#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
PDE6C	5146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	95381756	95381756	+	Missense_Mutation	SNP	C	C	T	rs143673530		TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr10:95381756C>T	ENST00000371447.3	+	4	929	c.791C>T	c.(790-792)gCg>gTg	p.A264V		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	264	GAF 2.				phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	TTTCACAAAGCGCTCTACACG	0.388													C|||	1	0.000199681	0.0	0.0	5008	,	,		19526	0.0		0.0	False		,,,				2504	0.001															0								C	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	162.0	147.0	152.0		791	4.0	0.9	10	dbSNP_134	152	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PDE6C	NM_006204.3	64	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	probably-damaging	264/859	95381756	3,13003	2203	4300	6503	SO:0001583	missense	5146			U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.791C>T	10.37:g.95381756C>T	ENSP00000360502:p.Ala264Val		A6NCR6|Q5VY29	Missense_Mutation	SNP	ENST00000371447.3	37	CCDS7429.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.725480	0.48833	4.54E-4	1.16E-4	ENSG00000095464	ENST00000371447	T	0.64803	-0.12	4.85	3.95	0.45737	GAF (2);	0.099518	0.64402	N	0.000002	T	0.53126	0.1777	M	0.65975	2.015	0.80722	D	1	P	0.37370	0.592	B	0.29077	0.098	T	0.53136	-0.8481	10	0.12766	T	0.61	.	13.5343	0.61639	0.0:0.9243:0.0:0.0757	.	264	P51160	PDE6C_HUMAN	V	264	ENSP00000360502:A264V	ENSP00000360502:A264V	A	+	2	0	PDE6C	95371746	1.000000	0.71417	0.860000	0.33809	0.940000	0.58332	4.789000	0.62446	1.406000	0.46857	0.561000	0.74099	GCG		0.388	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204		38	69	38	69
OR4A5	81318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	51411931	51411931	+	Silent	SNP	C	C	T	rs140587389	byFrequency	TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr11:51411931C>T	ENST00000319760.6	-	1	517	c.465G>A	c.(463-465)gcG>gcA	p.A155A		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A155A(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				CAATTTGAAACGCAGAATGTA	0.453													.|||	3	0.000599042	0.0008	0.0	5008	,	,		21566	0.002		0.0	False		,,,				2504	0.0															1	Substitution - coding silent(1)	NS(1)						C		3,4399		0,3,2198	86.0	78.0	81.0		465	0.9	0.0	11	dbSNP_134	81	1,8591		0,1,4295	no	coding-synonymous	OR4A5	NM_001005272.3		0,4,6493	TT,TC,CC		0.0116,0.0682,0.0308		155/316	51411931	4,12990	2201	4296	6497	SO:0001819	synonymous_variant	81318			AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.465G>A	11.37:g.51411931C>T			Q6IF84	Silent	SNP	ENST00000319760.6	37	CCDS31497.1																																																																																				0.453	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		28	41	28	41
IQSEC3	440073	hgsc.bcm.edu;ucsc.edu	37	12	280470	280470	+	Intron	SNP	A	A	T			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr12:280470A>T	ENST00000538872.1	+	13	3232				IQSEC3_ENST00000382841.2_Missense_Mutation_p.I755F|IQSEC3_ENST00000537151.1_Intron|IQSEC3_ENST00000326261.4_Intron|RP11-598F7.6_ENST00000537295.1_lincRNA			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3						actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		AAGAGATACAATTAAAAGTTA	0.493																																																0													161.0	160.0	160.0					12																	280470		2203	4300	6503	SO:0001627	intron_variant	440073			AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.3114+143A>T	12.37:g.280470A>T			A6NIF2|A6NKV9|Q8TB43	Missense_Mutation	SNP	ENST00000538872.1	37	CCDS53728.1	.	.	.	.	.	.	.	.	.	.	A	16.50	3.139922	0.56936	.	.	ENSG00000120645	ENST00000382841	T	0.10477	2.87	4.3	3.16	0.36331	.	.	.	.	.	T	0.12092	0.0294	.	.	.	0.80722	D	1	P	0.35908	0.527	B	0.40602	0.334	T	0.05920	-1.0856	8	0.46703	T	0.11	.	8.5324	0.33342	0.9109:0.0:0.0891:0.0	.	755	Q9UPP2-2	.	F	755	ENSP00000372292:I755F	ENSP00000372292:I755F	I	+	1	0	IQSEC3	150731	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.941000	0.56607	0.694000	0.31654	-0.411000	0.06167	ATT		0.493	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902		70	111	70	111
C12orf10	60314	hgsc.bcm.edu;ucsc.edu	37	12	53693542	53693542	+	Silent	SNP	C	C	G			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr12:53693542C>G	ENST00000267103.5	+	1	73	c.21C>G	c.(19-21)cgC>cgG	p.R7R	C12orf10_ENST00000548632.1_5'UTR|C12orf10_ENST00000549488.1_5'Flank|RP11-680A11.5_ENST00000550263.1_RNA	NM_021640.3	NP_067653	Q9HB07	MYG1_HUMAN	chromosome 12 open reading frame 10	7					locomotory exploration behavior (GO:0035641)|pigmentation (GO:0043473)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				cervix(1)|endometrium(3)|kidney(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	20						AATTCCTGCGCGGCCTCTTAA	0.672											OREG0021864	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													20.0	21.0	20.0					12																	53693542		2203	4298	6501	SO:0001819	synonymous_variant	0			AF289485	CCDS31810.1	12q13.13	2014-05-29			ENSG00000139637	ENSG00000139637			17590	protein-coding gene	gene with protein product	"""melanocyte related gene"", ""melanocyte proliferating gene 1"""	611366					Standard	NM_021640		Approved	MYG, MYG1, Gamm1	uc001scp.4	Q9HB07	OTTHUMG00000170030	ENST00000267103.5:c.21C>G	12.37:g.53693542C>G		994		Silent	SNP	ENST00000267103.5	37	CCDS31810.1																																																																																				0.672	C12orf10-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406906.1	NM_021640		8	15	8	15
DNAH10	196385	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	124358200	124358200	+	Silent	SNP	C	C	T	rs369269297		TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr12:124358200C>T	ENST00000409039.3	+	45	7552	c.7527C>T	c.(7525-7527)taC>taT	p.Y2509Y		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2509	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AAGATACTTACGGCCCACCCA	0.473																																																0								C		0,3856		0,0,1928	59.0	56.0	57.0		7527	-8.0	0.0	12		57	9,8273		0,9,4132	no	coding-synonymous	DNAH10	NM_207437.3		0,9,6060	TT,TC,CC		0.1087,0.0,0.0741		2509/4472	124358200	9,12129	1928	4141	6069	SO:0001819	synonymous_variant	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.7527C>T	12.37:g.124358200C>T			C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																				0.473	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			6	14	6	14
PCDH9	5101	hgsc.bcm.edu;broad.mit.edu	37	13	67800158	67800158	+	Silent	SNP	T	T	C			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr13:67800158T>C	ENST00000377865.2	-	1	2549	c.2415A>G	c.(2413-2415)caA>caG	p.Q805Q	PCDH9_ENST00000328454.5_Silent_p.Q805Q|PCDH9_ENST00000544246.1_Silent_p.Q805Q|PCDH9_ENST00000456367.1_Silent_p.Q805Q|PCDH9_ENST00000377861.3_Silent_p.Q805Q			Q9HC56	PCDH9_HUMAN	protocadherin 9	805					forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		TTTGATAGGGTTGGCTACTAT	0.483																																																0													235.0	213.0	220.0					13																	67800158		2203	4300	6503	SO:0001819	synonymous_variant	5101			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.2415A>G	13.37:g.67800158T>C			A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Silent	SNP	ENST00000377865.2	37	CCDS9444.1																																																																																				0.483	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		16	216	16	216
SLFN11	91607	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	33679774	33679774	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr17:33679774C>T	ENST00000394566.1	-	7	2579	c.2307G>A	c.(2305-2307)tgG>tgA	p.W769*	SLFN11_ENST00000308377.4_Nonsense_Mutation_p.W769*	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	769					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CACCCTGGGACCATTCGGCTT	0.443																																																0													66.0	62.0	63.0					17																	33679774		2203	4300	6503	SO:0001587	stop_gained	91607			AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.2307G>A	17.37:g.33679774C>T	ENSP00000378067:p.Trp769*		E1P643|Q8N3S8|Q8N762|Q8TEE0	Nonsense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	.	.	.	.	.	.	.	.	.	.	c	38	6.961096	0.97964	.	.	ENSG00000172716	ENST00000308377;ENST00000394566	.	.	.	3.85	3.85	0.44370	.	0.000000	0.45606	D	0.000357	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.4779	0.50308	0.0:1.0:0.0:0.0	.	.	.	.	X	769	.	ENSP00000312402:W769X	W	-	3	0	SLFN11	30703887	0.403000	0.25319	0.264000	0.24511	0.051000	0.14879	1.241000	0.32743	2.144000	0.66660	0.655000	0.94253	TGG		0.443	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		20	37	20	37
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	42798840	42798840	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr19:42798840G>A	ENST00000575354.2	+	19	4452	c.4412G>A	c.(4411-4413)cGg>cAg	p.R1471Q	CIC_ENST00000572681.2_Missense_Mutation_p.R2377Q|CIC_ENST00000160740.3_Missense_Mutation_p.R1469Q	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1471					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				GACCAGCGCCGGGCCCTGGTC	0.612			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0													72.0	71.0	71.0					19																	42798840		2203	4300	6503	SO:0001583	missense	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4412G>A	19.37:g.42798840G>A	ENSP00000458663:p.Arg1471Gln		Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.986595	0.93106	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.59	4.59	0.56863	.	.	.	.	.	T	0.64125	0.2570	L	0.29908	0.895	0.45403	D	0.998388	D	0.71674	0.998	D	0.66602	0.945	T	0.67979	-0.5530	8	0.87932	D	0	-10.608	15.2728	0.73717	0.0:0.0:1.0:0.0	.	1471	Q96RK0	CIC_HUMAN	Q	1471	.	ENSP00000160740:R1471Q	R	+	2	0	CIC	47490680	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.532000	0.90613	2.570000	0.86706	0.491000	0.48974	CGG		0.612	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			36	28	36	28
ZNF347	84671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	53652555	53652555	+	Silent	SNP	G	G	A	rs201753900		TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr19:53652555G>A	ENST00000334197.7	-	3	149	c.81C>T	c.(79-81)ccC>ccT	p.P27P	ZNF347_ENST00000601469.2_Silent_p.P27P|ZNF347_ENST00000452676.2_Silent_p.P27P|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	27	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P27P(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		TCCTCTGAGCGGGGTCCAGGC	0.502																																					Melanoma(64;205 1597 17324 45721)											1	Substitution - coding silent(1)	lung(1)											108.0	110.0	110.0					19																	53652555		2203	4300	6503	SO:0001819	synonymous_variant	84671			AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"""Zinc fingers, C2H2-type"", ""-"""	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.81C>T	19.37:g.53652555G>A			B3KU77|B9EG59|G5E9N4|Q8TCN1	Silent	SNP	ENST00000334197.7	37	CCDS33097.1																																																																																				0.502	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		54	57	54	57
LILRA2	11027	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	55086389	55086389	+	Missense_Mutation	SNP	G	G	A	rs559006483		TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr19:55086389G>A	ENST00000251377.3	+	5	677	c.544G>A	c.(544-546)Gtg>Atg	p.V182M	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA2_ENST00000251376.3_Missense_Mutation_p.V182M|LILRA2_ENST00000391737.1_Missense_Mutation_p.V170M|LILRB1_ENST00000418536.2_Intron|LILRA2_ENST00000391738.3_Missense_Mutation_p.V182M			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	182	Ig-like C2-type 2.				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)	p.V182M(1)		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)		CATCTTCTCCGTGGGCCCCGT	0.562													g|||	1	0.000199681	0.0	0.0	5008	,	,		19311	0.001		0.0	False		,,,				2504	0.0															1	Substitution - Missense(1)	prostate(1)											152.0	145.0	147.0					19																	55086389		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.544G>A	19.37:g.55086389G>A	ENSP00000251377:p.Val182Met		O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.225497	0.39300	.	.	ENSG00000239998	ENST00000439534;ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T;T	0.00792	5.69;5.69;5.69;5.69;5.69	2.93	-2.33	0.06724	Immunoglobulin-like fold (1);	0.499376	0.16837	N	0.197508	T	0.01489	0.0048	L	0.52905	1.665	0.09310	N	0.999999	D;D;D;D	0.89917	0.979;0.998;1.0;0.999	B;P;P;P	0.59643	0.314;0.846;0.846;0.861	T	0.47598	-0.9105	9	.	.	.	.	2.4237	0.04455	0.2676:0.0:0.3204:0.412	.	182;170;182;182	E9PDF4;A8MZH0;Q8N149;Q8N149-2	.;.;LIRA2_HUMAN;.	M	182;182;182;182;170	ENSP00000388131:V182M;ENSP00000251377:V182M;ENSP00000375618:V182M;ENSP00000251376:V182M;ENSP00000375617:V170M	.	V	+	1	0	LILRA2	59778201	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.035000	0.12205	-0.212000	0.10109	-0.442000	0.05670	GTG		0.562	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			67	50	67	50
OR10J5	127385	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	159505463	159505463	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr1:159505463C>T	ENST00000334857.2	-	1	379	c.335G>A	c.(334-336)tGc>tAc	p.C112Y		NM_001004469.1	NP_001004469.1	Q8NHC4	O10J5_HUMAN	olfactory receptor, family 10, subfamily J, member 5	112						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	22	all_hematologic(112;0.0429)					AAGCAGGAAGCAATTATTAGT	0.468																																																0													120.0	104.0	110.0					1																	159505463		2203	4300	6503	SO:0001583	missense	127385				CCDS30910.1	1q23.2	2012-08-09			ENSG00000184155	ENSG00000184155		"""GPCR / Class A : Olfactory receptors"""	14993	protein-coding gene	gene with protein product							Standard	NM_001004469		Approved		uc010piw.2	Q8NHC4	OTTHUMG00000022738	ENST00000334857.2:c.335G>A	1.37:g.159505463C>T	ENSP00000334441:p.Cys112Tyr		B9EH35|Q6IFH2	Missense_Mutation	SNP	ENST00000334857.2	37	CCDS30910.1	.	.	.	.	.	.	.	.	.	.	C	4.132	0.022855	0.08006	.	.	ENSG00000184155	ENST00000334857	T	0.02121	4.44	4.32	3.38	0.38709	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.02083	0.0065	M	0.84683	2.71	0.09310	N	1	B	0.31859	0.343	B	0.36030	0.216	T	0.33650	-0.9860	9	0.66056	D	0.02	.	7.453	0.27250	0.1913:0.6235:0.1852:0.0	.	112	Q8NHC4	O10J5_HUMAN	Y	112	ENSP00000334441:C112Y	ENSP00000334441:C112Y	C	-	2	0	OR10J5	157772087	0.000000	0.05858	0.901000	0.35422	0.107000	0.19398	-0.739000	0.04866	1.132000	0.42129	0.467000	0.42956	TGC		0.468	OR10J5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059021.1	NM_001004469		48	60	48	60
GGA1	26088	hgsc.bcm.edu;broad.mit.edu	37	22	38014515	38014515	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr22:38014515C>T	ENST00000343632.4	+	4	651	c.265C>T	c.(265-267)Cgc>Tgc	p.R89C	GGA1_ENST00000405147.3_Missense_Mutation_p.R89C|GGA1_ENST00000381756.5_Missense_Mutation_p.R106C|GGA1_ENST00000337437.4_Intron|GGA1_ENST00000406772.1_Missense_Mutation_p.R16C|GGA1_ENST00000325180.8_Missense_Mutation_p.R89C	NM_001172687.1|NM_013365.4	NP_001166158.1|NP_037497.1	Q9UJY5	GGA1_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 1	89	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				intracellular protein transport (GO:0006886)|positive regulation of protein catabolic process (GO:0045732)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	10	Melanoma(58;0.0574)					GGGCAAGTTCCGCTTTCTCAA	0.617																																																0													141.0	97.0	112.0					22																	38014515		2203	4300	6503	SO:0001583	missense	26088			AF190862	CCDS13951.1, CCDS33643.1, CCDS54526.1	22q13.31	2010-02-12	2010-02-12		ENSG00000100083	ENSG00000100083			17842	protein-coding gene	gene with protein product		606004				10747088, 10747089, 16407204	Standard	NM_013365		Approved		uc003atc.3	Q9UJY5	OTTHUMG00000030985	ENST00000343632.4:c.265C>T	22.37:g.38014515C>T	ENSP00000341344:p.Arg89Cys		A8K3D3|B0QYR7|Q5TG07|Q86YA9|Q8NCS6|Q9BW94|Q9UG00|Q9UGW0|Q9UGW1	Missense_Mutation	SNP	ENST00000343632.4	37	CCDS13951.1	.	.	.	.	.	.	.	.	.	.	C	35	5.507971	0.96386	.	.	ENSG00000100083	ENST00000343632;ENST00000381756;ENST00000405147;ENST00000429218;ENST00000325180;ENST00000439161;ENST00000449944;ENST00000411501;ENST00000453208;ENST00000447515;ENST00000406772;ENST00000431745;ENST00000326597;ENST00000413251;ENST00000423024	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88	5.35	5.35	0.76521	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.000000	0.85682	D	0.000000	T	0.64962	0.2646	H	0.94385	3.53	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.76146	-0.3066	10	0.87932	D	0	-24.1768	19.0552	0.93062	0.0:1.0:0.0:0.0	.	106;89;89	Q6IC75;Q86YA9;Q9UJY5	.;.;GGA1_HUMAN	C	89;106;89;16;89;16;81;16;16;16;16;16;16;16;16	ENSP00000341344:R89C;ENSP00000371175:R106C;ENSP00000384030:R89C;ENSP00000403534:R16C;ENSP00000321288:R89C;ENSP00000404453:R16C;ENSP00000390416:R81C;ENSP00000400159:R16C;ENSP00000416153:R16C;ENSP00000411727:R16C;ENSP00000385287:R16C;ENSP00000402930:R16C;ENSP00000411373:R16C;ENSP00000414413:R16C	ENSP00000321288:R89C	R	+	1	0	GGA1	36344461	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.981000	0.70524	2.507000	0.84556	0.655000	0.94253	CGC		0.617	GGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075873.3	NM_013365		4	59	4	59
CELSR1	9620	hgsc.bcm.edu;broad.mit.edu	37	22	46790148	46790148	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr22:46790148G>A	ENST00000262738.3	-	14	5854	c.5855C>T	c.(5854-5856)cCg>cTg	p.P1952L		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1952	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TCTGGGGCACGGAAGGTCGAG	0.562																																																0													40.0	39.0	39.0					22																	46790148		2203	4300	6503	SO:0001583	missense	9620			AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.5855C>T	22.37:g.46790148G>A	ENSP00000262738:p.Pro1952Leu		O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.466108	0.63625	.	.	ENSG00000075275	ENST00000262738	D	0.91124	-2.79	3.47	3.47	0.39725	.	0.000000	0.64402	U	0.000002	D	0.93877	0.8041	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.74023	0.982;0.767	D	0.93579	0.6911	10	0.42905	T	0.14	.	14.9317	0.70919	0.0:0.0:1.0:0.0	.	273;1952	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	L	1952	ENSP00000262738:P1952L	ENSP00000262738:P1952L	P	-	2	0	CELSR1	45168812	1.000000	0.71417	0.991000	0.47740	0.425000	0.31504	7.071000	0.76770	1.663000	0.50791	0.462000	0.41574	CCG		0.562	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		5	52	5	52
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			55	76	55	76
GLB1L	79411	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	220103270	220103270	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr2:220103270G>A	ENST00000295759.7	-	13	1487	c.1174C>T	c.(1174-1176)Ccc>Tcc	p.P392S	GLB1L_ENST00000409640.1_Missense_Mutation_p.P302S|GLB1L_ENST00000356283.3_Missense_Mutation_p.P302S|GLB1L_ENST00000497855.1_5'UTR|GLB1L_ENST00000392089.2_Missense_Mutation_p.P392S			Q6UWU2	GLB1L_HUMAN	galactosidase, beta 1-like	392					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		all_lung(227;1.19e-05)|Lung NSC(271;2.76e-05)|Medulloblastoma(418;0.0208)|Esophageal squamous(248;0.0559)		Epithelial(149;1.3e-11)|all cancers(144;2.07e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGCCCACGGGGGCAAAGCAAG	0.448																																																0													84.0	88.0	87.0					2																	220103270		2203	4300	6503	SO:0001583	missense	79411				CCDS2437.1, CCDS74657.1	2q36.1	2008-02-05			ENSG00000163521	ENSG00000163521			28129	protein-coding gene	gene with protein product						12975309	Standard	XM_005246850		Approved	MGC10771	uc002vkm.3	Q6UWU2	OTTHUMG00000133133	ENST00000295759.7:c.1174C>T	2.37:g.220103270G>A	ENSP00000295759:p.Pro392Ser		Q96DR0	Missense_Mutation	SNP	ENST00000295759.7	37	CCDS2437.1	.	.	.	.	.	.	.	.	.	.	G	11.30	1.599018	0.28534	.	.	ENSG00000163521	ENST00000295759;ENST00000409640;ENST00000392089;ENST00000356283	D;D;D;D	0.97138	-4.26;-4.02;-4.26;-4.02	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.97185	0.9080	L	0.45352	1.415	0.80722	D	1	D;P	0.89917	1.0;0.709	D;B	0.91635	0.999;0.156	D	0.94620	0.7812	10	0.08381	T	0.77	-14.0655	18.8727	0.92322	0.0:0.0:1.0:0.0	.	302;392	Q6UWU2-2;Q6UWU2	.;GLB1L_HUMAN	S	392;302;392;302	ENSP00000295759:P392S;ENSP00000386354:P302S;ENSP00000375939:P392S;ENSP00000348628:P302S	ENSP00000295759:P392S	P	-	1	0	GLB1L	219811514	1.000000	0.71417	0.948000	0.38648	0.037000	0.13140	8.344000	0.90055	2.779000	0.95612	0.655000	0.94253	CCC		0.448	GLB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256822.2	NM_024506		41	93	41	93
PIK3CA	5290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	178916645	178916645	+	Missense_Mutation	SNP	G	G	C			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr3:178916645G>C	ENST00000263967.3	+	2	189	c.32G>C	c.(31-33)tGg>tCg	p.W11S		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	11					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.W11L(2)|p.L10_M16del(1)|p.E9_R19del(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GGTGAACTGTGGGGCATCCAC	0.403		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	4	Substitution - Missense(2)|Deletion - In frame(2)	lung(2)|central_nervous_system(2)											52.0	52.0	52.0					3																	178916645		1856	4093	5949	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.32G>C	3.37:g.178916645G>C	ENSP00000263967:p.Trp11Ser		Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.077117	0.76415	.	.	ENSG00000121879	ENST00000477735;ENST00000263967;ENST00000468036	T;D	0.83837	-1.42;-1.77	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.91243	0.7240	M	0.78456	2.415	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.90403	0.4404	10	0.40728	T	0.16	-23.3132	19.1062	0.93296	0.0:0.0:1.0:0.0	.	11	P42336	PK3CA_HUMAN	S	11	ENSP00000263967:W11S;ENSP00000417479:W11S	ENSP00000263967:W11S	W	+	2	0	PIK3CA	180399339	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.409000	0.97331	2.506000	0.84524	0.650000	0.86243	TGG		0.403	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			34	42	34	42
PCDH7	5099	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	30725853	30725853	+	Missense_Mutation	SNP	G	G	C			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr4:30725853G>C	ENST00000361762.2	+	1	3817	c.2809G>C	c.(2809-2811)Gac>Cac	p.D937H	PCDH7_ENST00000543491.1_Missense_Mutation_p.D937H	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	937					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						GCCTAAAAAGGACAAGAAAAA	0.398																																																0													82.0	84.0	83.0					4																	30725853		2203	4300	6503	SO:0001583	missense	5099			AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"""Cadherins / Protocadherins : Non-clustered"""	8659	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 120"""	602988	"""BH-protocadherin (brain-heart)"""			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.2809G>C	4.37:g.30725853G>C	ENSP00000355243:p.Asp937His		O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	37	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.35|16.35	3.099395|3.099395	0.56183|0.56183	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000361762;ENST00000543491;ENST00000333135|ENST00000511884	T;T|.	0.33216|.	1.42;1.42|.	5.16|5.16	5.16|5.16	0.70880|0.70880	Protocadherin (1);|.	.|.	.|.	.|.	.|.	T|T	0.67776|0.67776	0.2929|0.2929	L|L	0.44542|0.44542	1.39|1.39	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D|.	0.89917|.	1.0;0.999;1.0|.	D;D;D|.	0.74674|.	0.982;0.973;0.984|.	T|T	0.63310|0.63310	-0.6666|-0.6666	9|5	0.48119|.	T|.	0.1|.	.|.	18.8391|18.8391	0.92174|0.92174	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	937;890;937|.	F5GWJ1;O60245-3;O60245|.	.;.;PCDH7_HUMAN|.	H|A	937;937;890|626	ENSP00000355243:D937H;ENSP00000441802:D937H|.	ENSP00000330302:D890H|.	D|G	+|+	1|2	0|0	PCDH7|PCDH7	30334951|30334951	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.445000|7.445000	0.80570|0.80570	2.683000|2.683000	0.91414|0.91414	0.655000|0.655000	0.94253|0.94253	GAC|GGA		0.398	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		14	39	14	39
EPHX2	2053	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	27401706	27401706	+	Missense_Mutation	SNP	C	C	A			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr8:27401706C>A	ENST00000521400.1	+	18	1964	c.1534C>A	c.(1534-1536)Ccc>Acc	p.P512T	EPHX2_ENST00000517536.1_Missense_Mutation_p.P329T|EPHX2_ENST00000518379.1_Missense_Mutation_p.P480T|EPHX2_ENST00000380476.3_Missense_Mutation_p.P459T|EPHX2_ENST00000521780.1_Missense_Mutation_p.P446T	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	512	Epoxide hydrolase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		CTTTCAGATTCCCCACCTGAA	0.572																																																0													140.0	132.0	135.0					8																	27401706		2203	4300	6503	SO:0001583	missense	2053			L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.1534C>A	8.37:g.27401706C>A	ENSP00000430269:p.Pro512Thr		B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Missense_Mutation	SNP	ENST00000521400.1	37	CCDS6060.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.221642	0.58560	.	.	ENSG00000120915	ENST00000521400;ENST00000517536;ENST00000521780;ENST00000380476;ENST00000415449;ENST00000518379	T;T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36;-0.36	4.05	4.05	0.47172	Alpha/beta hydrolase fold-1 (1);	0.108905	0.64402	D	0.000005	T	0.80660	0.4665	M	0.80616	2.505	0.58432	D	0.999996	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.983	T	0.82133	-0.0608	10	0.59425	D	0.04	0.0162	12.0213	0.53344	0.0:1.0:0.0:0.0	.	480;512	E5RFU2;P34913	.;HYES_HUMAN	T	512;329;446;459;459;480	ENSP00000430269:P512T;ENSP00000428875:P329T;ENSP00000430302:P446T;ENSP00000369843:P459T;ENSP00000427956:P480T	ENSP00000369843:P459T	P	+	1	0	EPHX2	27457623	0.995000	0.38212	1.000000	0.80357	0.865000	0.49528	4.763000	0.62257	2.549000	0.85964	0.491000	0.48974	CCC		0.572	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4			69	173	69	173
ABCA1	19	hgsc.bcm.edu;broad.mit.edu	37	9	107645364	107645364	+	Missense_Mutation	SNP	C	C	T	rs138438101		TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr9:107645364C>T	ENST00000374736.3	-	5	771	c.377G>A	c.(376-378)cGc>cAc	p.R126H	ABCA1_ENST00000374733.1_Missense_Mutation_p.R66H|ABCA1_ENST00000423487.2_Missense_Mutation_p.R126H	NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	126					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.R126H(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CAGAACTTTGCGCATGTCCTT	0.453																																																1	Substitution - Missense(1)	large_intestine(1)						C	HIS/ARG	0,4406		0,0,2203	167.0	157.0	160.0		377	1.9	0.6	9	dbSNP_134	160	1,8599	1.2+/-3.3	0,1,4299	no	missense	ABCA1	NM_005502.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	126/2262	107645364	1,13005	2203	4300	6503	SO:0001583	missense	19			AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.377G>A	9.37:g.107645364C>T	ENSP00000363868:p.Arg126His		Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	C	8.006	0.756436	0.15846	0.0	1.16E-4	ENSG00000165029	ENST00000374736;ENST00000423487;ENST00000374733	D;D;D	0.95918	-3.85;-3.85;-3.85	5.49	1.88	0.25563	.	0.567931	0.21605	N	0.071891	D	0.86690	0.5993	N	0.08118	0	0.26805	N	0.969127	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.75010	-0.3468	10	0.24483	T	0.36	.	8.7159	0.34411	0.0:0.2302:0.0:0.7698	.	66;126	B1AMI1;O95477	.;ABCA1_HUMAN	H	126;126;66	ENSP00000363868:R126H;ENSP00000416623:R126H;ENSP00000363865:R66H	ENSP00000363865:R66H	R	-	2	0	ABCA1	106685185	0.361000	0.24972	0.569000	0.28460	0.859000	0.49053	1.329000	0.33770	0.132000	0.18615	-0.302000	0.09304	CGC		0.453	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		6	75	6	75
CDK12	51755	broad.mit.edu;ucsc.edu	37	17	37676268	37676268	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr17:37676268G>A	ENST00000447079.4	+	11	3056	c.3023G>A	c.(3022-3024)cGg>cAg	p.R1008Q	CDK12_ENST00000430627.2_Missense_Mutation_p.R1008Q	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1008	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						CCTAGTAAGCGGTGCACAGCT	0.473			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)																													Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	0													215.0	180.0	192.0					17																	37676268		2203	4300	6503	SO:0001583	missense	51755			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.3023G>A	17.37:g.37676268G>A	ENSP00000398880:p.Arg1008Gln		A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	G	32	5.115609	0.94339	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.74632	-0.86;-0.86	5.56	5.56	0.83823	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.39210	N	0.001440	D	0.92805	0.7712	H	0.99357	4.53	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.996	D	0.95608	0.8669	10	0.87932	D	0	-5.6033	19.5353	0.95251	0.0:0.0:1.0:0.0	.	1007;1008;1008	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	Q	1008	ENSP00000407720:R1008Q;ENSP00000398880:R1008Q	ENSP00000407720:R1008Q	R	+	2	0	CDK12	34929794	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	9.824000	0.99380	2.607000	0.88179	0.655000	0.94253	CGG		0.473	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		66	181	66	181
ZNF148	7707	broad.mit.edu;hgsc.bcm.edu	37	3	124952387	124952387	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FG-7634-01A-11D-2086-08	TCGA-FG-7634-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc668076-5204-4c1b-8591-9ad354c15a6d	a5d74526-2420-4363-859f-becb06afe263	g.chr3:124952387delT	ENST00000360647.4	-	9	1668	c.1183delA	c.(1183-1185)attfs	p.I395fs	ZNF148_ENST00000492394.1_Frame_Shift_Del_p.I395fs|ZNF148_ENST00000497929.1_5'UTR|ZNF148_ENST00000485866.1_Frame_Shift_Del_p.I395fs|ZNF148_ENST00000468369.1_Intron|SLC12A8_ENST00000423114.2_Intron|ZNF148_ENST00000544464.1_Intron|ZNF148_ENST00000484491.1_Frame_Shift_Del_p.I395fs	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	395					cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						TTACTATTAATTTTTTTGAGA	0.383																																																0													74.0	78.0	77.0					3																	124952387		2203	4300	6503	SO:0001589	frameshift_variant	7707			U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848		"""Zinc fingers, C2H2-type"""	12933	protein-coding gene	gene with protein product		601897	"""zinc finger protein 148 (pHZ-52)"""			7557990, 9925940	Standard	NM_021964		Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.1183delA	3.37:g.124952387delT	ENSP00000353863:p.Ile395fs		D3DN27|O00389|O43591|Q58EY5|Q6PJ98	Frame_Shift_Del	DEL	ENST00000360647.4	37	CCDS3031.1																																																																																				0.383	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355452.4	NM_021964		46	22	46	22
