#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	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_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_classification	i_context	i_dataset	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_type
SZT2	23334	broad.mit.edu	37	1	43913627	43913627	+	Missense_Mutation	SNP	A	A	T			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr1:43913627A>T	ENST00000562955.1	+	67	9377	c.9377A>T	c.(9376-9378)gAg>gTg	p.E3126V	SZT2_ENST00000372442.1_Missense_Mutation_p.E2284V|SZT2-AS1_ENST00000396885.2_RNA	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	3183					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)		p.E2284V(2)		NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						GGAGAGGCTGAGCGGCACGTT	0.567																																																2	Substitution - Missense(2)	ovary(2)	1											92.0	87.0	89.0					1																	43913627		2203	4300	6503	43686214	SO:0001583	missense	23334			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.9377A>T	1.37:g.43913627A>T	ENSP00000457168:p.Glu3126Val		43686214	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	SNP	11	Broad	.	.	.	.	.	.	.	.	.	.	A	17.37	3.373054	0.61624	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.69	5.69	0.88448	.	0.046479	0.85682	D	0.000000	T	0.74898	0.3777	L	0.50333	1.59	0.38794	D	0.955042	D;D	0.89917	1.0;1.0	D;D	0.76575	0.97;0.988	T	0.78826	-0.2051	9	0.87932	D	0	.	15.9526	0.79855	1.0:0.0:0.0:0.0	.	3183;3126	Q5T011;Q5T011-5	SZT2_HUMAN;.	V	2284	.	ENSP00000361519:E2284V	E	+	2	0	SZT2	43686214	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.059000	0.76684	2.171000	0.68590	0.460000	0.39030	GAG		0.567	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		Missense_Mutation
NASP	4678	broad.mit.edu	37	1	46081049	46081049	+	Missense_Mutation	SNP	A	A	G			TCGA-13-1512-01	TCGA-13-1512-10			A	G	A	A	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr1:46081049A>G	ENST00000350030.3	+	11	2015	c.1928A>G	c.(1927-1929)aAg>aGg	p.K643R	NASP_ENST00000351223.3_Missense_Mutation_p.K304R|NASP_ENST00000530073.1_3'UTR|NASP_ENST00000372052.4_Missense_Mutation_p.K277R|NASP_ENST00000402363.3_Missense_Mutation_p.K645R|NASP_ENST00000537798.1_Missense_Mutation_p.K579R	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	643	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)	p.K645R(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					GAGGAACTAAAGGAACTGCTA	0.423																																																1	Substitution - Missense(1)	ovary(1)	1											100.0	98.0	99.0					1																	46081049		2203	4300	6503	45853636	SO:0001583	missense	4678			M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"""Tetratricopeptide (TTC) repeat domain containing"""	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.1928A>G	1.37:g.46081049A>G	ENSP00000255120:p.Lys643Arg		45853636	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Missense_Mutation	SNP	ENST00000350030.3	37	CCDS524.1	SNP	3	Broad	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.4|28.4	4.912732|4.912732	0.92178|0.92178	.|.	.|.	ENSG00000132780|ENSG00000132780	ENST00000537798;ENST00000402363;ENST00000341288;ENST00000528238;ENST00000350030;ENST00000372052;ENST00000351223|ENST00000531612	D;D;T;D;T;T|.	0.94862|.	-3.54;-3.54;0.83;-3.54;0.68;0.73|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73505|0.73505	0.3595|0.3595	M|M	0.71206|0.71206	2.165|2.165	0.58432|0.58432	D|D	0.999997|0.999997	D;D;D;D|.	0.76494|.	0.999;0.998;0.998;0.999|.	D;D;D;D|.	0.85130|.	0.997;0.989;0.993;0.997|.	T|T	0.74070|0.74070	-0.3783|-0.3783	10|5	0.87932|.	D|.	0|.	-16.9385|-16.9385	15.2619|15.2619	0.73631|0.73631	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	579;304;643;645|.	F5H3J2;Q5T626;P49321;P49321-3|.	.;.;NASP_HUMAN;.|.	R|G	579;645;543;240;643;277;304|168	ENSP00000438871:K579R;ENSP00000384529:K645R;ENSP00000432289:K240R;ENSP00000255120:K643R;ENSP00000361122:K277R;ENSP00000255121:K304R|.	ENSP00000345532:K543R|.	K|R	+|+	2|1	0|2	NASP|NASP	45853636|45853636	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	5.717000|5.717000	0.68446|0.68446	2.069000|2.069000	0.61940|0.61940	0.533000|0.533000	0.62120|0.62120	AAG|AGG		0.423	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482		Missense_Mutation
ZZZ3	26009	broad.mit.edu	37	1	78097567	78097567	+	Silent	SNP	T	T	C			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr1:78097567T>C	ENST00000370801.3	-	5	1948	c.1473A>G	c.(1471-1473)gaA>gaG	p.E491E	ZZZ3_ENST00000476275.1_5'UTR|ZZZ3_ENST00000370798.1_Intron	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	491					chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E491E(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						CATGATCTGATTCAAAGTAAT	0.368																																																1	Substitution - coding silent(1)	ovary(1)	1											120.0	113.0	116.0					1																	78097567		2203	4300	6503	77870155	SO:0001819	synonymous_variant	26009			AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549		"""Zinc fingers, ZZ-type"""	24523	protein-coding gene	gene with protein product	"""ATAC component 1 homolog (Drosophila)"""					16428443, 21304275	Standard	NM_015534		Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.1473A>G	1.37:g.78097567T>C			77870155	B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	Silent	SNP	ENST00000370801.3	37	CCDS677.1	SNP	52	Broad																																																																																				0.368	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026615.1	NM_015534		Silent
IQGAP3	128239	broad.mit.edu	37	1	156507007	156507007	+	Missense_Mutation	SNP	G	G	C			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr1:156507007G>C	ENST00000361170.2	-	27	3398	c.3388C>G	c.(3388-3390)Ctt>Gtt	p.L1130V	IQGAP3_ENST00000498755.1_5'UTR	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1130	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)	p.L1130V(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					ATGGCTAAAAGGAACTTATCA	0.582																																																1	Substitution - Missense(1)	ovary(1)	1											171.0	143.0	153.0					1																	156507007		2203	4300	6503	154773631	SO:0001583	missense	128239			AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.3388C>G	1.37:g.156507007G>C	ENSP00000354451:p.Leu1130Val		154773631	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	37	CCDS1144.1	SNP	35	Broad	.	.	.	.	.	.	.	.	.	.	G	18.47	3.629960	0.67015	.	.	ENSG00000183856	ENST00000361170	T	0.81330	-1.48	4.93	3.0	0.34707	Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.147081	0.47093	D	0.000250	T	0.61502	0.2352	M	0.65320	2	0.33717	D	0.616471	B	0.14805	0.011	B	0.22880	0.042	T	0.58183	-0.7681	10	0.72032	D	0.01	-4.407	4.9241	0.13885	0.1876:0.3421:0.4703:0.0	.	1130	Q86VI3	IQGA3_HUMAN	V	1130	ENSP00000354451:L1130V	ENSP00000354451:L1130V	L	-	1	0	IQGAP3	154773631	1.000000	0.71417	0.911000	0.35937	0.934000	0.57294	2.109000	0.41863	0.629000	0.30376	0.561000	0.74099	CTT		0.582	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		Missense_Mutation
F11R	50848	broad.mit.edu	37	1	160990824	160990824	+	Missense_Mutation	SNP	G	G	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr1:160990824G>A	ENST00000368026.6	-	1	314	c.40C>T	c.(40-42)Ctc>Ttc	p.L14F	F11R_ENST00000537746.1_Missense_Mutation_p.L14F|F11R_ENST00000289779.3_3'UTR	NM_016946.4	NP_058642.1	Q9Y624	JAM1_HUMAN	F11 receptor	14					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration (GO:0050900)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.L14F(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)	12	all_cancers(52;6.73e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00207)			AATATGAAGAGGCACAACAGT	0.587																																																1	Substitution - Missense(1)	ovary(1)	1											141.0	115.0	124.0					1																	160990824		2203	4300	6503	159257448	SO:0001583	missense	50848			AF111713	CCDS1213.1	1q21.2-q21.3	2013-01-29	2003-02-07	2003-02-14	ENSG00000158769	ENSG00000158769		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14685	protein-coding gene	gene with protein product		605721	"""junctional adhesion molecule 1"""	JAM1		10395639, 7646439	Standard	NM_016946		Approved	PAM-1, JCAM, JAM-1, JAM-A, JAMA, CD321	uc009wtt.3	Q9Y624	OTTHUMG00000028602	ENST00000368026.6:c.40C>T	1.37:g.160990824G>A	ENSP00000357005:p.Leu14Phe		159257448	B7Z941	Missense_Mutation	SNP	ENST00000368026.6	37	CCDS1213.1	SNP	35	Broad	.	.	.	.	.	.	.	.	.	.	G	10.85	1.466743	0.26335	.	.	ENSG00000158769	ENST00000368026;ENST00000335772;ENST00000289779;ENST00000537746	T;T	0.55413	1.35;0.52	3.94	0.674	0.17946	.	0.645917	0.13829	N	0.359884	T	0.21468	0.0517	L	0.61218	1.895	0.09310	N	1	B;B;B;B	0.17852	0.005;0.024;0.005;0.005	B;B;B;B	0.12837	0.003;0.008;0.003;0.003	T	0.16689	-1.0394	10	0.29301	T	0.29	.	3.1132	0.06365	0.2732:0.2332:0.4936:0.0	.	14;14;14;14	B7Z941;Q6FIB4;Q9Y624;D3DVF0	.;.;JAM1_HUMAN;.	F	14	ENSP00000357005:L14F;ENSP00000440812:L14F	ENSP00000289779:L14F	L	-	1	0	F11R	159257448	0.992000	0.36948	0.141000	0.22245	0.097000	0.18754	1.105000	0.31086	0.327000	0.23409	0.462000	0.41574	CTC		0.587	F11R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071458.3	NM_016946		Missense_Mutation
TNN	63923	broad.mit.edu	37	1	175049321	175049321	+	Missense_Mutation	SNP	G	G	C			TCGA-13-1512-01	TCGA-13-1512-10			G	C	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr1:175049321G>C	ENST00000239462.4	+	4	920	c.807G>C	c.(805-807)caG>caC	p.Q269H		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	269	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)		p.Q269H(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		AGGGCCTGCAGCTGCTCAAGA	0.607																																																1	Substitution - Missense(1)	ovary(1)	1											49.0	51.0	50.0					1																	175049321		2203	4300	6503	173315944	SO:0001583	missense	63923			AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.807G>C	1.37:g.175049321G>C	ENSP00000239462:p.Gln269His		173315944	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	SNP	34	Broad	.	.	.	.	.	.	.	.	.	.	G	15.48	2.845854	0.51164	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.57107	0.42	5.58	4.66	0.58398	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.247483	0.43260	D	0.000592	T	0.58538	0.2129	L	0.46157	1.445	0.27478	N	0.95266	D;D	0.58970	0.984;0.984	P;P	0.62491	0.852;0.903	T	0.51911	-0.8645	10	0.41790	T	0.15	.	8.2727	0.31853	0.0743:0.0:0.6691:0.2566	.	269;269	B3KXB6;Q9UQP3	.;TENN_HUMAN	H	269	ENSP00000239462:Q269H	ENSP00000239462:Q269H	Q	+	3	2	TNN	173315944	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	1.581000	0.36558	2.621000	0.88768	0.650000	0.86243	CAG		0.607	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		Missense_Mutation
LHX4	89884	broad.mit.edu	37	1	180241140	180241140	+	Splice_Site	SNP	A	A	T			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr1:180241140A>T	ENST00000263726.2	+	5	1021	c.777A>T	c.(775-777)cgA>cgT	p.R259R	RP5-1180C10.2_ENST00000440959.2_RNA|RP5-1180C10.2_ENST00000415414.1_RNA	NM_033343.3	NP_203129.1	Q969G2	LHX4_HUMAN	LIM homeobox 4	259					medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.R259R(1)		endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)	16						TGAGCTTCCGAGGTGAGCAGG	0.587																																																1	Substitution - coding silent(1)	ovary(1)	1											53.0	62.0	59.0					1																	180241140		2203	4300	6503	178507763	SO:0001630	splice_region_variant	89884			AB037683	CCDS1338.1	1q25.3	2011-06-20			ENSG00000121454	ENSG00000121454		"""Homeoboxes / LIM class"""	21734	protein-coding gene	gene with protein product		602146				11844481, 11567216	Standard	NM_033343		Approved	Gsh4	uc001goe.2	Q969G2	OTTHUMG00000035115	ENST00000263726.2:c.778+1A>T	1.37:g.180241140A>T			178507763	Q8NHE0|Q8NHM1|Q8TCJ1|Q8WWX2|Q969W2	Silent	SNP	ENST00000263726.2	37	CCDS1338.1	SNP	11	Broad																																																																																				0.587	LHX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084995.2	NM_033343	Silent	Silent
TTC13	79573	broad.mit.edu	37	1	231060661	231060661	+	Silent	SNP	C	C	T			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr1:231060661C>T	ENST00000366661.4	-	14	1654	c.1647G>A	c.(1645-1647)tcG>tcA	p.S549S	TTC13_ENST00000366662.4_Silent_p.S496S|TTC13_ENST00000414259.1_Silent_p.S496S	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	549								p.S549S(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		TTCGAACTTTCGAGTTGGTCC	0.438																																																1	Substitution - coding silent(1)	ovary(1)	1											211.0	172.0	185.0					1																	231060661		2203	4300	6503	229127284	SO:0001819	synonymous_variant	79573				CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"""Tetratricopeptide (TTC) repeat domain containing"""	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.1647G>A	1.37:g.231060661C>T			229127284	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Silent	SNP	ENST00000366661.4	37	CCDS1588.1	SNP	31	Broad																																																																																				0.438	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525		Silent
TRIM67	440730	broad.mit.edu	37	1	231351152	231351152	+	Missense_Mutation	SNP	C	C	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr1:231351152C>A	ENST00000366653.5	+	10	2318	c.2318C>A	c.(2317-2319)aCt>aAt	p.T773N	TRIM67_ENST00000444294.3_Missense_Mutation_p.T771N|TRIM67_ENST00000449018.3_Missense_Mutation_p.T711N|TRIM67_ENST00000366652.2_Intron			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	773	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				GAAGTGCCGACTAACCTGGGG	0.597																																																0			1											40.0	46.0	44.0					1																	231351152		2119	4240	6359	229417775	SO:0001583	missense	440730			AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"""Tripartite motif containing / Tripartite motif containing"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	31859	protein-coding gene	gene with protein product		610584	"""tripartite motif-containing 67"""				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.2318C>A	1.37:g.231351152C>A	ENSP00000355613:p.Thr773Asn		229417775	Q5TER7|Q5TER8|Q7Z4K7	Missense_Mutation	SNP	ENST00000366653.5	37	CCDS44333.1	SNP	20	Broad	.	.	.	.	.	.	.	.	.	.	C	12.31	1.898677	0.33535	.	.	ENSG00000119283	ENST00000444294;ENST00000449018;ENST00000366653	T;T;T	0.69685	-0.41;-0.34;-0.42	4.89	3.97	0.46021	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.44540	0.1298	N	0.14661	0.345	0.42793	D	0.993902	B	0.23650	0.089	B	0.24848	0.056	T	0.45041	-0.9288	9	0.39692	T	0.17	.	4.3159	0.10993	0.2492:0.5777:0.0:0.1731	.	773	Q6ZTA4	TRI67_HUMAN	N	771;711;773	ENSP00000412124:T771N;ENSP00000400163:T711N;ENSP00000355613:T773N	ENSP00000355613:T773N	T	+	2	0	TRIM67	229417775	0.822000	0.29219	0.986000	0.45419	0.943000	0.58893	1.507000	0.35758	2.688000	0.91661	0.557000	0.71058	ACT		0.597	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		Missense_Mutation
ZBTB18	10472	broad.mit.edu	37	1	244217893	244217893	+	Missense_Mutation	SNP	G	G	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr1:244217893G>A	ENST00000358704.4	+	2	966	c.817G>A	c.(817-819)Gtg>Atg	p.V273M		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	264					cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V264M(1)									TTCACAGGACGTGCTGAGAAG	0.483																																																1	Substitution - Missense(1)	ovary(1)	1											69.0	76.0	73.0					1																	244217893		2203	4300	6503	242284516	SO:0001583	missense	10472			U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13030	protein-coding gene	gene with protein product		608433	"""zinc finger protein 238"""	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.817G>A	1.37:g.244217893G>A	ENSP00000351539:p.Val273Met		242284516	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Missense_Mutation	SNP	ENST00000358704.4	37	CCDS1622.1	SNP	40	Broad	.	.	.	.	.	.	.	.	.	.	G	6.065	0.380392	0.11466	.	.	ENSG00000179456	ENST00000366538;ENST00000358704	T	0.11604	2.76	5.2	5.2	0.72013	.	0.243896	0.40385	N	0.001104	T	0.05640	0.0148	N	0.14661	0.345	0.33691	D	0.613322	B;P	0.35959	0.396;0.53	B;B	0.33690	0.081;0.168	T	0.20306	-1.0279	10	0.31617	T	0.26	.	6.2271	0.20714	0.2135:0.0:0.7865:0.0	.	264;273	Q99592;Q99592-2	ZN238_HUMAN;.	M	273	ENSP00000351539:V273M	ENSP00000351539:V273M	V	+	1	0	ZNF238	242284516	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.945000	0.49043	2.718000	0.92993	0.650000	0.86243	GTG		0.483	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768		Missense_Mutation
ZFYVE27	118813	broad.mit.edu	37	10	99510142	99510142	+	Missense_Mutation	SNP	A	A	G			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr10:99510142A>G	ENST00000393677.4	+	7	923	c.719A>G	c.(718-720)gAg>gGg	p.E240G	ZFYVE27_ENST00000370613.3_Missense_Mutation_p.E122G|ZFYVE27_ENST00000453958.2_Missense_Mutation_p.E240G|ZFYVE27_ENST00000337540.7_Missense_Mutation_p.E208G|ZFYVE27_ENST00000356257.4_Missense_Mutation_p.E240G|ZFYVE27_ENST00000370610.3_Missense_Mutation_p.E142G|ZFYVE27_ENST00000357540.4_Missense_Mutation_p.E154G|ZFYVE27_ENST00000359980.3_Missense_Mutation_p.E240G	NM_144588.6	NP_653189.3	Q5T4F4	ZFY27_HUMAN	zinc finger, FYVE domain containing 27	240					cell death (GO:0008219)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein localization to plasma membrane (GO:0072659)	axon (GO:0030424)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)	metal ion binding (GO:0046872)	p.E240G(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	8		Colorectal(252;0.0846)		Epithelial(162;7.08e-10)|all cancers(201;5.18e-08)		AAGCAGGAAGAGCATGCCTTT	0.552																																																1	Substitution - Missense(1)	ovary(1)	10											129.0	101.0	111.0					10																	99510142		2203	4300	6503	99500132	SO:0001583	missense	118813			BC030621	CCDS31263.1, CCDS31264.1, CCDS53562.1, CCDS53563.1, CCDS53564.1, CCDS53565.1	10q24.2	2013-09-11			ENSG00000155256	ENSG00000155256		"""Zinc fingers, FYVE domain containing"""	26559	protein-coding gene	gene with protein product	"""protrudin"""	610243				14702039	Standard	NM_144588		Approved	FLJ32919, SPG33	uc001kol.2	Q5T4F4	OTTHUMG00000018867	ENST00000393677.4:c.719A>G	10.37:g.99510142A>G	ENSP00000377282:p.Glu240Gly		99500132	B7Z3S0|B7Z404|B7Z626|G8JLC3|G8JLF0|J3KP98|Q5T4F1|Q5T4F2|Q5T4F3|Q8N1K0|Q8N6D6|Q8NCA0|Q8NDE4|Q96M08	Missense_Mutation	SNP	ENST00000393677.4	37	CCDS31263.1	SNP	11	Broad	.	.	.	.	.	.	.	.	.	.	A	13.10	2.137730	0.37728	.	.	ENSG00000155256	ENST00000337540;ENST00000357540;ENST00000370613;ENST00000370610;ENST00000393677;ENST00000453958;ENST00000359980;ENST00000356257;ENST00000423811	T;T;T;T;T;T;T	0.51817	0.71;0.69;1.28;1.27;1.27;1.25;1.27	5.51	1.76	0.24704	.	0.718423	0.14760	N	0.300038	T	0.28699	0.0711	N	0.24115	0.695	0.19575	N	0.999968	B;B;B;B;B;B;B	0.06786	0.0;0.0;0.001;0.001;0.0;0.0;0.0	B;B;B;B;B;B;B	0.10450	0.004;0.002;0.002;0.003;0.001;0.005;0.0	T	0.12967	-1.0527	10	0.35671	T	0.21	-2.8834	5.0708	0.14606	0.6986:0.0:0.1626:0.1388	.	208;142;122;154;240;240;240	B7Z404;B7Z3S0;B7Z626;Q5T4F4-5;Q5T4F4-3;Q5T4F4-2;Q5T4F4	.;.;.;.;.;.;ZFY27_HUMAN	G	208;154;122;142;240;240;240;240;218	ENSP00000337993:E208G;ENSP00000359642:E142G;ENSP00000377282:E240G;ENSP00000401580:E240G;ENSP00000353069:E240G;ENSP00000348593:E240G;ENSP00000409594:E218G	ENSP00000337993:E208G	E	+	2	0	ZFYVE27	99500132	0.987000	0.35691	0.736000	0.30914	0.862000	0.49288	2.260000	0.43267	0.935000	0.37341	0.459000	0.35465	GAG		0.552	ZFYVE27-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049745.2	NM_144588		Missense_Mutation
PDCD11	22984	broad.mit.edu	37	10	105178278	105178278	+	Missense_Mutation	SNP	C	C	T			TCGA-13-1512-01	TCGA-13-1512-10			C	T	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr10:105178278C>T	ENST00000369797.3	+	15	2087	c.1993C>T	c.(1993-1995)Ccc>Tcc	p.P665S		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	665	S1 motif 7. {ECO:0000255|PROSITE- ProRule:PRU00180}.				mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)	p.P665S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		TGCTTTCCTCCCCACATCTCA	0.542																																																1	Substitution - Missense(1)	ovary(1)	10											188.0	139.0	156.0					10																	105178278		2203	4300	6503	105168268	SO:0001583	missense	22984			D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.1993C>T	10.37:g.105178278C>T	ENSP00000358812:p.Pro665Ser		105168268	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	SNP	22	Broad	.	.	.	.	.	.	.	.	.	.	C	17.01	3.278933	0.59758	.	.	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.11821	2.74	5.93	5.93	0.95920	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);RNA-binding domain, S1 (1);Ribosomal protein S1, RNA-binding domain (1);	0.046420	0.85682	D	0.000000	T	0.34861	0.0912	L	0.61218	1.895	0.80722	D	1	D	0.56521	0.976	P	0.61275	0.886	T	0.00224	-1.1902	10	0.41790	T	0.15	-20.4719	20.3437	0.98782	0.0:1.0:0.0:0.0	.	665	Q14690	RRP5_HUMAN	S	665	ENSP00000358812:P665S	ENSP00000358812:P665S	P	+	1	0	PDCD11	105168268	1.000000	0.71417	0.845000	0.33349	0.109000	0.19521	7.254000	0.78329	2.815000	0.96918	0.561000	0.74099	CCC		0.542	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			Missense_Mutation
CTTN	2017	broad.mit.edu	37	11	70269076	70269076	+	Missense_Mutation	SNP	G	G	C			TCGA-13-1512-01	TCGA-13-1512-10			G	C	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr11:70269076G>C	ENST00000301843.8	+	12	1138	c.932G>C	c.(931-933)gGg>gCg	p.G311A	CTTN_ENST00000376561.3_Missense_Mutation_p.G274A|CTTN_ENST00000346329.3_Missense_Mutation_p.G274A|CTTN_ENST00000538675.1_5'UTR	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	311					negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)		p.G311A(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		GGGAAGTATGGGGTGCAGAAG	0.577																																																1	Substitution - Missense(1)	ovary(1)	11											178.0	151.0	160.0					11																	70269076		2200	4294	6494	69946724	SO:0001583	missense	2017			AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"""ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"""	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.932G>C	11.37:g.70269076G>C	ENSP00000301843:p.Gly311Ala		69946724	Q8N707|Q96H99	Missense_Mutation	SNP	ENST00000301843.8	37	CCDS41680.1	SNP	43	Broad	.	.	.	.	.	.	.	.	.	.	G	24.5	4.539263	0.85917	.	.	ENSG00000085733	ENST00000346329;ENST00000301843;ENST00000376561	T;T;T	0.44482	1.0;1.31;0.92	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.74053	0.3666	M	0.93328	3.405	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.996;0.998;0.996	T	0.80634	-0.1295	10	0.49607	T	0.09	-26.1983	18.4265	0.90611	0.0:0.0:1.0:0.0	.	274;311;274	Q96H99;Q14247;Q8N707	.;SRC8_HUMAN;.	A	274;311;274	ENSP00000317189:G274A;ENSP00000301843:G311A;ENSP00000365745:G274A	ENSP00000301843:G311A	G	+	2	0	CTTN	69946724	1.000000	0.71417	0.668000	0.29813	0.934000	0.57294	8.942000	0.92970	2.356000	0.79943	0.561000	0.74099	GGG		0.577	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565		Missense_Mutation
HOXC8	3224	broad.mit.edu	37	12	54405157	54405157	+	Missense_Mutation	SNP	A	A	C			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr12:54405157A>C	ENST00000040584.4	+	2	958	c.721A>C	c.(721-723)Aag>Cag	p.K241Q	RP11-834C11.12_ENST00000513209.1_Intron	NM_022658.3	NP_073149.1	P31273	HXC8_HUMAN	homeobox C8	241					anterior/posterior pattern specification (GO:0009952)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K241Q(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	8						ggaagaAAACAAGGACTAAGC	0.448																																					GBM(197;701 2226 7002 18822 41696)											1	Substitution - Missense(1)	ovary(1)	12											79.0	101.0	93.0					12																	54405157		2182	4289	6471	52691424	SO:0001583	missense	3224			X99680	CCDS8870.1	12q13.13	2011-06-20	2005-12-22			ENSG00000037965		"""Homeoboxes / ANTP class : HOXL subclass"""	5129	protein-coding gene	gene with protein product		142970	"""homeo box C8"""	HOX3, HOX3A		1973146, 1358459	Standard	NM_022658		Approved		uc001ser.3	P31273		ENST00000040584.4:c.721A>C	12.37:g.54405157A>C	ENSP00000040584:p.Lys241Gln		52691424	A8K4J4|O15221|O15362	Missense_Mutation	SNP	ENST00000040584.4	37	CCDS8870.1	SNP	5	Broad	.	.	.	.	.	.	.	.	.	.	A	14.13	2.443516	0.43429	.	.	ENSG00000037965	ENST00000040584	D	0.90955	-2.76	5.16	5.16	0.70880	.	0.179416	0.33959	N	0.004395	T	0.81216	0.4776	N	0.08118	0	0.44762	D	0.997764	B	0.17038	0.02	B	0.14578	0.011	T	0.76908	-0.2785	10	0.38643	T	0.18	.	14.2786	0.66196	1.0:0.0:0.0:0.0	.	241	P31273	HXC8_HUMAN	Q	241	ENSP00000040584:K241Q	ENSP00000040584:K241Q	K	+	1	0	HOXC8	52691424	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.074000	0.64401	2.075000	0.62263	0.528000	0.53228	AAG		0.448	HOXC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358957.2			Missense_Mutation
FAM109A	144717	broad.mit.edu	37	12	111800834	111800835	+	Missense_Mutation	DNP	CC	CC	AT	rs3840795|rs139032867|rs199734407|rs200911236	byFrequency	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr12:111800834_111800835CC>AT	ENST00000547838.2	-	2	494_495	c.397_398GG>AT	c.(397-399)GGg>ATg	p.G133M	FAM109A_ENST00000361483.3_Missense_Mutation_p.G146M|FAM109A_ENST00000450786.2_Missense_Mutation_p.G114W|FAM109A_ENST00000548163.1_Missense_Mutation_p.G133M|FAM109A_ENST00000392658.5_Missense_Mutation_p.G133M			Q8N4B1	SESQ1_HUMAN	family with sequence similarity 109, member A	133					endosome organization (GO:0007032)|receptor recycling (GO:0001881)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	protein homodimerization activity (GO:0042803)	p.G133M(1)|p.G146_G148delGGG(1)|p.G133_G135delGGG(1)		breast(1)|endometrium(1)|lung(1)|ovary(1)	4						CATGCCACCCCCGCCACGTACA	0.723																																																3	Deletion - In frame(2)|Substitution - Missense(1)	breast(2)|ovary(1)	12																																								110285218	SO:0001583	missense	144717			BC034809	CCDS9152.1, CCDS53833.1	12q24.12	2013-01-10			ENSG00000198324	ENSG00000198324		"""Pleckstrin homology (PH) domain containing"""	26509	protein-coding gene	gene with protein product		614239				12477932	Standard	NM_144671		Approved	FLJ32356	uc009zvu.3	Q8N4B1	OTTHUMG00000169547	ENST00000547838.2:c.397_398delinsAT	12.37:g.111800834_111800835delinsAT	ENSP00000447353:p.Gly133Met		110285217	J3KP50|Q6PJL9|Q96MH8	Missense_Mutation	DNP	ENST00000547838.2	37	CCDS9152.1	DNP	22	Broad																																																																																				0.723	FAM109A-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404768.2	NM_144671		Missense_Mutation
ATP8A2	51761	broad.mit.edu	37	13	26586707	26586707	+	Missense_Mutation	SNP	G	G	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr13:26586707G>A	ENST00000381655.2	+	36	3558	c.3416G>A	c.(3415-3417)cGg>cAg	p.R1139Q	ATP8A2_ENST00000255283.8_Missense_Mutation_p.R1074Q	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	1099					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R1139Q(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		AGGCTGGGCCGGAAGACGCCC	0.672																																																1	Substitution - Missense(1)	ovary(1)	13											8.0	10.0	10.0					13																	26586707		1819	3961	5780	25484707	SO:0001583	missense	51761			AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"""ATPases / P-type"""	13533	protein-coding gene	gene with protein product		605870	"""ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2"", ""ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"""			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.3416G>A	13.37:g.26586707G>A	ENSP00000371070:p.Arg1139Gln		25484707	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	37	CCDS41873.1	SNP	39	Broad	.	.	.	.	.	.	.	.	.	.	G	19.21	3.783267	0.70222	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	T;T	0.63417	0.41;-0.04	5.81	4.1	0.47936	.	0.234460	0.41097	D	0.000956	T	0.58779	0.2146	L	0.57536	1.79	0.31007	N	0.719663	D;B	0.53885	0.963;0.109	B;B	0.42495	0.389;0.059	T	0.66031	-0.6024	10	0.62326	D	0.03	.	12.351	0.55148	0.1355:0.0:0.8645:0.0	.	1074;1099	B7Z880;Q9NTI2	.;AT8A2_HUMAN	Q	1139;1074;919	ENSP00000371070:R1139Q;ENSP00000255283:R1074Q	ENSP00000255283:R1074Q	R	+	2	0	ATP8A2	25484707	1.000000	0.71417	0.952000	0.39060	0.819000	0.46315	2.608000	0.46308	0.829000	0.34733	0.650000	0.86243	CGG		0.672	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		Missense_Mutation
VPS13C	54832	broad.mit.edu	37	15	62167097	62167097	+	Missense_Mutation	SNP	T	T	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr15:62167097T>A	ENST00000261517.5	-	77	10465	c.10392A>T	c.(10390-10392)agA>agT	p.R3464S	VPS13C_ENST00000558919.1_5'Flank|VPS13C_ENST00000395896.4_Missense_Mutation_p.R3464S|VPS13C_ENST00000395898.3_Missense_Mutation_p.R3421S|VPS13C_ENST00000249837.3_Missense_Mutation_p.R3421S	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.R3464S(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CAAAGAGGCTTCTCACTCCAA	0.299																																																1	Substitution - Missense(1)	ovary(1)	15											99.0	101.0	100.0					15																	62167097		2203	4300	6503	59954389	SO:0001583	missense	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.10392A>T	15.37:g.62167097T>A	ENSP00000261517:p.Arg3464Ser		59954389		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	SNP	62	Broad	.	.	.	.	.	.	.	.	.	.	T	17.14	3.312715	0.60414	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.41400	1.0;1.01;1.18	5.83	3.54	0.40534	.	0.151909	0.56097	D	0.000023	T	0.34629	0.0904	N	0.25144	0.715	0.44771	D	0.997775	B;B;B;B	0.34226	0.247;0.123;0.443;0.075	B;B;B;B	0.43413	0.253;0.13;0.419;0.041	T	0.16778	-1.0391	10	0.45353	T	0.12	.	9.0528	0.36387	0.0:0.2037:0.0:0.7963	.	3421;3464;3421;3464	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	S	3421;3464;3464;3464	ENSP00000249837:R3421S;ENSP00000261517:R3464S;ENSP00000379233:R3464S	ENSP00000249837:R3421S	R	-	3	2	VPS13C	59954389	1.000000	0.71417	0.996000	0.52242	0.910000	0.53928	1.818000	0.39012	1.023000	0.39654	0.528000	0.53228	AGA		0.299	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		Missense_Mutation
GTF3C1	2975	broad.mit.edu	37	16	27549676	27549676	+	Splice_Site	SNP	A	A	C			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr16:27549676A>C	ENST00000356183.4	-	3	448	c.433T>G	c.(433-435)Tgg>Ggg	p.W145G	GTF3C1_ENST00000561623.1_Splice_Site_p.W145G	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	145					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.W145G(1)		breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						TTCTTCCCCCACCTGCAAATC	0.478																																																1	Substitution - Missense(1)	ovary(1)	16											57.0	54.0	55.0					16																	27549676		2197	4300	6497	27457177	SO:0001630	splice_region_variant	2975			U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.432-1T>G	16.37:g.27549676A>C			27457177	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	SNP	6	Broad	.	.	.	.	.	.	.	.	.	.	A	22.1	4.250277	0.80024	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.35973	1.28	5.38	5.38	0.77491	.	0.138323	0.52532	D	0.000061	T	0.60971	0.2310	M	0.74647	2.275	0.58432	D	0.999991	D;D	0.89917	1.0;1.0	D;D	0.91635	0.959;0.999	T	0.65360	-0.6187	10	0.72032	D	0.01	-5.6807	15.3533	0.74405	1.0:0.0:0.0:0.0	.	145;145	Q12789;Q12789-3	TF3C1_HUMAN;.	G	145	ENSP00000348510:W145G	ENSP00000348510:W145G	W	-	1	0	GTF3C1	27457177	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.867000	0.92314	2.161000	0.67846	0.460000	0.39030	TGG		0.478	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	Missense_Mutation	Missense_Mutation
SLC38A7	55238	broad.mit.edu	37	16	58713977	58713977	+	Silent	SNP	A	A	G			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr16:58713977A>G	ENST00000570101.1	-	2	937	c.54T>C	c.(52-54)gaT>gaC	p.D18D	SLC38A7_ENST00000564100.1_Silent_p.D18D|SLC38A7_ENST00000566953.1_Intron|SLC38A7_ENST00000564010.1_Intron|SLC38A7_ENST00000219320.4_Silent_p.D18D|SLC38A7_ENST00000564391.1_Silent_p.D18D			Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	18					sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	L-alanine transmembrane transporter activity (GO:0015180)|L-amino acid transmembrane transporter activity (GO:0015179)|L-asparagine transmembrane transporter activity (GO:0015182)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|L-glutamine transmembrane transporter activity (GO:0015186)|L-histidine transmembrane transporter activity (GO:0005290)|L-leucine transmembrane transporter activity (GO:0015190)|L-methionine transmembrane transporter activity (GO:0015191)|L-serine transmembrane transporter activity (GO:0015194)	p.D18D(1)		endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	13						GCTCCCCGGCATCCGTGCTCA	0.617																																																1	Substitution - coding silent(1)	ovary(1)	16											36.0	34.0	35.0					16																	58713977		2198	4300	6498	57271478	SO:0001819	synonymous_variant	55238			BC001961	CCDS10800.1	16q21	2013-05-22			ENSG00000103042	ENSG00000103042		"""Solute carriers"""	25582	protein-coding gene	gene with protein product		614236					Standard	XM_006721229		Approved	FLJ10815	uc002eod.1	Q9NVC3	OTTHUMG00000133491	ENST00000570101.1:c.54T>C	16.37:g.58713977A>G			57271478	Q53GJ9|Q9H9I5	Silent	SNP	ENST00000570101.1	37	CCDS10800.1	SNP	8	Broad																																																																																				0.617	SLC38A7-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422206.2	NM_018231		Silent
TP53	7157	broad.mit.edu	37	17	7577120	7577120	+	Missense_Mutation	SNP	C	C	A	rs28934576		TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr17:7577120C>A	ENST00000269305.4	-	8	1007	c.818G>T	c.(817-819)cGt>cTt	p.R273L	TP53_ENST00000420246.2_Missense_Mutation_p.R273L|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.R273L|TP53_ENST00000359597.4_Missense_Mutation_p.R273L|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R273L	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCACAAACACGCACCTCAAA	0.542	R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	669	Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1)	large_intestine(136)|lung(99)|breast(74)|ovary(59)|upper_aerodigestive_tract(55)|central_nervous_system(46)|oesophagus(35)|haematopoietic_and_lymphoid_tissue(30)|stomach(26)|urinary_tract(25)|pancreas(15)|endometrium(13)|liver(12)|skin(11)|bone(9)|biliary_tract(7)|penis(4)|cervix(2)|genital_tract(2)|NS(2)|soft_tissue(2)|vulva(1)|thyroid(1)|fallopian_tube(1)|prostate(1)|thymus(1)	17	GRCh37	CM004342|CM010472|CM920677	TP53	M	rs28934576						67.0	58.0	61.0					17																	7577120		2203	4300	6503	7517845	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.818G>T	17.37:g.7577120C>A	ENSP00000269305:p.Arg273Leu		7517845	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	SNP	19	Broad	.	.	.	.	.	.	.	.	.	.	C	24.6	4.554800	0.86231	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99866	-7.3;-7.3;-7.3;-7.3;-7.3;-7.3	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99871	0.9939	M	0.90759	3.145	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.77557	0.988;0.987;0.99;0.986	D	0.96378	0.9279	10	0.87932	D	0	-11.9995	15.662	0.77193	0.0:1.0:0.0:0.0	.	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	L	273;273;273;273;273;262;141	ENSP00000352610:R273L;ENSP00000269305:R273L;ENSP00000398846:R273L;ENSP00000391127:R273L;ENSP00000391478:R273L;ENSP00000425104:R141L	ENSP00000269305:R273L	R	-	2	0	TP53	7517845	1.000000	0.71417	0.068000	0.19968	0.665000	0.39181	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		Missense_Mutation
STAT5B	6777	broad.mit.edu	37	17	40379561	40379561	+	Missense_Mutation	SNP	C	C	A			TCGA-13-1512-01	TCGA-13-1512-10			C	A	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr17:40379561C>A	ENST00000293328.3	-	3	439	c.271G>T	c.(271-273)Gcc>Tcc	p.A91S		NM_012448.3	NP_036580.2	P51692	STA5B_HUMAN	signal transducer and activator of transcription 5B	91					2-oxoglutarate metabolic process (GO:0006103)|acute-phase response (GO:0006953)|allantoin metabolic process (GO:0000255)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hormone stimulus (GO:0032870)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|liver development (GO:0001889)|luteinization (GO:0001553)|natural killer cell differentiation (GO:0001779)|negative regulation of apoptotic process (GO:0043066)|negative regulation of erythrocyte differentiation (GO:0045647)|oxaloacetate metabolic process (GO:0006107)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cellular component movement (GO:0051272)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone metabolic process (GO:0042448)|prolactin signaling pathway (GO:0038161)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to lipopolysaccharide (GO:0032496)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription from RNA polymerase II promoter (GO:0006366)|valine metabolic process (GO:0006573)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|glucocorticoid receptor binding (GO:0035259)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.A91S(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)	AGCTGTGTGGCATAGTGCCCC	0.557																																																1	Substitution - Missense(1)	ovary(1)	17											108.0	104.0	106.0					17																	40379561		2203	4300	6503	37633087	SO:0001583	missense	6777			BC065227	CCDS11423.1	17q11.2	2014-09-17			ENSG00000173757	ENSG00000173757		"""SH2 domain containing"""	11367	protein-coding gene	gene with protein product		604260				8631883	Standard	NM_012448		Approved		uc002hzh.3	P51692	OTTHUMG00000150724	ENST00000293328.3:c.271G>T	17.37:g.40379561C>A	ENSP00000293328:p.Ala91Ser		37633087	Q8WWS8	Missense_Mutation	SNP	ENST00000293328.3	37	CCDS11423.1	SNP	25	Broad	.	.	.	.	.	.	.	.	.	.	C	21.7	4.190984	0.78789	.	.	ENSG00000173757	ENST00000293328;ENST00000415845	T;T	0.52526	0.66;0.66	5.44	5.44	0.79542	STAT transcription factor, protein interaction (4);	0.094300	0.64402	D	0.000001	T	0.54631	0.1870	L	0.46885	1.475	0.58432	D	0.999998	P;B	0.40731	0.728;0.433	P;B	0.47603	0.551;0.278	T	0.55373	-0.8151	10	0.66056	D	0.02	-10.2033	19.4483	0.94857	0.0:1.0:0.0:0.0	.	91;91	Q8WW55;P51692	.;STA5B_HUMAN	S	91	ENSP00000293328:A91S;ENSP00000398379:A91S	ENSP00000293328:A91S	A	-	1	0	STAT5B	37633087	1.000000	0.71417	0.999000	0.59377	0.950000	0.60333	7.259000	0.78381	2.835000	0.97688	0.591000	0.81541	GCC		0.557	STAT5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319797.1	NM_012448		Missense_Mutation
FAM117A	81558	broad.mit.edu	37	17	47794913	47794913	+	Missense_Mutation	SNP	C	C	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr17:47794913C>A	ENST00000240364.2	-	6	951	c.872G>T	c.(871-873)gGt>gTt	p.G291V	FAM117A_ENST00000514018.1_5'Flank|RP11-613C6.2_ENST00000512720.1_RNA|FAM117A_ENST00000513602.1_Missense_Mutation_p.G19V	NM_030802.3	NP_110429.1	Q9C073	F117A_HUMAN	family with sequence similarity 117, member A	291								p.G291V(1)		haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	17						CTCGGCGGCACCCCGATGTTC	0.642																																																1	Substitution - Missense(1)	ovary(1)	17											38.0	36.0	37.0					17																	47794913		2192	4284	6476	45149912	SO:0001583	missense	81558			BC037572	CCDS11553.1	17q21.33	2006-04-26				ENSG00000121104			24179	protein-coding gene	gene with protein product	"""C/EBP induced protein"""					12477932	Standard	NM_030802		Approved		uc002ipk.3	Q9C073		ENST00000240364.2:c.872G>T	17.37:g.47794913C>A	ENSP00000240364:p.Gly291Val		45149912	B7Z7Q3	Missense_Mutation	SNP	ENST00000240364.2	37	CCDS11553.1	SNP	18	Broad	.	.	.	.	.	.	.	.	.	.	C	10.47	1.359541	0.24598	.	.	ENSG00000121104	ENST00000240364;ENST00000511743	.	.	.	5.2	2.11	0.27256	.	1.208640	0.05677	N	0.589694	T	0.31420	0.0796	L	0.43923	1.385	0.26710	N	0.970997	P	0.38078	0.617	B	0.39738	0.308	T	0.22243	-1.0222	9	0.18276	T	0.48	-37.4037	6.1225	0.20161	0.0:0.676:0.155:0.169	.	291	Q9C073	F117A_HUMAN	V	291;181	.	ENSP00000240364:G291V	G	-	2	0	FAM117A	45149912	0.027000	0.19231	0.032000	0.17829	0.726000	0.41606	0.208000	0.17415	0.338000	0.23692	0.655000	0.94253	GGT		0.642	FAM117A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365736.1	NM_030802		Missense_Mutation
CHAD	1101	broad.mit.edu	37	17	48543071	48543071	+	Missense_Mutation	SNP	C	C	T	rs35218093	byFrequency	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr17:48543071C>T	ENST00000508540.1	-	2	1087	c.935G>A	c.(934-936)cGg>cAg	p.R312Q	ACSF2_ENST00000502667.1_Intron|ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000427954.2_Intron|CHAD_ENST00000258969.4_Missense_Mutation_p.R312Q|ACSF2_ENST00000300441.4_Intron|ACSF2_ENST00000541920.1_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	312	LRRCT.		R -> Q (in dbSNP:rs35218093).		bone development (GO:0060348)|cartilage condensation (GO:0001502)|negative regulation of bone trabecula formation (GO:1900155)	proteinaceous extracellular matrix (GO:0005578)		p.R312Q(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(2)|ovary(2)	15	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TTCTTACCGCCGAAGGCCCCG	0.562																																																1	Substitution - Missense(1)	ovary(1)	17											97.0	95.0	96.0					17																	48543071		2203	4300	6503	45898070	SO:0001583	missense	1101			U96767	CCDS11568.1	17q21.33	2008-02-05			ENSG00000136457	ENSG00000136457		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1909	protein-coding gene	gene with protein product	"""chondroadherin proteoglycan"""	602178				9344663	Standard	NM_001267		Approved	SLRR4A	uc010dbr.3	O15335	OTTHUMG00000162129	ENST00000508540.1:c.935G>A	17.37:g.48543071C>T	ENSP00000423812:p.Arg312Gln		45898070	A8K812|Q6GTU0|Q96RJ5	Missense_Mutation	SNP	ENST00000508540.1	37	CCDS11568.1	SNP	23	Broad	.	.	.	.	.	.	.	.	.	.	C	23.0	4.356835	0.82243	.	.	ENSG00000136457	ENST00000508540;ENST00000258969	T;T	0.04454	3.62;3.62	4.97	4.97	0.65823	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.06234	0.0161	M	0.64997	1.995	0.58432	D	0.999998	B	0.29612	0.251	B	0.14578	0.011	T	0.20974	-1.0259	10	0.32370	T	0.25	.	11.3247	0.49442	0.0:0.9126:0.0:0.0874	rs35218093	312	O15335	CHAD_HUMAN	Q	312	ENSP00000423812:R312Q;ENSP00000258969:R312Q	ENSP00000258969:R312Q	R	-	2	0	CHAD	45898070	1.000000	0.71417	0.998000	0.56505	0.881000	0.50899	4.092000	0.57707	2.578000	0.87016	0.655000	0.94253	CGG		0.562	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267		Missense_Mutation
ZNF521	25925	broad.mit.edu	37	18	22804982	22804982	+	Missense_Mutation	SNP	C	C	T			TCGA-13-1512-01	TCGA-13-1512-10			C	T	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr18:22804982C>T	ENST00000361524.3	-	4	3048	c.2900G>A	c.(2899-2901)cGg>cAg	p.R967Q	ZNF521_ENST00000538137.2_Missense_Mutation_p.R967Q|ZNF521_ENST00000584787.1_Missense_Mutation_p.R747Q|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	967					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)	p.R967Q(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GGAGGGAAACCGCTCTCCGCA	0.493			T	PAX5	ALL																																		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	1	Substitution - Missense(1)	ovary(1)	18											87.0	82.0	84.0					18																	22804982		2203	4300	6503	21058980	SO:0001583	missense	25925			AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2900G>A	18.37:g.22804982C>T	ENSP00000354794:p.Arg967Gln		21058980	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	SNP	23	Broad	.	.	.	.	.	.	.	.	.	.	C	15.00	2.703467	0.48412	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.19532	2.14;2.14	5.97	5.97	0.96955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.35364	0.0929	L	0.28504	0.86	0.43724	D	0.996203	D	0.89917	1.0	D	0.91635	0.999	T	0.02251	-1.1188	10	0.13470	T	0.59	-30.0479	20.4239	0.99064	0.0:1.0:0.0:0.0	.	967	Q96K83	ZN521_HUMAN	Q	967;1001;967	ENSP00000354794:R967Q;ENSP00000382352:R967Q	ENSP00000354794:R967Q	R	-	2	0	ZNF521	21058980	1.000000	0.71417	0.977000	0.42913	0.998000	0.95712	7.487000	0.81328	2.828000	0.97474	0.655000	0.94253	CGG		0.493	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		Missense_Mutation
MUC16	94025	broad.mit.edu	37	19	8977643	8977643	+	Missense_Mutation	SNP	T	T	C			TCGA-13-1512-01	TCGA-13-1512-10			T	C	T	T	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr19:8977643T>C	ENST00000397910.4	-	72	42405	c.42202A>G	c.(42202-42204)Aca>Gca	p.T14068A	MUC16_ENST00000380951.5_Missense_Mutation_p.T709A|MUC16_ENST00000596956.1_5'UTR	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	14099				Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.?(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAAATACCTGTTGTGGCTTCT	0.493																																																1	Unknown(1)	ovary(1)	19											57.0	59.0	58.0					19																	8977643		1923	4125	6048	8838643	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.42202A>G	19.37:g.8977643T>C	ENSP00000381008:p.Thr14068Ala		8838643	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	SNP	60	Broad	.	.	.	.	.	.	.	.	.	.	t	12.21	1.871078	0.33069	.	.	ENSG00000181143	ENST00000397910;ENST00000380951	T;T	0.30448	1.53;1.53	3.31	3.31	0.37934	.	0.254013	0.20507	U	0.090967	T	0.25865	0.0630	N	0.04162	-0.26	.	.	.	P	0.48911	0.917	P	0.60682	0.878	T	0.29579	-1.0007	9	0.40728	T	0.16	.	8.3873	0.32508	0.0:0.0:0.0:1.0	.	14068	B5ME49	.	A	14068;709	ENSP00000381008:T14068A;ENSP00000370338:T709A	ENSP00000370338:T709A	T	-	1	0	MUC16	8838643	1.000000	0.71417	1.000000	0.80357	0.416000	0.31233	0.915000	0.28638	1.749000	0.51849	0.370000	0.22315	ACA		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		Missense_Mutation
PKN1	5585	broad.mit.edu	37	19	14562650	14562650	+	Missense_Mutation	SNP	A	A	G			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr19:14562650A>G	ENST00000242783.6	+	7	1145	c.980A>G	c.(979-981)gAg>gGg	p.E327G	PKN1_ENST00000342216.4_Missense_Mutation_p.E333G	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	327	C2.				activation of JUN kinase activity (GO:0007257)|epithelial cell migration (GO:0010631)|histone H3-T11 phosphorylation (GO:0035407)|hyperosmotic response (GO:0006972)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|GTP-Rho binding (GO:0017049)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|histone kinase activity (H3-T11 specific) (GO:0035402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)	p.E327G(1)		breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)	31						GGGACCCTGGAGGTACGAGTG	0.687																																					NSCLC(185;2539 2965 10733 52867)											1	Substitution - Missense(1)	ovary(1)	19											23.0	30.0	27.0					19																	14562650		1975	4140	6115	14423650	SO:0001583	missense	5585			S75546	CCDS42513.1, CCDS42514.1	19p13.12	2008-05-14	2004-07-01	2004-07-01	ENSG00000123143	ENSG00000123143			9405	protein-coding gene	gene with protein product		601032	"""protein kinase C-like 1"""	PRKCL1		9570957	Standard	NM_002741		Approved	DBK, PRK1, PKN, MGC46204, PAK1	uc002myq.3	Q16512	OTTHUMG00000039611	ENST00000242783.6:c.980A>G	19.37:g.14562650A>G	ENSP00000242783:p.Glu327Gly		14423650	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Missense_Mutation	SNP	ENST00000242783.6	37	CCDS42513.1	SNP	11	Broad	.	.	.	.	.	.	.	.	.	.	A	10.99	1.507309	0.27036	.	.	ENSG00000123143	ENST00000242783;ENST00000342216	T;T	0.22945	1.93;1.93	4.34	1.89	0.25635	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.295883	0.27654	U	0.018406	T	0.25531	0.0621	M	0.77103	2.36	0.30660	N	0.754481	B;B	0.29646	0.253;0.035	B;B	0.22601	0.04;0.018	T	0.24119	-1.0169	10	0.87932	D	0	-22.1869	6.5557	0.22460	0.6916:0.1656:0.0:0.1427	.	333;327	Q16512-2;Q16512	.;PKN1_HUMAN	G	327;333	ENSP00000242783:E327G;ENSP00000343325:E333G	ENSP00000242783:E327G	E	+	2	0	PKN1	14423650	1.000000	0.71417	0.931000	0.37212	0.323000	0.28346	4.616000	0.61197	0.520000	0.28426	-0.695000	0.03696	GAG		0.687	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560		Missense_Mutation
FBL	2091	broad.mit.edu	37	19	40331298	40331298	+	Missense_Mutation	SNP	C	C	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr19:40331298C>A	ENST00000221801.3	-	2	253	c.140G>T	c.(139-141)gGa>gTa	p.G47V	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	47	DMA/Gly-rich.				histone glutamine methylation (GO:1990258)|osteoblast differentiation (GO:0001649)|rRNA processing (GO:0006364)|snoRNA metabolic process (GO:0016074)|tRNA processing (GO:0008033)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone-glutamine methyltransferase activity (GO:1990259)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.G47V(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)	9	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)	Renal(1328;0.000518)|Hepatocellular(1079;0.0893)	Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)	GBM - Glioblastoma multiforme(1328;0.000826)|STAD - Stomach adenocarcinoma(1328;0.138)		gcctccacctcctcctcgtcc	0.692																																																1	Substitution - Missense(1)	ovary(1)	19											19.0	22.0	21.0					19																	40331298		2201	4297	6498	45023138	SO:0001583	missense	2091			AC005393	CCDS12545.1	19q13.1	2010-02-17			ENSG00000105202	ENSG00000105202			3599	protein-coding gene	gene with protein product		134795				1846968, 2026646	Standard	NM_001436		Approved	RNU3IP1, FLRN, FIB	uc002omn.3	P22087		ENST00000221801.3:c.140G>T	19.37:g.40331298C>A	ENSP00000221801:p.Gly47Val		45023138	B5BUE8|O75259|Q6IAT5|Q9UPI6	Missense_Mutation	SNP	ENST00000221801.3	37	CCDS12545.1	SNP	30	Broad	.	.	.	.	.	.	.	.	.	.	C	16.10	3.028714	0.54790	.	.	ENSG00000105202	ENST00000221801	D	0.89123	-2.47	4.47	3.4	0.38934	.	0.297850	0.36234	N	0.002716	T	0.77678	0.4166	N	0.14661	0.345	0.80722	D	1	P;P	0.48911	0.917;0.531	B;B	0.41135	0.348;0.066	T	0.78969	-0.1994	10	0.54805	T	0.06	-0.0789	8.4791	0.33032	0.0:0.89:0.0:0.11	.	47;47	B4DLD4;P22087	.;FBRL_HUMAN	V	47	ENSP00000221801:G47V	ENSP00000221801:G47V	G	-	2	0	FBL	45023138	0.114000	0.22134	0.955000	0.39395	0.157000	0.22087	4.936000	0.63506	2.297000	0.77311	0.561000	0.74099	GGA		0.692	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436		Missense_Mutation
SPTBN4	57731	broad.mit.edu	37	19	41072244	41072244	+	Silent	SNP	C	C	T			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr19:41072244C>T	ENST00000352632.3	+	30	6401	c.6315C>T	c.(6313-6315)agC>agT	p.S2105S	SPTBN4_ENST00000598249.1_Silent_p.S2105S|SPTBN4_ENST00000338932.3_Silent_p.S2105S|SPTBN4_ENST00000392025.1_Silent_p.S848S			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	2105					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.S2105S(1)		breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			AGAGGTTCAGCTCTCTGCGGC	0.632																																																1	Substitution - coding silent(1)	ovary(1)	19											15.0	17.0	17.0					19																	41072244		2196	4295	6491	45764084	SO:0001819	synonymous_variant	57731			AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"""Pleckstrin homology (PH) domain containing"""	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.6315C>T	19.37:g.41072244C>T			45764084	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	37	CCDS12559.1	SNP	28	Broad																																																																																				0.632	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			Silent
AXL	558	broad.mit.edu	37	19	41725367	41725367	+	Missense_Mutation	SNP	T	T	G			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr19:41725367T>G	ENST00000301178.4	+	1	260	c.70T>G	c.(70-72)Tgc>Ggc	p.C24G	CTD-2195B23.3_ENST00000598541.1_RNA|AXL_ENST00000359092.3_Missense_Mutation_p.C24G	NM_001278599.1|NM_021913.3	NP_001265528.1|NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase	24					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interferon-alpha (GO:0035457)|cellular response to lipopolysaccharide (GO:0071222)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte homeostasis (GO:0034101)|forebrain cell migration (GO:0021885)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|natural killer cell differentiation (GO:0001779)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of tumor necrosis factor production (GO:0032720)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein kinase B signaling (GO:0051897)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|phosphatidylserine binding (GO:0001786)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.C24G(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	48						CGGCTGGGCGTGCATGGCCCC	0.692																																																1	Substitution - Missense(1)	ovary(1)	19											12.0	16.0	15.0					19																	41725367		2195	4287	6482	46417207	SO:0001583	missense	558			M76125	CCDS12574.1, CCDS12575.1, CCDS62677.1	19q13.1	2013-02-11				ENSG00000167601	2.7.10.1	"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	905	protein-coding gene	gene with protein product		109135				1656220	Standard	NM_021913		Approved	UFO, JTK11	uc010ehj.3	P30530		ENST00000301178.4:c.70T>G	19.37:g.41725367T>G	ENSP00000301178:p.Cys24Gly		46417207	Q8N5L2|Q9UD27	Missense_Mutation	SNP	ENST00000301178.4	37	CCDS12575.1	SNP	59	Broad	.	.	.	.	.	.	.	.	.	.	T	4.233	0.042169	0.08196	.	.	ENSG00000167601	ENST00000301178;ENST00000359092	T;T	0.74737	-0.87;-0.82	4.21	0.637	0.17735	.	0.134868	0.34338	N	0.004057	T	0.48352	0.1495	N	0.14661	0.345	0.09310	N	1	B;B	0.23249	0.082;0.049	B;B	0.18871	0.023;0.01	T	0.33854	-0.9852	10	0.52906	T	0.07	-3.483	1.052	0.01582	0.1898:0.1081:0.1966:0.5054	.	24;24	P30530-2;P30530	.;UFO_HUMAN	G	24	ENSP00000301178:C24G;ENSP00000351995:C24G	ENSP00000301178:C24G	C	+	1	0	AXL	46417207	0.008000	0.16893	0.033000	0.17914	0.048000	0.14542	1.037000	0.30241	0.276000	0.22118	0.369000	0.22263	TGC		0.692	AXL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463323.2			Missense_Mutation
ARHGEF1	9138	broad.mit.edu	37	19	42388541	42388541	+	Intron	SNP	T	T	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr19:42388541T>A	ENST00000354532.3	+	1	129				ARHGEF1_ENST00000347545.4_Intron|ARHGEF1_ENST00000337665.4_Missense_Mutation_p.S3T|ARHGEF1_ENST00000596957.1_Intron|ARHGEF1_ENST00000378152.4_Missense_Mutation_p.S3T|ARHGEF1_ENST00000599846.1_Intron	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1						cell proliferation (GO:0008283)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of axonogenesis (GO:0050770)|Rho protein signal transduction (GO:0007266)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|poly(A) RNA binding (GO:0044822)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S3T(1)		breast(2)|endometrium(8)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		GGCGATGGCTTCTCTTTCCAC	0.701																																																1	Substitution - Missense(1)	ovary(1)	19											50.0	43.0	45.0					19																	42388541		2203	4300	6503	47080381	SO:0001627	intron_variant	9138			U64105	CCDS12590.1, CCDS12591.1, CCDS12592.1	19q13.13	2014-06-19			ENSG00000076928	ENSG00000076928		"""Rho guanine nucleotide exchange factors"""	681	protein-coding gene	gene with protein product		601855				8810315, 9135076	Standard	NM_004706		Approved	P115-RHOGEF, SUB1.5, LBCL2	uc002osa.3	Q92888	OTTHUMG00000182679	ENST00000354532.3:c.-20+1185T>A	19.37:g.42388541T>A			47080381	O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Missense_Mutation	SNP	ENST00000354532.3	37	CCDS12591.1	SNP	62	Broad	.	.	.	.	.	.	.	.	.	.	T	12.83	2.054642	0.36277	.	.	ENSG00000076928	ENST00000337665;ENST00000378152	T;T	0.67865	0.03;-0.29	3.6	2.56	0.30785	.	.	.	.	.	T	0.37128	0.0992	.	.	.	0.42148	D	0.991542	B;B	0.14438	0.01;0.001	B;B	0.08055	0.003;0.003	T	0.26849	-1.0091	8	0.02654	T	1	.	6.2981	0.21097	0.2206:0.0:0.0:0.7794	.	3;3	Q6NX52;Q92888-3	.;.	T	3	ENSP00000337261:S3T;ENSP00000367394:S3T	ENSP00000337261:S3T	S	+	1	0	ARHGEF1	47080381	0.817000	0.29147	0.508000	0.27688	0.385000	0.30292	0.913000	0.28611	0.714000	0.32081	0.451000	0.29950	TCT		0.701	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000463360.1	NM_199002		Missense_Mutation
SCN3A	6328	broad.mit.edu	37	2	165947802	165947802	+	Nonsense_Mutation	SNP	G	G	A			TCGA-13-1512-01	TCGA-13-1512-10			G	A	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr2:165947802G>A	ENST00000360093.3	-	28	5352	c.4861C>T	c.(4861-4863)Cga>Tga	p.R1621*	SCN3A_ENST00000283254.7_Nonsense_Mutation_p.R1621*|AC013463.2_ENST00000431341.1_RNA|SCN3A_ENST00000465043.1_5'Flank|SCN3A_ENST00000540861.1_Nonsense_Mutation_p.R104*|SCN3A_ENST00000409101.3_Nonsense_Mutation_p.R1572*	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1621					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.R1621*(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CGGATCACTCGGAACAAGGTA	0.448																																																1	Substitution - Nonsense(1)	ovary(1)	2											109.0	112.0	111.0					2																	165947802		2203	4300	6503	165656048	SO:0001587	stop_gained	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.4861C>T	2.37:g.165947802G>A	ENSP00000353206:p.Arg1621*		165656048	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Nonsense_Mutation	SNP	ENST00000360093.3	37		SNP	39	Broad	.	.	.	.	.	.	.	.	.	.	G	45	11.651583	0.99587	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000540861	.	.	.	6.07	6.07	0.98685	.	0.000000	0.51477	D	0.000092	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.5344	0.67950	0.0:0.0:0.7423:0.2577	.	.	.	.	X	1621;1621;1572;104	.	ENSP00000283254:R1621X	R	-	1	2	SCN3A	165656048	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.659000	0.37387	2.890000	0.99128	0.585000	0.79938	CGA		0.448	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		Nonsense_Mutation
TMEM198	130612	broad.mit.edu	37	2	220412398	220412398	+	Missense_Mutation	SNP	G	G	T			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr2:220412398G>T	ENST00000344458.2	+	4	922	c.337G>T	c.(337-339)Gtg>Ttg	p.V113L	TMEM198_ENST00000373883.3_Missense_Mutation_p.V113L|RP11-256I23.1_ENST00000596829.1_RNA|MIR3132_ENST00000581997.1_RNA			Q66K66	TM198_HUMAN	transmembrane protein 198	113	Leu-rich.				multicellular organismal development (GO:0007275)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V113L(2)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	16		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		GGCCATGCTAGTGCGCAGCGT	0.697																																																2	Substitution - Missense(2)	ovary(2)	2											62.0	62.0	62.0					2																	220412398		2202	4298	6500	220120642	SO:0001583	missense	130612			BC068567	CCDS33385.1	2q35	2011-12-06			ENSG00000188760	ENSG00000188760			33704	protein-coding gene	gene with protein product							Standard	NM_001005209		Approved	MGC99813, TMEM198A	uc002vmf.3	Q66K66	OTTHUMG00000059156	ENST00000344458.2:c.337G>T	2.37:g.220412398G>T	ENSP00000343507:p.Val113Leu		220120642		Missense_Mutation	SNP	ENST00000344458.2	37	CCDS33385.1	SNP	36	Broad	.	.	.	.	.	.	.	.	.	.	G	22.3	4.275793	0.80580	.	.	ENSG00000188760	ENST00000344458;ENST00000421791;ENST00000373883	.	.	.	4.05	4.05	0.47172	.	0.058591	0.64402	D	0.000002	T	0.77644	0.4161	M	0.75447	2.3	0.54753	D	0.999985	D	0.63046	0.992	D	0.76071	0.987	T	0.77595	-0.2529	9	0.35671	T	0.21	-20.3095	16.3706	0.83357	0.0:0.0:1.0:0.0	.	113	Q66K66	TM198_HUMAN	L	113	.	ENSP00000343507:V113L	V	+	1	0	TMEM198	220120642	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.472000	0.97709	2.253000	0.74438	0.591000	0.81541	GTG		0.697	TMEM198-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131063.1	NM_001005209		Missense_Mutation
SIRPA	140885	broad.mit.edu	37	20	1903108	1903108	+	Missense_Mutation	SNP	G	G	A	rs2422666	byFrequency	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr20:1903108G>A	ENST00000358771.4	+	4	1056	c.904G>A	c.(904-906)Gtt>Att	p.V302I	SIRPA_ENST00000356025.3_Missense_Mutation_p.V302I|SIRPA_ENST00000400068.3_Missense_Mutation_p.V302I	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	302	Ig-like C1-type 2.		V -> L (in dbSNP:rs2422666).		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)		p.V302I(1)		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)		GGCCTCAACCGTTACAGAGAA	0.542																																					GBM(155;1668 1920 5945 42733 48121)											1	Substitution - Missense(1)	ovary(1)	20											215.0	176.0	189.0					20																	1903108		2203	4300	6503	1851108	SO:0001583	missense	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.904G>A	20.37:g.1903108G>A	ENSP00000351621:p.Val302Ile		1851108	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	SNP	40	Broad	.	.	.	.	.	.	.	.	.	.	C	10.59	1.393238	0.25118	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.00612	6.22;6.22;6.22	5.35	-0.247	0.13019	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	1.254340	0.05720	N	0.597593	T	0.00468	0.0015	N	0.16037	0.36	0.09310	N	1	B;B;B	0.22276	0.003;0.067;0.003	B;B;B	0.11329	0.001;0.006;0.001	T	0.45877	-0.9231	10	0.22109	T	0.4	.	1.5849	0.02642	0.1324:0.3821:0.2576:0.2279	.	282;302;302	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	I	302	ENSP00000382941:V302I;ENSP00000348307:V302I;ENSP00000351621:V302I	ENSP00000348307:V302I	V	+	1	0	SIRPA	1851108	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.154000	0.03166	-0.276000	0.09206	-0.120000	0.15030	GTT		0.542	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792		Missense_Mutation
PCSK2	5126	broad.mit.edu	37	20	17434587	17434587	+	Missense_Mutation	SNP	C	C	G			TCGA-13-1512-01	TCGA-13-1512-10			C	G	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr20:17434587C>G	ENST00000262545.2	+	9	1401	c.1086C>G	c.(1084-1086)aaC>aaG	p.N362K	PCSK2_ENST00000536609.1_Missense_Mutation_p.N327K|PCSK2_ENST00000377899.1_Missense_Mutation_p.N343K	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	362	Peptidase S8.				cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)	p.N362K(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GGAAAAGGAACCCCGAGGCCG	0.597																																																1	Substitution - Missense(1)	ovary(1)	20											95.0	79.0	85.0					20																	17434587		2203	4300	6503	17382587	SO:0001583	missense	5126			AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"""neuroendocrine convertase 2"", ""KEX2-like endoprotease 2"""	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.1086C>G	20.37:g.17434587C>G	ENSP00000262545:p.Asn362Lys		17382587	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Missense_Mutation	SNP	ENST00000262545.2	37	CCDS13125.1	SNP	18	Broad	.	.	.	.	.	.	.	.	.	.	C	14.25	2.478047	0.44044	.	.	ENSG00000125851	ENST00000377899;ENST00000262545;ENST00000536609	T;T;T	0.71222	-0.37;-0.37;-0.55	5.53	1.32	0.21799	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.85682	D	0.000000	T	0.56485	0.1988	N	0.14661	0.345	0.80722	D	1	B;B	0.29270	0.24;0.016	B;B	0.39771	0.309;0.013	T	0.54105	-0.8343	10	0.66056	D	0.02	-36.5633	8.7169	0.34416	0.0:0.5191:0.0:0.4809	.	327;362	B4DFQ3;P16519	.;NEC2_HUMAN	K	343;362;327	ENSP00000367131:N343K;ENSP00000262545:N362K;ENSP00000437458:N327K	ENSP00000262545:N362K	N	+	3	2	PCSK2	17382587	1.000000	0.71417	0.997000	0.53966	0.778000	0.44026	1.179000	0.31993	0.279000	0.22186	0.655000	0.94253	AAC		0.597	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		Missense_Mutation
DIDO1	11083	broad.mit.edu	37	20	61511873	61511873	+	Missense_Mutation	SNP	G	G	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr20:61511873G>A	ENST00000266070.4	-	16	5760	c.5435C>T	c.(5434-5436)tCg>tTg	p.S1812L	DIDO1_ENST00000395343.1_Missense_Mutation_p.S1812L	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1812	Pro-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.S1812L(1)		NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					ATGTTGCCCCGAGAATAAGGA	0.592																																					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											1	Substitution - Missense(1)	ovary(1)	20											74.0	87.0	83.0					20																	61511873		2203	4300	6503	60982318	SO:0001583	missense	11083			AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.5435C>T	20.37:g.61511873G>A	ENSP00000266070:p.Ser1812Leu		60982318	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	SNP	37	Broad	.	.	.	.	.	.	.	.	.	.	G	10.54	1.379178	0.24944	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.16324	2.35;2.35	5.03	2.03	0.26663	.	0.191876	0.25472	N	0.030433	T	0.19127	0.0459	M	0.67953	2.075	0.80722	D	1	B	0.12630	0.006	B	0.08055	0.003	T	0.04678	-1.0934	10	0.87932	D	0	-7.166	10.4095	0.44285	0.2073:0.0:0.7927:0.0	.	1812	Q9BTC0	DIDO1_HUMAN	L	1812	ENSP00000266070:S1812L;ENSP00000378752:S1812L	ENSP00000266070:S1812L	S	-	2	0	DIDO1	60982318	1.000000	0.71417	0.106000	0.21319	0.419000	0.31324	2.384000	0.44362	0.158000	0.19367	-1.069000	0.02264	TCG		0.592	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		Missense_Mutation
DIDO1	11083	broad.mit.edu	37	20	61541214	61541214	+	Missense_Mutation	SNP	G	G	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr20:61541214G>A	ENST00000266070.4	-	4	1323	c.998C>T	c.(997-999)gCa>gTa	p.A333V	DIDO1_ENST00000395343.1_Missense_Mutation_p.A333V|DIDO1_ENST00000354665.4_Missense_Mutation_p.A333V|DIDO1_ENST00000370368.1_Missense_Mutation_p.A333V|DIDO1_ENST00000395335.2_Missense_Mutation_p.A333V|DIDO1_ENST00000370371.4_Missense_Mutation_p.A333V|DIDO1_ENST00000395340.1_Missense_Mutation_p.A333V|DIDO1_ENST00000370366.1_Missense_Mutation_p.A333V|DIDO1_ENST00000266071.5_Missense_Mutation_p.A333V	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	333					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A333V(1)		NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					CTGCTGATCTGCCGTTTCTGA	0.483																																					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											1	Substitution - Missense(1)	ovary(1)	20											142.0	122.0	129.0					20																	61541214		2203	4300	6503	61011659	SO:0001583	missense	11083			AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.998C>T	20.37:g.61541214G>A	ENSP00000266070:p.Ala333Val		61011659	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	SNP	46	Broad	.	.	.	.	.	.	.	.	.	.	G	12.95	2.092150	0.36952	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335;ENST00000370371;ENST00000370368;ENST00000354665;ENST00000370366;ENST00000266071	T;T;T;T;T;T;T;T;T	0.19669	3.0;3.0;2.61;2.61;2.13;2.13;2.13;2.15;2.15	5.35	5.35	0.76521	.	0.859343	0.09627	N	0.776762	T	0.18425	0.0442	L	0.36672	1.1	0.09310	N	1	B;B;B;B	0.30406	0.023;0.213;0.003;0.278	B;B;B;B	0.29862	0.03;0.108;0.003;0.057	T	0.11299	-1.0593	10	0.27785	T	0.31	-3.8973	10.2329	0.43266	0.0733:0.136:0.7907:0.0	.	333;333;333;333	Q9BTC0-2;Q9BTC0-3;Q9BTC0-1;Q9BTC0	.;.;.;DIDO1_HUMAN	V	333	ENSP00000266070:A333V;ENSP00000378752:A333V;ENSP00000378749:A333V;ENSP00000378744:A333V;ENSP00000359397:A333V;ENSP00000359394:A333V;ENSP00000346692:A333V;ENSP00000359391:A333V;ENSP00000266071:A333V	ENSP00000266070:A333V	A	-	2	0	DIDO1	61011659	0.004000	0.15560	0.036000	0.18154	0.020000	0.10135	1.392000	0.34486	2.661000	0.90470	0.555000	0.69702	GCA		0.483	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		Missense_Mutation
UMODL1	89766	broad.mit.edu	37	21	43510524	43510524	+	Missense_Mutation	SNP	C	C	T	rs192021779	byFrequency	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr21:43510524C>T	ENST00000408910.2	+	6	907	c.907C>T	c.(907-909)Cgg>Tgg	p.R303W	UMODL1_ENST00000408989.2_Missense_Mutation_p.R303W|UMODL1_ENST00000400427.1_Missense_Mutation_p.R231W|UMODL1_ENST00000400424.2_Missense_Mutation_p.R231W	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	303	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)	p.R231W(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CACGTCTCCACGGAAGCTGAA	0.567																																					Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)											1	Substitution - Missense(1)	ovary(1)	21											88.0	92.0	91.0					21																	43510524		2083	4207	6290	42383593	SO:0001583	missense	89766				CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.907C>T	21.37:g.43510524C>T	ENSP00000386147:p.Arg303Trp		42383593	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	SNP	19	Broad	.	.	.	.	.	.	.	.	.	.	C	14.57	2.574676	0.45902	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910;ENST00000380462;ENST00000400417	T;T;T;T	0.72505	-0.66;-0.65;-0.66;-0.66	3.8	2.8	0.32819	.	1.482540	0.04875	U	0.446707	T	0.73916	0.3648	N	0.22421	0.69	0.09310	N	1	D;D	0.89917	1.0;0.998	D;P	0.67103	0.949;0.613	T	0.64076	-0.6492	10	0.66056	D	0.02	-2.4571	8.4692	0.32975	0.0:0.7593:0.2407:0.0	.	303;303	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	W	231;231;303;303;149;149	ENSP00000383279:R231W;ENSP00000383276:R231W;ENSP00000386126:R303W;ENSP00000386147:R303W	ENSP00000369829:R149W	R	+	1	2	UMODL1	42383593	0.001000	0.12720	0.018000	0.16275	0.017000	0.09413	0.483000	0.22292	2.050000	0.60909	0.313000	0.20887	CGG		0.567	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			Missense_Mutation
NUP210	23225	broad.mit.edu	37	3	13378308	13378308	+	Silent	SNP	G	G	A			TCGA-13-1512-01	TCGA-13-1512-10			G	A	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr3:13378308G>A	ENST00000254508.5	-	27	3745	c.3663C>T	c.(3661-3663)gaC>gaT	p.D1221D	NUP210_ENST00000485755.1_Intron	NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1221					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)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.D1221D(1)		NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					GCCCTCGGAGGTCCAGGACGT	0.647																																																1	Substitution - coding silent(1)	ovary(1)	3											84.0	72.0	76.0					3																	13378308		2203	4300	6503	13353308	SO:0001819	synonymous_variant	23225			AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.3663C>T	3.37:g.13378308G>A			13353308	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	37	CCDS33704.1	SNP	44	Broad																																																																																				0.647	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		Silent
TM4SF18	116441	broad.mit.edu	37	3	149042743	149042743	+	Missense_Mutation	SNP	C	C	T			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr3:149042743C>T	ENST00000296059.2	-	4	599	c.334G>A	c.(334-336)Gcc>Acc	p.A112T	TM4SF18_ENST00000470080.1_Missense_Mutation_p.A112T|RP11-206M11.7_ENST00000489011.1_RNA	NM_138786.3	NP_620141.1	Q96CE8	T4S18_HUMAN	transmembrane 4 L six family member 18	112						integral component of membrane (GO:0016021)		p.A112T(1)		lung(1)|ovary(1)|prostate(1)	3			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			AGACCCAAGGCAGAGATGACC	0.453																																																1	Substitution - Missense(1)	ovary(1)	3											87.0	82.0	84.0					3																	149042743		2203	4300	6503	150525433	SO:0001583	missense	116441			BC014339	CCDS3142.1	3q25.1	2005-08-09			ENSG00000163762	ENSG00000163762			25181	protein-coding gene	gene with protein product						10975581	Standard	NM_001184723		Approved	L6D	uc021xfl.1	Q96CE8	OTTHUMG00000159582	ENST00000296059.2:c.334G>A	3.37:g.149042743C>T	ENSP00000296059:p.Ala112Thr		150525433	B2R8K0|D3DNH5	Missense_Mutation	SNP	ENST00000296059.2	37	CCDS3142.1	SNP	25	Broad	.	.	.	.	.	.	.	.	.	.	C	14.36	2.511378	0.44660	.	.	ENSG00000163762	ENST00000296059;ENST00000470080;ENST00000474754	T;T;T	0.33865	1.39;1.39;1.39	5.8	4.93	0.64822	.	0.184598	0.48286	D	0.000199	T	0.30916	0.0780	L	0.49640	1.575	0.09310	N	1	B	0.06786	0.001	B	0.14578	0.011	T	0.20042	-1.0287	10	0.40728	T	0.16	-12.5648	8.1544	0.31160	0.0:0.7877:0.0:0.2123	.	112	Q96CE8	T4S18_HUMAN	T	112	ENSP00000296059:A112T;ENSP00000419278:A112T;ENSP00000418372:A112T	ENSP00000296059:A112T	A	-	1	0	TM4SF18	150525433	0.997000	0.39634	0.220000	0.23810	0.973000	0.67179	1.992000	0.40737	1.457000	0.47850	0.655000	0.94253	GCC		0.453	TM4SF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356326.1	NM_138786		Missense_Mutation
PIK3CA	5290	broad.mit.edu	37	3	178942593	178942593	+	Silent	SNP	C	C	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr3:178942593C>A	ENST00000263967.3	+	16	2557	c.2400C>A	c.(2398-2400)atC>atA	p.I800I		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	800	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.I800I(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATGAGATCATCTTTAAAAATG	0.363		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1	Substitution - coding silent(1)	ovary(1)	3											144.0	133.0	137.0					3																	178942593		1856	4093	5949	180425287	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2400C>A	3.37:g.178942593C>A			180425287	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1	SNP	32	Broad																																																																																				0.363	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			Silent
TACC3	10460	broad.mit.edu	37	4	1729572	1729572	+	Missense_Mutation	SNP	C	C	T			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr4:1729572C>T	ENST00000313288.4	+	4	549	c.443C>T	c.(442-444)gCc>gTc	p.A148V		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	148					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.A148V(1)		central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			GGCCCAGGTGCCCTGGCTGAC	0.592																																					Ovarian(120;482 2294 11894 35824)											1	Substitution - Missense(1)	ovary(1)	4											89.0	102.0	98.0					4																	1729572		2203	4299	6502	1699370	SO:0001583	missense	10460			AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810			11524	protein-coding gene	gene with protein product		605303				17675670	Standard	NM_006342		Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.443C>T	4.37:g.1729572C>T	ENSP00000326550:p.Ala148Val		1699370	Q2NKK4|Q3KQS5|Q9UMQ1	Missense_Mutation	SNP	ENST00000313288.4	37	CCDS3352.1	SNP	26	Broad	.	.	.	.	.	.	.	.	.	.	C	15.92	2.975360	0.53720	.	.	ENSG00000013810	ENST00000313288;ENST00000493975;ENST00000458173	T;T;T	0.44482	2.93;0.92;0.92	3.91	-5.63	0.02474	.	2.299200	0.02558	N	0.096395	T	0.25005	0.0607	L	0.36672	1.1	0.09310	N	1	B;B	0.13594	0.008;0.001	B;B	0.16289	0.015;0.002	T	0.08391	-1.0724	10	0.17832	T	0.49	1.7871	0.3812	0.00395	0.3749:0.1403:0.2264:0.2584	.	148;148	B4DYJ1;Q9Y6A5	.;TACC3_HUMAN	V	148	ENSP00000326550:A148V;ENSP00000418095:A148V;ENSP00000415914:A148V	ENSP00000326550:A148V	A	+	2	0	TACC3	1699370	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.894000	0.04123	-0.885000	0.03971	-0.251000	0.11542	GCC		0.592	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2			Missense_Mutation
SFRP2	6423	broad.mit.edu	37	4	154702675	154702675	+	Silent	SNP	C	C	G			TCGA-13-1512-01	TCGA-13-1512-10			C	G	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr4:154702675C>G	ENST00000274063.4	-	3	1100	c.816G>C	c.(814-816)tcG>tcC	p.S272S		NM_003013.2	NP_003004.1	Q96HF1	SFRP2_HUMAN	secreted frizzled-related protein 2	272	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				bone morphogenesis (GO:0060349)|brain development (GO:0007420)|cardiac left ventricle morphogenesis (GO:0003214)|cell-cell signaling (GO:0007267)|cellular response to extracellular stimulus (GO:0031668)|cellular response to X-ray (GO:0071481)|chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|embryonic digit morphogenesis (GO:0042733)|gonad development (GO:0008406)|hematopoietic stem cell proliferation (GO:0071425)|male gonad development (GO:0008584)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dermatome development (GO:0061185)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of gene expression (GO:0010629)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-anal tail morphogenesis (GO:0036342)|regulation of stem cell division (GO:2000035)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|sclerotome development (GO:0061056)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase activator activity (GO:0061133)|fibronectin binding (GO:0001968)|integrin binding (GO:0005178)|metalloenzyme activator activity (GO:0010577)|PDZ domain binding (GO:0030165)|receptor agonist activity (GO:0048018)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.S272S(1)		breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	16	all_hematologic(180;0.093)	Renal(120;0.117)				ACCGCTTCACCGAGGTGATCA	0.592																																																1	Substitution - coding silent(1)	ovary(1)	4											133.0	101.0	111.0					4																	154702675		2203	4300	6503	154922125	SO:0001819	synonymous_variant	6423			AF017986	CCDS34082.1	4q31.3	2008-08-29			ENSG00000145423	ENSG00000145423		"""Secreted frizzled-related proteins"""	10777	protein-coding gene	gene with protein product		604157				9391078	Standard	NM_003013		Approved	SARP1, SDF-5, FRP-2	uc003inv.1	Q96HF1	OTTHUMG00000161559	ENST00000274063.4:c.816G>C	4.37:g.154702675C>G			154922125	B3KQR2|O14778|Q9HAP5	Silent	SNP	ENST00000274063.4	37	CCDS34082.1	SNP	23	Broad																																																																																				0.592	SFRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365296.1			Silent
CEP120	153241	broad.mit.edu	37	5	122724242	122724242	+	Silent	SNP	T	T	C			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr5:122724242T>C	ENST00000306467.5	-	9	1618	c.1314A>G	c.(1312-1314)gaA>gaG	p.E438E	CEP120_ENST00000328236.5_Silent_p.E438E|CEP120_ENST00000306481.6_Silent_p.E412E			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	438					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.E438E(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						CTGAAGCTACTTCTGAAGCAT	0.388																																																1	Substitution - coding silent(1)	ovary(1)	5											183.0	171.0	175.0					5																	122724242		1868	4101	5969	122752141	SO:0001819	synonymous_variant	153241			AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"""coiled-coil domain containing 100"""	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.1314A>G	5.37:g.122724242T>C			122752141	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Silent	SNP	ENST00000306467.5	37	CCDS4134.2	SNP	56	Broad																																																																																				0.388	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223		Silent
SEPT8	23176	broad.mit.edu	37	5	132096666	132096666	+	Missense_Mutation	SNP	G	G	T			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr5:132096666G>T	ENST00000378719.2	-	9	1351	c.1114C>A	c.(1114-1116)Cac>Aac	p.H372N	SEPT8_ENST00000378706.1_Missense_Mutation_p.H372N|SEPT8_ENST00000458488.2_Missense_Mutation_p.H372N|SEPT8_ENST00000481030.1_5'Flank|SEPT8_ENST00000296873.7_Missense_Mutation_p.H372N|SEPT8_ENST00000378699.2_Missense_Mutation_p.H312N|SEPT8_ENST00000378701.1_Missense_Mutation_p.H370N|SEPT8_ENST00000448933.1_Missense_Mutation_p.H312N|SEPT8_ENST00000378721.4_Missense_Mutation_p.H370N	NM_001098811.1	NP_001092281.1	Q92599	SEPT8_HUMAN	septin 8	372					cell cycle (GO:0007049)	septin complex (GO:0031105)	GTP binding (GO:0005525)	p.H372N(1)	SEPT8/AFF4(2)	kidney(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CGCTTCAGGTGCTCAAACTTC	0.622																																																1	Substitution - Missense(1)	ovary(1)	5											81.0	85.0	84.0					5																	132096666		1985	4146	6131	132124565	SO:0001583	missense	23176			AF179995	CCDS43358.1, CCDS43359.1, CCDS43360.1, CCDS47262.1, CCDS75298.1	5q31	2013-01-21			ENSG00000164402	ENSG00000164402		"""Septins"""	16511	protein-coding gene	gene with protein product		608418				9039502, 9149945	Standard	NM_001098812		Approved	KIAA0202, SEP2	uc003kxr.2	Q92599	OTTHUMG00000059735	ENST00000378719.2:c.1114C>A	5.37:g.132096666G>T	ENSP00000367991:p.His372Asn		132124565	A6NC65|A6NKP6|F6W7K9|Q8IX36|Q8IX37|Q9BVB3	Missense_Mutation	SNP	ENST00000378719.2	37	CCDS43358.1	SNP	46	Broad	.	.	.	.	.	.	.	.	.	.	G	15.05	2.717061	0.48622	.	.	ENSG00000164402	ENST00000378719;ENST00000378721;ENST00000296873;ENST00000448933;ENST00000378706;ENST00000378699;ENST00000378701;ENST00000458488	D;D;D;D;D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65;-1.65;-1.65;-1.65;-1.65	5.34	3.47	0.39725	.	0.113488	0.64402	D	0.000008	T	0.73659	0.3615	L	0.29908	0.895	0.39396	D	0.966504	B;B;B;B	0.29571	0.016;0.033;0.249;0.058	B;B;B;B	0.25614	0.009;0.013;0.062;0.03	T	0.73936	-0.3825	10	0.49607	T	0.09	.	14.3863	0.66947	0.0:0.0:0.7314:0.2686	.	370;370;372;372	B7ZVZ1;A6NFQ9;F6W7K9;Q92599	.;.;.;SEPT8_HUMAN	N	372;370;372;312;372;312;370;372	ENSP00000367991:H372N;ENSP00000367993:H370N;ENSP00000296873:H372N;ENSP00000399840:H312N;ENSP00000367978:H372N;ENSP00000367971:H312N;ENSP00000367973:H370N;ENSP00000394766:H372N	ENSP00000296873:H372N	H	-	1	0	SEPT8	132124565	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.807000	0.86032	1.233000	0.43693	0.655000	0.94253	CAC		0.622	SEPT8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132827.2	XM_034872		Missense_Mutation
CCDC69	26112	broad.mit.edu	37	5	150585025	150585025	+	Missense_Mutation	SNP	T	T	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr5:150585025T>A	ENST00000355417.2	-	2	234	c.60A>T	c.(58-60)gaA>gaT	p.E20D	CCDC69_ENST00000521308.1_Intron	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	20								p.E20D(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGGTTCTGGTTCTTGGCGCT	0.572																																																1	Substitution - Missense(1)	ovary(1)	5											171.0	154.0	160.0					5																	150585025		2203	4300	6503	150565218	SO:0001583	missense	26112				CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624			24487	protein-coding gene	gene with protein product						12477932	Standard	NM_015621		Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.60A>T	5.37:g.150585025T>A	ENSP00000347586:p.Glu20Asp		150565218	A8K9X6	Missense_Mutation	SNP	ENST00000355417.2	37	CCDS4312.1	SNP	60	Broad	.	.	.	.	.	.	.	.	.	.	T	13.56	2.273397	0.40194	.	.	ENSG00000198624	ENST00000355417	T	0.23950	1.88	4.32	-0.767	0.11016	.	1.077990	0.07209	N	0.858869	T	0.11922	0.0290	N	0.08118	0	0.18873	N	0.999987	B	0.34290	0.447	B	0.30105	0.111	T	0.26573	-1.0099	10	0.49607	T	0.09	-1.8048	7.143	0.25566	0.0:0.5028:0.0:0.4972	.	20	A6NI79	CCD69_HUMAN	D	20	ENSP00000347586:E20D	ENSP00000347586:E20D	E	-	3	2	CCDC69	150565218	0.764000	0.28473	0.864000	0.33941	0.796000	0.44982	0.144000	0.16135	-0.037000	0.13646	-0.388000	0.06559	GAA		0.572	CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252435.1	NM_015621		Missense_Mutation
ERVFRD-1	405754	broad.mit.edu	37	6	11105465	11105465	+	Missense_Mutation	SNP	T	T	C			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr6:11105465T>C	ENST00000472091.1	-	2	454	c.79A>G	c.(79-81)Aaa>Gaa	p.K27E	ERVFRD-1_ENST00000542862.1_Missense_Mutation_p.K27E|SMIM13_ENST00000416247.2_Intron	NM_207582.2	NP_997465.1	P60508	SYCY2_HUMAN	endogenous retrovirus group FRD, member 1	27					syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)		p.K27E(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(4)|stomach(1)	15						TGCTGAGCTTTTTCCAATAAC	0.507																																																1	Substitution - Missense(1)	ovary(1)	6											59.0	60.0	59.0					6																	11105465		2203	4300	6503	11213451	SO:0001583	missense	405754			AK075092, AK123938, AY358244	CCDS4519.1	6p24.2	2014-05-02			ENSG00000244476	ENSG00000244476			33823	other	endogenous retrovirus		610524				12970426, 14557543, 15476554, 21542922	Standard	NM_207582		Approved	HERV-W/FRD, HERV-FRD, envFRD, ERVFRDE1, syncytin-2	uc003mzt.3	P60508	OTTHUMG00000159193	ENST00000472091.1:c.79A>G	6.37:g.11105465T>C	ENSP00000420174:p.Lys27Glu		11213451		Missense_Mutation	SNP	ENST00000472091.1	37	CCDS4519.1	SNP	64	Broad	.	.	.	.	.	.	.	.	.	.	T	13.94	2.386946	0.42308	.	.	ENSG00000244476	ENST00000472091;ENST00000542862	T;T	0.15372	2.43;2.43	0.235	0.235	0.15431	.	.	.	.	.	T	0.02267	0.0070	N	0.14661	0.345	0.19575	N	0.999966	P	0.38110	0.618	B	0.25759	0.063	T	0.39482	-0.9612	8	0.62326	D	0.03	.	.	.	.	.	27	P60508	EFRD1_HUMAN	E	27	ENSP00000420174:K27E;ENSP00000444461:K27E	ENSP00000420174:K27E	K	-	1	0	ERVFRD-1	11213451	0.763000	0.28462	0.735000	0.30896	0.740000	0.42216	0.310000	0.19356	0.263000	0.21812	0.260000	0.18958	AAA		0.507	ERVFRD-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353776.1	NM_207582		Missense_Mutation
TRIM26	7726	broad.mit.edu	37	6	30164385	30164385	+	Missense_Mutation	SNP	T	T	G			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr6:30164385T>G	ENST00000454678.2	-	6	1109	c.673A>C	c.(673-675)Aag>Cag	p.K225Q	TRIM26_ENST00000453195.1_Missense_Mutation_p.K225Q|TRIM26_ENST00000437089.1_Missense_Mutation_p.K225Q|TRIM26_ENST00000487829.1_5'Flank	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26	225					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)	p.K225Q(1)		lung(1)|ovary(2)	3						CCCCGGCTCTTGAACTTCTCC	0.647																																																1	Substitution - Missense(1)	ovary(1)	6											39.0	40.0	39.0					6																	30164385		2203	4300	6503	30272364	SO:0001583	missense	7726			AB088090	CCDS4678.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000234127	ENSG00000234127		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12962	protein-coding gene	gene with protein product		600830	"""tripartite motif-containing 26"""	ZNF173		8530076	Standard	NM_003449		Approved	RNF95	uc003npt.3	Q12899	OTTHUMG00000031041	ENST00000454678.2:c.673A>C	6.37:g.30164385T>G	ENSP00000410446:p.Lys225Gln		30272364	A6NG96|Q5SRL2	Missense_Mutation	SNP	ENST00000454678.2	37	CCDS4678.1	SNP	63	Broad	.	.	.	.	.	.	.	.	.	.	T	8.496	0.863203	0.17250	.	.	ENSG00000234127	ENST00000453195;ENST00000454678;ENST00000437089;ENST00000416596;ENST00000420345	T;T;T;T	0.70631	3.75;3.75;3.75;-0.5	5.62	3.22	0.36961	.	0.812496	0.10595	N	0.656344	T	0.33059	0.0850	L	0.44542	1.39	0.09310	N	1	B	0.25441	0.126	B	0.15484	0.013	T	0.17531	-1.0366	10	0.11794	T	0.64	.	5.1998	0.15258	0.0:0.0906:0.1829:0.7265	.	225	Q12899	TRI26_HUMAN	Q	225;225;225;225;150	ENSP00000391879:K225Q;ENSP00000410446:K225Q;ENSP00000395491:K225Q;ENSP00000413673:K225Q	ENSP00000413673:K225Q	K	-	1	0	TRIM26	30272364	0.000000	0.05858	0.030000	0.17652	0.746000	0.42486	-0.176000	0.09811	0.949000	0.37715	0.467000	0.42956	AAG		0.647	TRIM26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253442.1	NM_003449		Missense_Mutation
RUNX2	860	broad.mit.edu	37	6	45480092	45480092	+	Silent	SNP	C	C	A			TCGA-13-1512-01	TCGA-13-1512-10			C	A	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr6:45480092C>A	ENST00000371438.1	+	6	1327	c.969C>A	c.(967-969)tcC>tcA	p.S323S	RUNX2_ENST00000371432.3_Silent_p.S309S|RUNX2_ENST00000359524.5_Silent_p.S309S|RUNX2_ENST00000371436.6_Silent_p.S323S|RUNX2_ENST00000541979.1_Silent_p.S391S|RUNX2_ENST00000465038.2_Silent_p.S323S|RUNX2_ENST00000352853.5_Silent_p.S391S|RUNX2_ENST00000576263.1_Silent_p.S323S	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	323	Pro/Ser/Thr-rich.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.S323S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						CGCTGTCTTCCACACGGGGCA	0.587																																																1	Substitution - coding silent(1)	ovary(1)	6											120.0	98.0	105.0					6																	45480092		2203	4300	6503	45588070	SO:0001819	synonymous_variant	860			AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.969C>A	6.37:g.45480092C>A			45588070	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	37	CCDS43467.2	SNP	21	Broad																																																																																				0.587	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		Silent
THSD7A	221981	broad.mit.edu	37	7	11676209	11676209	+	Silent	SNP	A	A	C			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr7:11676209A>C	ENST00000423059.4	-	2	821	c.570T>G	c.(568-570)ccT>ccG	p.P190P	THSD7A_ENST00000480061.1_5'Flank	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	190					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P190P(1)		NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CTTGCTGGCAAGGAATGAGGC	0.557										HNSCC(18;0.044)																																						1	Substitution - coding silent(1)	ovary(1)	7											71.0	68.0	69.0					7																	11676209		2004	4184	6188	11642734	SO:0001819	synonymous_variant	221981				CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.570T>G	7.37:g.11676209A>C			11642734		Silent	SNP	ENST00000423059.4	37	CCDS47543.1	SNP	3	Broad																																																																																				0.557	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		Silent
NT5C3A	51251	broad.mit.edu	37	7	33057184	33057184	+	Missense_Mutation	SNP	A	A	T			TCGA-13-1512-01	TCGA-13-1512-10			A	T	A	A	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr7:33057184A>T	ENST00000242210.7	-	7	651	c.575T>A	c.(574-576)cTc>cAc	p.L192H	NT5C3A_ENST00000381626.2_Missense_Mutation_p.L141H|NT5C3A_ENST00000409467.1_Missense_Mutation_p.L141H|AVL9_ENST00000404479.1_Intron|NT5C3A_ENST00000409787.1_Missense_Mutation_p.L153H|NT5C3A_ENST00000405342.1_Missense_Mutation_p.L153H|NT5C3A_ENST00000396152.2_Missense_Mutation_p.L153H|NT5C3A_ENST00000610140.1_Missense_Mutation_p.L187H	NM_001002009.2|NM_001002010.2	NP_001002009.1|NP_001002010.1	Q9H0P0	5NT3A_HUMAN	5'-nucleotidase, cytosolic IIIA	192					dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside metabolic process (GO:0006213)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	2'-phosphotransferase activity (GO:0008665)|5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)	p.L192H(1)									ATGTTGTTGGAGCTTATCAAA	0.368																																																1	Substitution - Missense(1)	ovary(1)	7											142.0	138.0	140.0					7																	33057184		2203	4300	6503	33023709	SO:0001583	missense	51251			AF312735	CCDS34616.1, CCDS34617.1, CCDS55101.1	7p14.3	2013-03-06	2013-03-06	2013-03-06	ENSG00000122643	ENSG00000122643	3.1.3.5		17820	protein-coding gene	gene with protein product	"""lupin"""	606224	"""5'-nucleotidase, cytosolic III"""	NT5C3		11042152, 10942414	Standard	NM_001002010		Approved	UMPH1, PSN1, PN-I, UMPH, P5'N-1, cN-III, p36, POMP, hUMP1	uc003tdk.4	Q9H0P0	OTTHUMG00000152983	ENST00000242210.7:c.575T>A	7.37:g.33057184A>T	ENSP00000242210:p.Leu192His		33023709	A8K253|B2RAA5|B8ZZC4|Q6IPZ1|Q6NXS6|Q7L3G6|Q9P0P5|Q9UC42|Q9UC43|Q9UC44|Q9UC45	Missense_Mutation	SNP	ENST00000242210.7	37	CCDS34616.1	SNP	11	Broad	.	.	.	.	.	.	.	.	.	.	A	21.1	4.091900	0.76756	.	.	ENSG00000122643	ENST00000381626;ENST00000396152;ENST00000242210;ENST00000405342;ENST00000409467;ENST00000409787	D;D;D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32;-2.32;-2.32	5.19	4.04	0.47022	HAD-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94670	0.8281	H	0.94183	3.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94576	0.7775	10	0.87932	D	0	.	10.9177	0.47146	0.9262:0.0:0.0738:0.0	.	192;153	Q9H0P0;Q9H0P0-1	5NT3_HUMAN;.	H	141;153;192;153;141;153	ENSP00000371039:L141H;ENSP00000379456:L153H;ENSP00000242210:L192H;ENSP00000385261:L153H;ENSP00000387166:L141H;ENSP00000387205:L153H	ENSP00000242210:L192H	L	-	2	0	NT5C3	33023709	1.000000	0.71417	0.811000	0.32455	0.876000	0.50452	9.288000	0.96055	0.816000	0.34421	0.533000	0.62120	CTC		0.368	NT5C3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328880.1	NM_016489		Missense_Mutation
PEX1	5189	broad.mit.edu	37	7	92147160	92147160	+	Silent	SNP	C	C	T			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr7:92147160C>T	ENST00000248633.4	-	5	764	c.669G>A	c.(667-669)gtG>gtA	p.V223V	PEX1_ENST00000438045.1_Intron|PEX1_ENST00000428214.1_Silent_p.V223V|PEX1_ENST00000541751.1_5'Flank	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	223					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)	p.V223V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			CAGTGATTCCCACAGTATTTG	0.353																																																1	Substitution - coding silent(1)	ovary(1)	7											89.0	88.0	89.0					7																	92147160		2203	4300	6503	91985096	SO:0001819	synonymous_variant	5189			AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"""ATPases / AAA-type"""	8850	protein-coding gene	gene with protein product		602136	"""peroxisome biogenesis factor 1"", ""Zellweger syndrome 1"", ""Zellweger syndrome"""	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.669G>A	7.37:g.92147160C>T			91985096	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Silent	SNP	ENST00000248633.4	37	CCDS5627.1	SNP	21	Broad																																																																																				0.353	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		Silent
CCDC132	55610	broad.mit.edu	37	7	92926064	92926064	+	Missense_Mutation	SNP	T	T	G			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr7:92926064T>G	ENST00000305866.5	+	15	1306	c.1178T>G	c.(1177-1179)cTa>cGa	p.L393R	CCDC132_ENST00000317751.6_Missense_Mutation_p.L124R|CCDC132_ENST00000544910.1_Missense_Mutation_p.L363R|CCDC132_ENST00000541136.1_Missense_Mutation_p.L204R|CCDC132_ENST00000535481.1_Missense_Mutation_p.L113R	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	393						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.L393R(1)		endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			GATGTTCAGCTAAAAGTAAAA	0.289																																																1	Substitution - Missense(1)	ovary(1)	7											85.0	81.0	82.0					7																	92926064		1795	4064	5859	92764000	SO:0001583	missense	55610			AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.1178T>G	7.37:g.92926064T>G	ENSP00000307666:p.Leu393Arg		92764000	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	37	CCDS43617.1	SNP	53	Broad	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.892|8.892	0.954249|0.954249	0.18431|0.18431	.|.	.|.	ENSG00000004766|ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481;ENST00000317751|ENST00000458707	T|.	0.39592|.	1.07|.	4.95|4.95	4.95|4.95	0.65309|0.65309	.|.	0.000000|.	0.64402|.	D|.	0.000006|.	T|.	0.51736|.	0.1692|.	N|N	0.24115|0.24115	0.695|0.695	0.58432|0.58432	D|D	0.999997|0.999997	P;P;P|.	0.43701|.	0.808;0.815;0.808|.	B;B;B|.	0.37387|.	0.222;0.248;0.222|.	T|.	0.48811|.	-0.9002|.	10|.	0.46703|.	T|.	0.11|.	-14.6567|-14.6567	14.9369|14.9369	0.70964|0.70964	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	113;363;393|.	B4DS55;F5H5U7;Q96JG6|.	.;.;CC132_HUMAN|.	R|E	393;363;204;113;124|180	ENSP00000325582:L124R|.	ENSP00000307666:L393R|.	L|X	+|+	2|1	0|0	CCDC132|CCDC132	92764000|92764000	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.022000|6.022000	0.70839|0.70839	2.006000|2.006000	0.58801|0.58801	0.528000|0.528000	0.53228|0.53228	CTA|TAA		0.289	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		Missense_Mutation
SCARA3	51435	broad.mit.edu	37	8	27528615	27528615	+	Missense_Mutation	SNP	G	G	C			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr8:27528615G>C	ENST00000301904.3	+	6	1588	c.1568G>C	c.(1567-1569)gGc>gCc	p.G523A	SCARA3_ENST00000337221.4_Intron	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	523					receptor-mediated endocytosis (GO:0006898)|response to oxidative stress (GO:0006979)|UV protection (GO:0009650)	collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)	p.G523A(1)		breast(1)|large_intestine(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	9		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)		GGCCTCAAAGGCTCAAAGGGC	0.697																																																1	Substitution - Missense(1)	ovary(1)	8											10.0	12.0	11.0					8																	27528615		2193	4270	6463	27584534	SO:0001583	missense	51435			AB007829	CCDS34870.1, CCDS34871.1	8p21	2010-03-24			ENSG00000168077	ENSG00000168077			19000	protein-coding gene	gene with protein product	"""macrophage scavenger receptor-like 1"""	602728				9747040, 9580669	Standard	NM_182826		Approved	CSR1, CSR, MSLR1, APC7, MSRL1	uc003xga.1	Q6AZY7	OTTHUMG00000163898	ENST00000301904.3:c.1568G>C	8.37:g.27528615G>C	ENSP00000301904:p.Gly523Ala		27584534	Q9UM15|Q9UM16	Missense_Mutation	SNP	ENST00000301904.3	37	CCDS34871.1	SNP	42	Broad	.	.	.	.	.	.	.	.	.	.	G	19.38	3.815665	0.70912	.	.	ENSG00000168077	ENST00000301904	D	0.98234	-4.81	5.72	5.72	0.89469	.	0.054609	0.64402	D	0.000001	D	0.99223	0.9730	H	0.96048	3.76	0.58432	D	0.999998	D	0.62365	0.991	P	0.61070	0.883	D	0.99123	1.0850	10	0.87932	D	0	-25.5726	17.366	0.87364	0.0:0.0:1.0:0.0	.	523	Q6AZY7	SCAR3_HUMAN	A	523	ENSP00000301904:G523A	ENSP00000301904:G523A	G	+	2	0	SCARA3	27584534	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.178000	0.94855	2.700000	0.92200	0.561000	0.74099	GGC		0.697	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376258.2	NM_016240		Missense_Mutation
BAG4	9530	broad.mit.edu	37	8	38067870	38067870	+	Silent	SNP	T	T	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr8:38067870T>A	ENST00000287322.4	+	5	1504	c.1233T>A	c.(1231-1233)ctT>ctA	p.L411L	BAG4_ENST00000432471.2_Silent_p.L375L	NM_004874.3	NP_004865.1	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	411	BAG. {ECO:0000255|PROSITE- ProRule:PRU00369}.				cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to tumor necrosis factor (GO:0071356)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA modification (GO:0090367)|negative regulation of phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:2001145)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein localization to plasma membrane (GO:0072659)|ruffle assembly (GO:0097178)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)	p.L411L(1)		breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	11	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				CATACTGGCTTCTGGAAGAAA	0.418																																																1	Substitution - coding silent(1)	ovary(1)	8											38.0	42.0	41.0					8																	38067870		2202	4300	6502	38187027	SO:0001819	synonymous_variant	9530			AF095194	CCDS6104.1, CCDS56533.1	8p11.23	2008-08-07			ENSG00000156735	ENSG00000156735			940	protein-coding gene	gene with protein product	"""silencer of death domains"""	603884				9873016, 9915703	Standard	NM_004874		Approved	SODD	uc003xky.2	O95429	OTTHUMG00000164064	ENST00000287322.4:c.1233T>A	8.37:g.38067870T>A			38187027	B4E217|O95818	Silent	SNP	ENST00000287322.4	37	CCDS6104.1	SNP	62	Broad																																																																																				0.418	BAG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377038.2	NM_004874		Silent
MROH6	642475	broad.mit.edu	37	8	144657403	144657403	+	5'Flank	SNP	G	G	C			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr8:144657403G>C	ENST00000398882.3	-	0	0				RP11-661A12.9_ENST00000531730.1_RNA|NAPRT1_ENST00000460623.1_5'UTR|NAPRT1_ENST00000426292.3_Silent_p.A468A|NAPRT1_ENST00000435154.3_Silent_p.A468A|NAPRT1_ENST00000449291.2_Silent_p.A468A|NAPRT1_ENST00000276844.7_Silent_p.A468A	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6									p.A444A(1)									GCTCCACCTGGGCTGGCCTCA	0.687																																																1	Substitution - coding silent(1)	ovary(1)	8											22.0	23.0	23.0					8																	144657403		2196	4297	6493	144728546	SO:0001631	upstream_gene_variant	93100			AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"""maestro heat-like repeat containing"""	27814	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 73"""	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164		8.37:g.144657403G>C	Exception_encountered		144728546	A8MWB1	Silent	SNP	ENST00000398882.3	37	CCDS47928.1	SNP	43	Broad																																																																																				0.687	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878		Silent
C9orf41	138199	broad.mit.edu	37	9	77631295	77631295	+	Missense_Mutation	SNP	G	G	A			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr9:77631295G>A	ENST00000376834.3	-	3	631	c.479C>T	c.(478-480)tCc>tTc	p.S160F	C9orf41_ENST00000376837.3_Missense_Mutation_p.S160F|RP11-197P3.5_ENST00000455336.2_RNA	NM_152420.1	NP_689633.1	Q8N4J0	CI041_HUMAN	chromosome 9 open reading frame 41	160								p.S160F(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|urinary_tract(2)	17						TTTCAGCGTGGATTTTAACTT	0.368																																																1	Substitution - Missense(1)	ovary(1)	9											183.0	187.0	186.0					9																	77631295		2203	4300	6503	76821115	SO:0001583	missense	138199			AK098661	CCDS6649.1	9q21.31	2012-03-15			ENSG00000156017	ENSG00000156017			23435	protein-coding gene	gene with protein product						12477932	Standard	NM_152420		Approved	FLJ25795	uc004ajq.3	Q8N4J0	OTTHUMG00000020032	ENST00000376834.3:c.479C>T	9.37:g.77631295G>A	ENSP00000366030:p.Ser160Phe		76821115	Q7Z383|Q8N7C5	Missense_Mutation	SNP	ENST00000376834.3	37	CCDS6649.1	SNP	41	Broad	.	.	.	.	.	.	.	.	.	.	G	23.2	4.386265	0.82902	.	.	ENSG00000156017	ENST00000376834;ENST00000376837;ENST00000451153	T;T	0.04119	3.7;3.7	5.75	5.75	0.90469	N2227-like (1);	0.000000	0.85682	D	0.000000	T	0.30665	0.0772	M	0.90759	3.145	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.09596	-1.0667	10	0.66056	D	0.02	-11.004	19.9522	0.97203	0.0:0.0:1.0:0.0	.	160	Q8N4J0	CI041_HUMAN	F	160;160;99	ENSP00000366030:S160F;ENSP00000396353:S99F	ENSP00000366030:S160F	S	-	2	0	C9orf41	76821115	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.444000	0.97578	2.725000	0.93324	0.655000	0.94253	TCC		0.368	C9orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052703.1	NM_152420		Missense_Mutation
COL5A1	1289	broad.mit.edu	37	9	137717652	137717652	+	Missense_Mutation	SNP	G	G	A			TCGA-13-1512-01	TCGA-13-1512-10			G	A	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chr9:137717652G>A	ENST00000371817.3	+	63	5383	c.4969G>A	c.(4969-4971)Gat>Aat	p.D1657N		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1657	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.D1657N(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		ATACTGGGTCGATCCTAACCA	0.552																																																1	Substitution - Missense(1)	ovary(1)	9											72.0	64.0	67.0					9																	137717652		2203	4300	6503	136857473	SO:0001583	missense	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4969G>A	9.37:g.137717652G>A	ENSP00000360882:p.Asp1657Asn		136857473	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	SNP	37	Broad	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.3|21.3	4.124433|4.124433	0.77436|0.77436	.|.	.|.	ENSG00000130635|ENSG00000130635	ENST00000371817;ENST00000355306|ENST00000371820	D|.	0.86030|.	-2.06|.	4.05|4.05	4.05|4.05	0.47172|0.47172	Fibrillar collagen, C-terminal (3);|.	0.000000|.	0.64402|.	U|.	0.000001|.	D|D	0.85660|0.85660	0.5748|0.5748	M|M	0.93283|0.93283	3.4|3.4	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.83275|.	0.996|.	D|D	0.90412|0.90412	0.4410|0.4410	10|5	0.87932|.	D|.	0|.	.|.	16.3981|16.3981	0.83630|0.83630	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1657|.	P20908|.	CO5A1_HUMAN|.	N|Q	1657;194|76	ENSP00000360882:D1657N|.	ENSP00000347458:D194N|.	D|R	+|+	1|2	0|0	COL5A1|COL5A1	136857473|136857473	1.000000|1.000000	0.71417|0.71417	0.965000|0.965000	0.40720|0.40720	0.974000|0.974000	0.67602|0.67602	9.694000|9.694000	0.98686|0.98686	1.851000|1.851000	0.53745|0.53745	0.280000|0.280000	0.19369|0.19369	GAT|CGA		0.552	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		Missense_Mutation
IRAK1	3654	broad.mit.edu	37	X	153278665	153278665	+	Missense_Mutation	SNP	C	C	T			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1512-01	TCGA-13-1512-10	g.chrX:153278665C>T	ENST00000369980.3	-	12	1926	c.1759G>A	c.(1759-1761)Gag>Aag	p.E587K	IRAK1_ENST00000429936.2_Missense_Mutation_p.E583K|IRAK1_ENST00000393687.2_Missense_Mutation_p.E557K|IRAK1_ENST00000477274.1_Intron|IRAK1_ENST00000369974.2_Missense_Mutation_p.E508K|IRAK1_ENST00000393682.1_Missense_Mutation_p.E568K	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	587					activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|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)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)	p.E587K(1)		breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCGTCACTCTCCACGGGCTGG	0.692																																																1	Substitution - Missense(1)	ovary(1)	X											16.0	17.0	17.0					X																	153278665		2197	4286	6483	152931859	SO:0001583	missense	3654			L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.1759G>A	X.37:g.153278665C>T	ENSP00000358997:p.Glu587Lys		152931859	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Missense_Mutation	SNP	ENST00000369980.3	37	CCDS14740.1	SNP	30	Broad	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	20.8|20.8|20.8	4.050317|4.050317|4.050317	0.75846|0.75846|0.75846	.|.|.	.|.|.	ENSG00000184216|ENSG00000184216|ENSG00000184216	ENST00000369980;ENST00000369974;ENST00000393682;ENST00000393687;ENST00000429936|ENST00000444254;ENST00000443220|ENST00000437278	T;T;T;T;T|.|.	0.27720|.|.	1.65;1.65;1.65;1.65;1.65|.|.	5.38|5.38|5.38	5.38|5.38|5.38	0.77491|0.77491|0.77491	.|.|.	0.000000|.|.	0.56097|.|.	D|.|.	0.000040|.|.	T|T|.	0.50360|0.50360|.	0.1611|0.1611|.	L|L|L	0.34521|0.34521|0.34521	1.04|1.04|1.04	0.35456|0.35456|0.35456	D|D|D	0.796072|0.796072|0.796072	D;D;D|.|.	0.89917|.|.	0.999;1.0;1.0|.|.	D;D;D|.|.	0.91635|.|.	0.996;0.997;0.999|.|.	T|T|.	0.58763|0.58763|.	-0.7579|-0.7579|.	10|5|.	0.52906|.|.	T|.|.	0.07|.|.	-29.0142|-29.0142|-29.0142	13.4486|13.4486|13.4486	0.61155|0.61155|0.61155	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	508;587;557|.|.	P51617-4;P51617;P51617-2|.|.	.;IRAK1_HUMAN;.|.|.	K|E|X	587;508;568;557;583|142;335|150	ENSP00000358997:E587K;ENSP00000358991:E508K;ENSP00000377287:E568K;ENSP00000377291:E557K;ENSP00000392662:E583K|.|.	ENSP00000358991:E508K|.|.	E|G|W	-|-|-	1|2|3	0|0|0	IRAK1|IRAK1|IRAK1	152931859|152931859|152931859	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.347000|0.347000|0.347000	0.29111|0.29111|0.29111	4.245000|4.245000|4.245000	0.58734|0.58734|0.58734	2.239000|2.239000|2.239000	0.73571|0.73571|0.73571	0.513000|0.513000|0.513000	0.50165|0.50165|0.50165	GAG|GGA|TGG		0.692	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3			Missense_Mutation
SPRR1B	6699	broad.mit.edu	37	1	153004942	153005013	+	In_Frame_Del	DEL	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	-	rs2339500|rs145337134|rs201925274|rs367847286|rs12195|rs368848590|rs200829544|rs551505658	byFrequency	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	TCGA-13-1512-01	TCGA-13-1512-10	g.chr1:153004942_153005013delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	ENST00000307098.4	+	2	186_257	c.121_192delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	c.(121-192)tgccaccccaaggtgcctgagccctgccaccccaaagtgcccgagccctgccagcccaaggttccagagccadel	p.CHPKVPEPCHPKVPEPCQPKVPEP41del	SPRR1B_ENST00000392661.3_Splice_Site_p.CHPKVPEPCHPK41del	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	41	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.C41_P64delCHPKVPEPCHPKVPEPCQPKVPEP(1)|p.P43A(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAAGGAGCCCTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCATGCCACCCCA	0.621																																																2	Substitution - Missense(1)|Deletion - In frame(1)	ovary(1)|haematopoietic_and_lymphoid_tissue(1)	1																																								151271637	SO:0001651	inframe_deletion	6699			M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"""cornifin"""	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.121_192delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	1.37:g.153004942_153005013delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	ENSP00000306461:p.Cys41_Pro64del		151271566	B2R5H7|P22529|P22530|Q5T524	In_Frame_Del	DEL	ENST00000307098.4	37	CCDS30863.1	DEL	55	Broad																																																																																				0.621	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125		In_Frame_Del
E2F4	1874	broad.mit.edu	37	16	67234581	67234586	+	IGR	DEL	AACCTC	AACCTC	-			TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	TCGA-13-1512-01	TCGA-13-1512-10	g.chr16:67234581_67234586delAACCTC	ENST00000379378.3	+	0	2096				ELMO3_ENST00000393997.2_In_Frame_Del_p.NL232del|MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000477898.1_In_Frame_Del_p.NL66del|ELMO3_ENST00000571638.1_3'UTR|ELMO3_ENST00000360833.1_In_Frame_Del_p.NL215del	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding						blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.N232_L233delNL(1)		breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		CGTGAACATGAACCTCATGGATGCCT	0.655																																																1	Deletion - In frame(1)	ovary(1)	16																																								65792087	SO:0001628	intergenic_variant	79767			BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975		16.37:g.67234581_67234586delAACCTC			65792082	A6NGR8|B5BU56|Q12991|Q15328	In_Frame_Del	DEL	ENST00000379378.3	37	CCDS32464.1	DEL	9	Broad																																																																																				0.655	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950		In_Frame_Del
