SNP	G	G	A	rs370981552		TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr6:97063550G>A	ENST00000326771.2	+	7	1137	c.757G>A	c.(757-759)Ggg>Agg	p.G253R	FHL5_ENST00000541107.1_Missense_Mutation_p.G253R	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	253	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.G253W(2)|p.G253R(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		CTTTAACTGCGGGAAATGCTC	0.458																																																	3	Substitution - Missense(3)	lung(2)|kidney(1)						G	ARG/GLY,ARG/GLY	0,4406		0,0,2203	113.0	110.0	111.0		757,757	3.9	1.0	6		111	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FHL5	NM_001170807.1,NM_020482.4	125,125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	253/285,253/285	97063550	1,13005	2203	4300	6503	SO:0001583	missense	9457			AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.757G>A	6.37:g.97063550G>A	ENSP00000326022:p.Gly253Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Missense_Mutation	SNP	ENST00000326771.2	37	CCDS5035.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.614403	0.28712	0.0	1.16E-4	ENSG00000112214	ENST00000541107;ENST00000326771	D;D	0.86956	-2.19;-2.19	5.66	3.87	0.44632	Zinc finger, LIM-type (5);	0.181180	0.27004	N	0.021405	T	0.63510	0.2517	N	0.16862	0.45	0.25789	N	0.984641	B	0.14012	0.009	B	0.13407	0.009	T	0.58092	-0.7697	10	0.44086	T	0.13	.	11.6625	0.51356	0.1973:0.0:0.8027:0.0	.	253	Q5TD97	FHL5_HUMAN	R	253	ENSP00000442357:G253R;ENSP00000326022:G253R	ENSP00000326022:G253R	G	+	1	0	FHL5	97170271	0.043000	0.20138	0.978000	0.43139	0.976000	0.68499	1.908000	0.39907	1.393000	0.46605	0.655000	0.94253	GGG		0.458	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1		NM_020482	
G6PD	2539	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	153762612	153762612	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chrX:153762612C>A	ENST00000393564.2	-	6	697	c.585G>T	c.(583-585)caG>caT	p.Q195H	G6PD_ENST00000497281.1_5'Flank|G6PD_ENST00000369620.2_Missense_Mutation_p.Q195H|G6PD_ENST00000393562.2_Missense_Mutation_p.Q225H	NM_001042351.1	NP_001035810.1	P11413	G6PD_HUMAN	glucose-6-phosphate dehydrogenase	195					carbohydrate metabolic process (GO:0005975)|cellular response to oxidative stress (GO:0034599)|cholesterol biosynthetic process (GO:0006695)|cytokine production (GO:0001816)|erythrocyte maturation (GO:0043249)|glucose 6-phosphate metabolic process (GO:0051156)|glutathione metabolic process (GO:0006749)|lipid metabolic process (GO:0006629)|NADP metabolic process (GO:0006739)|NADPH regeneration (GO:0006740)|negative regulation of protein glutathionylation (GO:0010734)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|regulation of neuron apoptotic process (GO:0043523)|response to ethanol (GO:0045471)|response to food (GO:0032094)|response to organic cyclic compound (GO:0014070)|ribose phosphate biosynthetic process (GO:0046390)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	glucose binding (GO:0005536)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)	p.Q195H(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(3)|ovary(4)	18	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-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)					TGCGGTAGATCTGGTCCTCAC	0.637																																																	1	Substitution - Missense(1)	kidney(1)											98.0	81.0	87.0					X																	153762612		2203	4300	6503	SO:0001583	missense	2539			X03674	CCDS14756.2, CCDS44023.1	Xq28	2014-09-17			ENSG00000160211	ENSG00000160211	1.1.1.49		4057	protein-coding gene	gene with protein product		305900				3012556, 2428611	Standard	NM_000402		Approved	G6PD1	uc004flx.1	P11413	OTTHUMG00000024237	ENST00000393564.2:c.585G>T	X.37:g.153762612C>A	ENSP00000377194:p.Gln195His	Somatic		WXS	Illumina HiSeq	Phase_I	D3DWX9|Q16000|Q16765|Q8IU70|Q8IU88|Q8IUA6|Q96PQ2	Missense_Mutation	SNP	ENST00000393564.2	37	CCDS44023.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.946008	0.73672	.	.	ENSG00000160211	ENST00000393562;ENST00000291567;ENST00000393564;ENST00000369620;ENST00000439227;ENST00000440967;ENST00000433845	D;D;D;D;D;D	0.98633	-5.04;-5.04;-5.04;-5.04;-5.04;-5.04	5.65	4.78	0.61160	NAD(P)-binding domain (1);Glucose-6-phosphate dehydrogenase, NAD-binding (1);	0.000000	0.85682	D	0.000000	D	0.99180	0.9716	M	0.91510	3.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.99113	1.0847	10	0.72032	D	0.01	.	11.696	0.51544	0.0:0.9096:0.0:0.0904	.	195;225	P11413;P11413-3	G6PD_HUMAN;.	H	225;195;195;195;196;196;195	ENSP00000377192:Q225H;ENSP00000377194:Q195H;ENSP00000358633:Q195H;ENSP00000395599:Q196H;ENSP00000400648:Q196H;ENSP00000394690:Q195H	ENSP00000291567:Q195H	Q	-	3	2	G6PD	153415806	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	2.474000	0.45154	2.361000	0.80049	0.513000	0.50165	CAG		0.637	G6PD-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061170.3		NM_000402	
GEN1	348654	hgsc.bcm.edu	37	2	17946312	17946312	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr2:17946312delT	ENST00000381254.2	+	4	711	c.497delT	c.(496-498)gttfs	p.V166fs	SMC6_ENST00000402989.1_Intron|GEN1_ENST00000317402.7_Frame_Shift_Del_p.V166fs	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	166	I-domain.				DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|resolution of recombination intermediates (GO:0071139)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GCCCAGACTGTTTACAGGAAT	0.398								Homologous recombination																																									0													136.0	133.0	134.0					2																	17946312		2203	4300	6503	SO:0001589	frameshift_variant	348654			AK098188	CCDS1691.1	2p24.2	2013-06-04	2013-06-04		ENSG00000178295	ENSG00000178295			26881	protein-coding gene	gene with protein product	"""Holliday junction resolvase"""	612449	"""Gen endonuclease homolog 1 (Drosophila)"""			15576351	Standard	NM_182625		Approved	FLJ40869, Gen	uc002rct.2	Q17RS7	OTTHUMG00000121173	ENST00000381254.2:c.497delT	2.37:g.17946312delT	ENSP00000370653:p.Val166fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q17RS9|Q6ZN37	Frame_Shift_Del	DEL	ENST00000381254.2	37	CCDS1691.1																																																																																				0.398	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2		NM_182625	
GPR183	1880	hgsc.bcm.edu;ucsc.edu	37	13	99947650	99947652	+	In_Frame_Del	DEL	AAT	AAT	-			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr13:99947650_99947652delAAT	ENST00000376414.4	-	2	831_833	c.748_750delATT	c.(748-750)attdel	p.I250del	UBAC2_ENST00000376440.2_Intron|UBAC2_ENST00000403766.3_Intron	NM_004951.4	NP_004942.1	P32249	GP183_HUMAN	G protein-coupled receptor 183	250					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)			cervix(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	23						CAAACACAACAATAATAAGAATA	0.365																																																	0																																										SO:0001651	inframe_deletion	1880			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.748_750delATT	13.37:g.99947653_99947655delAAT	ENSP00000365596:p.Ile250del	Somatic		WXS	Illumina HiSeq	Phase_I	B2R8N5|Q53F99|Q5JUH7	In_Frame_Del	DEL	ENST00000376414.4	37	CCDS9492.1																																																																																				0.365	GPR183-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045582.2		NM_004951	
GPRC5B	51704	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	19883415	19883415	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr16:19883415C>T	ENST00000300571.2	-	2	944	c.753G>A	c.(751-753)atG>atA	p.M251I	GPRC5B_ENST00000569847.1_Missense_Mutation_p.M251I|GPRC5B_ENST00000535671.1_Missense_Mutation_p.M251I|GPRC5B_ENST00000537135.1_Missense_Mutation_p.M277I|GPRC5B_ENST00000569479.1_Missense_Mutation_p.M251I	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, class C, group 5, member B	251					glucose homeostasis (GO:0042593)|locomotory behavior (GO:0007626)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein tyrosine kinase activity (GO:0061098)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)	p.M251I(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						GGTACATGGTCATCCAGGCCA	0.607																																																	1	Substitution - Missense(1)	kidney(1)											97.0	102.0	100.0					16																	19883415		2197	4300	6497	SO:0001583	missense	51704			AF202640	CCDS10581.1	16p12	2014-01-30	2014-01-30		ENSG00000167191	ENSG00000167191		"""GPCR / Class C : Orphans"""	13308	protein-coding gene	gene with protein product		605948	"""G protein-coupled receptor, family C, group 1, member B"", ""G protein-coupled receptor, family C, group 5, member B"""			10493829, 10783259	Standard	XM_005255357		Approved	RAIG-2	uc002dgt.3	Q9NZH0	OTTHUMG00000131460	ENST00000300571.2:c.753G>A	16.37:g.19883415C>T	ENSP00000300571:p.Met251Ile	Somatic		WXS	Illumina HiSeq	Phase_I	D2DFB0|O75205|Q8NBZ8	Missense_Mutation	SNP	ENST00000300571.2	37	CCDS10581.1	.	.	.	.	.	.	.	.	.	.	C	0.550	-0.849735	0.02651	.	.	ENSG00000167191	ENST00000300571;ENST00000535671;ENST00000538074;ENST00000537135	D;D;D	0.85339	-1.97;-1.97;-1.97	5.44	-0.136	0.13473	GPCR, family 3, C-terminal (2);	0.343111	0.34652	N	0.003792	T	0.67487	0.2898	N	0.11154	0.105	0.37915	D	0.931484	B;B	0.06786	0.0;0.001	B;B	0.09377	0.0;0.004	T	0.53337	-0.8453	9	.	.	.	.	12.0003	0.53226	0.0:0.4633:0.471:0.0658	.	277;251	B7Z831;Q9NZH0	.;GPC5B_HUMAN	I	251;251;100;277	ENSP00000300571:M251I;ENSP00000442858:M251I;ENSP00000441775:M277I	.	M	-	3	0	GPRC5B	19790916	1.000000	0.71417	0.980000	0.43619	0.888000	0.51559	1.127000	0.31357	-0.107000	0.12088	-0.961000	0.02630	ATG		0.607	GPRC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254285.1			
HCFC2	29915	hgsc.bcm.edu;ucsc.edu	37	12	104476286	104476286	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr12:104476286delT	ENST00000229330.4	+	6	880	c.776delT	c.(775-777)attfs	p.I259fs		NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	259					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						AGGATGTACATTTTTGGTGGA	0.353																																					Esophageal Squamous(184;1814 2036 4771 6974 15702)												0													97.0	96.0	96.0					12																	104476286		2203	4300	6503	SO:0001589	frameshift_variant	29915			AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.776delT	12.37:g.104476286delT	ENSP00000229330:p.Ile259fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2R8Q5|C0H5X3	Frame_Shift_Del	DEL	ENST00000229330.4	37	CCDS9097.1																																																																																				0.353	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1		NM_013320	
HIST1H2AH	85235	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	27115055	27115055	+	Missense_Mutation	SNP	G	G	A	rs201037769		TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr6:27115055G>A	ENST00000377459.1	+	1	195	c.148G>A	c.(148-150)Gtg>Atg	p.V50M	MIR3143_ENST00000584253.1_RNA|HIST1H2BK_ENST00000356950.1_5'Flank|HIST1H2BK_ENST00000396891.4_5'Flank	NM_080596.1	NP_542163.1	Q96KK5	H2A1H_HUMAN	histone cluster 1, H2ah	50						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.V50M(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|prostate(1)|skin(1)	12						CGGCGCGCCAGTGTACCTGGC	0.657																																																	1	Substitution - Missense(1)	kidney(1)											46.0	50.0	49.0					6																	27115055		2203	4300	6503	SO:0001583	missense	85235			AY131988	CCDS4622.1	6p22.1	2011-01-27	2006-10-11			ENSG00000274997		"""Histones / Replication-dependent"""	13671	protein-coding gene	gene with protein product		615013	"""histone 1, H2ah"""			12408966	Standard	NM_080596		Approved	H2AFALii, dJ86C11.1, H2A/S	uc003niz.4	Q96KK5		ENST00000377459.1:c.148G>A	6.37:g.27115055G>A	ENSP00000366679:p.Val50Met	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000377459.1	37	CCDS4622.1	.	.	.	.	.	.	.	.	.	.	G	13.58	2.280328	0.40294	.	.	ENSG00000184825	ENST00000377459	D	0.87809	-2.3	3.95	3.95	0.45737	Histone-fold (2);Histone core (1);Histone H2A (2);	0.000000	0.37012	N	0.002290	D	0.96318	0.8799	H	0.99697	4.71	0.38930	D	0.957911	D	0.89917	1.0	D	0.97110	1.0	D	0.97875	1.0288	10	0.87932	D	0	.	14.3093	0.66405	0.0:0.0:1.0:0.0	.	50	Q96KK5	H2A1H_HUMAN	M	50	ENSP00000366679:V50M	ENSP00000366679:V50M	V	+	1	0	HIST1H2AH	27223034	1.000000	0.71417	0.750000	0.31169	0.049000	0.14656	8.845000	0.92153	2.142000	0.66516	0.655000	0.94253	GTG		0.657	HIST1H2AH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040136.1		NM_080596	
HTR7	3363	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	92617162	92617162	+	Silent	SNP	C	C	G			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr10:92617162C>G	ENST00000336152.3	-	1	293	c.267G>C	c.(265-267)acG>acC	p.T89T	HTR7_ENST00000277874.6_Silent_p.T89T|HTR7_ENST00000371721.3_Silent_p.T89T|HTR7_ENST00000371719.2_Silent_p.T89T	NM_019859.3	NP_062873.1	P34969	5HT7R_HUMAN	5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled	89					blood circulation (GO:0008015)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)	p.T89T(2)		NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30					Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Eletriptan(DB00216)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Methysergide(DB00247)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	GCGTGATGAGCGTCAGGATGG	0.627																																																	2	Substitution - coding silent(2)	kidney(2)											77.0	69.0	72.0					10																	92617162		2203	4300	6503	SO:0001819	synonymous_variant	3363			BC047526	CCDS7408.1, CCDS7409.1, CCDS7410.1	10q21-q24	2012-08-08	2012-02-03		ENSG00000148680	ENSG00000148680		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5302	protein-coding gene	gene with protein product		182137	"""5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)"""			8226867	Standard	NM_000872		Approved	5-HT7	uc001kha.3	P34969	OTTHUMG00000018732	ENST00000336152.3:c.267G>C	10.37:g.92617162C>G		Somatic		WXS	Illumina HiSeq	Phase_I	B5BUP6|P78336|P78372|P78516|Q5VX01|Q5VX02|Q5VX03	Silent	SNP	ENST00000336152.3	37	CCDS7408.1																																																																																				0.627	HTR7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049343.1		NM_000872	
IL21R	50615	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	27460474	27460474	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr16:27460474G>T	ENST00000337929.3	+	9	1960	c.1487G>T	c.(1486-1488)gGc>gTc	p.G496V	IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000564089.1_Missense_Mutation_p.G496V|IL21R_ENST00000395755.1_Missense_Mutation_p.G496V|IL21R_ENST00000395754.4_Missense_Mutation_p.G496V	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	496					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)	p.G496V(1)		breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						GGCTTTGTGGGCTCTGACTGC	0.667			T	BCL6	NHL																																			Dom	yes		16	16p11	50615	interleukin 21 receptor		L	1	Substitution - Missense(1)	kidney(1)											50.0	44.0	46.0					16																	27460474		2197	4299	6496	SO:0001583	missense	50615			AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"""Interleukins and interleukin receptors"", ""CD molecules"""	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1487G>T	16.37:g.27460474G>T	ENSP00000338010:p.Gly496Val	Somatic		WXS	Illumina HiSeq	Phase_I	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	37	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	G	19.97	3.925061	0.73213	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.24538	1.85;1.85;1.85	4.9	3.93	0.45458	.	0.168550	0.41605	D	0.000858	T	0.41858	0.1177	L	0.56769	1.78	0.58432	D	0.999995	D	0.76494	0.999	D	0.71870	0.975	T	0.22941	-1.0202	10	0.59425	D	0.04	-27.6999	8.053	0.30589	0.1175:0.0:0.8825:0.0	.	496	Q9HBE5	IL21R_HUMAN	V	496	ENSP00000338010:G496V;ENSP00000379104:G496V;ENSP00000379103:G496V	ENSP00000338010:G496V	G	+	2	0	IL21R	27367975	1.000000	0.71417	0.969000	0.41365	0.949000	0.60115	2.113000	0.41902	1.020000	0.39573	0.561000	0.74099	GGC		0.667	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2		NM_181078	
IWS1	55677	broad.mit.edu;ucsc.edu	37	2	128262532	128262533	+	Missense_Mutation	DNP	TC	TC	AA			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr2:128262532_128262533TC>AA	ENST00000295321.4	-	3	1205_1206	c.946_947GA>TT	c.(946-948)GAa>TTa	p.E316L	IWS1_ENST00000486662.1_5'Flank|IWS1_ENST00000455721.2_Missense_Mutation_p.E323L|AC010976.2_ENST00000599001.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	316	Glu-rich.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E316*(1)|p.E316V(1)|p.E316>?(1)		cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		ATCCTCAGTTTCTGAGTCACTG	0.525																																																	3	Substitution - Missense(1)|Substitution - Nonsense(1)|Complex(1)	kidney(3)																																								SO:0001583	missense	55677			AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.946_947delinsAA	2.37:g.128262532_128262533delinsAA	ENSP00000295321:p.Glu316Leu	Somatic		WXS	Illumina GAIIx	Phase_I	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000295321.4	37	CCDS2146.1																																																																																				0.525	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2		NM_017969	
KIAA1755	85449	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	36869596	36869596	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr20:36869596C>A	ENST00000279024.4	-	3	1208	c.937G>T	c.(937-939)Gaa>Taa	p.E313*		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	313								p.E313*(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				AAGGGAGTTTCCTTAGTTCCA	0.517																																																	1	Substitution - Nonsense(1)	kidney(1)											132.0	142.0	138.0					20																	36869596		2203	4300	6503	SO:0001587	stop_gained	85449			AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.937G>T	20.37:g.36869596C>A	ENSP00000279024:p.Glu313*	Somatic		WXS	Illumina HiSeq	Phase_I	Q9C0A8	Nonsense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	C	37	6.103826	0.97286	.	.	ENSG00000149633	ENST00000279024	.	.	.	5.07	3.06	0.35304	.	0.943820	0.08795	N	0.892589	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	.	5.5199	0.16927	0.1981:0.7026:0.0:0.0993	.	.	.	.	X	313	.	ENSP00000279024:E313X	E	-	1	0	KIAA1755	36303010	0.002000	0.14202	0.457000	0.27056	0.181000	0.23173	0.370000	0.20433	2.629000	0.89072	0.655000	0.94253	GAA		0.517	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3		NM_001029864	
LMAN1	3998	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	57013225	57013225	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr18:57013225T>C	ENST00000251047.5	-	8	1598	c.881A>G	c.(880-882)gAg>gGg	p.E294G	LMAN1_ENST00000587940.1_5'UTR	NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	294					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)	p.E294G(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	TTGAAAGTGCTCAAATTCCTC	0.398																																																	1	Substitution - Missense(1)	kidney(1)											137.0	139.0	138.0					18																	57013225		2203	4300	6503	SO:0001583	missense	3998			X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"""endoplasmic reticulum-golgi intermediate compartment protein 53"""	601567	"""coagulation factor V-factor VIII combined deficiency"""	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.881A>G	18.37:g.57013225T>C	ENSP00000251047:p.Glu294Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Missense_Mutation	SNP	ENST00000251047.5	37	CCDS11974.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.026272	0.93518	.	.	ENSG00000074695	ENST00000251047	D	0.99462	-5.94	5.71	5.71	0.89125	.	0.151252	0.64402	D	0.000019	D	0.99121	0.9697	L	0.59436	1.845	0.80722	D	1	D	0.62365	0.991	P	0.56700	0.804	D	0.99360	1.0917	10	0.54805	T	0.06	-26.6017	15.6453	0.77042	0.0:0.0:0.0:1.0	.	294	P49257	LMAN1_HUMAN	G	294	ENSP00000251047:E294G	ENSP00000251047:E294G	E	-	2	0	LMAN1	55164205	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.665000	0.83852	2.178000	0.69098	0.533000	0.62120	GAG		0.398	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2		NM_005570	
RP11-38M15.11	0	broad.mit.edu	37	13	19432891	19432891	+	lincRNA	SNP	C	C	A	rs1937748	byFrequency	TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr13:19432891C>A	ENST00000418741.1	+	0	0																											AGTAAATACTCTGCAAAACTA	0.353													.|||	1239	0.247404	0.503	0.1571	5008	,	,		16920	0.0972		0.2048	False		,,,				2504	0.1646																0																																												0																															13.37:g.19432891C>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000418741.1	37																																																																																					0.353	RP11-38M15.11-001	KNOWN	not_best_in_genome_evidence|basic	lincRNA	lincRNA	OTTHUMT00000043983.1			
LRRC42	115353	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	54433413	54433413	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr1:54433413T>A	ENST00000371370.3	+	9	1609	c.1088T>A	c.(1087-1089)cTc>cAc	p.L363H	LRRC42_ENST00000319223.4_Missense_Mutation_p.L363H	NM_001256409.1	NP_001243338.1	Q9Y546	LRC42_HUMAN	leucine rich repeat containing 42	363								p.L363H(1)		breast(2)|kidney(1)|large_intestine(1)|lung(5)	9						TCCGAGAAACTCCAGTTCTAT	0.507																																																	1	Substitution - Missense(1)	kidney(1)											55.0	55.0	55.0					1																	54433413		2203	4300	6503	SO:0001583	missense	115353			AK075201	CCDS585.1	1p33-p32.1	2014-02-12			ENSG00000116212	ENSG00000116212			28792	protein-coding gene	gene with protein product						12477932	Standard	NM_001256409		Approved	MGC8974	uc001cwj.2	Q9Y546	OTTHUMG00000008436	ENST00000371370.3:c.1088T>A	1.37:g.54433413T>A	ENSP00000360421:p.Leu363His	Somatic		WXS	Illumina HiSeq	Phase_I	D3DQ46|Q8N2Q8	Missense_Mutation	SNP	ENST00000371370.3	37	CCDS585.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.396658	0.83011	.	.	ENSG00000116212	ENST00000371370;ENST00000319223	.	.	.	5.74	5.74	0.90152	.	0.063495	0.64402	D	0.000007	T	0.66944	0.2841	L	0.29908	0.895	0.54753	D	0.999984	D	0.76494	0.999	D	0.85130	0.997	T	0.70802	-0.4773	9	0.87932	D	0	-13.1267	16.0351	0.80621	0.0:0.0:0.0:1.0	.	363	Q9Y546	LRC42_HUMAN	H	363	.	ENSP00000318185:L363H	L	+	2	0	LRRC42	54206001	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	5.505000	0.66981	2.186000	0.69663	0.533000	0.62120	CTC		0.507	LRRC42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023250.1		NM_052940	
MIS12	79003	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	5392574	5392574	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr17:5392574A>C	ENST00000381165.3	+	3	945	c.392A>C	c.(391-393)gAa>gCa	p.E131A	MIS12_ENST00000573759.1_Missense_Mutation_p.E131A|DERL2_ENST00000571968.1_5'Flank	NM_001258217.1|NM_001258219.1|NM_001258220.1|NM_024039.2	NP_001245146.1|NP_001245148.1|NP_001245149.1|NP_076944.1			MIS12 kinetochore complex component									p.E131A(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(2)	12						TACAAGACTGAATTATGTACT	0.373																																																	1	Substitution - Missense(1)	kidney(1)											110.0	106.0	107.0					17																	5392574		2203	4300	6503	SO:0001583	missense	79003			AL136906	CCDS11074.1	17p13.3	2013-07-03	2013-07-03		ENSG00000167842	ENSG00000167842			24967	protein-coding gene	gene with protein product		609178	"""MIS12, MIND kinetochore complex component, homolog (yeast)"", ""MIS12, MIND kinetochore complex component, homolog (S. pombe)"""			11230166, 12515822	Standard	NM_001258217		Approved	MGC2488, hMIS12, KNTC2AP, MTW1	uc031qyj.1	Q9H081	OTTHUMG00000102042	ENST00000381165.3:c.392A>C	17.37:g.5392574A>C	ENSP00000370557:p.Glu131Ala	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000381165.3	37	CCDS11074.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.518962	0.85495	.	.	ENSG00000167842	ENST00000381165	T	0.52057	0.68	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.65123	0.2661	L	0.55481	1.735	0.58432	D	0.999993	D	0.89917	1.0	D	0.91635	0.999	T	0.65705	-0.6103	10	0.56958	D	0.05	-9.9653	15.8323	0.78764	1.0:0.0:0.0:0.0	.	131	Q9H081	MIS12_HUMAN	A	131	ENSP00000370557:E131A	ENSP00000370557:E131A	E	+	2	0	MIS12	5333298	1.000000	0.71417	0.986000	0.45419	0.976000	0.68499	7.942000	0.87708	2.333000	0.79357	0.482000	0.46254	GAA		0.373	MIS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219827.1		NM_024039	
MAP2K3	5606	hgsc.bcm.edu	37	17	21203907	21203907	+	Silent	SNP	T	T	C	rs73311539	byFrequency	TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr17:21203907T>C	ENST00000342679.4	+	4	465	c.216T>C	c.(214-216)cgT>cgC	p.R72R	MAP2K3_ENST00000361818.5_Silent_p.R43R|MAP2K3_ENST00000316920.6_Silent_p.R43R	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	72	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|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)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.R76R(2)|p.R43R(1)							COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		AACTGGGCCGTGGAGCCTATG	0.607																																																	3	Substitution - coding silent(3)	prostate(2)|haematopoietic_and_lymphoid_tissue(1)											59.0	54.0	55.0					17																	21203907		2203	4300	6503	SO:0001819	synonymous_variant	5606			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.216T>C	17.37:g.21203907T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B3KSK7|Q99441|Q9UE71|Q9UE72	Silent	SNP	ENST00000342679.4	37	CCDS11217.1																																																																																				0.607	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2		NM_145109	
MRGPRD	116512	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	68747868	68747868	+	Silent	SNP	C	C	G			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr11:68747868C>G	ENST00000309106.3	-	1	587	c.588G>C	c.(586-588)ctG>ctC	p.L196L		NM_198923.2	NP_944605.2	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D	196						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L196L(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)	22			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TCAGGCTGGACAGAGTCATCA	0.597																																																	1	Substitution - coding silent(1)	kidney(1)											51.0	45.0	47.0					11																	68747868		2200	4294	6494	SO:0001819	synonymous_variant	116512			AB083627	CCDS31625.1	11q13.3	2012-08-21			ENSG00000172938	ENSG00000172938		"""GPCR / Class A : Orphans"""	29626	protein-coding gene	gene with protein product		607231				11551509, 12909716	Standard	NM_198923		Approved	mrgD	uc010rqf.2	Q8TDS7	OTTHUMG00000167896	ENST00000309106.3:c.588G>C	11.37:g.68747868C>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q8NGK7	Silent	SNP	ENST00000309106.3	37	CCDS31625.1																																																																																				0.597	MRGPRD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396874.1		NM_198923	
MRO	83876	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	48335764	48335764	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr18:48335764G>T	ENST00000428869.2	-	4	265	c.7C>A	c.(7-9)Caa>Aaa	p.Q3K	MRO_ENST00000588444.1_Missense_Mutation_p.Q3K|MRO_ENST00000398439.3_Missense_Mutation_p.Q3K|MRO_ENST00000256425.2_Missense_Mutation_p.Q3K|MRO_ENST00000431965.2_Intron|MRO_ENST00000587291.1_Intron|MRO_ENST00000436348.2_Intron			Q9BYG7	MSTRO_HUMAN	maestro	3						nucleolus (GO:0005730)		p.Q3K(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|skin(2)	10		Colorectal(6;0.0596)		Colorectal(21;0.082)		CTCTGTCTTTGGTCCATGGAA	0.433																																																	1	Substitution - Missense(1)	kidney(1)											84.0	78.0	80.0					18																	48335764		2203	4300	6503	SO:0001583	missense	83876			AK054702	CCDS11947.1, CCDS45867.1, CCDS45868.1, CCDS45869.1	18q21	2012-12-19	2004-06-15		ENSG00000134042	ENSG00000134042		"""maestro heat-like repeat containing"""	24121	protein-coding gene	gene with protein product	"""B29 protein"", ""beside the Ma29 deletion"""	608080	"""chromosome 18 open reading frame 3"""	C18orf3		11401430	Standard	NM_031939		Approved	B29, FLJ30140	uc010dpa.3	Q9BYG7	OTTHUMG00000132692	ENST00000428869.2:c.7C>A	18.37:g.48335764G>T	ENSP00000409509:p.Gln3Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z2I5|B7Z3B2|E9PAT5|E9PBI3|K7EKJ8|Q8N6K5	Missense_Mutation	SNP	ENST00000428869.2	37	CCDS11947.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.801683	0.50315	.	.	ENSG00000134042	ENST00000428869;ENST00000398439;ENST00000256425	T;T;T	0.15718	2.4;2.4;2.4	5.24	4.31	0.51392	.	1.272030	0.05949	N	0.638344	T	0.44561	0.1299	M	0.78223	2.4	0.24338	N	0.994977	P;D	0.67145	0.587;0.996	B;D	0.72982	0.266;0.979	T	0.16571	-1.0398	10	0.46703	T	0.11	.	10.9695	0.47431	0.0:0.1889:0.811:0.0	.	3;3	E9PFU2;Q9BYG7	.;MSTRO_HUMAN	K	3	ENSP00000409509:Q3K;ENSP00000381465:Q3K;ENSP00000256425:Q3K	ENSP00000256425:Q3K	Q	-	1	0	MRO	46589762	0.974000	0.33945	0.987000	0.45799	0.776000	0.43924	1.394000	0.34509	2.473000	0.83533	0.650000	0.86243	CAA		0.433	MRO-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449478.2		NM_031939	
NCOA2	10499	hgsc.bcm.edu;ucsc.edu	37	8	71069452	71069452	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr8:71069452delT	ENST00000452400.2	-	11	1329	c.1148delA	c.(1147-1149)aatfs	p.N383fs	NCOA2_ENST00000524223.1_5'Flank	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	383					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			CAGATCCGGATTCATCACACA	0.413			T	"""RUNXBP2, HEY1"""	"""AML, Chondrosarcoma"""																																			Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	0													63.0	59.0	60.0					8																	71069452		1924	4135	6059	SO:0001589	frameshift_variant	10499			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.1148delA	8.37:g.71069452delT	ENSP00000399968:p.Asn383fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q14CD2	Frame_Shift_Del	DEL	ENST00000452400.2	37	CCDS47872.1																																																																																				0.413	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			
NFXL1	152518	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	47880552	47880552	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr4:47880552C>A	ENST00000507489.1	-	17	2245	c.2069G>T	c.(2068-2070)gGa>gTa	p.G690V	NFXL1_ENST00000329043.3_Missense_Mutation_p.G690V|NFXL1_ENST00000381538.3_Missense_Mutation_p.G690V	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	690						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G690V(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						CTTGTTTTTTCCAGTGCAGCC	0.338																																																	1	Substitution - Missense(1)	kidney(1)											247.0	243.0	244.0					4																	47880552		2203	4300	6503	SO:0001583	missense	152518			AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"""ovarian zinc finger protein"""						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.2069G>T	4.37:g.47880552C>A	ENSP00000422037:p.Gly690Val	Somatic		WXS	Illumina HiSeq	Phase_I	B1Q2K1|Q86VG1|Q8WVH1	Missense_Mutation	SNP	ENST00000507489.1	37	CCDS3478.2	.	.	.	.	.	.	.	.	.	.	C	6.818	0.520094	0.13005	.	.	ENSG00000170448	ENST00000381538;ENST00000507489;ENST00000329043	T;T;T	0.60672	0.17;0.17;1.57	5.33	-0.877	0.10621	.	0.536026	0.18225	N	0.147742	T	0.51517	0.1679	M	0.80508	2.5	0.09310	N	0.999993	B	0.02656	0.0	B	0.06405	0.002	T	0.44298	-0.9337	10	0.30078	T	0.28	0.2712	6.7727	0.23602	0.0:0.3933:0.1245:0.4822	.	690	Q6ZNB6	NFXL1_HUMAN	V	690	ENSP00000370949:G690V;ENSP00000422037:G690V;ENSP00000333113:G690V	ENSP00000333113:G690V	G	-	2	0	NFXL1	47575309	0.007000	0.16637	0.123000	0.21794	0.797000	0.45037	-0.048000	0.11944	-0.115000	0.11915	0.591000	0.81541	GGA		0.338	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1		NM_152995	
POM121	9883	hgsc.bcm.edu;ucsc.edu	37	7	72419464	72419464	+	IGR	SNP	T	T	G	rs138398938	byFrequency	TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr7:72419464T>G	ENST00000434423.2	+	0	3750				NSUN5P2_ENST00000388955.4_RNA|POM121_ENST00000395270.1_3'UTR			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin						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.Q163P(1)		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)				CAGCGCATCTTGTACCATGTC	0.632																																																	1	Substitution - Missense(1)	prostate(1)											41.0	46.0	44.0					7																	72419464		2202	4300	6502	SO:0001628	intergenic_variant	260294			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		7.37:g.72419464T>G		Somatic		WXS	Illumina HiSeq	Phase_I	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	RNA	SNP	ENST00000434423.2	37																																																																																					0.632	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1			
OSBPL7	114881	broad.mit.edu	37	17	45891939	45891939	+	Silent	SNP	G	G	C			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr17:45891939G>C	ENST00000007414.3	-	14	1490	c.1299C>G	c.(1297-1299)acC>acG	p.T433T	OSBPL7_ENST00000392507.3_Silent_p.T433T	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	433					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)	p.T433T(1)		autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						CAGACAGGCTGGTGGTGATTT	0.657																																																	1	Substitution - coding silent(1)	kidney(1)											70.0	57.0	61.0					17																	45891939		2203	4300	6503	SO:0001819	synonymous_variant	114881			AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.1299C>G	17.37:g.45891939G>C		Somatic		WXS	Illumina GAIIx	Phase_I	D3DTT6|Q6PIV6	Silent	SNP	ENST00000007414.3	37	CCDS11515.1																																																																																				0.657	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1		NM_017731	
PBRM1	55193	broad.mit.edu;ucsc.edu	37	3	52696148	52696148	+	Splice_Site	SNP	C	C	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr3:52696148C>A	ENST00000296302.7	-	4	530		c.e4+1		PBRM1_ENST00000356770.4_Splice_Site|PBRM1_ENST00000394830.3_Splice_Site|PBRM1_ENST00000409767.1_Splice_Site|PBRM1_ENST00000410007.1_Splice_Site|PBRM1_ENST00000337303.4_Splice_Site|PBRM1_ENST00000409114.3_Splice_Site|PBRM1_ENST00000409057.1_Splice_Site			Q86U86	PB1_HUMAN	polybromo 1						chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.?(3)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TACACACTTACTCCTTCAGTC	0.488			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	3	Unknown(3)	kidney(3)											366.0	333.0	344.0					3																	52696148		2203	4300	6503	SO:0001630	splice_region_variant	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.528+1G>T	3.37:g.52696148C>A		Somatic		WXS	Illumina GAIIx	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Splice_Site	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	C	21.0	4.084633	0.76642	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103;ENST00000431678	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4035	0.94640	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PBRM1	52671188	1.000000	0.71417	0.999000	0.59377	0.906000	0.53458	4.881000	0.63114	2.590000	0.87494	0.650000	0.86243	.		0.488	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	Intron
PCSK5	5125	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	78601100	78601100	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr9:78601100A>C	ENST00000545128.1	+	3	888	c.350A>C	c.(349-351)gAc>gCc	p.D117A	PCSK5_ENST00000376752.4_Missense_Mutation_p.D117A|PCSK5_ENST00000376767.3_Missense_Mutation_p.D117A	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	117					anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)	p.D117A(3)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						AGGGATTATGACTTCAGTCGT	0.468																																																	3	Substitution - Missense(3)	kidney(3)											208.0	176.0	187.0					9																	78601100		2203	4300	6503	SO:0001583	missense	5125				CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.350A>C	9.37:g.78601100A>C	ENSP00000446280:p.Asp117Ala	Somatic		WXS	Illumina HiSeq	Phase_I	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	.	.	.	.	.	.	.	.	.	.	A	10.28	1.306940	0.23821	.	.	ENSG00000099139	ENST00000545128;ENST00000376767;ENST00000396108;ENST00000376752	T;T;T	0.41400	1.0;1.0;1.0	5.83	5.83	0.93111	.	.	.	.	.	T	0.22898	0.0553	N	0.08118	0	0.39255	D	0.96411	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.0	T	0.14448	-1.0472	9	0.06494	T	0.89	.	16.1968	0.82036	1.0:0.0:0.0:0.0	.	117;117	Q92824-2;B1AMG5	.;.	A	117	ENSP00000446280:D117A;ENSP00000365958:D117A;ENSP00000365943:D117A	ENSP00000365943:D117A	D	+	2	0	PCSK5	77790920	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.058000	0.76676	2.225000	0.72522	0.533000	0.62120	GAC		0.468	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				
PLTP	5360	broad.mit.edu	37	20	44534935	44534935	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr20:44534935G>A	ENST00000477313.1	-	7	1271	c.677C>T	c.(676-678)tCc>tTc	p.S226F	PLTP_ENST00000354050.4_Missense_Mutation_p.S174F|PLTP_ENST00000420868.2_Missense_Mutation_p.S131F|PLTP_ENST00000372431.3_Missense_Mutation_p.S226F|PLTP_ENST00000542937.1_Missense_Mutation_p.S246F|PLTP_ENST00000372420.1_Missense_Mutation_p.S138F			P55058	PLTP_HUMAN	phospholipid transfer protein	226					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.S226F(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				GTTGCTGGTGGAAGCCACAGG	0.527																																																	1	Substitution - Missense(1)	kidney(1)											104.0	81.0	89.0					20																	44534935		2203	4300	6503	SO:0001583	missense	5360			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.677C>T	20.37:g.44534935G>A	ENSP00000417138:p.Ser226Phe	Somatic		WXS	Illumina GAIIx	Phase_I	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Missense_Mutation	SNP	ENST00000477313.1	37	CCDS13386.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.794838	0.90453	.	.	ENSG00000100979	ENST00000372420;ENST00000372431;ENST00000354050;ENST00000477313;ENST00000542937;ENST00000420868	T;T;T;T;T;T	0.05447	3.44;3.44;3.44;3.44;3.44;3.44	5.4	5.4	0.78164	Lipid-binding serum glycoprotein, N-terminal (1);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.051523	0.85682	D	0.000000	T	0.24586	0.0596	M	0.68952	2.095	0.58432	D	0.999999	D;D;D;D;D;D;D	0.71674	0.998;0.998;0.997;0.997;0.998;0.997;0.997	D;D;P;P;D;P;P	0.67725	0.938;0.938;0.898;0.898;0.953;0.898;0.898	T	0.00076	-1.2118	10	0.87932	D	0	-33.2314	19.359	0.94428	0.0:0.0:1.0:0.0	.	131;131;138;226;174;226;246	E7EV16;B4DRB4;B4DDD5;Q53H91;P55058-2;P55058;B3KUE5	.;.;.;.;.;PLTP_HUMAN;.	F	138;226;174;226;246;131	ENSP00000361497:S138F;ENSP00000361508:S226F;ENSP00000335290:S174F;ENSP00000417138:S226F;ENSP00000440296:S246F;ENSP00000411671:S131F	ENSP00000335290:S174F	S	-	2	0	PLTP	43968342	1.000000	0.71417	0.359000	0.25824	0.990000	0.78478	8.544000	0.90654	2.811000	0.96726	0.555000	0.69702	TCC		0.527	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1		NM_006227	
PRMT8	56341	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	3659255	3659255	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr12:3659255G>A	ENST00000382622.3	+	3	805	c.415G>A	c.(415-417)Ggg>Agg	p.G139R	PRMT8_ENST00000261252.4_3'UTR|PRMT8_ENST00000452611.2_Missense_Mutation_p.G130R	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8	139	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.G139R(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			GAAGGTGTTTGGGGTGAGCAC	0.562																																																	1	Substitution - Missense(1)	kidney(1)											134.0	112.0	119.0					12																	3659255		2203	4300	6503	SO:0001583	missense	56341			AF263539	CCDS8521.2, CCDS58200.1	12p13.3	2006-03-03	2006-02-16	2006-02-16	ENSG00000111218	ENSG00000111218		"""Protein arginine methyltransferases"""	5188	protein-coding gene	gene with protein product		610086	"""HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)"", ""HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)"""	HRMT1L3, HRMT1L4		16051612	Standard	NM_019854		Approved		uc001qmf.4	Q9NR22	OTTHUMG00000128493	ENST00000382622.3:c.415G>A	12.37:g.3659255G>A	ENSP00000372067:p.Gly139Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B2RDP0|Q8TBJ8	Missense_Mutation	SNP	ENST00000382622.3	37	CCDS8521.2	.	.	.	.	.	.	.	.	.	.	G	26.1	4.701530	0.88924	.	.	ENSG00000111218	ENST00000452611;ENST00000382622	T;T	0.36340	1.26;1.26	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.74412	0.3713	H	0.97415	4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.83968	0.0325	10	0.87932	D	0	.	16.9998	0.86378	0.0:0.0:1.0:0.0	.	130;139	Q9NR22-2;Q9NR22	.;ANM8_HUMAN	R	130;139	ENSP00000414507:G130R;ENSP00000372067:G139R	ENSP00000372067:G139R	G	+	1	0	PRMT8	3529516	1.000000	0.71417	1.000000	0.80357	0.704000	0.40688	9.813000	0.99286	2.610000	0.88304	0.561000	0.74099	GGG		0.562	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2		NM_019854	
PSG6	5675	broad.mit.edu;hgsc.bcm.edu	37	19	43415010	43415010	+	Splice_Site	SNP	G	G	A	rs186311462	byFrequency	TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr19:43415010G>A	ENST00000292125.2	-	3	472	c.428C>T	c.(427-429)tCg>tTg	p.S143L	PSG6_ENST00000187910.2_Splice_Site_p.S143L|PSG6_ENST00000402603.4_Splice_Site_p.S143L	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	143	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.S143L(2)		central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				GGGAGTCTCCGCTGTGCAGAA	0.527													.|||	2	0.000399361	0.0	0.0014	5008	,	,		19656	0.001		0.0	False		,,,				2504	0.0																2	Substitution - Missense(2)	kidney(1)|endometrium(1)											122.0	124.0	123.0					19																	43415010		2201	4298	6499	SO:0001630	splice_region_variant	5675				CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.428-1C>T	19.37:g.43415010G>A		Somatic		WXS	Illumina HiSeq	Phase_I	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	37	CCDS12613.1	5	0.0022893772893772895	1	0.0020325203252032522	1	0.0027624309392265192	3	0.005244755244755245	0	0.0	N	0.448	-0.895161	0.02491	.	.	ENSG00000170848	ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456	T;T;T	0.31510	1.49;1.83;1.51	1.64	-3.28	0.05033	.	.	.	.	.	T	0.03695	0.0105	N	0.00170	-1.935	0.80722	D	1	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.04013	0.001;0.001;0.0	T	0.31475	-0.9942	9	0.30854	T	0.27	.	6.1077	0.20084	0.3266:0.0:0.6734:0.0	.	143;143;143	Q00889;Q00889-2;B5MCE1	PSG6_HUMAN;.;.	L	143	ENSP00000187910:S143L;ENSP00000385736:S143L;ENSP00000292125:S143L	ENSP00000187910:S143L	S	-	2	0	PSG6	48106850	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	-1.316000	0.02710	-0.994000	0.03463	-1.441000	0.01070	TCG		0.527	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1		NM_002782	Missense_Mutation
PTPN4	5775	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	120720267	120720267	+	Nonsense_Mutation	SNP	G	G	T			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr2:120720267G>T	ENST00000263708.2	+	24	3127	c.2356G>T	c.(2356-2358)Gaa>Taa	p.E786*	PTPN4_ENST00000544261.1_Nonsense_Mutation_p.E419*	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	786	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)	p.E786*(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	CTGCCACTCTGAAGAAGGAAA	0.388																																																	1	Substitution - Nonsense(1)	kidney(1)											76.0	70.0	72.0					2																	120720267		2203	4300	6503	SO:0001587	stop_gained	5775				CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.2356G>T	2.37:g.120720267G>T	ENSP00000263708:p.Glu786*	Somatic		WXS	Illumina HiSeq	Phase_I	B2RBV8|Q9UDA7	Nonsense_Mutation	SNP	ENST00000263708.2	37	CCDS2129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	6.983819|6.983819	0.97983|0.97983	.|.	.|.	ENSG00000088179|ENSG00000088179	ENST00000263708;ENST00000544261|ENST00000441089	.|.	.|.	.|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.87932|.	D|.	0|.	.|.	19.4142|19.4142	0.94688|0.94688	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	786;419|69	.|.	ENSP00000263708:E786X|.	E|X	+|+	1|2	0|2	PTPN4|PTPN4	120436737|120436737	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.849000|0.849000	0.48306|0.48306	9.481000|9.481000	0.97933|0.97933	2.592000|2.592000	0.87571|0.87571	0.460000|0.460000	0.39030|0.39030	GAA|TGA		0.388	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2			
PTPRR	5801	broad.mit.edu;hgsc.bcm.edu	37	12	71029653	71029653	+	IGR	SNP	G	G	T			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr12:71029653G>T	ENST00000283228.2	-	0	3529				PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000551525.1_Silent_p.I82I|PTPRR_ENST00000537619.2_5'Flank|PTPRB_ENST00000550358.1_Silent_p.I83I|PTPRB_ENST00000334414.6_Silent_p.I83I	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R						ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.I83I(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		AGCGGTCCAAGATGGCTGAGC	0.547																																																	1	Substitution - coding silent(1)	kidney(1)											57.0	57.0	57.0					12																	71029653		1980	4142	6122	SO:0001628	intergenic_variant	5787			D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502		12.37:g.71029653G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Silent	SNP	ENST00000283228.2	37	CCDS8998.1																																																																																				0.547	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1		NM_002849	
RAB40B	10966	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	80622419	80622419	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr17:80622419C>A	ENST00000571995.1	-	2	287	c.156G>T	c.(154-156)aaG>aaT	p.K52N	RAB40B_ENST00000538809.2_Missense_Mutation_p.K52N|RAB40B_ENST00000269347.6_5'UTR	NM_006822.2	NP_006813.1	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family	52					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.K52N(1)		central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(2)	10	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			TGGTGGTCGTCTTGTAGTCGA	0.617																																																	1	Substitution - Missense(1)	kidney(1)											111.0	97.0	102.0					17																	80622419		2203	4300	6503	SO:0001583	missense	10966			U05227	CCDS11816.1	17q25.3	2014-08-12			ENSG00000141542	ENSG00000141542		"""RAB, member RAS oncogene"""	18284	protein-coding gene	gene with protein product						11697911	Standard	NM_006822		Approved	SEC4L, RAR	uc002kft.3	Q12829	OTTHUMG00000177806	ENST00000571995.1:c.156G>T	17.37:g.80622419C>A	ENSP00000461785:p.Lys52Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q8WVG3	Missense_Mutation	SNP	ENST00000571995.1	37	CCDS11816.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.903948	0.52333	.	.	ENSG00000141542	ENST00000269347;ENST00000538809	.	.	.	3.97	1.94	0.25998	Small GTP-binding protein domain (1);	0.087971	0.42821	U	0.000642	T	0.74951	0.3784	M	0.77486	2.375	0.49687	D	0.999814	D	0.54397	0.966	D	0.66979	0.948	T	0.75260	-0.3380	9	0.87932	D	0	.	9.7918	0.40710	0.0:0.8231:0.0:0.1769	.	52	Q12829	RB40B_HUMAN	N	52;86	.	ENSP00000269347:K52N	K	-	3	2	RAB40B	78215708	0.966000	0.33281	0.996000	0.52242	0.729000	0.41735	0.205000	0.17356	0.420000	0.25954	-0.266000	0.10368	AAG		0.617	RAB40B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439007.1			
RGS18	64407	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	192150572	192150572	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr1:192150572C>G	ENST00000367460.3	+	4	615	c.434C>G	c.(433-435)aCt>aGt	p.T145S		NM_130782.2	NP_570138.1	Q9NS28	RGS18_HUMAN	regulator of G-protein signaling 18	145	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.T145S(1)		kidney(1)|large_intestine(2)|lung(15)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TTTATACAGACTGATGCCCCA	0.264																																																	1	Substitution - Missense(1)	kidney(1)											45.0	47.0	46.0					1																	192150572		2201	4289	6490	SO:0001583	missense	64407			AF268036	CCDS1374.1	1q31.2	2008-02-05	2007-08-14		ENSG00000150681	ENSG00000150681		"""Regulators of G-protein signaling"""	14261	protein-coding gene	gene with protein product		607192	"""regulator of G-protein signalling 18"""			11042171	Standard	NM_130782		Approved	RGS13	uc001gsg.3	Q9NS28	OTTHUMG00000035592	ENST00000367460.3:c.434C>G	1.37:g.192150572C>G	ENSP00000356430:p.Thr145Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B2RD23	Missense_Mutation	SNP	ENST00000367460.3	37	CCDS1374.1	.	.	.	.	.	.	.	.	.	.	C	0.051	-1.249572	0.01469	.	.	ENSG00000150681	ENST00000367460	T	0.01804	4.63	5.34	-3.09	0.05331	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.630657	0.16815	N	0.198398	T	0.00695	0.0023	N	0.04805	-0.155	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43909	-0.9362	10	0.07813	T	0.8	.	2.183	0.03879	0.2984:0.3736:0.2142:0.1138	.	145	Q9NS28	RGS18_HUMAN	S	145	ENSP00000356430:T145S	ENSP00000356430:T145S	T	+	2	0	RGS18	190417195	0.000000	0.05858	0.267000	0.24556	0.172000	0.22775	-0.594000	0.05733	-0.905000	0.03871	-0.535000	0.04281	ACT		0.264	RGS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086382.1		NM_130782	
SAMD15	161394	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	77844922	77844922	+	Silent	SNP	C	C	T			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr14:77844922C>T	ENST00000216471.4	+	1	1447	c.1161C>T	c.(1159-1161)atC>atT	p.I387I	SAMD15_ENST00000533095.2_Intron|TMED8_ENST00000216468.7_5'Flank	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	387								p.I387I(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CACAGGAGATCAACCCACAAG	0.403																																																	1	Substitution - coding silent(1)	kidney(1)											87.0	89.0	88.0					14																	77844922		2203	4300	6503	SO:0001819	synonymous_variant	161394			AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"""Sterile alpha motif (SAM) domain containing"""	18631	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.1161C>T	14.37:g.77844922C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q2M3P3	Silent	SNP	ENST00000216471.4	37	CCDS32126.1																																																																																				0.403	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2		NM_001010860	
SHF	90525	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	45470431	45470431	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr15:45470431C>A	ENST00000560734.1	-	2	572	c.572G>T	c.(571-573)gGa>gTa	p.G191V	SHF_ENST00000318390.6_Missense_Mutation_p.G183V|SHF_ENST00000561091.1_5'UTR|SHF_ENST00000458022.2_5'UTR|RP11-519G16.2_ENST00000560034.1_RNA|SHF_ENST00000560540.1_Missense_Mutation_p.G191V|SHF_ENST00000290894.8_Missense_Mutation_p.G126V|SHF_ENST00000560471.1_Missense_Mutation_p.G191V					Src homology 2 domain containing F									p.G126V(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		CTCTGGGGCTCCTGAAGCTCC	0.567																																																	1	Substitution - Missense(1)	kidney(1)											71.0	66.0	68.0					15																	45470431		2198	4298	6496	SO:0001583	missense	90525			BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606		"""SH2 domain containing"""	25116	protein-coding gene	gene with protein product						11095946	Standard	NM_138356		Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000560734.1:c.572G>T	15.37:g.45470431C>A	ENSP00000453168:p.Gly191Val	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000560734.1	37		.	.	.	.	.	.	.	.	.	.	C	21.1	4.092537	0.76756	.	.	ENSG00000138606	ENST00000290894;ENST00000361989;ENST00000318390;ENST00000413198	T;T	0.31247	1.5;1.5	5.92	5.0	0.66597	.	0.364158	0.26048	N	0.026644	T	0.27524	0.0676	L	0.39898	1.24	0.54753	D	0.999985	B	0.15473	0.013	B	0.15870	0.014	T	0.03043	-1.1079	10	0.39692	T	0.17	-5.5913	14.2081	0.65748	0.1507:0.8493:0.0:0.0	.	126	Q7M4L6	SHF_HUMAN	V	126;126;183;116	ENSP00000290894:G126V;ENSP00000315978:G183V	ENSP00000290894:G126V	G	-	2	0	SHF	43257723	0.000000	0.05858	1.000000	0.80357	0.959000	0.62525	0.291000	0.18994	1.496000	0.48567	0.655000	0.94253	GGA		0.567	SHF-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000416338.1		NM_138356	
SIPA1L3	23094	broad.mit.edu	37	19	38632053	38632053	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr19:38632053T>C	ENST00000222345.6	+	11	3882	c.3373T>C	c.(3373-3375)Tcc>Ccc	p.S1125P		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1125					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.S1125P(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)			CTTCCGGGAGTCCCAGCCACT	0.657																																																	1	Substitution - Missense(1)	kidney(1)											48.0	55.0	53.0					19																	38632053		2203	4299	6502	SO:0001583	missense	23094			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.3373T>C	19.37:g.38632053T>C	ENSP00000222345:p.Ser1125Pro	Somatic		WXS	Illumina GAIIx	Phase_I	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	T	8.854	0.945239	0.18356	.	.	ENSG00000105738	ENST00000222345	T	0.75589	-0.95	4.57	0.598	0.17512	.	0.563973	0.19037	N	0.124390	T	0.49287	0.1548	N	0.14661	0.345	0.28520	N	0.913106	B	0.02656	0.0	B	0.01281	0.0	T	0.25572	-1.0128	10	0.22706	T	0.39	-13.7756	4.4315	0.11529	0.1562:0.3345:0.0:0.5094	.	1125	O60292	SI1L3_HUMAN	P	1125	ENSP00000222345:S1125P	ENSP00000222345:S1125P	S	+	1	0	SIPA1L3	43323893	0.995000	0.38212	0.999000	0.59377	0.994000	0.84299	0.444000	0.21661	0.185000	0.20105	0.377000	0.23210	TCC		0.657	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2		XM_032278	
SIRPA	140885	hgsc.bcm.edu	37	20	1895842	1895842	+	Silent	SNP	T	T	C	rs17853847	byFrequency	TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr20:1895842T>C	ENST00000358771.4	+	2	329	c.177T>C	c.(175-177)tcT>tcC	p.S59S	SIRPA_ENST00000356025.3_Silent_p.S59S|SIRPA_ENST00000400068.3_Silent_p.S59S	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	59	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CTGCGACCTCTCTGATCCCTG	0.582													T|||	1687	0.336861	0.1982	0.3631	5008	,	,		12012	0.5506		0.2604	False		,,,				2504	0.364				GBM(155;1668 1920 5945 42733 48121)												0								T	,,	134,4184		5,124,2030	56.0	49.0	51.0		177,177,177	0.8	0.0	20	dbSNP_123	51	424,7940		16,392,3774	no	coding-synonymous,coding-synonymous,coding-synonymous	SIRPA	NM_001040022.1,NM_001040023.1,NM_080792.2	,,	21,516,5804	CC,CT,TT		5.0693,3.1033,4.3999	,,	59/505,59/505,59/505	1895842	558,12124	2159	4182	6341	SO:0001819	synonymous_variant	140885			D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.177T>C	20.37:g.1895842T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Silent	SNP	ENST00000358771.4	37	CCDS13022.1																																																																																				0.582	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2		NM_080792	
STIL	6491	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	47725984	47725984	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr1:47725984A>C	ENST00000360380.3	-	17	3417	c.3054T>G	c.(3052-3054)aaT>aaG	p.N1018K	STIL_ENST00000243182.6_Missense_Mutation_p.N1018K|STIL_ENST00000371877.3_Missense_Mutation_p.N1019K|STIL_ENST00000396221.2_Missense_Mutation_p.N1001K|STIL_ENST00000337817.5_Missense_Mutation_p.N1018K	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	1018					cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.N1018K(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				CGTTATGTGCATTTTTCTTCA	0.299																																																	1	Substitution - Missense(1)	kidney(1)											111.0	108.0	109.0					1																	47725984		2203	4299	6502	SO:0001583	missense	6491			M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"""TAL1 (SCL) interrupting locus"""	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.3054T>G	1.37:g.47725984A>C	ENSP00000353544:p.Asn1018Lys	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T0C5|Q68CN9	Missense_Mutation	SNP	ENST00000360380.3	37	CCDS548.1	.	.	.	.	.	.	.	.	.	.	A	11.83	1.754905	0.31046	.	.	ENSG00000123473	ENST00000360380;ENST00000337817;ENST00000371877;ENST00000396221;ENST00000243182	T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21	5.93	3.63	0.41609	.	0.334264	0.38959	N	0.001515	T	0.14657	0.0354	L	0.47716	1.5	0.30353	N	0.784595	P;P;P;P	0.45902	0.868;0.868;0.868;0.868	B;B;B;B	0.44044	0.439;0.439;0.439;0.439	T	0.06180	-1.0841	10	0.22706	T	0.39	-12.3643	5.3457	0.16008	0.6496:0.1413:0.209:0.0	.	1001;1001;1019;1018	E9PSF2;B7ZLW5;Q15468-2;Q15468	.;.;.;STIL_HUMAN	K	1018;1018;1019;1001;1018	ENSP00000353544:N1018K;ENSP00000337367:N1018K;ENSP00000360944:N1019K;ENSP00000379523:N1001K;ENSP00000243182:N1018K	ENSP00000243182:N1018K	N	-	3	2	STIL	47498571	0.125000	0.22332	1.000000	0.80357	0.940000	0.58332	0.138000	0.16016	1.053000	0.40415	0.533000	0.62120	AAT		0.299	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2		NM_003035	
SYNGAP1	8831	broad.mit.edu	37	6	33411625	33411625	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr6:33411625A>G	ENST00000418600.2	+	15	3397	c.3296A>G	c.(3295-3297)tAt>tGt	p.Y1099C	SYNGAP1_ENST00000293748.5_Missense_Mutation_p.Y1099C|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.Y1040C	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	1099					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)	p.Y1099C(1)|p.Y1084C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GAGCCAAGTTATGGCCCCGCC	0.667																																																	2	Substitution - Missense(2)	kidney(2)											26.0	32.0	30.0					6																	33411625		2201	4295	6496	SO:0001583	missense	8831			AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.3296A>G	6.37:g.33411625A>G	ENSP00000403636:p.Tyr1099Cys	Somatic		WXS	Illumina GAIIx	Phase_I	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	A	12.68	2.010592	0.35511	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.11930	2.73;2.73;2.73	4.39	4.39	0.52855	.	2.065980	0.01685	N	0.026381	T	0.13415	0.0325	L	0.29908	0.895	0.33918	D	0.640545	D;D;D	0.69078	0.997;0.99;0.997	P;P;P	0.58520	0.84;0.634;0.753	T	0.01753	-1.1281	10	0.39692	T	0.17	.	11.6227	0.51128	1.0:0.0:0.0:0.0	.	1099;1099;1099	Q96PV0;Q96PV0-2;Q96PV0-4	SYGP1_HUMAN;.;.	C	1099;1099;1085;1040	ENSP00000293748:Y1099C;ENSP00000403636:Y1099C;ENSP00000412475:Y1040C	ENSP00000293748:Y1099C	Y	+	2	0	SYNGAP1	33519603	0.590000	0.26815	0.931000	0.37212	0.995000	0.86356	1.658000	0.37376	1.850000	0.53721	0.482000	0.46254	TAT		0.667	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4		XM_166407	
SYT15	83849	hgsc.bcm.edu	37	10	46968675	46968679	+	Frame_Shift_Del	DEL	ATCTC	ATCTC	-	rs557452410	byFrequency	TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	ATCTC	ATCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr10:46968675_46968679delATCTC	ENST00000374321.4	-	3	323_327	c.257_261delGAGAT	c.(256-261)cgagatfs	p.RD86fs	SYT15_ENST00000503753.1_Frame_Shift_Del_p.RD86fs|SYT15_ENST00000374323.4_Frame_Shift_Del_p.RD139fs|RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374325.3_Frame_Shift_Del_p.RD86fs	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	86						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						GGGGCACCCAATCTCGGCCTTGAAG	0.629														9	0.00179712	0.0	0.0029	5008	,	,		39241	0.0		0.005	False		,,,				2504	0.002				Ovarian(57;1152 1428 19651 37745)												0									,	8,4094		0,8,2043					,	-0.7	0.4		dbSNP_119	65	59,8075		0,59,4008	no	frameshift,frameshift	SYT15	NM_181519.2,NM_031912.4	,	0,67,6051	A1A1,A1R,RR		0.7254,0.195,0.5476	,	,		67,12169				SO:0001589	frameshift_variant	83849			AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"""Synaptotagmins"""	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.257_261delGAGAT	10.37:g.46968675_46968679delATCTC	ENSP00000363441:p.Arg86fs	Somatic		WXS	Illumina HiSeq	Phase_I	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Frame_Shift_Del	DEL	ENST00000374321.4	37	CCDS44376.1																																																																																				0.629	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1		NM_031912	
TOP3A	7156	hgsc.bcm.edu;ucsc.edu	37	17	18178133	18178133	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr17:18178133delA	ENST00000321105.5	-	19	3203	c.2989delT	c.(2989-2991)tgtfs	p.C997fs	TOP3A_ENST00000542570.1_Frame_Shift_Del_p.C902fs|TOP3A_ENST00000540524.1_Frame_Shift_Del_p.C527fs	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	997					DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						TTCTGAGGACAAAAGGGACGG	0.542																																																	0													119.0	105.0	110.0					17																	18178133		2203	4300	6503	SO:0001589	frameshift_variant	7156			U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 7"""	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.2989delT	17.37:g.18178133delA	ENSP00000321636:p.Cys997fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8KA61|B4DK80|D3DXC7|Q13473	Frame_Shift_Del	DEL	ENST00000321105.5	37	CCDS11194.1																																																																																				0.542	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			
TRAF3IP1	26146	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	239233980	239233980	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr2:239233980T>C	ENST00000373327.4	+	2	379	c.157T>C	c.(157-159)Tac>Cac	p.Y53H	TRAF3IP1_ENST00000391994.2_Missense_Mutation_p.Y53H|TRAF3IP1_ENST00000391993.3_Missense_Mutation_p.Y53H	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	53	Abolishes microtubules-binding when missing.				cilium assembly (GO:0042384)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic heart tube development (GO:0035050)|intraciliary transport (GO:0042073)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube patterning (GO:0021532)|post-anal tail morphogenesis (GO:0036342)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)		p.Y53H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(2)	23		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		GAAGGGCCTCTACACAGACGC	0.493																																																	1	Substitution - Missense(1)	kidney(1)											174.0	172.0	173.0					2																	239233980		2203	4300	6503	SO:0001583	missense	26146			AF230877	CCDS33415.1, CCDS46557.1	2q37.3	2014-02-21			ENSG00000204104	ENSG00000204104		"""Intraflagellar transport homologs"""	17861	protein-coding gene	gene with protein product	"""microtubule interacting protein that associates with TRAF3"""	607380				10791955, 12935900	Standard	NM_015650		Approved	MIP-T3, DKFZP434F124, MIPT3, IFT54	uc002vye.3	Q8TDR0	OTTHUMG00000152872	ENST00000373327.4:c.157T>C	2.37:g.239233980T>C	ENSP00000362424:p.Tyr53His	Somatic		WXS	Illumina HiSeq	Phase_I	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Missense_Mutation	SNP	ENST00000373327.4	37	CCDS33415.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250807	0.80135	.	.	ENSG00000204104	ENST00000391993;ENST00000373327;ENST00000391994;ENST00000440998	T;T;T	0.34275	1.37;1.37;1.37	4.45	4.45	0.53987	.	0.121261	0.64402	D	0.000020	T	0.60983	0.2311	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.67067	-0.5764	10	0.87932	D	0	-24.0579	12.9001	0.58121	0.0:0.0:0.0:1.0	.	53;53	Q8TDR0-2;Q8TDR0	.;MIPT3_HUMAN	H	53	ENSP00000375851:Y53H;ENSP00000362424:Y53H;ENSP00000375852:Y53H	ENSP00000362424:Y53H	Y	+	1	0	TRAF3IP1	238898719	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.993000	0.76245	1.637000	0.50538	0.533000	0.62120	TAC		0.493	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1		NM_015650	
TSC2	7249	hgsc.bcm.edu	37	16	2126068	2126068	+	Splice_Site	SNP	G	G	A	rs397515203		TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr16:2126068G>A	ENST00000219476.3	+	24	3269		c.e24-1		TSC2_ENST00000439673.2_Splice_Site|TSC2_ENST00000382538.6_Splice_Site|TSC2_ENST00000401874.2_Splice_Site|TSC2_ENST00000353929.4_Splice_Site|TSC2_ENST00000350773.4_Splice_Site|TSC2_ENST00000568454.1_Splice_Site	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2						acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				TCTCATCTCAGGTTTAATCAG	0.552			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																														yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	0													98.0	84.0	89.0					16																	2126068		2198	4299	6497	SO:0001630	splice_region_variant	7249	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.2640-1G>A	16.37:g.2126068G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Splice_Site	SNP	ENST00000219476.3	37	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.353457	0.61293	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	.	.	.	5.09	5.09	0.68999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5131	0.90925	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TSC2	2066069	1.000000	0.71417	0.999000	0.59377	0.931000	0.56810	9.787000	0.99055	2.367000	0.80283	0.561000	0.74099	.		0.552	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2		NM_000548	Intron
TSC2	7249	hgsc.bcm.edu	37	16	2126070	2126070	+	Splice_Site	SNP	T	T	A	rs45463498|rs137854030		TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr16:2126070T>A	ENST00000219476.3	+	24	3271	c.2641T>A	c.(2641-2643)Ttt>Att	p.F881I	TSC2_ENST00000439673.2_Splice_Site_p.F844I|TSC2_ENST00000382538.6_Splice_Site_p.F832I|TSC2_ENST00000401874.2_Splice_Site_p.F881I|TSC2_ENST00000353929.4_Splice_Site_p.F881I|TSC2_ENST00000350773.4_Splice_Site_p.F881I|TSC2_ENST00000568454.1_Splice_Site_p.F892I	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	881					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				TCATCTCAGGTTTAATCAGTA	0.542			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																														yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	0													99.0	85.0	90.0					16																	2126070		2198	4299	6497	SO:0001630	splice_region_variant	7249	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.2640-1T>A	16.37:g.2126070T>A		Somatic		WXS	Illumina HiSeq	Phase_I	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	37	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.888044	0.91814	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D;D	0.88509	-2.39;-2.39;-2.39;-2.39;-2.39;-2.39	5.09	5.09	0.68999	Tuberin-type domain (1);	0.000000	0.85682	D	0.000000	D	0.93304	0.7866	M	0.65498	2.005	0.80722	D	1	P;D;D;D;D;D	0.65815	0.909;0.984;0.971;0.971;0.995;0.994	P;P;P;P;D;D	0.75020	0.837;0.885;0.804;0.729;0.97;0.985	D	0.93831	0.7128	10	0.62326	D	0.03	-39.5133	14.8891	0.70594	0.0:0.0:0.0:1.0	.	832;844;881;881;881;881	B4DIL8;P49815-6;P49815-4;P49815-3;P49815-5;P49815	.;.;.;.;.;TSC2_HUMAN	I	881;881;881;844;832;881	ENSP00000219476:F881I;ENSP00000384468:F881I;ENSP00000248099:F881I;ENSP00000399232:F844I;ENSP00000371978:F832I;ENSP00000344383:F881I	ENSP00000219476:F881I	F	+	1	0	TSC2	2066071	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.975000	0.88055	1.919000	0.55581	0.459000	0.35465	TTT		0.542	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2		NM_000548	Missense_Mutation
TSPY10	100289087	broad.mit.edu	37	Y	9366667	9366672	+	In_Frame_Del	DEL	GAAGAT	GAAGAT	-			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	GAAGAT	GAAGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chrY:9366667_9366672delGAAGAT	ENST00000428845.2	+	2	572_577	c.526_531delGAAGAT	c.(526-531)gaagatdel	p.ED178del	TSPY10_ENST00000489397.1_3'UTR|TSPY10_ENST00000429039.1_In_Frame_Del_p.ED91del|TSPY10_ENST00000444056.1_In_Frame_Del_p.ED178del|FAM197Y2_ENST00000598351.1_RNA	NM_001282469.1	NP_001269398.1	P0CW01	TSPYA_HUMAN	testis specific protein, Y-linked 10	184					cell differentiation (GO:0030154)|gonadal mesoderm development (GO:0007506)|nucleosome assembly (GO:0006334)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											GATCACTGACGAAGATGAAGACATGC	0.515																																																	0																																										SO:0001651	inframe_deletion	728137				CCDS65365.1	Yp11.2	2010-07-28			ENSG00000236424	ENSG00000236424			37473	protein-coding gene	gene with protein product							Standard	NM_001282469		Approved			P0CW01	OTTHUMG00000041524	ENST00000428845.2:c.526_531delGAAGAT	Y.37:g.9366667_9366672delGAAGAT	ENSP00000406407:p.Glu178_Asp179del	Somatic		WXS	Illumina GAIIx	Phase_I		In_Frame_Del	DEL	ENST00000428845.2	37																																																																																					0.515	TSPY10-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000099482.1		XM_002344198	
TSR1	55720	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	2238674	2238674	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr17:2238674C>A	ENST00000301364.5	-	4	1515	c.436G>T	c.(436-438)Gtg>Ttg	p.V146L	TSR1_ENST00000576112.2_Missense_Mutation_p.V146L|SGSM2_ENST00000426855.2_5'Flank|SGSM2_ENST00000574563.1_5'Flank|SGSM2_ENST00000268989.3_5'Flank	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	146	Bms1-type G.				ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.V146L(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						ATGTCTAACACAACGTGCAGA	0.438																																																	1	Substitution - Missense(1)	kidney(1)											101.0	88.0	92.0					17																	2238674		2203	4300	6503	SO:0001583	missense	55720			AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"""TSR1, 20S rRNA accumulation, homolog (yeast)"""			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.436G>T	17.37:g.2238674C>A	ENSP00000301364:p.Val146Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q8WUY5|Q9NVT0|Q9P2E6	Missense_Mutation	SNP	ENST00000301364.5	37	CCDS32525.1	.	.	.	.	.	.	.	.	.	.	C	4.704	0.130859	0.08981	.	.	ENSG00000167721	ENST00000301364	T	0.41400	1.0	5.84	-0.145	0.13436	.	0.343565	0.29995	N	0.010661	T	0.22085	0.0532	N	0.17764	0.52	0.30016	N	0.814784	B	0.06786	0.001	B	0.10450	0.005	T	0.16571	-1.0398	10	0.20519	T	0.43	-4.7494	7.8853	0.29646	0.1099:0.3758:0.4482:0.0661	.	146	Q2NL82	TSR1_HUMAN	L	146	ENSP00000301364:V146L	ENSP00000301364:V146L	V	-	1	0	TSR1	2185424	0.897000	0.30589	0.947000	0.38551	0.301000	0.27625	0.789000	0.26886	0.325000	0.23359	-0.181000	0.13052	GTG		0.438	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2		NM_018128	
TTN	7273	broad.mit.edu	37	2	179604751	179604751	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr2:179604751C>G	ENST00000591111.1	-	46	12482	c.12258G>C	c.(12256-12258)ttG>ttC	p.L4086F	TTN_ENST00000589042.1_Missense_Mutation_p.L4403F|TTN_ENST00000460472.2_Missense_Mutation_p.L4040F|TTN_ENST00000342992.6_Intron|TTN_ENST00000342175.6_Missense_Mutation_p.L4232F|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L4165F|TTN-AS1_ENST00000582847.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0					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.L4165F(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)			CGGCTGCTTGCAAAGCCCGGC	0.488																																																	1	Substitution - Missense(1)	kidney(1)											61.0	62.0	62.0					2																	179604751		1870	4099	5969	SO:0001583	missense	7273			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.12258G>C	2.37:g.179604751C>G	ENSP00000465570:p.Leu4086Phe	Somatic		WXS	Illumina GAIIx	Phase_I	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	7.421	0.636734	0.14386	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;D;D	0.82081	-1.45;-1.57;-1.57	5.46	3.65	0.41850	.	.	.	.	.	D	0.84279	0.5437	L	0.36672	1.1	0.22639	N	0.998904	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.65233	0.933;0.933;0.933	T	0.73069	-0.4099	9	0.87932	D	0	.	7.8823	0.29629	0.0:0.698:0.0:0.302	.	4040;4165;4232	D3DPF9;E7EQE6;E7ET18	.;.;.	F	4040;4232;4165;4040	ENSP00000434586:L4040F;ENSP00000340554:L4232F;ENSP00000352154:L4165F	ENSP00000340554:L4232F	L	-	3	2	TTN	179312996	0.049000	0.20398	1.000000	0.80357	0.603000	0.37013	-0.640000	0.05440	1.309000	0.44985	0.655000	0.94253	TTG		0.488	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
TUBA4A	7277	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	220115231	220115231	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr2:220115231A>C	ENST00000248437.4	-	4	1363	c.1190T>G	c.(1189-1191)cTg>cGg	p.L397R	TUBA4B_ENST00000490341.1_RNA|TUBA4A_ENST00000392088.2_Missense_Mutation_p.L382R|TUBA4A_ENST00000498660.1_5'Flank	NM_006000.2	NP_005991.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	397					'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.L382R(1)|p.L397R(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	GGCATACATCAGGTCGAACTT	0.637																																																	2	Substitution - Missense(2)	kidney(2)											119.0	106.0	110.0					2																	220115231		2203	4300	6503	SO:0001583	missense	7277			AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824		"""Tubulins"""	12407	protein-coding gene	gene with protein product		191110	"""tubulin, alpha 1 (testis specific)"", ""tubulin, alpha 1"""	TUBA1		3785200	Standard	NM_006000		Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000248437.4:c.1190T>G	2.37:g.220115231A>C	ENSP00000248437:p.Leu397Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A8MUB1|B3KNQ6|P05215	Missense_Mutation	SNP	ENST00000248437.4	37	CCDS2438.1	.	.	.	.	.	.	.	.	.	.	A	15.24	2.776167	0.49786	.	.	ENSG00000127824	ENST00000248437;ENST00000392088	D;D	0.85088	-1.94;-1.94	5.06	5.06	0.68205	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.53938	D	0.000047	D	0.92509	0.7621	M	0.87097	2.86	0.80722	D	1	D	0.64830	0.994	D	0.64506	0.926	D	0.93858	0.7151	10	0.87932	D	0	.	14.9593	0.71144	1.0:0.0:0.0:0.0	.	397	P68366	TBA4A_HUMAN	R	397;382	ENSP00000248437:L397R;ENSP00000375938:L382R	ENSP00000248437:L397R	L	-	2	0	TUBA4A	219823475	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.107000	0.94261	2.111000	0.64477	0.533000	0.62120	CTG		0.637	TUBA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256816.3		NM_006000	
UBA6	55236	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	68547886	68547886	+	Silent	SNP	G	G	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr4:68547886G>A	ENST00000322244.5	-	3	239	c.180C>T	c.(178-180)gcC>gcT	p.A60A	UBA6_ENST00000420827.2_Silent_p.A60A	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	60					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)	p.A60A(1)		central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						CATGGGACTTGGCCATCTTCT	0.348																																																	1	Substitution - coding silent(1)	kidney(1)											97.0	96.0	96.0					4																	68547886		2203	4300	6503	SO:0001819	synonymous_variant	55236			AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"""Ubiquitin-like modifier activating enzymes"""	25581	protein-coding gene	gene with protein product	"""UBA6, ubiquitin-activating enzyme E1"""	611361	"""ubiquitin-activating enzyme E1-like 2"""	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.180C>T	4.37:g.68547886G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Silent	SNP	ENST00000322244.5	37	CCDS3516.1																																																																																				0.348	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2		NM_018227	
DDX11L1	100287102	broad.mit.edu	37	1	13281	13281	+	RNA	SNP	C	C	G			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr1:13281C>G	ENST00000456328.2	+	0	529					NR_046018.2|NR_051986.1				DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1																		CAGTGATACACCCGGCACCCT	0.572																																																	0																																												0			AM992871		1p36.33	2012-02-23	2012-02-23		ENSG00000223972	ENSG00000223972			37102	pseudogene	pseudogene			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 1"""			19476624	Standard	NR_046018		Approved		uc010nxq.1		OTTHUMG00000000961		1.37:g.13281C>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000456328.2	37																																																																																					0.572	DDX11L1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000362751.1			
WTAP	9589	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	160174528	160174528	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr6:160174528G>A	ENST00000358372.4	+	7	2246	c.489G>A	c.(487-489)atG>atA	p.M163I	SOD2_ENST00000546087.1_Intron	NM_001270531.1|NM_004906.4	NP_001257460.1|NP_004897.2	Q15007	FL2D_HUMAN	Wilms tumor 1 associated protein	163					cell cycle (GO:0007049)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	MIS complex (GO:0036396)|nuclear membrane (GO:0031965)|nuclear speck (GO:0016607)|nucleus (GO:0005634)		p.M163I(1)|p.M163_L164delML(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	18		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)		AGTGTCGAATGCTTATCCAGG	0.438																																																	2	Substitution - Missense(1)|Deletion - In frame(1)	prostate(1)|kidney(1)											125.0	118.0	121.0					6																	160174528		2203	4300	6503	SO:0001583	missense	9589			AJ276706	CCDS5266.1, CCDS5267.1, CCDS75542.1	6q25-q27	2008-02-05			ENSG00000146457	ENSG00000146457			16846	protein-coding gene	gene with protein product		605442				7788527, 11001926	Standard	NM_004906		Approved	KIAA0105, MGC3925	uc003qsl.4	Q15007	OTTHUMG00000015933	ENST00000358372.4:c.489G>A	6.37:g.160174528G>A	ENSP00000351141:p.Met163Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TCL8|Q5TCL9|Q96T28|Q9BYJ7|Q9H4E2	Missense_Mutation	SNP	ENST00000358372.4	37	CCDS5266.1	.	.	.	.	.	.	.	.	.	.	G	35	5.488666	0.96323	.	.	ENSG00000146457	ENST00000358372	T	0.50001	0.76	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.49643	0.1569	L	0.36672	1.1	0.80722	D	1	D;P	0.67145	0.996;0.512	P;B	0.59056	0.851;0.199	T	0.25398	-1.0133	10	0.37606	T	0.19	1.3765	20.8794	0.99867	0.0:0.0:1.0:0.0	.	163;163	A8K489;Q15007	.;FL2D_HUMAN	I	163	ENSP00000351141:M163I	ENSP00000351141:M163I	M	+	3	0	WTAP	160094518	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.841000	0.99482	2.941000	0.99782	0.655000	0.94253	ATG		0.438	WTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042905.1		NM_152857	
SPRED1	161742	broad.mit.edu	37	15	38591664	38591664	+	Silent	SNP	C	C	T			TCGA-BP-4801-01A-02D-1421-08	TCGA-BP-4801-11A-01D-1421-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM	.		Illumina GAIIx	d3e62cb1-5ced-42cb-a360-479ee01877aa	8e5edfea-ec07-46dd-824f-6b0ea9a34e3e	g.chr15:38591664C>T	ENST00000299084.4	+	2	983	c.123C>T	c.(121-123)agC>agT	p.S41S	SPRED1_ENST00000561205.1_3'UTR	NM_152594.2	NP_689807.1	Q7Z699	SPRE1_HUMAN	sprouty-related, EVH1 domain containing 1	41	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)	p.S41S(1)		kidney(6)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		GACTAAGCAGCGTCACTGTCT	0.458									Legius syndrome																												Melanoma(196;2146 2959 7698 16532)	.											1	Substitution - coding silent(1)	kidney(1)											131.0	115.0	120.0					15																	38591664		2200	4297	6497	SO:0001819	synonymous_variant	161742	Familial Cancer Database	Neurofibromatosis type 1 - like syndrome, SPRED1 disorder	AK091222	CCDS32193.1	15q14	2014-06-13			ENSG00000166068	ENSG00000166068			20249	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 147"""	609291					Standard	NM_152594		Approved	FLJ33903, PPP1R147	uc001zka.4	Q7Z699		ENST00000299084.4:c.123C>T	15.37:g.38591664C>T		Somatic		WXS	Illumina GAIIx	Phase_I	B2RPJ8|Q05D53|Q8N256	Silent	SNP	ENST00000299084.4	37	CCDS32193.1																																																																																				0.458	SPRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418217.1			
