#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
KIF20B	9585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	91498265	91498265	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr10:91498265C>T	ENST00000371728.3	+	20	3732	c.3667C>T	c.(3667-3669)Ctc>Ttc	p.L1223F	KIF20B_ENST00000260753.4_Missense_Mutation_p.L1183F|KIF20B_ENST00000394289.2_Missense_Mutation_p.L1223F|KIF20B_ENST00000416354.1_Missense_Mutation_p.L1253F|KIF20B_ENST00000478929.1_3'UTR	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1223					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						TGTAAAGGAACTCAAGCTGAA	0.299																																																0													52.0	57.0	55.0					10																	91498265		2147	4278	6425	SO:0001583	missense	9585			L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"""cancer/testis antigen 90"""	605498	"""M-phase phosphoprotein 1"""	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.3667C>T	10.37:g.91498265C>T	ENSP00000360793:p.Leu1223Phe		A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37		.	.	.	.	.	.	.	.	.	.	C	3.104	-0.184074	0.06340	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.68181	-0.25;-0.26;-0.31;-0.25	5.82	-2.72	0.05968	.	0.857438	0.09882	N	0.743494	T	0.39809	0.1092	N	0.08118	0	0.09310	N	1	B;B	0.23806	0.055;0.091	B;B	0.23716	0.021;0.048	T	0.23797	-1.0178	10	0.59425	D	0.04	0.0863	3.926	0.09263	0.5066:0.1071:0.2781:0.1082	.	1223;1183	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	F	1183;1253;1223;1223	ENSP00000260753:L1183F;ENSP00000411545:L1253F;ENSP00000377830:L1223F;ENSP00000360793:L1223F	ENSP00000260753:L1183F	L	+	1	0	KIF20B	91488245	0.000000	0.05858	0.055000	0.19348	0.053000	0.15095	-0.709000	0.05030	-0.606000	0.05746	-0.378000	0.06908	CTC		0.299	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		19	26	19	26
CABP2	51475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	67287316	67287316	+	Silent	SNP	G	G	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr11:67287316G>A	ENST00000294288.4	-	6	654	c.585C>T	c.(583-585)gaC>gaT	p.D195D	CABP2_ENST00000353903.5_Silent_p.D138D	NM_016366.2	NP_057450.2	Q9NPB3	CABP2_HUMAN	calcium binding protein 2	195	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	9						GGAGGATCTCGTCCACCTCCC	0.667																																																0													76.0	74.0	74.0					11																	67287316		2200	4295	6495	SO:0001819	synonymous_variant	51475			AF169154	CCDS8170.1	11q13.1	2013-01-10			ENSG00000167791	ENSG00000167791		"""EF-hand domain containing"""	1385	protein-coding gene	gene with protein product		607314				10625670	Standard	NM_016366		Approved		uc001omc.1	Q9NPB3	OTTHUMG00000168014	ENST00000294288.4:c.585C>T	11.37:g.67287316G>A				Silent	SNP	ENST00000294288.4	37	CCDS8170.1																																																																																				0.667	CABP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397516.1			20	65	20	65
GPC5	2262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	92101015	92101015	+	Splice_Site	SNP	G	G	T			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr13:92101015G>T	ENST00000377067.3	+	2	536	c.164G>T	c.(163-165)gGa>gTa	p.G55V		NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	55					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				TGTGTTCCAGGACCTGATCTT	0.413																																																0													122.0	116.0	118.0					13																	92101015		2203	4300	6503	SO:0001630	splice_region_variant	2262			AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"""Proteoglycans / Cell Surface : Glypicans"""	4453	protein-coding gene	gene with protein product	"""glypican proteoglycan 5"""	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.164-1G>T	13.37:g.92101015G>T			B2R726|O60436|Q9BX27	Splice_Site	SNP	ENST00000377067.3	37	CCDS9468.1	.	.	.	.	.	.	.	.	.	.	G	19.77	3.888701	0.72524	.	.	ENSG00000179399	ENST00000377067	T	0.64618	-0.11	5.5	5.5	0.81552	.	0.210963	0.43579	D	0.000557	T	0.76371	0.3978	L	0.60455	1.87	0.58432	D	0.999999	D	0.71674	0.998	D	0.72625	0.978	T	0.74777	-0.3550	9	.	.	.	.	18.3999	0.90513	0.0:0.0:1.0:0.0	.	55	P78333	GPC5_HUMAN	V	55	ENSP00000366267:G55V	.	G	+	2	0	GPC5	90899016	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	5.332000	0.65911	2.580000	0.87095	0.467000	0.42956	GGA		0.413	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466	Missense_Mutation	22	53	22	53
ACIN1	22985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	23550990	23550990	+	Silent	SNP	C	C	T			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr14:23550990C>T	ENST00000262710.1	-	5	993	c.666G>A	c.(664-666)agG>agA	p.R222R	ACIN1_ENST00000605057.1_Silent_p.R164R|ACIN1_ENST00000555053.1_Silent_p.R222R|ACIN1_ENST00000457657.1_Silent_p.R182R|ACIN1_ENST00000555352.1_5'Flank	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	222	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		TTTCTCCTTTCCTTGGTTTCT	0.388																																																0													279.0	249.0	259.0					14																	23550990		2203	4300	6503	SO:0001819	synonymous_variant	22985			AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.666G>A	14.37:g.23550990C>T			B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	37	CCDS9587.1																																																																																				0.388	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		39	80	39	80
AK7	122481	hgsc.bcm.edu;broad.mit.edu	37	14	96875258	96875258	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr14:96875258C>T	ENST00000267584.4	+	4	522	c.478C>T	c.(478-480)Cgc>Tgc	p.R160C	AK7_ENST00000554313.1_3'UTR	NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	160					axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GACTTGGGCGCGCTCCAAAGC	0.473																																																0													84.0	82.0	83.0					14																	96875258		2203	4300	6503	SO:0001583	missense	122481			AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"""Adenylate kinases"""	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.478C>T	14.37:g.96875258C>T	ENSP00000267584:p.Arg160Cys		Q8IYP6	Missense_Mutation	SNP	ENST00000267584.4	37	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	C	13.02	2.111582	0.37242	.	.	ENSG00000140057	ENST00000267584	T	0.57107	0.42	5.1	3.2	0.36748	NAD(P)-binding domain (1);	0.675264	0.14346	N	0.325382	T	0.51193	0.1660	M	0.71581	2.175	0.80722	D	1	B	0.26775	0.159	B	0.18561	0.022	T	0.51655	-0.8678	10	0.87932	D	0	-13.3972	11.6219	0.51124	0.3348:0.6652:0.0:0.0	.	160	Q96M32	KAD7_HUMAN	C	160	ENSP00000267584:R160C	ENSP00000267584:R160C	R	+	1	0	AK7	95945011	0.001000	0.12720	0.117000	0.21633	0.043000	0.13939	0.237000	0.17985	0.602000	0.29896	-0.152000	0.13540	CGC		0.473	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			6	76	6	76
PLA2G4D	283748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	42371771	42371771	+	Silent	SNP	C	C	G			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr15:42371771C>G	ENST00000290472.3	-	13	1375	c.1281G>C	c.(1279-1281)ctG>ctC	p.L427L		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	427	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		CTAGCGCCCACAGGTCCACAA	0.701																																																0													27.0	28.0	28.0					15																	42371771		2202	4297	6499	SO:0001819	synonymous_variant	283748			AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1281G>C	15.37:g.42371771C>G			Q8N176	Silent	SNP	ENST00000290472.3	37	CCDS32203.1																																																																																				0.701	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034		11	21	11	21
CDYL2	124359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	80646582	80646582	+	Missense_Mutation	SNP	G	G	A	rs536459738		TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr16:80646582G>A	ENST00000570137.2	-	5	1314	c.1159C>T	c.(1159-1161)Cgc>Tgc	p.R387C	CDYL2_ENST00000563890.1_Missense_Mutation_p.R388C|CDYL2_ENST00000562812.1_Missense_Mutation_p.R388C|CDYL2_ENST00000566173.1_Missense_Mutation_p.R388C	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	387						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						GGCGTGAGGCGGATGGTGGCG	0.657																																																0													90.0	89.0	89.0					16																	80646582		2203	4300	6503	SO:0001583	missense	124359			AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"""chromodomain Y-like protein 2"""			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.1159C>T	16.37:g.80646582G>A	ENSP00000476295:p.Arg387Cys		Q7Z5I8	Missense_Mutation	SNP	ENST00000570137.2	37	CCDS32493.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.207508	0.79240	.	.	ENSG00000166446	ENST00000299564	T	0.66995	-0.24	4.95	4.95	0.65309	Crotonase, core (1);	0.123452	0.56097	D	0.000028	T	0.74921	0.3780	L	0.40543	1.245	0.80722	D	1	D	0.71674	0.998	D	0.65443	0.935	T	0.77477	-0.2573	10	0.72032	D	0.01	.	17.3496	0.87320	0.0:0.0:1.0:0.0	.	387	Q8N8U2	CDYL2_HUMAN	C	387	ENSP00000299564:R387C	ENSP00000299564:R387C	R	-	1	0	CDYL2	79204083	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.564000	0.53791	2.562000	0.86427	0.650000	0.86243	CGC		0.657	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342		37	93	37	93
MYOCD	93649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	12656007	12656007	+	Missense_Mutation	SNP	G	G	A	rs531377746		TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr17:12656007G>A	ENST00000343344.4	+	10	1402	c.1402G>A	c.(1402-1404)Gct>Act	p.A468T	AC005358.1_ENST00000609971.1_Missense_Mutation_p.A372T|MYOCD_ENST00000395988.1_3'UTR|MYOCD_ENST00000425538.1_Missense_Mutation_p.A468T			Q8IZQ8	MYCD_HUMAN	myocardin	468	Ser-rich.				cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.A468T(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		CCTGTCAGTCGCTGGGTCCCT	0.627																																																1	Substitution - Missense(1)	prostate(1)											73.0	69.0	71.0					17																	12656007		2203	4300	6503	SO:0001583	missense	93649			AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.1402G>A	17.37:g.12656007G>A	ENSP00000341835:p.Ala468Thr		Q5UBU5|Q8N7Q1	Missense_Mutation	SNP	ENST00000343344.4	37	CCDS11163.1	.	.	.	.	.	.	.	.	.	.	G	2.498	-0.315834	0.05422	.	.	ENSG00000141052	ENST00000395982;ENST00000425538;ENST00000343344;ENST00000395988;ENST00000443061	T;T	0.43688	0.94;0.94	5.66	-1.8	0.07907	.	0.287999	0.41001	N	0.000978	T	0.23171	0.0560	L	0.34521	1.04	0.09310	N	1	B;B;B;B	0.12013	0.003;0.005;0.005;0.003	B;B;B;B	0.08055	0.001;0.002;0.003;0.001	T	0.12426	-1.0548	10	0.22109	T	0.4	-0.7432	5.8551	0.18714	0.5174:0.0:0.3524:0.1302	.	187;372;468;468	E9PEP9;Q8IZQ8-2;Q8IZQ8-3;Q8IZQ8	.;.;.;MYCD_HUMAN	T	187;468;468;372;173	ENSP00000341835:A468T;ENSP00000400148:A173T	ENSP00000341835:A468T	A	+	1	0	MYOCD	12596732	0.991000	0.36638	0.000000	0.03702	0.378000	0.30076	3.173000	0.50839	-0.129000	0.11620	-0.229000	0.12294	GCT		0.627	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		37	75	37	75
HGS	9146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	79657241	79657241	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr17:79657241G>A	ENST00000329138.4	+	6	580	c.445G>A	c.(445-447)Gat>Aat	p.D149N		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	149					endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			CAAAGAGAGCGATGCCATGTT	0.617																																																0													120.0	107.0	111.0					17																	79657241		2203	4300	6503	SO:0001583	missense	9146			D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"""Zinc fingers, FYVE domain containing"""	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		ENST00000329138.4:c.445G>A	17.37:g.79657241G>A	ENSP00000331201:p.Asp149Asn		Q9NR36	Missense_Mutation	SNP	ENST00000329138.4	37	CCDS11784.1	.	.	.	.	.	.	.	.	.	.	G	19.25	3.792321	0.70452	.	.	ENSG00000185359	ENST00000329138;ENST00000442335	T	0.48201	0.82	5.55	5.55	0.83447	.	0.273175	0.40385	N	0.001110	T	0.64450	0.2599	L	0.46567	1.45	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.64922	-0.6293	10	0.62326	D	0.03	-38.9887	18.4687	0.90765	0.0:0.0:1.0:0.0	.	149	O14964	HGS_HUMAN	N	149	ENSP00000331201:D149N	ENSP00000331201:D149N	D	+	1	0	HGS	77267646	1.000000	0.71417	0.954000	0.39281	0.372000	0.29890	9.101000	0.94219	2.607000	0.88179	0.561000	0.74099	GAT		0.617	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712		45	88	45	88
ZNF555	148254	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	2852903	2852903	+	Silent	SNP	C	C	T	rs148620935		TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr19:2852903C>T	ENST00000334241.4	+	4	978	c.840C>T	c.(838-840)ggC>ggT	p.G280G	AC006130.3_ENST00000589365.1_RNA|ZNF555_ENST00000591539.1_Silent_p.G279G	NM_001172775.1|NM_152791.4	NP_001166246.1|NP_690004.4	Q8NEP9	ZN555_HUMAN	zinc finger protein 555	280					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)|urinary_tract(4)	23				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACACACTGGCGAGAAGCCAT	0.408																																																0								T	,	0,4406		0,0,2203	62.0	57.0	59.0		837,840	0.9	1.0	19	dbSNP_134	59	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ZNF555	NM_001172775.1,NM_152791.4	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	279/628,280/629	2852903	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	148254			AL832140	CCDS12096.1, CCDS59329.1	19p13.3	2013-09-20			ENSG00000186300	ENSG00000186300		"""Zinc fingers, C2H2-type"", ""-"""	28382	protein-coding gene	gene with protein product						12477932	Standard	NM_152791		Approved	MGC26707	uc002lwo.3	Q8NEP9	OTTHUMG00000180500	ENST00000334241.4:c.840C>T	19.37:g.2852903C>T			A8KA89|K7EQM2|Q8NA46|Q96MP1	Silent	SNP	ENST00000334241.4	37	CCDS12096.1																																																																																				0.408	ZNF555-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451637.3	NM_152791		25	58	25	58
CEP89	84902	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	33392199	33392199	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr19:33392199T>C	ENST00000305768.5	-	15	1773	c.1685A>G	c.(1684-1686)cAa>cGa	p.Q562R		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	562					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						TGCTTTGTTTTGCTCTGTCAA	0.408																																																0													205.0	201.0	202.0					19																	33392199		2203	4300	6503	SO:0001583	missense	84902			AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.1685A>G	19.37:g.33392199T>C	ENSP00000306105:p.Gln562Arg		B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	T	0.039	-1.291994	0.01375	.	.	ENSG00000121289	ENST00000305768	D	0.87256	-2.23	5.15	0.135	0.14775	.	0.795595	0.11954	N	0.513402	T	0.71117	0.3302	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.54970	-0.8213	10	0.27082	T	0.32	-0.1792	5.0835	0.14668	0.0:0.2618:0.1421:0.596	.	562	Q96ST8	CEP89_HUMAN	R	562	ENSP00000306105:Q562R	ENSP00000306105:Q562R	Q	-	2	0	CEP89	38084039	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.149000	0.10204	-0.210000	0.10140	-0.911000	0.02809	CAA		0.408	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		37	145	37	145
GPATCH1	55094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	33608853	33608853	+	Silent	SNP	A	A	G			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr19:33608853A>G	ENST00000170564.2	+	16	2633	c.2319A>G	c.(2317-2319)caA>caG	p.Q773Q		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	773					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					AGGATGAGCAAGGTGACAGTG	0.537																																					Pancreas(67;88 1713 4567 18227)											0													95.0	82.0	87.0					19																	33608853		2203	4300	6503	SO:0001819	synonymous_variant	55094			AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"""G patch domain containing"""	24658	protein-coding gene	gene with protein product	"""evolutionarily conserved G patch domain containing"""			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.2319A>G	19.37:g.33608853A>G			Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																				0.537	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025		26	59	26	59
LILRA2	11027	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	55087420	55087420	+	Missense_Mutation	SNP	C	C	G	rs370378058		TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr19:55087420C>G	ENST00000251377.3	+	7	1232	c.1099C>G	c.(1099-1101)Ctg>Gtg	p.L367V	LILRA2_ENST00000251376.3_Missense_Mutation_p.L367V|LILRA2_ENST00000391738.3_Missense_Mutation_p.L367V|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000396321.2_Intron|LILRA2_ENST00000391737.1_Missense_Mutation_p.L355V|LILRB1_ENST00000418536.2_Intron			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	367	Ig-like C2-type 4.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		CCCACTGCATCTGAGATCAGA	0.587																																																0													108.0	90.0	96.0					19																	55087420		2203	4300	6503	SO:0001583	missense	11027			U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.1099C>G	19.37:g.55087420C>G	ENSP00000251377:p.Leu367Val		O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	.	.	.	.	.	.	.	.	.	.	C	7.359	0.624444	0.14193	.	.	ENSG00000239998	ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T	0.03124	4.04;4.04;4.04;4.04	2.19	1.14	0.20703	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.567530	0.04672	N	0.410877	T	0.11153	0.0272	M	0.83118	2.625	0.09310	N	1	P;B;B	0.35872	0.525;0.148;0.282	P;B;B	0.44811	0.461;0.344;0.22	T	0.32693	-0.9897	9	.	.	.	.	4.7815	0.13204	0.0:0.8121:0.0:0.1879	.	355;367;367	A8MZH0;Q8N149;Q8N149-2	.;LIRA2_HUMAN;.	V	367;367;367;355	ENSP00000251377:L367V;ENSP00000375618:L367V;ENSP00000251376:L367V;ENSP00000375617:L355V	.	L	+	1	2	LILRA2	59779232	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.017000	0.12590	0.456000	0.26937	0.508000	0.49915	CTG		0.587	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			37	105	37	105
NOTCH2	4853	hgsc.bcm.edu;broad.mit.edu	37	1	120502127	120502127	+	Splice_Site	SNP	T	T	C			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr1:120502127T>C	ENST00000256646.2	-	12	2135		c.e12-2			NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2						apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		AATTAACCCCTGGAAGAGAAA	0.403			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																														Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0													62.0	62.0	62.0					1																	120502127		2203	4300	6503	SO:0001630	splice_region_variant	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.1916-2A>G	1.37:g.120502127T>C			Q5T3X7|Q99734|Q9H240	Splice_Site	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.936461	0.73442	.	.	ENSG00000134250	ENST00000256646;ENST00000539617	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3851	0.74691	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NOTCH2	120303650	1.000000	0.71417	0.943000	0.38184	0.771000	0.43674	7.776000	0.85560	2.288000	0.76882	0.533000	0.62120	.		0.403	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	Intron	14	42	14	42
NUP210L	91181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	154062057	154062057	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr1:154062057C>T	ENST00000368559.3	-	16	2272	c.2201G>A	c.(2200-2202)cGa>cAa	p.R734Q	NUP210L_ENST00000271854.3_Missense_Mutation_p.R734Q	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	734					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			ATTTCCAATTCGGAATGTGAG	0.423																																																0													77.0	77.0	77.0					1																	154062057		1892	4122	6014	SO:0001583	missense	91181			AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2201G>A	1.37:g.154062057C>T	ENSP00000357547:p.Arg734Gln		E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	C	10.05	1.244852	0.22796	.	.	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.22945	1.93;1.93	4.57	1.51	0.23008	.	0.150747	0.30752	N	0.008943	T	0.07098	0.0180	L	0.47716	1.5	0.38637	D	0.951515	B;B	0.13594	0.003;0.008	B;B	0.08055	0.003;0.003	T	0.19976	-1.0289	10	0.14656	T	0.56	-27.8864	7.693	0.28579	0.0:0.6275:0.0:0.3725	.	734;734	E7EP56;Q5VU65	.;P210L_HUMAN	Q	734	ENSP00000357547:R734Q;ENSP00000271854:R734Q	ENSP00000271854:R734Q	R	-	2	0	NUP210L	152328681	0.635000	0.27199	0.958000	0.39756	0.942000	0.58702	-0.037000	0.12164	0.129000	0.18514	-0.444000	0.05651	CGA		0.423	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		45	80	45	80
OR2T8	343172	hgsc.bcm.edu;broad.mit.edu	37	1	248084419	248084419	+	Silent	SNP	T	T	C			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr1:248084419T>C	ENST00000319968.4	+	1	100	c.100T>C	c.(100-102)Ttg>Ctg	p.L34L		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	34						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GAGTATCGTTTTGACCTCCCT	0.488																																																0													74.0	71.0	72.0					1																	248084419		2203	4297	6500	SO:0001819	synonymous_variant	343172				CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.100T>C	1.37:g.248084419T>C				Silent	SNP	ENST00000319968.4	37	CCDS31100.1																																																																																				0.488	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522		31	73	31	73
OR2L8	391190	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	248112252	248112252	+	Silent	SNP	T	T	C			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr1:248112252T>C	ENST00000357191.3	+	1	93	c.93T>C	c.(91-93)gtT>gtC	p.V31V	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TTCTCATTGTTTTCATTTTCC	0.393																																																0													235.0	218.0	224.0					1																	248112252		2203	4300	6503	SO:0001819	synonymous_variant	391190			BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"""GPCR / Class A : Olfactory receptors"""	15014	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily L, member 8"""				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.93T>C	1.37:g.248112252T>C			Q6IF03	Silent	SNP	ENST00000357191.3	37	CCDS31101.1																																																																																				0.393	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			77	164	77	164
RIPK4	54101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	43161015	43161015	+	Missense_Mutation	SNP	G	G	A	rs140909597		TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr21:43161015G>A	ENST00000352483.2	-	9	2546	c.2482C>T	c.(2482-2484)Cgg>Tgg	p.R828W	RIPK4_ENST00000544709.1_Missense_Mutation_p.R717W|RIPK4_ENST00000542057.1_Missense_Mutation_p.R717W|RIPK4_ENST00000332512.3_Missense_Mutation_p.R780W|AP001615.9_ENST00000423276.1_RNA			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	828					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TTGCTTCGCCGCAGGAGCGTG	0.667													G|||	1	0.000199681	0.0	0.0014	5008	,	,		15911	0.0		0.0	False		,,,				2504	0.0															0								G	TRP/ARG	1,4389		0,1,2194	23.0	25.0	24.0		2338	3.7	0.0	21	dbSNP_134	24	0,8546		0,0,4273	no	missense	RIPK4	NM_020639.2	101	0,1,6467	AA,AG,GG		0.0,0.0228,0.0077	probably-damaging	780/785	43161015	1,12935	2195	4273	6468	SO:0001583	missense	54101			AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.2482C>T	21.37:g.43161015G>A	ENSP00000330161:p.Arg828Trp		Q96KH0	Missense_Mutation	SNP	ENST00000352483.2	37		.	.	.	.	.	.	.	.	.	.	G	9.220	1.033156	0.19590	2.28E-4	0.0	ENSG00000183421	ENST00000332512;ENST00000352483;ENST00000544709;ENST00000542057	T;T;T;T	0.79247	-1.02;-1.06;-1.25;-1.25	4.65	3.72	0.42706	.	0.290214	0.24204	N	0.040590	T	0.74306	0.3699	L	0.32530	0.975	0.09310	N	1	D	0.64830	0.994	P	0.53224	0.721	T	0.65639	-0.6119	10	0.62326	D	0.03	-12.2004	8.8313	0.35085	0.0:0.1645:0.6652:0.1703	.	780	P57078-2	.	W	780;828;717;717	ENSP00000332454:R780W;ENSP00000330161:R828W;ENSP00000441754:R717W;ENSP00000442901:R717W	ENSP00000332454:R780W	R	-	1	2	RIPK4	42034084	0.065000	0.20965	0.005000	0.12908	0.011000	0.07611	1.973000	0.40550	0.880000	0.35969	0.655000	0.94253	CGG		0.667	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639		16	33	16	33
HJURP	55355	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	234750376	234750376	+	Missense_Mutation	SNP	C	C	G			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr2:234750376C>G	ENST00000411486.2	-	8	1115	c.1050G>C	c.(1048-1050)aaG>aaC	p.K350N	HJURP_ENST00000434039.1_5'Flank|HJURP_ENST00000441687.1_Missense_Mutation_p.K265N|HJURP_ENST00000432087.1_Missense_Mutation_p.K296N	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	350					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		TTAAACCTGTCTTACGGCAAG	0.443																																																0													73.0	74.0	74.0					2																	234750376		2203	4300	6503	SO:0001583	missense	55355				CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.1050G>C	2.37:g.234750376C>G	ENSP00000414109:p.Lys350Asn		A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	.	.	.	.	.	.	.	.	.	.	C	9.769	1.172262	0.21704	.	.	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	4.3	1.48	0.22813	Holliday junction recognition protein, HJURP (1);	1.527910	0.03482	N	0.215265	T	0.36110	0.0955	N	0.24115	0.695	0.09310	N	1	B;B;B	0.12630	0.003;0.006;0.003	B;B;B	0.17433	0.008;0.018;0.013	T	0.29058	-1.0024	10	0.51188	T	0.08	-1.9282	6.55	0.22427	0.0:0.5514:0.3517:0.0969	.	265;296;350	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	N	350;296;265;265	ENSP00000414109:K350N;ENSP00000407208:K296N;ENSP00000401944:K265N;ENSP00000393253:K265N	ENSP00000414109:K350N	K	-	3	2	HJURP	234415115	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.008000	0.12788	0.328000	0.23435	-0.176000	0.13171	AAG		0.443	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410		21	41	21	41
TRA2B	6434	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	185639892	185639892	+	Missense_Mutation	SNP	A	A	C			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr3:185639892A>C	ENST00000453386.2	-	5	820	c.545T>G	c.(544-546)aTg>aGg	p.M182R	TRA2B_ENST00000382191.4_Missense_Mutation_p.M82R	NM_004593.2	NP_004584.1	P62995	TRA2B_HUMAN	transformer 2 beta homolog (Drosophila)	182	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(3)|prostate(1)|urinary_tract(1)	18						ATCAAGCTCCATTCCATTGGC	0.408																																																0													133.0	125.0	128.0					3																	185639892		2203	4300	6503	SO:0001583	missense	6434			AF057159	CCDS33905.1, CCDS58872.1	3q26.2-q27	2014-06-13	2009-02-27	2009-02-27	ENSG00000136527	ENSG00000136527		"""RNA binding motif (RRM) containing"""	10781	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 156"""	602719	"""splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)"""	SFRS10		9790768	Standard	NM_004593		Approved	Htra2-beta, PPP1R156	uc003fpv.3	P62995	OTTHUMG00000156641	ENST00000453386.2:c.545T>G	3.37:g.185639892A>C	ENSP00000416959:p.Met182Arg		B4DVK2|D3DNU3|O15449|Q15815|Q64283	Missense_Mutation	SNP	ENST00000453386.2	37	CCDS33905.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.5|26.5	4.741312|4.741312	0.89573|0.89573	.|.	.|.	ENSG00000136527|ENSG00000136527	ENST00000453386;ENST00000382191|ENST00000259043;ENST00000414862	D;D|.	0.85258|.	-1.96;-1.96|.	6.17|6.17	6.17|6.17	0.99709|0.99709	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.39886|0.39886	0.1095|0.1095	N|N	0.05383|0.05383	-0.06|-0.06	0.80722|0.80722	D|D	1|1	P;P|.	0.48016|.	0.904;0.904|.	P;P|.	0.61132|.	0.884;0.884|.	T|T	0.36089|0.36089	-0.9762|-0.9762	10|5	0.27082|.	T|.	0.32|.	-4.208|-4.208	15.8048|15.8048	0.78491|0.78491	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	182;182|.	B2RDQ3;P62995|.	.;TRA2B_HUMAN|.	R|G	182;82|41;2	ENSP00000416959:M182R;ENSP00000371626:M82R|.	ENSP00000371626:M82R|.	M|W	-|-	2|1	0|0	TRA2B|TRA2B	187122586|187122586	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	9.287000|9.287000	0.95975|0.95975	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	ATG|TGG		0.408	TRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344984.1	NM_004593		12	54	12	54
NCAPG	64151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	17843981	17843981	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr4:17843981C>T	ENST00000251496.2	+	20	3079	c.2903C>T	c.(2902-2904)aCt>aTt	p.T968I	LCORL_ENST00000326877.4_3'UTR	NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	968					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		AGGTGTCAGACTGCTGAAGCC	0.353																																																0													81.0	79.0	80.0					4																	17843981		2203	4299	6502	SO:0001583	missense	64151			AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"""chromosome condensation protein G"""	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.2903C>T	4.37:g.17843981C>T	ENSP00000251496:p.Thr968Ile		Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000251496.2	37	CCDS3424.1	.	.	.	.	.	.	.	.	.	.	C	9.493	1.101217	0.20632	.	.	ENSG00000109805	ENST00000251496	T	0.30448	1.53	5.45	0.309	0.15820	.	0.709707	0.14243	N	0.331965	T	0.16128	0.0388	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.17776	-1.0358	10	0.33940	T	0.23	-1.9033	3.8966	0.09143	0.1675:0.4797:0.0:0.3528	.	968	Q9BPX3	CND3_HUMAN	I	968	ENSP00000251496:T968I	ENSP00000251496:T968I	T	+	2	0	NCAPG	17453079	0.000000	0.05858	0.001000	0.08648	0.627000	0.37826	-0.190000	0.09615	0.125000	0.18397	0.655000	0.94253	ACT		0.353	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346		17	30	17	30
FDCSP	260436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	71096961	71096961	+	Missense_Mutation	SNP	G	G	T			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr4:71096961G>T	ENST00000317987.5	+	2	162	c.50G>T	c.(49-51)gGt>gTt	p.G17V		NM_152997.3	NP_694542.1	Q8NFU4	FDSCP_HUMAN	follicular dendritic cell secreted protein	17						extracellular region (GO:0005576)											GTGGCTGTTGGTTTCCCAGTA	0.378																																																0													83.0	86.0	85.0					4																	71096961		2203	4299	6502	SO:0001583	missense	260436			AF435080	CCDS3537.1	4q13	2011-12-12	2011-12-12	2011-12-12	ENSG00000181617	ENSG00000181617			19215	protein-coding gene	gene with protein product		607241	"""chromosome 4 open reading frame 7"""	C4orf7		12193705, 17548624, 20811673	Standard	NM_152997		Approved	FDC-SP	uc003hfd.3	Q8NFU4	OTTHUMG00000129393	ENST00000317987.5:c.50G>T	4.37:g.71096961G>T	ENSP00000318437:p.Gly17Val			Missense_Mutation	SNP	ENST00000317987.5	37	CCDS3537.1	.	.	.	.	.	.	.	.	.	.	G	8.600	0.886675	0.17540	.	.	ENSG00000181617	ENST00000317987	.	.	.	4.05	0.0164	0.14108	.	0.713707	0.12170	N	0.493151	T	0.62841	0.2461	.	.	.	0.09310	N	1	D	0.63046	0.992	P	0.61070	0.883	T	0.59295	-0.7481	8	0.87932	D	0	-1.9885	13.7032	0.62622	0.0:0.648:0.352:0.0	.	17	Q8NFU4	FDSCP_HUMAN	V	17	.	ENSP00000318437:G17V	G	+	2	0	C4orf7	71131550	0.075000	0.21258	0.010000	0.14722	0.030000	0.12068	0.114000	0.15520	-0.032000	0.13758	-0.172000	0.13284	GGT		0.378	FDCSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251549.1	NM_152997		55	120	55	120
ADAMTS12	81792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	33648939	33648939	+	Silent	SNP	G	G	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr5:33648939G>A	ENST00000504830.1	-	9	1802	c.1467C>T	c.(1465-1467)tgC>tgT	p.C489C	ADAMTS12_ENST00000352040.3_Silent_p.C489C|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	489	Disintegrin.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						CTACTTCCTGGCAGAAGGTAG	0.473										HNSCC(64;0.19)																																						0													136.0	129.0	131.0					5																	33648939		2203	4300	6503	SO:0001819	synonymous_variant	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.1467C>T	5.37:g.33648939G>A			A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	CCDS34140.1																																																																																				0.473	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		29	124	29	124
SHROOM1	134549	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	132159379	132159379	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr5:132159379G>A	ENST00000378679.3	-	8	2693	c.1889C>T	c.(1888-1890)cCt>cTt	p.P630L	SHROOM1_ENST00000378676.1_Missense_Mutation_p.P561L|SHROOM1_ENST00000319854.3_Missense_Mutation_p.P630L|SHROOM1_ENST00000488072.1_5'UTR	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	630	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTCAAGCACAGGGTGGGTGGC	0.612																																																0													60.0	61.0	60.0					5																	132159379		2203	4300	6503	SO:0001583	missense	134549			AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.1889C>T	5.37:g.132159379G>A	ENSP00000367950:p.Pro630Leu		B7WP40|B7ZL01|Q8TDP0|Q8TF41	Missense_Mutation	SNP	ENST00000378679.3	37	CCDS54902.1	.	.	.	.	.	.	.	.	.	.	G	10.41	1.343904	0.24339	.	.	ENSG00000164403	ENST00000378679;ENST00000319854;ENST00000378676	T;T;T	0.24538	1.85;1.85;1.86	4.89	2.13	0.27403	Apx/shroom, ASD2 (2);	1.070980	0.07260	N	0.867292	T	0.22975	0.0555	L	0.47716	1.5	0.09310	N	0.999999	B;B	0.17852	0.019;0.024	B;B	0.21917	0.022;0.037	T	0.36335	-0.9752	10	0.20519	T	0.43	0.0212	7.3954	0.26934	0.2829:0.0:0.7171:0.0	.	630;630	Q2M3G4-2;Q2M3G4	.;SHRM1_HUMAN	L	630;630;561	ENSP00000367950:P630L;ENSP00000324245:P630L;ENSP00000367947:P561L	ENSP00000324245:P630L	P	-	2	0	SHROOM1	132187278	0.025000	0.19082	0.000000	0.03702	0.386000	0.30323	1.917000	0.39996	0.340000	0.23745	0.561000	0.74099	CCT		0.612	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		40	100	40	100
PCDHA4	56144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	140188796	140188796	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr5:140188796C>T	ENST00000530339.1	+	1	2024	c.2024C>T	c.(2023-2025)gCg>gTg	p.A675V	PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.A675V|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.A675V	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	675	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGTGGACAGGCGCCAAAGGCC	0.657																																																0													57.0	59.0	59.0					5																	140188796		2203	4300	6503	SO:0001583	missense	56144			AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.2024C>T	5.37:g.140188796C>T	ENSP00000435300:p.Ala675Val		O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	N	10.95	1.496466	0.26861	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.52295	0.73;0.67;0.7	3.93	-0.505	0.11993	Cadherin (2);	0.703928	0.11608	U	0.547081	T	0.37865	0.1019	L	0.60957	1.885	0.09310	N	1	B;B;B	0.18310	0.027;0.015;0.012	B;B;B	0.18263	0.021;0.009;0.004	T	0.29427	-1.0012	10	0.32370	T	0.25	.	5.2108	0.15316	0.3918:0.4593:0.0:0.1488	.	675;675;675	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	V	675	ENSP00000423470:A675V;ENSP00000349344:A675V;ENSP00000435300:A675V	ENSP00000349344:A675V	A	+	2	0	PCDHA4	140168980	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.197000	0.09518	-0.016000	0.14127	-0.336000	0.08194	GCG		0.657	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		17	79	17	79
SLC36A2	153201	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	150704990	150704990	+	Missense_Mutation	SNP	C	C	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr5:150704990C>A	ENST00000335244.4	-	8	996	c.867G>T	c.(865-867)atG>atT	p.M289I	SLC36A2_ENST00000450886.1_Missense_Mutation_p.M13I|SLC36A2_ENST00000521967.1_Missense_Mutation_p.M289I	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	289					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	GGGCATTCTTCATCTTGTTTT	0.468																																																0													82.0	75.0	77.0					5																	150704990		2203	4300	6503	SO:0001583	missense	153201			AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"""Solute carriers"""	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.867G>T	5.37:g.150704990C>A	ENSP00000334223:p.Met289Ile		Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Missense_Mutation	SNP	ENST00000335244.4	37	CCDS4315.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.0|23.0	4.368682|4.368682	0.82463|0.82463	.|.	.|.	ENSG00000186335|ENSG00000186335	ENST00000335244;ENST00000450886;ENST00000521967|ENST00000523044	T;T;T|.	0.02812|.	4.15;4.15;4.15|.	4.82|4.82	4.82|4.82	0.62117|0.62117	.|.	0.162750|.	0.64402|.	D|.	0.000005|.	D|.	0.87537|.	0.6202|.	H|H	0.95645|0.95645	3.7|3.7	0.80722|0.80722	D|D	1|1	P;P|.	0.46220|.	0.874;0.576|.	P;P|.	0.53760|.	0.734;0.513|.	D|.	0.91189|.	0.4982|.	10|.	0.72032|.	D|.	0.01|.	-42.7873|-42.7873	18.4691|18.4691	0.90766|0.90766	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	289;289|.	E5RJJ5;Q495M3|.	.;S36A2_HUMAN|.	I|L	289;13;289|42	ENSP00000334223:M289I;ENSP00000399479:M13I;ENSP00000430535:M289I|.	ENSP00000334223:M289I|.	M|X	-|-	3|2	0|2	SLC36A2|SLC36A2	150685183|150685183	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.643000|0.643000	0.38383|0.38383	7.317000|7.317000	0.79018|0.79018	2.660000|2.660000	0.90430|0.90430	0.467000|0.467000	0.42956|0.42956	ATG|TGA		0.468	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1			24	52	24	52
FAT2	2196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	150922417	150922417	+	Silent	SNP	G	G	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr5:150922417G>A	ENST00000261800.5	-	9	8283	c.8271C>T	c.(8269-8271)caC>caT	p.H2757H		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2757	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGTGGATTCGTGGTCCATGG	0.512																																																0													198.0	172.0	180.0					5																	150922417		2203	4300	6503	SO:0001819	synonymous_variant	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.8271C>T	5.37:g.150922417G>A			O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																				0.512	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		50	122	50	122
ATP10B	23120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	160047525	160047525	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr5:160047525G>A	ENST00000327245.5	-	15	3091	c.2245C>T	c.(2245-2247)Cgc>Tgc	p.R749C	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	749					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGGGGCAGGCGCACAGTCACC	0.617																																																0													32.0	35.0	34.0					5																	160047525		2106	4219	6325	SO:0001583	missense	23120			AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.2245C>T	5.37:g.160047525G>A	ENSP00000313600:p.Arg749Cys		Q9H725	Missense_Mutation	SNP	ENST00000327245.5	37	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.702604	0.68501	.	.	ENSG00000118322	ENST00000327245;ENST00000520108	T;T	0.63580	-0.05;-0.05	5.36	5.36	0.76844	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	T	0.76870	0.4048	M	0.76574	2.34	0.51233	D	0.999911	D;D	0.89917	1.0;1.0	D;D	0.70935	0.95;0.971	T	0.77702	-0.2489	9	.	.	.	.	13.1254	0.59351	0.0:0.0:0.8402:0.1598	.	357;749	Q2YDW8;O94823	.;AT10B_HUMAN	C	749;357	ENSP00000313600:R749C;ENSP00000431081:R357C	.	R	-	1	0	ATP10B	159980103	0.999000	0.42202	1.000000	0.80357	0.991000	0.79684	1.765000	0.38481	2.523000	0.85059	0.655000	0.94253	CGC		0.617	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		16	42	16	42
DSP	1832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	7571618	7571618	+	Silent	SNP	G	G	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr6:7571618G>A	ENST00000379802.3	+	14	2045	c.1704G>A	c.(1702-1704)ctG>ctA	p.L568L	DSP_ENST00000418664.2_Silent_p.L568L	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	568	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		CCTTTCAGCTGAAAACAATGC	0.453																																																0													217.0	218.0	218.0					6																	7571618		2203	4300	6503	SO:0001819	synonymous_variant	1832			J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.1704G>A	6.37:g.7571618G>A			B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	37	CCDS4501.1																																																																																				0.453	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		126	244	126	244
DSP	1832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	7571689	7571689	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr6:7571689G>A	ENST00000379802.3	+	14	2116	c.1775G>A	c.(1774-1776)aGa>aAa	p.R592K	DSP_ENST00000418664.2_Missense_Mutation_p.R592K	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	592	Globular 1.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GAGTTCATCAGAAATAGCCAA	0.453																																																0													233.0	226.0	229.0					6																	7571689		2203	4300	6503	SO:0001583	missense	1832			J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.1775G>A	6.37:g.7571689G>A	ENSP00000369129:p.Arg592Lys		B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.420919	0.62622	.	.	ENSG00000096696	ENST00000379802;ENST00000418664;ENST00000397483	T;T	0.75260	-0.58;-0.92	5.64	3.85	0.44370	.	0.000000	0.64402	D	0.000006	T	0.74045	0.3665	L	0.55743	1.74	0.37738	D	0.925524	D;D	0.54397	0.966;0.966	D;D	0.66497	0.944;0.944	T	0.74785	-0.3547	10	0.42905	T	0.14	.	11.7301	0.51732	0.145:0.0:0.855:0.0	.	639;592	Q4LE79;P15924	.;DESP_HUMAN	K	592;592;397	ENSP00000369129:R592K;ENSP00000396591:R592K	ENSP00000369129:R592K	R	+	2	0	DSP	7516688	1.000000	0.71417	0.515000	0.27774	0.990000	0.78478	5.417000	0.66423	0.723000	0.32274	0.655000	0.94253	AGA		0.453	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		95	186	95	186
HLA-F	3134	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	29693049	29693049	+	Silent	SNP	C	C	T	rs374197706		TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr6:29693049C>T	ENST00000376861.1	+	5	1236	c.852C>T	c.(850-852)caC>caT	p.H284H	HLA-F_ENST00000434407.2_Intron|HLA-F_ENST00000334668.4_Silent_p.H284H|HLA-F_ENST00000259951.7_Silent_p.H284H|HLA-F_ENST00000440587.2_Silent_p.H166H			P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	284	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						ATGTGCAGCACGAGGGGCTGC	0.597																																																0								C	,,	0,4406		0,0,2203	44.0	43.0	44.0		,852,852	-0.1	0.7	6		44	2,8598		0,2,4298	no	intron,coding-synonymous,coding-synonymous	HLA-F	NM_001098478.1,NM_001098479.1,NM_018950.2	,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,	,284/443,284/347	29693049	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3134			AY253269	CCDS43437.1, CCDS43438.1, CCDS43439.1	6p21.3	2013-01-11			ENSG00000204642	ENSG00000204642		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4963	protein-coding gene	gene with protein product		143110				1688605	Standard	NM_018950		Approved		uc003nno.4	P30511	OTTHUMG00000031156	ENST00000376861.1:c.852C>T	6.37:g.29693049C>T			Q5JQI8|Q5JQJ1|Q5SPT5|Q860R0|Q8MGQ1|Q8WLP5|Q95HC0|Q9TP68	Silent	SNP	ENST00000376861.1	37	CCDS43438.1	.	.	.	.	.	.	.	.	.	.	.	0.023	-1.394921	0.01175	0.0	2.33E-4	ENSG00000204642	ENST00000429294	.	.	.	1.92	-0.091	0.13662	.	.	.	.	.	T	0.28732	0.0712	.	.	.	0.58432	D	0.999992	.	.	.	.	.	.	T	0.17561	-1.0365	4	.	.	.	.	4.2368	0.10630	0.0:0.5965:0.0:0.4035	.	.	.	.	M	163	.	.	T	+	2	0	HLA-F	29801028	0.035000	0.19736	0.680000	0.29994	0.003000	0.03518	-0.575000	0.05861	-0.244000	0.09639	-0.436000	0.05848	ACG		0.597	HLA-F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195083.1	NM_018950		24	67	24	67
CRISP3	10321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	49701500	49701500	+	Missense_Mutation	SNP	G	G	C			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr6:49701500G>C	ENST00000393666.1	-	4	345	c.339C>G	c.(337-339)atC>atG	p.I113M	CRISP3_ENST00000433368.2_Missense_Mutation_p.I136M|CRISP3_ENST00000423399.2_Missense_Mutation_p.I23M|CRISP3_ENST00000263045.4_Missense_Mutation_p.I126M|CRISP3_ENST00000371159.4_Missense_Mutation_p.I144M			P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	113	SCP.				defense response (GO:0006952)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|specific granule (GO:0042581)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|skin(6)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			ACCAGCTTTGGATTGCTTGTG	0.433																																																0													154.0	143.0	146.0					6																	49701500		2203	4300	6503	SO:0001583	missense	10321			X94323	CCDS4929.1, CCDS4929.2, CCDS55019.1	6p12.3	2008-02-05			ENSG00000096006	ENSG00000096006			16904	protein-coding gene	gene with protein product						8665901, 12223513	Standard	NM_006061		Approved	SGP28, CRISP-3, CRS3, dJ442L6.3, Aeg2	uc003ozs.3	P54108	OTTHUMG00000014823	ENST00000393666.1:c.339C>G	6.37:g.49701500G>C	ENSP00000377274:p.Ile113Met		A8K9S1|B2R8I8|Q15512|Q3MJ82|Q53FA9|Q5JW83|Q9H108	Missense_Mutation	SNP	ENST00000393666.1	37		.	.	.	.	.	.	.	.	.	.	g	10.19	1.280753	0.23392	.	.	ENSG00000096006	ENST00000263045;ENST00000433368;ENST00000393666;ENST00000423399;ENST00000371159;ENST00000354620	T;T;T;T;T;T	0.48201	2.79;2.79;2.79;0.82;2.79;2.79	5.1	0.693	0.18056	CAP domain (3);	0.080976	0.47455	U	0.000230	T	0.46347	0.1388	M	0.74546	2.27	0.33747	D	0.620126	D	0.71674	0.998	D	0.74674	0.984	T	0.43621	-0.9380	10	0.51188	T	0.08	.	3.9078	0.09190	0.3257:0.0:0.5148:0.1595	.	113	P54108	CRIS3_HUMAN	M	126;136;113;23;144;136	ENSP00000263045:I126M;ENSP00000389026:I136M;ENSP00000377274:I113M;ENSP00000410469:I23M;ENSP00000360201:I144M;ENSP00000346636:I136M	ENSP00000263045:I126M	I	-	3	3	CRISP3	49809459	0.999000	0.42202	0.553000	0.28255	0.038000	0.13279	0.501000	0.22578	0.060000	0.16281	-1.130000	0.01982	ATC		0.433	CRISP3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006061		49	99	49	99
BAI3	577	hgsc.bcm.edu;broad.mit.edu	37	6	70048901	70048901	+	Silent	SNP	C	C	T	rs138734026		TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr6:70048901C>T	ENST00000370598.1	+	25	4103	c.3282C>T	c.(3280-3282)aaC>aaT	p.N1094N	BAI3_ENST00000238918.8_Silent_p.N300N|BAI3_ENST00000546190.1_Silent_p.N58N	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1094					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				CCGCCAGTAACGCCATGTTAG	0.398													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17098	0.0		0.0	False		,,,				2504	0.0															0								C		0,4406		0,0,2203	154.0	148.0	150.0		3282	0.6	1.0	6	dbSNP_134	150	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BAI3	NM_001704.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1094/1523	70048901	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.3282C>T	6.37:g.70048901C>T			B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	37	CCDS4968.1																																																																																				0.398	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			52	151	52	151
LACE1	246269	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	108768486	108768486	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr6:108768486A>G	ENST00000368977.4	+	8	1063	c.877A>G	c.(877-879)Aaa>Gaa	p.K293E		NM_145315.3	NP_660358.2	Q8WV93	LACE1_HUMAN	lactation elevated 1	293						mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)		TGCTGCAGGAAAACTCTACTA	0.328																																																0													95.0	98.0	97.0					6																	108768486		2203	4300	6503	SO:0001583	missense	246269			AF520418	CCDS5067.1	6q22.1	2006-11-10			ENSG00000135537	ENSG00000135537			16411	protein-coding gene	gene with protein product	"""ATPase family gene 1 homolog (S. cerevisiae)"""					12079282	Standard	XM_005266885		Approved	AFG1	uc003psj.3	Q8WV93	OTTHUMG00000015324	ENST00000368977.4:c.877A>G	6.37:g.108768486A>G	ENSP00000357973:p.Lys293Glu		Q8N6A3	Missense_Mutation	SNP	ENST00000368977.4	37	CCDS5067.1	.	.	.	.	.	.	.	.	.	.	A	11.52	1.662694	0.29515	.	.	ENSG00000135537	ENST00000368977	.	.	.	5.73	4.56	0.56223	.	0.047145	0.85682	D	0.000000	T	0.22666	0.0547	N	0.25031	0.7	0.50467	D	0.999879	B	0.13145	0.007	B	0.16722	0.016	T	0.07829	-1.0752	9	0.15499	T	0.54	-11.6653	11.8592	0.52457	0.9313:0.0:0.0687:0.0	.	293	Q8WV93	LACE1_HUMAN	E	293	.	ENSP00000357973:K293E	K	+	1	0	LACE1	108875179	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.423000	0.66458	0.983000	0.38602	0.533000	0.62120	AAA		0.328	LACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041719.4	NM_145315		26	46	26	46
CDC40	51362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	110533410	110533410	+	Missense_Mutation	SNP	A	A	G	rs147439944	byFrequency	TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr6:110533410A>G	ENST00000368932.1	+	8	903	c.802A>G	c.(802-804)Act>Gct	p.T268A	CDC40_ENST00000368930.1_Missense_Mutation_p.T268A|CDC40_ENST00000307731.1_Missense_Mutation_p.T268A			O60508	PRP17_HUMAN	cell division cycle 40	268					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)		TCTACGGTCAACTATGCCACC	0.383													A|||	13	0.00259585	0.0098	0.0	5008	,	,		20911	0.0		0.0	False		,,,				2504	0.0															0								A	ALA/THR	24,4382	31.7+/-61.6	0,24,2179	152.0	139.0	143.0		802	-6.5	0.5	6	dbSNP_134	143	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CDC40	NM_015891.2	58	0,25,6478	GG,GA,AA		0.0116,0.5447,0.1922	benign	268/580	110533410	25,12981	2203	4300	6503	SO:0001583	missense	51362			AF015044	CCDS5081.1	6q22.1	2013-01-17	2013-01-17		ENSG00000168438	ENSG00000168438		"""WD repeat domain containing"""	17350	protein-coding gene	gene with protein product		605585	"""cell division cycle 40 homolog (yeast)"", ""cell division cycle 40 homolog (S. cerevisiae)"""			9769104, 9830021	Standard	NM_015891		Approved	PRP17, EHB3, PRPF17, FLJ10564	uc003pua.3	O60508	OTTHUMG00000015358	ENST00000368932.1:c.802A>G	6.37:g.110533410A>G	ENSP00000357928:p.Thr268Ala		B2RBC5|O75471|Q5SRN0|Q9UPG1	Missense_Mutation	SNP	ENST00000368932.1	37	CCDS5081.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	8.268	0.812644	0.16537	0.005447	1.16E-4	ENSG00000168438	ENST00000368932;ENST00000368933;ENST00000368930;ENST00000307731	T;T;T;T	0.61158	0.25;0.13;0.13;0.25	5.84	-6.52	0.01872	WD40 repeat-like-containing domain (1);	0.556571	0.20879	N	0.084030	T	0.07369	0.0186	N	0.08118	0	0.22511	N	0.999038	B	0.02656	0.0	B	0.06405	0.002	T	0.34925	-0.9809	10	0.10377	T	0.69	-14.3555	2.6764	0.05082	0.2971:0.2899:0.0612:0.3518	.	268	O60508	PRP17_HUMAN	A	268	ENSP00000357928:T268A;ENSP00000357929:T268A;ENSP00000357926:T268A;ENSP00000304370:T268A	ENSP00000304370:T268A	T	+	1	0	CDC40	110640103	0.035000	0.19736	0.549000	0.28204	0.990000	0.78478	0.439000	0.21575	-0.866000	0.04068	0.482000	0.46254	ACT		0.383	CDC40-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041791.1	NM_015891		38	54	38	54
COL1A2	1278	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	94043557	94043557	+	Silent	SNP	C	C	T	rs183493537		TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr7:94043557C>T	ENST00000297268.6	+	29	2160	c.1689C>T	c.(1687-1689)ccC>ccT	p.P563P		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	563					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CCTCAGGTCCCGCTGGTGAAG	0.428										HNSCC(75;0.22)			C|||	1	0.000199681	0.0	0.0	5008	,	,		17457	0.001		0.0	False		,,,				2504	0.0															0													64.0	65.0	65.0					7																	94043557		2203	4300	6503	SO:0001819	synonymous_variant	1278			Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.1689C>T	7.37:g.94043557C>T			P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	37	CCDS34682.1																																																																																				0.428	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		14	55	14	55
LRRC17	10234	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	102574365	102574365	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr7:102574365G>A	ENST00000339431.4	+	2	300	c.5G>A	c.(4-6)cGt>cAt	p.R2H	FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000379306.3_Intron|FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000393772.2_Intron|FBXL13_ENST00000379308.3_Intron|LRRC17_ENST00000249377.4_Missense_Mutation_p.R2H	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	2					bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						GTCAGGATGCGTGTGGTTACC	0.493																																																0													46.0	41.0	43.0					7																	102574365		2203	4300	6503	SO:0001583	missense	10234			U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.5G>A	7.37:g.102574365G>A	ENSP00000344242:p.Arg2His		Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	37	CCDS34721.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.110768	0.56398	.	.	ENSG00000128606	ENST00000339431;ENST00000249377;ENST00000455453	T;T;T	0.63580	0.19;-0.05;0.67	5.77	2.5	0.30297	.	0.121001	0.37955	N	0.001867	T	0.50616	0.1626	L	0.45581	1.43	0.41125	D	0.985841	B;B	0.13145	0.004;0.007	B;B	0.06405	0.001;0.002	T	0.51841	-0.8654	10	0.72032	D	0.01	-12.9213	7.3201	0.26523	0.3827:0.0:0.6173:0.0	.	2;2	Q8N6Y2;Q8N6Y2-2	LRC17_HUMAN;.	H	2	ENSP00000344242:R2H;ENSP00000249377:R2H;ENSP00000394194:R2H	ENSP00000249377:R2H	R	+	2	0	LRRC17	102361601	0.996000	0.38824	0.762000	0.31397	0.983000	0.72400	1.779000	0.38624	0.897000	0.36392	0.650000	0.86243	CGT		0.493	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824		14	25	14	25
RELN	5649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	103338477	103338477	+	Silent	SNP	C	C	T			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr7:103338477C>T	ENST00000428762.1	-	10	1125	c.966G>A	c.(964-966)gaG>gaA	p.E322E	RELN_ENST00000343529.5_Silent_p.E322E|RELN_ENST00000424685.2_Silent_p.E322E	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	322					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		ATTGGACATTCTCCCCTTTGG	0.458																																					NSCLC(146;835 1944 15585 22231 52158)											0													218.0	199.0	205.0					7																	103338477		2203	4300	6503	SO:0001819	synonymous_variant	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.966G>A	7.37:g.103338477C>T			A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																				0.458	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		66	188	66	188
RAB11FIP1	80223	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	37729419	37729419	+	Silent	SNP	C	C	T			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr8:37729419C>T	ENST00000330843.4	-	4	2913	c.2901G>A	c.(2899-2901)tcG>tcA	p.S967S	RAB11FIP1_ENST00000287263.4_Intron|RAB11FIP1_ENST00000523182.1_5'UTR|RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000524118.1_Intron	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	967					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			TTTCATCATCCGATGCGACTT	0.453																																																0													156.0	128.0	137.0					8																	37729419		2203	4300	6503	SO:0001819	synonymous_variant	80223			AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.2901G>A	8.37:g.37729419C>T			J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Silent	SNP	ENST00000330843.4	37	CCDS34882.1																																																																																				0.453	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		42	97	42	97
EPPK1	83481	hgsc.bcm.edu;broad.mit.edu	37	8	144942253	144942253	+	Silent	SNP	G	G	A	rs368824447	byFrequency	TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr8:144942253G>A	ENST00000525985.1	-	2	5240	c.5169C>T	c.(5167-5169)gaC>gaT	p.D1723D				P58107	EPIPL_HUMAN	epiplakin 1	1723						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCTTGGTGTCGTCGCTGGGGT	0.657													G|||	2	0.000399361	0.0015	0.0	5008	,	,		16863	0.0		0.0	False		,,,				2504	0.0															0								G		5,4173		0,5,2084	91.0	96.0	95.0		5169	-5.0	0.1	8		95	1,8391		0,1,4195	no	coding-synonymous	EPPK1	NM_031308.1		0,6,6279	AA,AG,GG		0.0119,0.1197,0.0477		1723/2420	144942253	6,12564	2089	4196	6285	SO:0001819	synonymous_variant	83481			AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.5169C>T	8.37:g.144942253G>A			Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																					0.657	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		50	94	50	94
AKAP2	11217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	112900626	112900626	+	Silent	SNP	C	C	T	rs370870911	byFrequency	TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr9:112900626C>T	ENST00000259318.7	+	2	2316	c.2109C>T	c.(2107-2109)gaC>gaT	p.D703D	AKAP2_ENST00000482335.1_3'UTR|AKAP2_ENST00000434623.2_Silent_p.D792D|AKAP2_ENST00000374525.1_Silent_p.D792D|PALM2-AKAP2_ENST00000374530.3_Silent_p.D934D|AKAP2_ENST00000555236.1_Silent_p.D934D|PALM2-AKAP2_ENST00000302798.7_Silent_p.D934D|AKAP2_ENST00000510514.5_Silent_p.D934D	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	703										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						AAGAATCTGACGTGATGGTTG	0.547													C|||	6	0.00119808	0.0	0.0	5008	,	,		20960	0.0		0.0	False		,,,				2504	0.0061															0													77.0	69.0	71.0					9																	112900626		2203	4300	6503	SO:0001819	synonymous_variant	445815			AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.2109C>T	9.37:g.112900626C>T			B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Silent	SNP	ENST00000259318.7	37	CCDS48003.1																																																																																				0.547	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065		13	43	13	43
VPS11	55823	broad.mit.edu;ucsc.edu	37	11	118941054	118941054	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr11:118941054C>T	ENST00000300793.6	+	5	622	c.580C>T	c.(580-582)Cgc>Tgc	p.R194C	VPS11_ENST00000527798.1_3'UTR|RP11-110I1.13_ENST00000607709.1_RNA	NM_021729.4	NP_068375.3	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11 homolog (S. cerevisiae)	195					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	29	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)		ATTGGCCTTTCGCCAAGCAGG	0.517																																																0													65.0	67.0	67.0					11																	118941054		1944	4137	6081	SO:0001583	missense	55823			AB027508	CCDS73404.1	11q23	2008-02-05	2006-12-19			ENSG00000160695		"""RING-type (C3HC4) zinc fingers"""	14583	protein-coding gene	gene with protein product		608549	"""vacuolar protein sorting 11 (yeast homolog)"""				Standard	NM_021729		Approved	RNF108, PEP5	uc010ryx.2	Q9H270		ENST00000300793.6:c.580C>T	11.37:g.118941054C>T	ENSP00000475301:p.Arg194Cys		Q8WY89|Q96EP8|Q9H6D9|Q9HCS6	Missense_Mutation	SNP	ENST00000300793.6	37																																																																																					0.517	VPS11-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021729		13	23	13	23
SLC2A3	6515	broad.mit.edu;ucsc.edu	37	12	8083869	8083869	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr12:8083869C>T	ENST00000075120.7	-	4	722	c.482G>A	c.(481-483)gGc>gAc	p.G161D		NM_006931.2	NP_008862.1	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 3	161					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(14)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				Kidney(36;0.0866)		AACAACGATGCCCAGCTGGTT	0.488																																					Colon(96;424 1461 14416 20933 23688)											0													73.0	70.0	71.0					12																	8083869		2203	4300	6503	SO:0001583	missense	6515			M20681	CCDS8586.1	12p13.3	2013-05-22			ENSG00000059804	ENSG00000059804		"""Solute carriers"""	11007	protein-coding gene	gene with protein product		138170		GLUT3			Standard	NM_006931		Approved		uc001qtr.3	P11169	OTTHUMG00000133685	ENST00000075120.7:c.482G>A	12.37:g.8083869C>T	ENSP00000075120:p.Gly161Asp		B2R606|D3DUU6|Q6I9U2|Q9UG15	Missense_Mutation	SNP	ENST00000075120.7	37	CCDS8586.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.878659	0.51801	.	.	ENSG00000059804	ENST00000075120;ENST00000540978;ENST00000544291	D;D	0.83335	-1.71;-1.71	4.37	3.45	0.39498	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.048354	0.85682	D	0.000000	D	0.92034	0.7476	M	0.93978	3.48	0.54753	D	0.999981	D;D	0.62365	0.989;0.991	D;D	0.72625	0.949;0.978	D	0.91800	0.5451	10	0.36615	T	0.2	.	12.0028	0.53241	0.0:0.8235:0.1765:0.0	.	87;161	F5H2H8;P11169	.;GTR3_HUMAN	D	161;87;130	ENSP00000075120:G161D;ENSP00000440750:G130D	ENSP00000075120:G161D	G	-	2	0	SLC2A3	7975136	1.000000	0.71417	1.000000	0.80357	0.302000	0.27658	5.157000	0.64911	1.138000	0.42230	0.555000	0.69702	GGC		0.488	SLC2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257914.1	NM_006931		26	104	26	104
KRT19P2	160313	broad.mit.edu;ucsc.edu	37	12	95228505	95228505	+	RNA	SNP	G	G	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr12:95228505G>A	ENST00000405395.2	+	0	276				MIR492_ENST00000385303.1_RNA	NR_036685.1				keratin 19 pseudogene 2																		TGAGTGACAGGCAAAGCCAAT	0.552																																																0																																												160313					12q22	2013-06-25			ENSG00000216306	ENSG00000216306			33423	pseudogene	pseudogene			"""keratin 19 pseudogene 5"""	KRT19P5			Standard	NR_036685		Approved		uc001tdk.2		OTTHUMG00000170700		12.37:g.95228505G>A				RNA	SNP	ENST00000405395.2	37																																																																																					0.552	KRT19P2-002	PUTATIVE	basic	processed_transcript	pseudogene	OTTHUMT00000410053.1	NT_019546		8	5	8	5
OR3A4P	390756	broad.mit.edu;ucsc.edu	37	17	3213993	3213993	+	RNA	SNP	G	G	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr17:3213993G>A	ENST00000573491.1	-	0	359																											CTGGCCATCTGCCAGTCCCTC	0.562																																																0													77.0	79.0	78.0					17																	3213993		2203	4300	6503			0																															17.37:g.3213993G>A				RNA	SNP	ENST00000573491.1	37																																																																																					0.562	RP11-64J4.2-001	KNOWN	basic	sense_overlapping	sense_overlapping	OTTHUMT00000438371.1			42	80	42	80
HERC2P3	283755	broad.mit.edu;ucsc.edu	37	15	20644046	20644046	+	RNA	SNP	G	G	A	rs375784648		TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr15:20644046G>A	ENST00000428453.1	-	0	3413							Q9BVR0	HRC23_HUMAN	hect domain and RLD 2 pseudogene 3								metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(1)|lung(14)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35						CAGGGTTCTCGGAATCAGGGA	0.597																																																0								G		1,4383		0,1,2191	44.0	35.0	38.0			-5.0	0.6	15		38	1,8549		0,1,4274	no	intergenic				0,2,6465	AA,AG,GG		0.0117,0.0228,0.0155			20644046	2,12932	2192	4275	6467			283755			AF041081		15q11.2	2010-08-02			ENSG00000180229	ENSG00000180229			4871	pseudogene	pseudogene						9730612	Standard	NR_036432		Approved	D15F37S4, LOC283755	uc001ytg.3	Q9BVR0	OTTHUMG00000157175		15.37:g.20644046G>A				RNA	SNP	ENST00000428453.1	37																																																																																					0.597	HERC2P3-014	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000347772.2	NG_008269		16	20	16	20
OLFM1	10439	broad.mit.edu;ucsc.edu	37	9	137998621	137998621	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr9:137998621G>A	ENST00000371793.3	+	5	954	c.703G>A	c.(703-705)Gac>Aac	p.D235N	OLFM1_ENST00000371796.3_Missense_Mutation_p.D208N|OLFM1_ENST00000252854.4_Missense_Mutation_p.D217N	NM_001282611.1	NP_001269540.1	Q99784	NOE1_HUMAN	olfactomedin 1	235	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of neuron migration (GO:2001223)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)	21		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)		GGGCATCAGTGACCCCGTGAC	0.637																																																0													75.0	63.0	67.0					9																	137998621		2203	4300	6503	SO:0001583	missense	10439			AF035301	CCDS6986.1, CCDS6987.1, CCDS65183.1, CCDS65184.1	9q34.3	2014-01-20			ENSG00000130558	ENSG00000130558			17187	protein-coding gene	gene with protein product	"""pancortin"""	605366				9039501	Standard	NM_006334		Approved	NOE1, OlfA, AMY, NOELIN	uc004cfl.4	Q99784	OTTHUMG00000020897	ENST00000371793.3:c.703G>A	9.37:g.137998621G>A	ENSP00000360858:p.Asp235Asn		Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	Missense_Mutation	SNP	ENST00000371793.3	37		.	.	.	.	.	.	.	.	.	.	G	17.21	3.332599	0.60853	.	.	ENSG00000130558	ENST00000252854;ENST00000371796;ENST00000371793;ENST00000539877	D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4	4.75	4.75	0.60458	Olfactomedin-like (3);	0.101398	0.64402	D	0.000003	T	0.81847	0.4909	N	0.10645	0.015	0.80722	D	1	B;B	0.31655	0.334;0.002	B;B	0.40444	0.329;0.014	T	0.78339	-0.2242	10	0.15066	T	0.55	.	17.75	0.88430	0.0:0.0:1.0:0.0	.	235;217	Q99784;Q6IMJ8	NOE1_HUMAN;.	N	217;208;235;132	ENSP00000252854:D217N;ENSP00000360861:D208N;ENSP00000360858:D235N;ENSP00000443806:D132N	ENSP00000252854:D217N	D	+	1	0	OLFM1	137138442	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.613000	0.74192	2.147000	0.66899	0.561000	0.74099	GAC		0.637	OLFM1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000054974.1	NM_014279		9	25	9	25
PIK3R1	5295	broad.mit.edu;hgsc.bcm.edu	37	5	67589632	67589634	+	In_Frame_Del	DEL	ATT	ATT	-			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr5:67589632_67589634delATT	ENST00000521381.1	+	11	2011_2013	c.1395_1397delATT	c.(1393-1398)agatta>aga	p.L466del	PIK3R1_ENST00000320694.8_In_Frame_Del_p.L166del|PIK3R1_ENST00000336483.5_In_Frame_Del_p.L196del|PIK3R1_ENST00000396611.1_In_Frame_Del_p.L466del|PIK3R1_ENST00000521657.1_In_Frame_Del_p.L466del|PIK3R1_ENST00000274335.5_In_Frame_Del_p.L466del|PIK3R1_ENST00000523872.1_In_Frame_Del_p.L103del	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	466					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|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)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|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 cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.Y463_L466del(1)|p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AATATGATAGATTATATGAAGAA	0.291			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	3	Whole gene deletion(1)|Deletion - In frame(1)|Unknown(1)	large_intestine(1)|lung(1)|endometrium(1)																																								SO:0001651	inframe_deletion	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1395_1397delATT	5.37:g.67589632_67589634delATT	ENSP00000428056:p.Leu466del		B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	In_Frame_Del	DEL	ENST00000521381.1	37	CCDS3993.1																																																																																				0.291	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		14	50	14	50
FAM135B	51059	broad.mit.edu;hgsc.bcm.edu	37	8	139158292	139158292	+	Splice_Site	DEL	C	C	-			TCGA-CS-6188-01A-11D-1893-08	TCGA-CS-6188-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	adacd0a6-53f0-46c1-9f59-e30cb1b56164	1026b480-665c-4646-8fec-982cc07dca1e	g.chr8:139158292delC	ENST00000395297.1	-	15	3620	c.3450delG	c.(3448-3450)ggg>gg	p.G1150fs		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1150										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CTGCACTGTTCCCTAAAAATG	0.448										HNSCC(54;0.14)																																						0													81.0	86.0	84.0					8																	139158292		2203	4300	6503	SO:0001630	splice_region_variant	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3449-1G>-	8.37:g.139158292delC			B5MDB3|O95879|Q2WGJ7|Q3KP46	Splice_Site	DEL	ENST00000395297.1	37	CCDS6375.2																																																																																				0.448	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	Frame_Shift_Del	32	97	32	97
