#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
WRN	7486	broad.mit.edu	37	8	31004953	31004953	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr8:31004953T>C	ENST00000298139.5	+	30	3782	c.3533T>C	c.(3532-3534)cTg>cCg	p.L1178P		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	1178	HRDC. {ECO:0000255|PROSITE- ProRule:PRU00328}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		CCAGCTATTCTGGCAACAAAC	0.343			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												Ovarian(18;161 598 2706 14834 27543)	ENST00000298139.5			yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	"""Mis, N, F, S"""	Werner syndrome (RECQL2)			"""L, E, M, O"""		"""osteosarcoma, meningioma, others"""			0				central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60						c.(3532-3534)cTg>cCg	Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome, RecQ helicase-like							98.0	98.0	98.0					8																	31004953		2203	4300	6503	SO:0001583	missense	7486	Werner syndrome	Familial Cancer Database	WS, Adult Progeria	base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding	g.chr8:31004953T>C		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.3533T>C	8.37:g.31004953T>C	ENSP00000298139:p.Leu1178Pro						p.L1178P	NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)	30	3782	+		Breast(100;0.195)	1178			HRDC.		A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	37	c.3533T>C	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	T	19.11	3.764768	0.69878	.	.	ENSG00000165392	ENST00000298139	T	0.50001	0.76	4.97	4.97	0.65823	HRDC-like (1);Helicase/RNase D C-terminal, HRDC domain (3);	0.000000	0.64402	D	0.000013	T	0.69922	0.3165	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.75300	-0.3366	10	0.87932	D	0	-8.2858	14.6037	0.68460	0.0:0.0:0.0:1.0	.	588;1178	Q59F09;Q14191	.;WRN_HUMAN	P	1178	ENSP00000298139:L1178P	ENSP00000298139:L1178P	L	+	2	0	WRN	31124495	1.000000	0.71417	0.992000	0.48379	0.876000	0.50452	6.143000	0.71756	1.990000	0.58119	0.533000	0.62120	CTG		0.343	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			21	32	0	0	0	0.003330	0	21	32				
PYGB	5834	broad.mit.edu	37	20	25257360	25257360	+	Missense_Mutation	SNP	G	G	A	rs200914374		TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr20:25257360G>A	ENST00000216962.4	+	6	849	c.739G>A	c.(739-741)Gcc>Acc	p.A247T		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	247					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						GCTGTGGTCCGCCAAGGCTCC	0.617																																						ENST00000216962.4																			0				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						c.(739-741)Gcc>Acc		phosphorylase, glycogen; brain	Pyridoxal Phosphate(DB00114)	G	THR/ALA	2,4404	4.2+/-10.8	0,2,2201	139.0	94.0	109.0		739	3.5	1.0	20		109	0,8600		0,0,4300	no	missense	PYGB	NM_002862.3	58	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	247/844	25257360	2,13004	2203	4300	6503	SO:0001583	missense	5834				glucose metabolic process|glycogen catabolic process	cytoplasm	glycogen phosphorylase activity|pyridoxal phosphate binding	g.chr20:25257360G>A		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.739G>A	20.37:g.25257360G>A	ENSP00000216962:p.Ala247Thr						p.A247T	NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN			6	849	+			247					Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	37	c.739G>A	CCDS13171.1	.	.	.	.	.	.	.	.	.	.	G	31	5.077262	0.94000	4.54E-4	0.0	ENSG00000100994	ENST00000216962	D	0.94862	-3.54	3.49	3.49	0.39957	.	0.000000	0.85682	D	0.000000	D	0.97049	0.9036	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.97802	1.0245	10	0.87932	D	0	-25.5524	15.1631	0.72801	0.0:0.0:1.0:0.0	.	247	P11216	PYGB_HUMAN	T	247	ENSP00000216962:A247T	ENSP00000216962:A247T	A	+	1	0	PYGB	25205360	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	9.492000	0.97957	1.974000	0.57490	0.557000	0.71058	GCC		0.617	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862		3	32	0	0	0	0.000248	0	3	32				
SEMG1	6406	broad.mit.edu	37	20	43836652	43836652	+	Silent	SNP	C	C	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr20:43836652C>T	ENST00000372781.3	+	2	771	c.714C>T	c.(712-714)ctC>ctT	p.L238L	SEMG1_ENST00000244069.6_Silent_p.L238L	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	238	Interaction with EPPIN.|Repeat-rich region. {ECO:0000250}.				insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				AAACCTCACTCTGTCCTGCGC	0.378																																						ENST00000372781.3																			0				cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32						c.(712-714)ctC>ctT		semenogelin I							114.0	99.0	104.0					20																	43836652		2203	4300	6503	SO:0001819	synonymous_variant	6406							g.chr20:43836652C>T		CCDS13345.1	20q12-q13.2	2009-08-06			ENSG00000124233	ENSG00000124233			10742	protein-coding gene	gene with protein product	"""semen coagulating protein"", ""cancer/testis antigen 103"""	182140		SEMG		2912989, 15563730	Standard	NM_003007		Approved	CT103		P04279	OTTHUMG00000032565	ENST00000372781.3:c.714C>T	20.37:g.43836652C>T						SEMG1_ENST00000244069.6_Silent_p.L238L	p.L238L	NM_003007.3	NP_002998.1					2	771	+		Myeloproliferative disorder(115;0.0122)						Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Silent	SNP	ENST00000372781.3	37	c.714C>T	CCDS13345.1																																																																																				0.378	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007		6	131	0	0	0	0.001168	0	6	131				
TUBB8P7	197331	broad.mit.edu	37	16	90162513	90162513	+	RNA	SNP	T	T	C			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr16:90162513T>C	ENST00000564451.1	+	0	1866				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7									p.N415N(2)									GCAACATGAATGACCTGGTGT	0.537																																						ENST00000567960.1																			2	Substitution - coding silent(2)	p.N415N(2)	prostate(1)|kidney(1)																																																0							g.chr16:90162513T>C			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162513T>C						TUBB8P7_ENST00000564451.1_RNA								0	1249	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.537	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		4	107	0	0	0	0.000602	0	4	107				
USP28	57646	broad.mit.edu	37	11	113705033	113705033	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr11:113705033G>A	ENST00000003302.4	-	6	627	c.559C>T	c.(559-561)Cga>Tga	p.R187*	USP28_ENST00000260188.5_Nonsense_Mutation_p.R187*|USP28_ENST00000542033.1_5'UTR|USP28_ENST00000537706.1_Nonsense_Mutation_p.R187*|USP28_ENST00000545540.1_Nonsense_Mutation_p.R62*	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	187	USP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.R187*(1)		breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		ACAAGTCTTCGAAATTCAGGC	0.343																																					Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	ENST00000003302.4																			1	Substitution - Nonsense(1)	p.R187*(1)	skin(1)	breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59						c.(559-561)Cga>Tga		ubiquitin specific peptidase 28							104.0	95.0	98.0					11																	113705033		2201	4296	6497	SO:0001587	stop_gained	57646				cell proliferation|DNA damage checkpoint|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA repair|protein deubiquitination|response to ionizing radiation|ubiquitin-dependent protein catabolic process	nucleolus|nucleoplasm	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	g.chr11:113705033G>A	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"""Ubiquitin-specific peptidases"""	12625	protein-coding gene	gene with protein product		610748	"""ubiquitin specific protease 28"""			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.559C>T	11.37:g.113705033G>A	ENSP00000003302:p.Arg187*					USP28_ENST00000260188.5_Nonsense_Mutation_p.R187*|USP28_ENST00000537706.1_Nonsense_Mutation_p.R187*|USP28_ENST00000542033.1_5'UTR|USP28_ENST00000545540.1_Nonsense_Mutation_p.R62*	p.R187*	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)	6	627	-		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)	187					B0YJC0|B0YJC1|Q9P213	Nonsense_Mutation	SNP	ENST00000003302.4	37	c.559C>T	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	G	38	7.006134	0.97998	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000545540;ENST00000537706	.	.	.	5.08	5.08	0.68730	.	0.063315	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6665	17.4468	0.87580	0.0:0.0:1.0:0.0	.	.	.	.	X	187;187;62;187	.	ENSP00000003302:R187X	R	-	1	2	USP28	113210243	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.022000	0.70839	2.357000	0.79964	0.460000	0.39030	CGA		0.343	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			16	35	0	0	0	0.004007	0	16	35				
HS3ST4	9951	broad.mit.edu	37	16	26147154	26147154	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr16:26147154G>A	ENST00000331351.5	+	2	1348	c.956G>A	c.(955-957)cGg>cAg	p.R319Q	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	319					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		TTCAAAAACCGGACCCTCGGG	0.552																																						ENST00000331351.5																			0				breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15						c.(955-957)cGg>cAg		heparan sulfate (glucosamine) 3-O-sulfotransferase 4							175.0	166.0	169.0					16																	26147154		1568	3582	5150	SO:0001583	missense	9951				heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity	g.chr16:26147154G>A	AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.956G>A	16.37:g.26147154G>A	ENSP00000330606:p.Arg319Gln					HS3ST4_ENST00000475436.1_3'UTR	p.R319Q	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN		GBM - Glioblastoma multiforme(48;0.0988)	2	1348	+			319					Q5QI42|Q8NDC2	Missense_Mutation	SNP	ENST00000331351.5	37	c.956G>A	CCDS53995.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.977846	0.74360	.	.	ENSG00000182601	ENST00000331351	T	0.55052	0.54	5.35	5.35	0.76521	Sulfotransferase domain (1);	0.000000	0.64402	U	0.000011	T	0.42154	0.1190	L	0.42686	1.345	0.58432	D	0.999998	P	0.48998	0.918	B	0.32583	0.148	T	0.46076	-0.9217	10	0.38643	T	0.18	.	18.0433	0.89325	0.0:0.0:1.0:0.0	.	319	Q9Y661	HS3S4_HUMAN	Q	319	ENSP00000330606:R319Q	ENSP00000330606:R319Q	R	+	2	0	HS3ST4	26054655	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.823000	0.99369	2.491000	0.84063	0.655000	0.94253	CGG		0.552	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		81	105	0	0	0	0.003610	0	81	105				
C9orf72	203228	broad.mit.edu	37	9	27567087	27567087	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr9:27567087G>A	ENST00000380003.3	-	2	95	c.32C>T	c.(31-33)gCt>gTt	p.A11V	C9orf72_ENST00000488117.1_5'UTR|C9orf72_ENST00000379997.3_Missense_Mutation_p.A11V	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN	chromosome 9 open reading frame 72	11					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634)	Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		CTTGGCAACAGCTGGAGATGG	0.423																																						ENST00000380003.3																			0				breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23						c.(31-33)gCt>gTt		chromosome 9 open reading frame 72							69.0	66.0	67.0					9																	27567087		2203	4298	6501	SO:0001583	missense	203228							g.chr9:27567087G>A	AL832467	CCDS6522.1, CCDS6523.1	9p21.1	2014-09-17			ENSG00000147894	ENSG00000147894			28337	protein-coding gene	gene with protein product		614260				21944778, 24549040	Standard	NM_145005		Approved	MGC23980	uc003zqq.3	Q96LT7	OTTHUMG00000019716	ENST00000380003.3:c.32C>T	9.37:g.27567087G>A	ENSP00000369339:p.Ala11Val					C9orf72_ENST00000379997.3_Missense_Mutation_p.A11V|C9orf72_ENST00000488117.1_5'UTR	p.A11V	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)	2	95	-		all_neural(11;7.57e-10)	11					A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Missense_Mutation	SNP	ENST00000380003.3	37	c.32C>T	CCDS6522.1	.	.	.	.	.	.	.	.	.	.	G	33	5.222152	0.95139	.	.	ENSG00000147894	ENST00000380003;ENST00000379997;ENST00000379995	T;T;T	0.52754	0.68;0.65;0.65	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.57475	0.2056	N	0.24115	0.695	0.80722	D	1	D;D	0.67145	0.996;0.994	D;D	0.75484	0.986;0.909	T	0.51663	-0.8677	9	.	.	.	.	20.4777	0.99188	0.0:0.0:1.0:0.0	.	11;11	Q96LT7-2;Q96LT7	.;CI072_HUMAN	V	11	ENSP00000369339:A11V;ENSP00000369333:A11V;ENSP00000369331:A11V	.	A	-	2	0	C9orf72	27557087	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.420000	0.97426	2.840000	0.97914	0.655000	0.94253	GCT		0.423	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325		22	30	0	0	0	0.002780	0	22	30				
ZGRF1	55345	broad.mit.edu	37	4	113508691	113508691	+	Silent	SNP	C	C	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr4:113508691C>T	ENST00000505019.1	-	12	3647	c.3522G>A	c.(3520-3522)gaG>gaA	p.E1174E		NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		1174						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		CAGAAACAGCCTCAGCAAAGA	0.413																																						ENST00000505019.1																			0				breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						c.(3520-3522)gaG>gaA		chromosome 4 open reading frame 21							188.0	199.0	195.0					4																	113508691		2203	4300	6503	SO:0001819	synonymous_variant	55345							g.chr4:113508691C>T																												ENST00000505019.1:c.3522G>A	4.37:g.113508691C>T							p.E1174E	NM_018392.4	NP_060862.3	Q86YA3	CD021_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.000676)	12	3647	-		Ovarian(17;0.156)	0					B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Silent	SNP	ENST00000505019.1	37	c.3522G>A																																																																																					0.413	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1			77	145	0	0	0	0.003610	0	77	145				
EDEM1	9695	broad.mit.edu	37	3	5255103	5255103	+	Missense_Mutation	SNP	C	C	T	rs183693683	byFrequency	TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr3:5255103C>T	ENST00000256497.4	+	11	1913	c.1780C>T	c.(1780-1782)Cca>Tca	p.P594S		NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	594					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	calcium ion binding (GO:0005509)|misfolded protein binding (GO:0051787)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		TCGGGAATTGCCATGGAAGGA	0.478													C|||	2	0.000399361	0.0	0.0029	5008	,	,		20006	0.0		0.0	False		,,,				2504	0.0					ENST00000256497.4																			0				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						c.(1780-1782)Cca>Tca		ER degradation enhancer, mannosidase alpha-like 1							91.0	82.0	85.0					3																	5255103		2203	4300	6503	SO:0001583	missense	9695				ER-associated protein catabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	integral to endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding	g.chr3:5255103C>T	D86967	CCDS33686.1	3p26.1	2008-02-05			ENSG00000134109	ENSG00000134109			18967	protein-coding gene	gene with protein product		607673				12610306	Standard	NM_014674		Approved	KIAA0212, EDEM	uc003bqi.3	Q92611	OTTHUMG00000154896	ENST00000256497.4:c.1780C>T	3.37:g.5255103C>T	ENSP00000256497:p.Pro594Ser						p.P594S	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN		Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)	11	1913	+			594					A8K9C8|B4DXP3	Missense_Mutation	SNP	ENST00000256497.4	37	c.1780C>T	CCDS33686.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	11.12	1.544647	0.27563	.	.	ENSG00000134109	ENST00000256497	D	0.81996	-1.56	5.42	5.42	0.78866	.	0.445764	0.26927	N	0.021783	T	0.56031	0.1958	N	0.08118	0	0.35331	D	0.785656	B	0.13594	0.008	B	0.06405	0.002	T	0.61307	-0.7089	10	0.06625	T	0.88	-25.6372	12.5698	0.56331	0.0:0.9244:0.0:0.0756	.	594	Q92611	EDEM1_HUMAN	S	594	ENSP00000256497:P594S	ENSP00000256497:P594S	P	+	1	0	EDEM1	5230103	0.058000	0.20735	0.808000	0.32385	0.750000	0.42670	1.909000	0.39917	2.530000	0.85305	0.655000	0.94253	CCA		0.478	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674		3	33	0	0	0	0.000248	0	3	33				
RP11-423O2.5	0	broad.mit.edu	37	1	142803543	142803543	+	lincRNA	SNP	C	C	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr1:142803543C>T	ENST00000423385.1	-	0	1422																											TGTTGGAATTCCTGATGAATC	0.269																																						ENST00000423385.1																			0																																																			0							g.chr1:142803543C>T																													1.37:g.142803543C>T														0	1422	-									RNA	SNP	ENST00000423385.1	37																																																																																						0.269	RP11-423O2.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000193203.1			7	227	0	0	0	0.001984	0	7	227				
SLC22A11	55867	broad.mit.edu	37	11	64326627	64326627	+	Silent	SNP	C	C	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr11:64326627C>T	ENST00000301891.4	+	2	788	c.414C>T	c.(412-414)tcC>tcT	p.S138S	SLC22A11_ENST00000490834.1_Intron|SLC22A11_ENST00000377581.3_Silent_p.S138S|SLC22A11_ENST00000377585.3_Silent_p.S138S	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 11	138					organic anion transport (GO:0015711)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23					Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495)	TGTGCAGCTCCCAGGGCTTGA	0.637																																						ENST00000301891.4																			0				breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23						c.(412-414)tcC>tcT		solute carrier family 22 (organic anion/urate transporter), member 11	Probenecid(DB01032)						122.0	110.0	114.0					11																	64326627		2201	4297	6498	SO:0001819	synonymous_variant	55867				urate metabolic process	apical plasma membrane|external side of plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium-independent organic anion transmembrane transporter activity	g.chr11:64326627C>T	AB026116	CCDS8074.1	11q13.3	2013-05-22	2008-01-11		ENSG00000168065	ENSG00000168065		"""Solute carriers"""	18120	protein-coding gene	gene with protein product		607097				10660625, 15576633, 17229912	Standard	NM_018484		Approved	OAT4	uc001oai.3	Q9NSA0	OTTHUMG00000045142	ENST00000301891.4:c.414C>T	11.37:g.64326627C>T						SLC22A11_ENST00000490834.1_Intron|SLC22A11_ENST00000377585.3_Silent_p.S138S|SLC22A11_ENST00000377581.3_Silent_p.S138S	p.S138S	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN			2	788	+			138					A8K426|Q53GR2|Q6ZP72|Q8NBU4	Silent	SNP	ENST00000301891.4	37	c.414C>T	CCDS8074.1																																																																																				0.637	SLC22A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104886.4	NM_018484		33	60	0	0	0	0.003271	0	33	60				
SLITRK3	22865	broad.mit.edu	37	3	164906912	164906912	+	Missense_Mutation	SNP	G	G	C			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr3:164906912G>C	ENST00000475390.1	-	2	2150	c.1707C>G	c.(1705-1707)gaC>gaG	p.D569E	SLITRK3_ENST00000241274.3_Missense_Mutation_p.D569E			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	569	LRRCT 2.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						AGGGGACCAGGTCACAGGTGC	0.517										HNSCC(40;0.11)																												ENST00000475390.1																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						c.(1705-1707)gaC>gaG		SLIT and NTRK-like family, member 3							99.0	91.0	93.0					3																	164906912		2203	4300	6503	SO:0001583	missense	22865					integral to membrane		g.chr3:164906912G>C	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1707C>G	3.37:g.164906912G>C	ENSP00000420091:p.Asp569Glu	HNSCC(40;0.11)				SLITRK3_ENST00000241274.3_Missense_Mutation_p.D569E	p.D569E			O94933	SLIK3_HUMAN			2	2150	-			569			LRRCT 2.		Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	37	c.1707C>G	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	G	10.09	1.254251	0.22965	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.52983	0.64;0.64	5.81	3.99	0.46301	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.40064	N	0.001194	T	0.43964	0.1271	L	0.58969	1.84	0.43084	D	0.99474	B	0.11235	0.004	B	0.12156	0.007	T	0.38735	-0.9647	10	0.56958	D	0.05	-17.5076	10.8945	0.47015	0.0677:0.2442:0.688:0.0	.	569	O94933	SLIK3_HUMAN	E	569	ENSP00000420091:D569E;ENSP00000241274:D569E	ENSP00000241274:D569E	D	-	3	2	SLITRK3	166389606	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.717000	0.25851	0.884000	0.36064	0.655000	0.94253	GAC		0.517	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		19	33	0	0	0	0.001523	0	19	33				
TUBBP5	643224	broad.mit.edu	37	9	141070111	141070111	+	RNA	SNP	T	T	C	rs139643347		TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr9:141070111T>C	ENST00000503395.1	+	0	1191									tubulin, beta pseudogene 5									p.S75S(1)									CCATGGACTCTGTGCGCTCGG	0.697																																						ENST00000503395.1																			1	Substitution - coding silent(1)	p.S75S(1)	prostate(1)																																																0							g.chr9:141070111T>C	AF355123		9q34.3	2012-03-06	2005-11-15		ENSG00000159247	ENSG00000159247			23674	pseudogene	pseudogene			"""tubulin, beta polypeptide pseudogene 5"""			11731935	Standard	NR_027156		Approved		uc010ncq.3		OTTHUMG00000021001		9.37:g.141070111T>C														0	1191	+									RNA	SNP	ENST00000503395.1	37																																																																																						0.697	TUBBP5-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000373087.1	NR_027156		4	97	0	0	0	0.001984	0	4	97				
GALNT18	374378	broad.mit.edu	37	11	11400737	11400737	+	Missense_Mutation	SNP	G	G	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr11:11400737G>T	ENST00000227756.4	-	4	1081	c.670C>A	c.(670-672)Cgt>Agt	p.R224S		NM_198516.2	NP_940918.2	Q6P9A2	GLT18_HUMAN	polypeptide N-acetylgalactosaminyltransferase 18	224	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										TTGCTGTGACGCACGACTTTG	0.567																																						ENST00000227756.4																			0											c.(670-672)Cgt>Agt		UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18							152.0	124.0	133.0					11																	11400737		2201	4294	6495	SO:0001583	missense	374378							g.chr11:11400737G>T	AK055111	CCDS7807.1	11p15	2014-03-13	2014-03-13	2013-01-25	ENSG00000110328	ENSG00000110328	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	30488	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 18"""	615136	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 4"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18"""	GALNTL4		22186971	Standard	NM_198516		Approved	MGC71806, GALNT15, GalNAc-T18	uc001mjo.2	Q6P9A2	OTTHUMG00000165707	ENST00000227756.4:c.670C>A	11.37:g.11400737G>T	ENSP00000227756:p.Arg224Ser						p.R224S	NM_198516.2	NP_940918.2					4	1081	-								O95903|Q8NDY9	Missense_Mutation	SNP	ENST00000227756.4	37	c.670C>A	CCDS7807.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.517763	0.85495	.	.	ENSG00000110328	ENST00000227756	T	0.64260	-0.09	5.98	5.98	0.97165	Glycosyl transferase, family 2 (1);	0.202272	0.41605	D	0.000858	D	0.83248	0.5213	M	0.88310	2.945	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	D	0.85391	0.1125	10	0.87932	D	0	.	19.0102	0.92870	0.0:0.0:1.0:0.0	.	224	Q6P9A2	GLTL4_HUMAN	S	224	ENSP00000227756:R224S	ENSP00000227756:R224S	R	-	1	0	GALNTL4	11357313	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.786000	0.99046	2.838000	0.97847	0.514000	0.50259	CGT		0.567	GALNT18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385848.1	NM_198516		18	39	1	0	8.00594e-06	0.007413	1.08316e-05	18	39				
PPFIA4	8497	broad.mit.edu	37	1	203013072	203013072	+	Missense_Mutation	SNP	A	A	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr1:203013072A>T	ENST00000447715.2	+	8	791	c.350A>T	c.(349-351)cAt>cTt	p.H117L	PPFIA4_ENST00000367240.2_Missense_Mutation_p.H117L|PPFIA4_ENST00000414050.2_5'Flank|PPFIA4_ENST00000295706.4_5'UTR			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	117					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						CTTCTGGAACATCTGGAGTGC	0.637																																						ENST00000367240.2																			0				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						c.(349-351)cAt>cTt		protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4							43.0	40.0	41.0					1																	203013072		876	1991	2867	SO:0001583	missense	8497				cell communication	cell surface|cytoplasm	protein binding	g.chr1:203013072A>T	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.350A>T	1.37:g.203013072A>T	ENSP00000402576:p.His117Leu					PPFIA4_ENST00000295706.4_5'UTR|PPFIA4_ENST00000447715.2_Missense_Mutation_p.H117L	p.H117L			O75335	LIPA4_HUMAN			4	877	+			119					A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37	c.350A>T		.	.	.	.	.	.	.	.	.	.	A	27.5	4.833045	0.91036	.	.	ENSG00000143847	ENST00000367240;ENST00000447715	T;T	0.51071	0.72;0.72	4.87	4.87	0.63330	.	0.000000	0.46442	D	0.000282	T	0.69160	0.3080	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74188	-0.3746	9	0.87932	D	0	-17.1364	14.9377	0.70970	1.0:0.0:0.0:0.0	.	117	B1N949	.	L	117	ENSP00000356209:H117L;ENSP00000402576:H117L	ENSP00000356209:H117L	H	+	2	0	PPFIA4	201279695	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	9.087000	0.94110	2.189000	0.69895	0.459000	0.35465	CAT		0.637	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053		12	22	0	0	0	0.001855	0	12	22				
RAD54L2	23132	broad.mit.edu	37	3	51675796	51675796	+	Missense_Mutation	SNP	G	G	C			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr3:51675796G>C	ENST00000409535.2	+	14	2388	c.2263G>C	c.(2263-2265)Gaa>Caa	p.E755Q	RAD54L2_ENST00000296477.3_Missense_Mutation_p.E449Q	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	755	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		TCTCATCGAGGAATTCCTTGG	0.483																																						ENST00000409535.1																			0				NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31						c.(2263-2265)Gaa>Caa		RAD54-like 2 (S. cerevisiae)							135.0	109.0	118.0					3																	51675796		2203	4298	6501	SO:0001583	missense	23132					nucleus	ATP binding|DNA binding|helicase activity	g.chr3:51675796G>C	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.2263G>C	3.37:g.51675796G>C	ENSP00000386520:p.Glu755Gln					RAD54L2_ENST00000296477.3_Missense_Mutation_p.E449Q	p.E755Q	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)	14	2388	+			755			Helicase C-terminal.		Q8TB57|Q9BV54	Missense_Mutation	SNP	ENST00000409535.2	37	c.2263G>C	CCDS33765.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.14|15.14	2.746006|2.746006	0.49151|0.49151	.|.	.|.	ENSG00000164080|ENSG00000164080	ENST00000409535;ENST00000296477|ENST00000432863	T;T|.	0.76839|.	-1.05;-1.05|.	5.95|5.95	5.95|5.95	0.96441|0.96441	Helicase, C-terminal (2);|.	0.093439|.	0.64402|.	D|.	0.000001|.	T|T	0.53578|0.53578	0.1805|0.1805	N|N	0.17278|0.17278	0.47|0.47	0.49299|0.49299	D|D	0.999777|0.999777	B;B|.	0.18863|.	0.031;0.031|.	B;B|.	0.14023|.	0.01;0.01|.	T|T	0.45702|0.45702	-0.9243|-0.9243	10|5	0.34782|.	T|.	0.22|.	-22.2683|-22.2683	19.3906|19.3906	0.94581|0.94581	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	755;346|.	Q9Y4B4;B3KV54|.	ARIP4_HUMAN;.|.	Q|A	755;449|583	ENSP00000386520:E755Q;ENSP00000296477:E449Q|.	ENSP00000296477:E449Q|.	E|G	+|+	1|2	0|0	RAD54L2|RAD54L2	51650836|51650836	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.564000|0.564000	0.35744|0.35744	7.879000|7.879000	0.87236|0.87236	2.827000|2.827000	0.97445|0.97445	0.650000|0.650000	0.86243|0.86243	GAA|GGA		0.483	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106		2	8	0	0	0	0.004672	0	2	8				
NEIL2	252969	broad.mit.edu	37	8	11637219	11637219	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr8:11637219C>T	ENST00000284503.6	+	3	850	c.251C>T	c.(250-252)gCg>gTg	p.A84V	NEIL2_ENST00000455213.2_Missense_Mutation_p.A84V|NEIL2_ENST00000403422.3_Missense_Mutation_p.A23V|NEIL2_ENST00000528323.1_Intron|NEIL2_ENST00000436750.3_Missense_Mutation_p.A84V	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	84					base-excision repair (GO:0006284)|nucleotide-excision repair (GO:0006289)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		GAAGGGGCTGCGGACCCAAAG	0.557								Base excision repair (BER), DNA glycosylases																														ENST00000284503.6																			0				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10						c.(250-252)gCg>gTg	Base excision repair (BER), DNA glycosylases	nei endonuclease VIII-like 2 (E. coli)							59.0	70.0	66.0					8																	11637219		2203	4300	6503	SO:0001583	missense	252969				base-excision repair|nucleotide-excision repair	nucleus	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|hydrolase activity, hydrolyzing N-glycosyl compounds|zinc ion binding	g.chr8:11637219C>T	AK056206	CCDS5984.1, CCDS47802.1, CCDS47803.1	8p23.1	2010-04-27	2010-04-27		ENSG00000154328	ENSG00000154328			18956	protein-coding gene	gene with protein product		608933	"""nei like 2 (E. coli)"""			12097317, 17686777	Standard	NM_145043		Approved	NEH2, FLJ31644, MGC2832, MGC4505	uc003wue.2	Q969S2	OTTHUMG00000090753	ENST00000284503.6:c.251C>T	8.37:g.11637219C>T	ENSP00000284503:p.Ala84Val					NEIL2_ENST00000528323.1_Intron|NEIL2_ENST00000455213.2_Missense_Mutation_p.A84V|NEIL2_ENST00000436750.3_Missense_Mutation_p.A84V|NEIL2_ENST00000403422.3_Missense_Mutation_p.A23V	p.A84V	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)	3	850	+	all_epithelial(15;0.103)		84					B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Missense_Mutation	SNP	ENST00000284503.6	37	c.251C>T	CCDS5984.1	.	.	.	.	.	.	.	.	.	.	C	11.43	1.636330	0.29068	.	.	ENSG00000154328	ENST00000530433;ENST00000455213;ENST00000403422;ENST00000436750;ENST00000284503	T;T;T;T	0.04758	3.56;3.56;3.56;3.56	5.41	-10.8	0.00216	DNA glycosylase/AP lyase, catalytic domain (2);	2.894660	0.01553	N	0.019747	T	0.01661	0.0053	N	0.03608	-0.345	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.43669	-0.9377	10	0.33141	T	0.24	-31.8102	1.0944	0.01670	0.2093:0.225:0.3141:0.2516	.	84	Q969S2	NEIL2_HUMAN	V	84;84;23;84;84	ENSP00000397538:A84V;ENSP00000384070:A23V;ENSP00000394023:A84V;ENSP00000284503:A84V	ENSP00000284503:A84V	A	+	2	0	NEIL2	11674628	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-3.429000	0.00474	-2.073000	0.00878	-0.380000	0.06706	GCG		0.557	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043		4	132	0	0	0	0.000602	0	4	132				
MUC16	94025	broad.mit.edu	37	19	9070335	9070335	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr19:9070335G>A	ENST00000397910.4	-	3	17314	c.17111C>T	c.(17110-17112)aCt>aTt	p.T5704I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5706	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGTGTGCGCAGTGTCTTTGTA	0.502																																						ENST00000397910.4																			0				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						c.(17110-17112)aCt>aTt		mucin 16, cell surface associated							167.0	163.0	164.0					19																	9070335		2093	4212	6305	SO:0001583	missense	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:9070335G>A	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.17111C>T	19.37:g.9070335G>A	ENSP00000381008:p.Thr5704Ile						p.T5704I	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN			3	17314	-			5706			Thr-rich.		Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	c.17111C>T	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	5.060	0.196782	0.09599	.	.	ENSG00000181143	ENST00000397910	T	0.27890	1.64	1.54	1.54	0.23209	.	.	.	.	.	T	0.23410	0.0566	N	0.19112	0.55	.	.	.	D	0.62365	0.991	P	0.48840	0.592	T	0.26883	-1.0090	8	0.87932	D	0	.	6.5715	0.22541	0.0:0.0:1.0:0.0	.	5704	B5ME49	.	I	5704	ENSP00000381008:T5704I	ENSP00000381008:T5704I	T	-	2	0	MUC16	8931335	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.347000	0.20014	1.176000	0.42840	0.456000	0.33151	ACT		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		6	70	0	0	0	0.001168	0	6	70				
MALAT1	378938	broad.mit.edu	37	11	65268279	65268279	+	lincRNA	SNP	A	A	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr11:65268279A>T	ENST00000534336.1	+	0	3047				AP000769.7_ENST00000602344.1_lincRNA	NR_002819.2		Q9UHZ2	MALAT_HUMAN	metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)																		TCTGGAACTTACTTATGGTAA	0.448																																						ENST00000534336.1																			0																				52.0	53.0	52.0					11																	65268279		874	1988	2862			0							g.chr11:65268279A>T	AF001540		11q13.1	2013-12-11	2007-11-20		ENSG00000251562	ENSG00000251562		"""Long non-coding RNAs"", ""-"""	29665	non-coding RNA	RNA, long non-coding	"""metastasis associated in lung adenocarcinoma transcript 1"", ""non-protein coding RNA 47"", ""hepcarcin"", ""nuclear enriched abundant transcript 2"", ""nuclear paraspeckle assembly transcript 2 (non-protein coding)"", ""long intergenic non-protein coding RNA 47"""	607924				12970751, 22560368	Standard	NR_002819		Approved	PRO1073, MALAT-1, NCRNA00047, HCN, NEAT2, LINC00047, mascRNA	uc010roh.3	Q9UHZ2	OTTHUMG00000166322		11.37:g.65268279A>T								NR_002819.2						0	3047	+									RNA	SNP	ENST00000534336.1	37																																																																																						0.448	MALAT1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000389143.1	NR_002819		15	21	0	0	0	0.004007	0	15	21				
DNM1P47	100216544	broad.mit.edu	37	15	102292785	102292785	+	RNA	SNP	C	C	G	rs61084368|rs143389223	byFrequency	TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr15:102292785C>G	ENST00000561463.1	+	0	831									DNM1 pseudogene 47									p.Q125E(1)									TGCTGCTTCTCAGAGCTGCTG	0.602																																						ENST00000561463.1																			1	Substitution - Missense(1)	p.Q125E(1)	kidney(1)																																																0							g.chr15:102292785C>G	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102292785C>G														0	831	+									RNA	SNP	ENST00000561463.1	37																																																																																						0.602	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149		3	20	0	0	0	0.001984	0	3	20				
ATP10B	23120	broad.mit.edu	37	5	160047602	160047602	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr5:160047602T>C	ENST00000327245.5	-	15	3014	c.2168A>G	c.(2167-2169)gAt>gGt	p.D723G	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	723					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGCGGCCTCATCAGGGCTCTC	0.642																																						ENST00000327245.5																			0				NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75						c.(2167-2169)gAt>gGt		ATPase, class V, type 10B							33.0	38.0	36.0					5																	160047602		2095	4228	6323	SO:0001583	missense	23120				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity	g.chr5:160047602T>C	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.2168A>G	5.37:g.160047602T>C	ENSP00000313600:p.Asp723Gly					CTC-348L5.1_ENST00000523598.1_RNA	p.D723G	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		15	3014	-	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	723					Q9H725	Missense_Mutation	SNP	ENST00000327245.5	37	c.2168A>G	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.606952	0.87157	.	.	ENSG00000118322	ENST00000327245;ENST00000520108	T;T	0.78595	-1.19;-1.19	5.36	5.36	0.76844	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.91352	0.7272	H	0.95745	3.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.93771	0.7075	9	.	.	.	.	14.5725	0.68220	0.0:0.0:0.0:1.0	.	331;723	Q2YDW8;O94823	.;AT10B_HUMAN	G	723;331	ENSP00000313600:D723G;ENSP00000431081:D331G	.	D	-	2	0	ATP10B	159980180	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	7.888000	0.87302	2.042000	0.60477	0.533000	0.62120	GAT		0.642	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		6	39	0	0	0	0.003080	0	6	39				
TAF1L	138474	broad.mit.edu	37	9	32631455	32631455	+	Missense_Mutation	SNP	G	G	A	rs533523762	byFrequency	TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr9:32631455G>A	ENST00000242310.4	-	1	4212	c.4123C>T	c.(4123-4125)Cgg>Tgg	p.R1375W	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1375					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CCAACTCGCCGTTTCTTCTTT	0.458													G|||	2	0.000399361	0.0	0.0	5008	,	,		21262	0.002		0.0	False		,,,				2504	0.0					ENST00000242310.4																			0				breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159						c.(4123-4125)Cgg>Tgg		TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like							210.0	208.0	209.0					9																	32631455		2203	4300	6503	SO:0001583	missense	138474				male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding	g.chr9:32631455G>A	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4123C>T	9.37:g.32631455G>A	ENSP00000418379:p.Arg1375Trp						p.R1375W	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)	1	4212	-			1375					Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	c.4123C>T	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.605499	0.66445	.	.	ENSG00000122728	ENST00000242310	T	0.10860	2.83	0.479	0.479	0.16796	.	0.000000	0.85682	D	0.000000	T	0.18676	0.0448	M	0.64170	1.965	0.49483	D	0.999799	D	0.71674	0.998	P	0.56916	0.809	T	0.01839	-1.1263	10	0.87932	D	0	.	6.6915	0.23174	2.0E-4:0.0:0.9998:0.0	.	1375	Q8IZX4	TAF1L_HUMAN	W	1375	ENSP00000418379:R1375W	ENSP00000418379:R1375W	R	-	1	2	TAF1L	32621455	1.000000	0.71417	0.976000	0.42696	0.811000	0.45836	2.826000	0.48104	0.507000	0.28148	0.195000	0.17529	CGG		0.458	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			87	141	0	0	0	0.003610	0	87	141				
PCDHGC3	5098	broad.mit.edu	37	5	140857072	140857072	+	Silent	SNP	C	C	T			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr5:140857072C>T	ENST00000308177.3	+	1	1493	c.1389C>T	c.(1387-1389)gaC>gaT	p.D463D	PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	463	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTCCTACGACGTTTACATTG	0.512																																						ENST00000308177.3																			0				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29						c.(1387-1389)gaC>gaT									138.0	145.0	143.0					5																	140857072		2203	4300	6503	SO:0001819	synonymous_variant	0							g.chr5:140857072C>T	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"""Cadherins / Protocadherins : Clustered"""	8716	other	protocadherin	"""cadherin-like 2"", ""protocadherin 2"", ""protocadherin 43"""	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.1389C>T	5.37:g.140857072C>T						PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron	p.D463D	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	1493	+								O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	37	c.1389C>T	CCDS4261.1																																																																																				0.512	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		5	158	0	0	0	0.001168	0	5	158				
SIDT1	54847	broad.mit.edu	37	3	113300224	113300224	+	Missense_Mutation	SNP	T	T	G			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr3:113300224T>G	ENST00000264852.4	+	6	1406	c.680T>G	c.(679-681)cTc>cGc	p.L227R	SIDT1_ENST00000393830.3_Missense_Mutation_p.L227R	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	227					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						GTGTATGATCTCGACCACAAT	0.458																																						ENST00000264852.4																			0				breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						c.(679-681)cTc>cGc		SID1 transmembrane family, member 1							192.0	150.0	165.0					3																	113300224		2203	4300	6503	SO:0001583	missense	54847					integral to membrane		g.chr3:113300224T>G	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.680T>G	3.37:g.113300224T>G	ENSP00000264852:p.Leu227Arg					SIDT1_ENST00000393830.3_Missense_Mutation_p.L227R	p.L227R	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN			6	1406	+			227					Q17RR4	Missense_Mutation	SNP	ENST00000264852.4	37	c.680T>G	CCDS2974.1	.	.	.	.	.	.	.	.	.	.	T	17.71	3.457753	0.63401	.	.	ENSG00000072858	ENST00000264852;ENST00000393830	T;T	0.24350	1.86;1.86	5.12	5.12	0.69794	.	0.000000	0.51477	D	0.000097	T	0.53690	0.1812	M	0.85197	2.74	0.52099	D	0.999944	D	0.89917	1.0	D	0.91635	0.999	T	0.56177	-0.8022	10	0.32370	T	0.25	-15.5368	14.1901	0.65633	0.0:0.0:0.0:1.0	.	227	Q9NXL6	SIDT1_HUMAN	R	227	ENSP00000264852:L227R;ENSP00000377416:L227R	ENSP00000264852:L227R	L	+	2	0	SIDT1	114782914	1.000000	0.71417	0.797000	0.32132	0.586000	0.36452	5.746000	0.68681	2.045000	0.60652	0.482000	0.46254	CTC		0.458	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699		30	42	0	0	0	0.002096	0	30	42				
KRTAP4-8	728224	broad.mit.edu	37	17	39254054	39254054	+	Missense_Mutation	SNP	A	A	T	rs76270529		TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr17:39254054A>T	ENST00000333822.4	-	1	339	c.283T>A	c.(283-285)Tgc>Agc	p.C95S		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	95	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.C95S(4)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						ctggagatgcagcagcTAGGG	0.677																																						ENST00000333822.4																			4	Substitution - Missense(4)	p.C95S(4)	endometrium(3)|kidney(1)	endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						c.(283-285)Tgc>Agc		keratin associated protein 4-8							7.0	11.0	10.0					17																	39254054		685	1582	2267	SO:0001583	missense	728224					keratin filament		g.chr17:39254054A>T	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.283T>A	17.37:g.39254054A>T	ENSP00000328444:p.Cys95Ser						p.C95S	NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN			1	339	-			95			25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].		A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	c.283T>A	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	15.18	2.755714	0.49362	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.02280	4.36	3.11	2.01	0.26516	.	0.000000	0.52532	U	0.000067	T	0.04497	0.0123	M	0.83223	2.63	0.25182	N	0.99019	B	0.21606	0.058	B	0.27887	0.084	T	0.21793	-1.0235	10	0.54805	T	0.06	.	6.3859	0.21559	0.8715:0.0:0.1285:0.0	.	95	Q9BYQ9	KRA48_HUMAN	S	95;80	ENSP00000328444:C95S	ENSP00000414561:C80S	C	-	1	0	KRTAP4-8	36507580	0.999000	0.42202	0.393000	0.26258	0.649000	0.38597	3.122000	0.50446	0.404000	0.25506	0.374000	0.22700	TGC		0.677	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960		5	45	0	0	0	0.000602	0	5	45				
IGLV2-23	28813	broad.mit.edu	37	22	23040595	23040595	+	RNA	SNP	C	C	G			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr22:23040595C>G	ENST00000390306.2	+	0	208				D86994.1_ENST00000385095.1_RNA					immunoglobulin lambda variable 2-23																		CTCCCTCTTTCCAGGGTCCTG	0.617																																						ENST00000390306.2																			0																				64.0	81.0	75.0					22																	23040595		2060	4194	6254			0							g.chr22:23040595C>G	X14616		22q11.2	2012-02-08			ENSG00000211660	ENSG00000211660		"""Immunoglobulins / IGL locus"""	5890	other	immunoglobulin gene							Standard	NG_000002		Approved				OTTHUMG00000151234		22.37:g.23040595C>G														0	208	+									RNA	SNP	ENST00000390306.2	37																																																																																						0.617	IGLV2-23-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000321839.2	NG_000002		20	136	0	0	0	0.002780	0	20	136				
RNF145	153830	broad.mit.edu	37	5	158630630	158630630	+	5'UTR	DEL	T	T	-	rs76451527		TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr5:158630630delT	ENST00000424310.2	-	0	355				RNF145_ENST00000519865.1_5'UTR|RNF145_ENST00000518802.1_Frame_Shift_Del_p.N30fs|RNF145_ENST00000520638.1_Frame_Shift_Del_p.N14fs|RNF145_ENST00000274542.2_Frame_Shift_Del_p.N28fs|RNF145_ENST00000521606.2_Frame_Shift_Del_p.N17fs	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145							integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGCCATGTTGttttttttttt	0.378																																						ENST00000274542.2																			0				endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30						c.(79-81)acfs		ring finger protein 145							47.0	49.0	48.0					5																	158630630		2203	4300	6503	SO:0001623	5_prime_UTR_variant	153830					integral to membrane	zinc ion binding	g.chr5:158630630delT	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"""RING-type (C3HC4) zinc fingers"""	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.-5A>-	5.37:g.158630630delT						RNF145_ENST00000520638.1_Frame_Shift_Del_p.N14fs|RNF145_ENST00000521606.2_Frame_Shift_Del_p.N17fs|RNF145_ENST00000424310.2_5'UTR|RNF145_ENST00000519865.1_5'UTR|RNF145_ENST00000518802.1_Frame_Shift_Del_p.N30fs	p.N28fs	NM_144726.2	NP_653327.1	Q96MT1	RN145_HUMAN	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		2	106	-	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	0					B7Z903|B7Z949|E7EVI7|Q8IVP7	Frame_Shift_Del	DEL	ENST00000424310.2	37	c.80delA	CCDS56390.1																																																																																				0.378	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726		7	55						7	55	---	---	---	---
HERC2P2	400322	broad.mit.edu	37	15	23299147	23299147	+	RNA	DEL	A	A	-	rs572079359	byFrequency	TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr15:23299147delA	ENST00000560464.1	-	0	4510									hect domain and RLD 2 pseudogene 2																		ACATTCAAAGAAAAAAAAAAA	0.313													|||unknown(HR)	437	0.0872604	0.1884	0.1182	5008	,	,		18000	0.0308		0.0268	False		,,,				2504	0.0491					ENST00000560464.1																			0																																																			0							g.chr15:23299147delA	AF041080		15q11.2	2014-03-18			ENSG00000140181				4870	pseudogene	pseudogene						9730612	Standard	NR_002824		Approved	D15F37S3	uc001yvq.2		OTTHUMG00000171926		15.37:g.23299147delA														0	4510	-									RNA	DEL	ENST00000560464.1	37																																																																																						0.313	HERC2P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000415936.1			4	5						4	5	---	---	---	---
ZNF528-AS1	102724105	broad.mit.edu	37	19	52896073	52896074	+	RNA	DEL	TA	TA	-			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr19:52896073_52896074delTA	ENST00000601562.1	-	0	784																											GTGGAAGCTGTATATATATATA	0.46																																						ENST00000601562.1																			0																																																			0							g.chr19:52896073_52896074delTA																													19.37:g.52896083_52896084delTA														0	784	-									RNA	DEL	ENST00000601562.1	37																																																																																						0.460	CTD-3018O17.3-001	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000462867.1			2	4						2	4	---	---	---	---
CD93	22918	broad.mit.edu	37	20	23066789	23066791	+	In_Frame_Del	DEL	AGC	AGC	-			TCGA-DJ-A1QL-01A-11D-A14W-08	TCGA-DJ-A1QL-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79169c46-7049-4576-9885-63973db76ab9	d6ea054f-372b-4fc7-a9f4-c61f74f8f1ee	g.chr20:23066789_23066791delAGC	ENST00000246006.4	-	1	186_188	c.39_41delGCT	c.(37-42)ctgctc>ctc	p.13_14LL>L		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	13					macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					CTGGGTcaggagcagcagcagca	0.709																																						ENST00000246006.4																			0				NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						c.(37-42)ctc>ct		CD93 molecule				4,187,3873		0,0,4,17,153,1858						-10.7	0.0			6	5,391,7426		0,0,5,22,347,3537	no	codingComplex	CD93	NM_012072.3		0,0,9,39,500,5395	A1A1,A1A2,A1R,A2A2,A2R,RR		5.0626,4.6998,4.9386				9,578,11299				SO:0001651	inframe_deletion	22918				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding	g.chr20:23066789_23066791delAGC	U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"""CD molecules"""	15855	protein-coding gene	gene with protein product		120577	"""matrix-remodelling associated 4"", ""complement component 1, q subcomponent, receptor 1"", ""CD93 antigen"""	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.39_41delGCT	20.37:g.23066798_23066800delAGC	ENSP00000246006:p.Leu15del						p.LL13del	NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN			1	186_188	-	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)		13					O00274	In_Frame_Del	DEL	ENST00000246006.4	37	c.39_41delGCT	CCDS13149.1																																																																																				0.709	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072		2	4						2	4	---	---	---	---
