#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
TAF5	6877	hgsc.bcm.edu;broad.mit.edu	37	10	105145230	105145230	+	Silent	SNP	C	C	T	rs145434074		TCGA-HT-7691-01A-11D-2253-08	TCGA-HT-7691-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	efd30f39-5200-4c80-957d-a4f3898dd711	2891bd1f-d811-43da-b76f-60eb95191d34	g.chr10:105145230C>T	ENST00000369839.3	+	8	1835	c.1812C>T	c.(1810-1812)ggC>ggT	p.G604G	TAF5_ENST00000351396.4_Intron	NM_006951.3	NP_008882.2	Q15542	TAF5_HUMAN	TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 100kDa	604					chromatin modification (GO:0016568)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	protein dimerization activity (GO:0046983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)	15		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		TGTCAGGGGGCCATGACCGAG	0.413																																																0								C		1,4405	2.1+/-5.4	0,1,2202	72.0	63.0	66.0		1812	0.9	1.0	10	dbSNP_134	66	0,8600		0,0,4300	no	coding-synonymous	TAF5	NM_006951.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		604/801	105145230	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	6877			X95525	CCDS7547.1	10q24-q25.2	2013-01-10	2002-08-29	2001-12-07	ENSG00000148835	ENSG00000148835		"""WD repeat domain containing"""	11539	protein-coding gene	gene with protein product		601787	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, D, 100kD"""	TAF2D		8884287, 8942982	Standard	NM_006951		Approved	TAFII100	uc001kwv.3	Q15542	OTTHUMG00000018985	ENST00000369839.3:c.1812C>T	10.37:g.105145230C>T			A8K5B4|B2RMR0|B7ZKJ6|Q53EM4|Q5SYD5|Q86UZ7|Q9Y4K5	Silent	SNP	ENST00000369839.3	37	CCDS7547.1																																																																																				0.413	TAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050144.1			3	45	3	45
SACS	26278	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	23908606	23908606	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7691-01A-11D-2253-08	TCGA-HT-7691-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	efd30f39-5200-4c80-957d-a4f3898dd711	2891bd1f-d811-43da-b76f-60eb95191d34	g.chr13:23908606C>T	ENST00000382292.3	-	9	9682	c.9409G>A	c.(9409-9411)Gat>Aat	p.D3137N	SACS_ENST00000382298.3_Missense_Mutation_p.D3137N|SACS_ENST00000402364.1_Missense_Mutation_p.D2387N			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3137					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		AAACAATAATCAACTAAAAGT	0.373																																																0													31.0	33.0	32.0					13																	23908606		2201	4294	6495	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.9409G>A	13.37:g.23908606C>T	ENSP00000371729:p.Asp3137Asn		O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	23.9	4.472705	0.84640	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.86562	-2.0;-2.14;-2.0	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.89763	0.6809	L	0.27053	0.805	0.51233	D	0.999915	D	0.71674	0.998	D	0.68621	0.959	D	0.90260	0.4300	10	0.56958	D	0.05	.	19.9379	0.97147	0.0:1.0:0.0:0.0	.	3137	Q9NZJ4	SACS_HUMAN	N	3137;2387;3137	ENSP00000371729:D3137N;ENSP00000385844:D2387N;ENSP00000371735:D3137N	ENSP00000371729:D3137N	D	-	1	0	SACS	22806606	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.710000	0.92621	0.555000	0.69702	GAT		0.373	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		11	24	11	24
TMC6	11322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	76120700	76120700	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-7691-01A-11D-2253-08	TCGA-HT-7691-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	efd30f39-5200-4c80-957d-a4f3898dd711	2891bd1f-d811-43da-b76f-60eb95191d34	g.chr17:76120700G>C	ENST00000590602.1	-	8	955	c.796C>G	c.(796-798)Ctg>Gtg	p.L266V	TMC6_ENST00000322914.3_Missense_Mutation_p.L266V|TMC6_ENST00000589553.1_Missense_Mutation_p.L39V|TMC6_ENST00000592076.1_5'Flank|TMC6_ENST00000322933.4_5'UTR|TMC6_ENST00000591436.1_5'Flank|TMC6_ENST00000392467.3_Missense_Mutation_p.L266V|TMC6_ENST00000306591.7_Missense_Mutation_p.L266V			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	266				L -> P (in Ref. 2; AAP69874). {ECO:0000305}.	ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			AAGGCCACCAGCAGCAGCAGC	0.672																																																0													19.0	19.0	19.0					17																	76120700		2183	4244	6427	SO:0001583	missense	11322			AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"""epidermodysplasia verruciformis 1"""	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.796C>G	17.37:g.76120700G>C	ENSP00000465261:p.Leu266Val		O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	37	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	G	11.48	1.650996	0.29336	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000306591	T;T;T	0.54279	0.58;0.58;0.58	3.64	1.38	0.22167	.	1.022600	0.07798	N	0.955959	T	0.53498	0.1800	L	0.53249	1.67	0.33038	D	0.531028	P;D;D;D;B	0.58268	0.713;0.981;0.981;0.982;0.23	B;P;P;P;B	0.57101	0.246;0.813;0.761;0.664;0.082	T	0.56974	-0.7890	10	0.06891	T	0.86	-10.1151	4.5808	0.12257	0.211:0.184:0.605:0.0	.	103;266;39;266;266	B4E003;Q7Z403-2;Q7Z403-4;B3KTU5;Q7Z403	.;.;.;.;TMC6_HUMAN	V	266	ENSP00000313408:L266V;ENSP00000376260:L266V;ENSP00000306405:L266V	ENSP00000306405:L266V	L	-	1	2	TMC6	73632295	0.228000	0.23718	0.981000	0.43875	0.146000	0.21551	0.651000	0.24873	0.497000	0.27926	0.462000	0.41574	CTG		0.672	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1			4	23	4	23
IL12RB1	3594	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	18183118	18183118	+	Silent	SNP	C	C	T	rs141737618		TCGA-HT-7691-01A-11D-2253-08	TCGA-HT-7691-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	efd30f39-5200-4c80-957d-a4f3898dd711	2891bd1f-d811-43da-b76f-60eb95191d34	g.chr19:18183118C>T	ENST00000600835.2	-	10	1123	c.825G>A	c.(823-825)gcG>gcA	p.A275A	IL12RB1_ENST00000322153.7_Silent_p.A275A|IL12RB1_ENST00000593993.2_Silent_p.A275A			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	275	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						CCGTGCCAGGCGCCAGCCCTT	0.587																																																0								C	,	0,4406		0,0,2203	57.0	48.0	51.0		825,825	-5.0	0.0	19	dbSNP_134	51	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	IL12RB1	NM_005535.1,NM_153701.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	275/663,275/382	18183118	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	3594			U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.825G>A	19.37:g.18183118C>T			A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Silent	SNP	ENST00000600835.2	37	CCDS54232.1																																																																																				0.587	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3			10	21	10	21
PCDHB10	56126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	140572688	140572688	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-7691-01A-11D-2253-08	TCGA-HT-7691-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	efd30f39-5200-4c80-957d-a4f3898dd711	2891bd1f-d811-43da-b76f-60eb95191d34	g.chr5:140572688G>T	ENST00000239446.4	+	1	747	c.563G>T	c.(562-564)gGc>gTc	p.G188V		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	188	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGTGATGAAGGCATGATATAT	0.498																																																0													116.0	137.0	129.0					5																	140572688		2203	4300	6503	SO:0001583	missense	56126			AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.563G>T	5.37:g.140572688G>T	ENSP00000239446:p.Gly188Val		Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	G	16.17	3.046514	0.55110	.	.	ENSG00000120324	ENST00000239446	T	0.04502	3.61	3.52	2.64	0.31445	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.28400	0.0702	H	0.95470	3.675	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	T	0.28713	-1.0035	9	0.87932	D	0	.	10.8847	0.46960	0.0956:0.0:0.9044:0.0	.	188	Q9UN67	PCDBA_HUMAN	V	188	ENSP00000239446:G188V	ENSP00000239446:G188V	G	+	2	0	PCDHB10	140552872	0.990000	0.36364	0.605000	0.28930	0.774000	0.43823	2.439000	0.44846	0.831000	0.34780	0.556000	0.70494	GGC		0.498	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		63	171	63	171
BRAT1	221927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	2583295	2583295	+	Silent	SNP	C	C	A			TCGA-HT-7691-01A-11D-2253-08	TCGA-HT-7691-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	efd30f39-5200-4c80-957d-a4f3898dd711	2891bd1f-d811-43da-b76f-60eb95191d34	g.chr7:2583295C>A	ENST00000340611.4	-	5	988	c.732G>T	c.(730-732)gtG>gtT	p.V244V	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	244					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						GCAGACAGGCCACGCGGGGAC	0.701																																																0													31.0	39.0	37.0					7																	2583295		2203	4296	6499	SO:0001819	synonymous_variant	221927			BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.732G>T	7.37:g.2583295C>A			A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Silent	SNP	ENST00000340611.4	37	CCDS5334.1																																																																																				0.701	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743		9	72	9	72
BRWD3	254065	hgsc.bcm.edu;broad.mit.edu	37	X	79932312	79932312	+	Silent	SNP	G	G	A			TCGA-HT-7691-01A-11D-2253-08	TCGA-HT-7691-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	efd30f39-5200-4c80-957d-a4f3898dd711	2891bd1f-d811-43da-b76f-60eb95191d34	g.chrX:79932312G>A	ENST00000373275.4	-	41	5421	c.5205C>T	c.(5203-5205)acC>acT	p.T1735T	BRWD3_ENST00000473691.1_5'Flank	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1735					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						CTGAAAACATGGTATCAAATT	0.443																																																0													146.0	113.0	124.0					X																	79932312		2203	4300	6503	SO:0001819	synonymous_variant	254065				CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"""WD repeat domain containing"""	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.5205C>T	X.37:g.79932312G>A			C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Silent	SNP	ENST00000373275.4	37	CCDS14447.1																																																																																				0.443	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		6	103	6	103
SLC6A17	388662	broad.mit.edu;ucsc.edu	37	1	110740737	110740737	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7691-01A-11D-2253-08	TCGA-HT-7691-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	efd30f39-5200-4c80-957d-a4f3898dd711	2891bd1f-d811-43da-b76f-60eb95191d34	g.chr1:110740737G>A	ENST00000331565.4	+	12	2340	c.1855G>A	c.(1855-1857)Gca>Aca	p.A619T		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	619					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		CTGGGCCATGGCACTCCTGAT	0.657																																																0													86.0	76.0	79.0					1																	110740737		2203	4300	6503	SO:0001583	missense	388662				CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"""Solute carriers"""	31399	protein-coding gene	gene with protein product		610299	"""solute carrier family 6 (neurotransmitter transporter), member 17"", ""solute carrier family 6, member 17"""				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.1855G>A	1.37:g.110740737G>A	ENSP00000330199:p.Ala619Thr		A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	37	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.383390	0.82792	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.74947	-0.89	4.63	4.63	0.57726	.	0.242352	0.40818	N	0.001020	T	0.68988	0.3061	M	0.68728	2.09	0.36989	D	0.894673	B	0.26445	0.149	B	0.39419	0.299	T	0.74494	-0.3647	10	0.62326	D	0.03	.	12.56	0.56275	0.0:0.0:0.8334:0.1666	.	619	Q9H1V8	S6A17_HUMAN	T	619	ENSP00000330199:A619T	ENSP00000330199:A619T	A	+	1	0	SLC6A17	110542260	1.000000	0.71417	0.993000	0.49108	0.860000	0.49131	5.227000	0.65305	2.114000	0.64651	0.455000	0.32223	GCA		0.657	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		4	35	4	35
CTNS	1497	broad.mit.edu;ucsc.edu	37	17	3560060	3560060	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7691-01A-11D-2253-08	TCGA-HT-7691-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	efd30f39-5200-4c80-957d-a4f3898dd711	2891bd1f-d811-43da-b76f-60eb95191d34	g.chr17:3560060A>G	ENST00000046640.3	+	9	1245	c.652A>G	c.(652-654)Atc>Gtc	p.I218V	CTNS_ENST00000381870.3_Missense_Mutation_p.I218V|CTNS_ENST00000414524.2_Missense_Mutation_p.I71V|RP11-235E17.6_ENST00000575741.1_RNA|CTNS_ENST00000441220.2_Missense_Mutation_p.I110V	NM_004937.2	NP_004928.2	O60931	CTNS_HUMAN	cystinosin, lysosomal cystine transporter	218					adult walking behavior (GO:0007628)|ATP metabolic process (GO:0046034)|brain development (GO:0007420)|cellular amino acid metabolic process (GO:0006520)|cognition (GO:0050890)|glutathione metabolic process (GO:0006749)|grooming behavior (GO:0007625)|L-cystine transport (GO:0015811)|lens development in camera-type eye (GO:0002088)|long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	L-cystine transmembrane transporter activity (GO:0015184)			NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)	10				COAD - Colon adenocarcinoma(5;0.0829)	L-Cystine(DB00138)	CCTCACGCTGATCATCATCGT	0.592																																																0													121.0	96.0	105.0					17																	3560060		2203	4300	6503	SO:0001583	missense	1497			AJ222967	CCDS11031.1, CCDS32530.1	17p13	2011-06-07	2011-06-07		ENSG00000040531	ENSG00000040531			2518	protein-coding gene	gene with protein product		606272	"""cystinosis, nephropathic"""			9537412, 15128704	Standard	NM_004937		Approved	CTNS-LSB, PQLC4	uc002fwa.3	O60931	OTTHUMG00000090693	ENST00000046640.3:c.652A>G	17.37:g.3560060A>G	ENSP00000046640:p.Ile218Val		D3DTJ5|Q8IZ01|Q9UNK6	Missense_Mutation	SNP	ENST00000046640.3	37	CCDS11031.1	.	.	.	.	.	.	.	.	.	.	a	5.117	0.207271	0.09704	.	.	ENSG00000040531	ENST00000046640;ENST00000381870;ENST00000441220;ENST00000414524	D;D;D;D	0.96685	-3.62;-3.66;-4.09;-3.91	4.92	3.91	0.45181	.	0.192581	0.45606	N	0.000359	D	0.85678	0.5752	N	0.04787	-0.16	0.35227	D	0.776554	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.77667	-0.2502	10	0.06365	T	0.9	-11.1631	2.9994	0.06009	0.3624:0.2739:0.3637:0.0	.	110;218;218	F8W6Z1;O60931;O60931-2	.;CTNS_HUMAN;.	V	218;218;110;71	ENSP00000046640:I218V;ENSP00000371294:I218V;ENSP00000411465:I110V;ENSP00000395471:I71V	ENSP00000046640:I218V	I	+	1	0	CTNS	3506809	0.965000	0.33210	0.963000	0.40424	0.374000	0.29953	0.139000	0.16036	1.036000	0.39998	0.398000	0.26397	ATC		0.592	CTNS-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317696.1	NM_004937		26	93	26	93
