#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
PKD1L2	114780	broad.mit.edu	37	16	81157274	81157274	+	RNA	SNP	G	G	A			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr16:81157274G>A	ENST00000534142.1	-	0	853				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000525539.1_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CTGGTCTCTAGCGTCAGCGTG	0.597																																						uc002fgh.1																			0				breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						c.(6460-6462)Cta>Tta		Homo sapiens polycystic kidney disease 1-like 2 (PKD1L2), transcript variant 1, mRNA.							114.0	114.0	114.0					16																	81157274		2038	4195	6233			114780				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding	g.chr16:81157274G>A	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81157274G>A						PKD1L2_uc002fgf.1_5'UTR|PKD1L2_uc002fgg.1_Non-coding_Transcript	p.L2154L	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN			38	6460	-			2156					Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000534142.1	37	c.6460C>T																																																																																					0.597	PKD1L2-009	PUTATIVE	basic|exp_conf	processed_transcript	polymorphic_pseudogene	OTTHUMT00000387969.1			4	94	0	0	0	1	0	4	94				
SENP7	57337	broad.mit.edu	37	3	101090962	101090962	+	Missense_Mutation	SNP	T	T	G			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr3:101090962T>G	ENST00000394095.2	-	7	739	c.686A>C	c.(685-687)cAa>cCa	p.Q229P	SENP7_ENST00000394091.1_Missense_Mutation_p.Q65P|SENP7_ENST00000314261.7_Missense_Mutation_p.Q163P|SENP7_ENST00000358203.3_Missense_Mutation_p.Q65P|SENP7_ENST00000394094.2_Missense_Mutation_p.Q164P|SENP7_ENST00000348610.3_Missense_Mutation_p.Q196P	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	229						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CTTACTTCGTTGTGAGCCCCT	0.348																																						uc003dut.3																			0				breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						c.(685-687)cAa>cCa		Homo sapiens SUMO1/sentrin specific peptidase 7 (SENP7), transcript variant 1, mRNA.							114.0	109.0	111.0					3																	101090962		2203	4300	6503	SO:0001583	missense	57337				proteolysis	nucleus	cysteine-type peptidase activity	g.chr3:101090962T>G		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.686A>C	3.37:g.101090962T>G	ENSP00000377655:p.Gln229Pro					SENP7_uc003duu.3_Missense_Mutation_p.Q164P|SENP7_uc003duv.3_Missense_Mutation_p.Q196P|SENP7_uc003duw.3_Missense_Mutation_p.Q163P|SENP7_uc003dux.3_Missense_Mutation_p.Q65P	p.Q229P	NM_020654	NP_065705	Q9BQF6	SENP7_HUMAN			6	797	-			229					A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	c.686A>C	CCDS2941.2	.	.	.	.	.	.	.	.	.	.	T	10.49	1.364298	0.24684	.	.	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.21031	2.12;2.11;2.13;2.03;2.03;2.12	5.1	3.94	0.45596	.	0.420489	0.20548	N	0.090172	T	0.32133	0.0819	L	0.56769	1.78	0.09310	N	1	D;D;D;P	0.57571	0.98;0.98;0.967;0.944	P;P;P;P	0.56088	0.731;0.731;0.791;0.623	T	0.09058	-1.0692	10	0.56958	D	0.05	-2.4716	7.7962	0.29148	0.0:0.0961:0.0:0.9039	.	65;163;196;229	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	P	229;164;163;65;65;196	ENSP00000377655:Q229P;ENSP00000377654:Q164P;ENSP00000313624:Q163P;ENSP00000377651:Q65P;ENSP00000350936:Q65P;ENSP00000342159:Q196P	ENSP00000313624:Q163P	Q	-	2	0	SENP7	102573652	0.914000	0.31030	0.039000	0.18376	0.006000	0.05464	1.358000	0.34102	0.897000	0.36392	-0.361000	0.07541	CAA		0.348	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		3	88	0	0	0	1	0	3	88				
SMG1	23049	broad.mit.edu	37	16	18860687	18860687	+	Silent	SNP	T	T	C	rs376900887		TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr16:18860687T>C	ENST00000446231.2	-	36	5887	c.5475A>G	c.(5473-5475)caA>caG	p.Q1825Q	SMG1_ENST00000389467.3_Silent_p.Q1825Q			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1825	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						GTGAGAAAAGTTGCGGAATAA	0.388																																						uc002dfm.3																			0				NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						c.(5473-5475)caA>caG		Homo sapiens smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans) (SMG1), mRNA.		T		0,3744		0,0,1872	99.0	93.0	95.0		5475	0.4	1.0	16		95	1,8213		0,1,4106	no	coding-synonymous	SMG1	NM_015092.4		0,1,5978	CC,CT,TT		0.0122,0.0,0.0084		1825/3662	18860687	1,11957	1872	4107	5979	SO:0001819	synonymous_variant	23049				DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr16:18860687T>C	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.5475A>G	16.37:g.18860687T>C						SMG1_uc010bwb.3_Silent_p.Q1685Q|SMG1_uc010bwa.3_Silent_p.Q556Q|SMG1_uc021ted.1_Silent_p.Q123Q	p.Q1825Q	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN			35	5838	-			1825			FAT.|Interaction with SMG8 and SMG9.		O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	c.5475A>G	CCDS45430.1																																																																																				0.388	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		7	70	0	0	0	1	0	7	70				
SLCO1A2	6579	broad.mit.edu	37	12	21467494	21467494	+	Missense_Mutation	SNP	G	G	C			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr12:21467494G>C	ENST00000307378.6	-	5	1044	c.324C>G	c.(322-324)ttC>ttG	p.F108L	SLCO1A2_ENST00000452078.1_Missense_Mutation_p.F108L|SLCO1A2_ENST00000537524.1_Intron|SLCO1A2_ENST00000390670.3_Missense_Mutation_p.F106L|SLCO1A2_ENST00000473830.1_Intron|SLCO1A2_ENST00000458504.1_Intron	NM_134431.3	NP_602307.1	P46721	SO1A2_HUMAN	solute carrier organic anion transporter family, member 1A2	108					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(6)|upper_aerodigestive_tract(1)	48					Aminohippurate(DB00345)|Atorvastatin(DB01076)|Bumetanide(DB00887)|Chlorambucil(DB00291)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Enalapril(DB00584)|Erythromycin(DB00199)|Estradiol(DB00783)|Estriol(DB04573)|Estrone(DB00655)|Fexofenadine(DB00950)|Glyburide(DB01016)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Indinavir(DB00224)|Indomethacin(DB00328)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Mirabegron(DB08893)|Naloxone(DB01183)|Naproxen(DB00788)|Nelfinavir(DB00220)|Ouabain(DB01092)|Pravastatin(DB00175)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rocuronium(DB00728)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Simvastatin(DB00641)|Spironolactone(DB00421)|Sumatriptan(DB00669)|Tauroursodeoxycholic acid(DB08834)|Testosterone(DB00624)|Tolbutamide(DB01124)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)	GGTTCATGAGGAAATGAGGTA	0.398																																						uc001res.3																			0				breast(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(6)|upper_aerodigestive_tract(1)	48						c.(322-324)ttC>ttG		Homo sapiens solute carrier organic anion transporter family, member 1A2 (SLCO1A2), transcript variant 1, mRNA.							155.0	141.0	146.0					12																	21467494		2203	4300	6503	SO:0001583	missense	6579				bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity	g.chr12:21467494G>C		CCDS8686.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000084453	ENSG00000084453		"""Solute carriers"""	10956	protein-coding gene	gene with protein product		602883	"""solute carrier family 21 (organic anion transporter), member 3"""	SLC21A3		9007731	Standard	NM_134431		Approved	OATP, OATP1A2, OATP-A	uc001rer.3	P46721	OTTHUMG00000156259	ENST00000307378.6:c.324C>G	12.37:g.21467494G>C	ENSP00000305974:p.Phe108Leu					SLCO1A2_uc010siq.2_Intron|SLCO1A2_uc010sio.2_Intron|SLCO1A2_uc001rer.3_Missense_Mutation_p.F108L|SLCO1A2_uc010sip.2_Intron|SLCO1A2_uc001ret.3_Missense_Mutation_p.F106L|SLCO1A2_uc001reu.2_Missense_Mutation_p.F88L	p.F108L	NM_134431	NP_602307	P46721	SO1A2_HUMAN			4	1045	-			108					Q9UGP7|Q9UL38	Missense_Mutation	SNP	ENST00000307378.6	37	c.324C>G	CCDS8686.1	.	.	.	.	.	.	.	.	.	.	G	19.77	3.889813	0.72524	.	.	ENSG00000084453	ENST00000307378;ENST00000452078;ENST00000390670;ENST00000422327;ENST00000453443	T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68	5.32	0.355	0.16069	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.67154	0.2863	M	0.87617	2.895	0.38331	D	0.943794	P;P;D	0.64830	0.955;0.944;0.994	P;P;D	0.71870	0.657;0.526;0.975	T	0.70396	-0.4883	10	0.66056	D	0.02	.	10.2403	0.43308	0.4831:0.0:0.5169:0.0	.	88;106;108	Q8IV69;P46721-2;P46721	.;.;SO1A2_HUMAN	L	108;108;106;108;108	ENSP00000305974:F108L;ENSP00000393973:F108L;ENSP00000375088:F106L;ENSP00000416190:F108L;ENSP00000409314:F108L	ENSP00000305974:F108L	F	-	3	2	SLCO1A2	21358761	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	0.718000	0.25866	-0.090000	0.12462	0.655000	0.94253	TTC		0.398	SLCO1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343648.3	NM_021094		3	85	0	0	0	1	0	3	85				
IFIT1B	439996	broad.mit.edu	37	10	91144286	91144286	+	Silent	SNP	T	T	C			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr10:91144286T>C	ENST00000371809.3	+	2	1296	c.1216T>C	c.(1216-1218)Ttg>Ctg	p.L406L	LIPA_ENST00000371837.1_Intron	NM_001010987.2	NP_001010987.1	Q5T764	IFT1B_HUMAN	interferon-induced protein with tetratricopeptide repeats 1B	406										endometrium(2)|large_intestine(3)|lung(8)	13						TTTAAAAGGTTTGAAAATAGA	0.363																																						uc001kgh.3																			0				endometrium(2)|large_intestine(3)|lung(8)	13						c.(1216-1218)Ttg>Ctg		Homo sapiens interferon-induced protein with tetratricopeptide repeats 1B (IFIT1B), mRNA.							74.0	77.0	76.0					10																	91144286		2203	4300	6503	SO:0001819	synonymous_variant	439996						binding	g.chr10:91144286T>C		CCDS31242.1	10q23.31	2014-05-22	2010-03-22	2010-03-22	ENSG00000204010	ENSG00000204010		"""Tetratricopeptide (TTC) repeat domain containing"""	23442	protein-coding gene	gene with protein product			"""interferon-induced protein with tetratricopeptide repeats 1-like"""	IFIT1L			Standard	NM_001010987		Approved	bA149I23.6	uc001kgh.3	Q5T764	OTTHUMG00000018709	ENST00000371809.3:c.1216T>C	10.37:g.91144286T>C						LIPA_uc001kgb.4_Intron|LIPA_uc001kgc.4_Intron	p.L406L	NM_001010987	NP_001010987	Q5T764	IFT1B_HUMAN			1	1296	+			406					A7E245	Silent	SNP	ENST00000371809.3	37	c.1216T>C	CCDS31242.1																																																																																				0.363	IFIT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049296.3	NM_001010987		36	66	0	0	0	1	0	36	66				
KCTD3	51133	broad.mit.edu	37	1	215792548	215792548	+	Silent	SNP	T	T	C			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr1:215792548T>C	ENST00000259154.4	+	17	2095	c.1801T>C	c.(1801-1803)Ttg>Ctg	p.L601L	KCTD3_ENST00000495537.1_3'UTR	NM_016121.3	NP_057205.2	Q9Y597	KCTD3_HUMAN	potassium channel tetramerization domain containing 3	601					protein homooligomerization (GO:0051260)					breast(4)|endometrium(2)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)	33				all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)		TCAATGTGATTTGAGCACATC	0.393																																						uc001hks.3																			0				breast(4)|endometrium(2)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)	33						c.(1801-1803)Ttg>Ctg		Homo sapiens potassium channel tetramerisation domain containing 3 (KCTD3), mRNA.							132.0	135.0	134.0					1																	215792548		2203	4300	6503	SO:0001819	synonymous_variant	51133					voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity	g.chr1:215792548T>C	AK024547	CCDS1515.1	1q41	2013-06-20	2013-06-20		ENSG00000136636	ENSG00000136636			21305	protein-coding gene	gene with protein product		613272	"""potassium channel tetramerisation domain containing 3"""			10508479	Standard	NM_016121		Approved	NY-REN-45	uc001hks.3	Q9Y597	OTTHUMG00000037019	ENST00000259154.4:c.1801T>C	1.37:g.215792548T>C						KCTD3_uc001hkt.3_Silent_p.L599L|KCTD3_uc010pub.2_Silent_p.L499L|KCTD3_uc009xdn.3_Silent_p.L325L	p.L601L	NM_016121	NP_057205	Q9Y597	KCTD3_HUMAN		all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)	16	2095	+			601					A0AV15|D3DTA6|Q49AG7|Q504Q9|Q6PJN6|Q8ND58|Q8NDJ0|Q8WX16	Silent	SNP	ENST00000259154.4	37	c.1801T>C	CCDS1515.1																																																																																				0.393	KCTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089871.2	NM_016121		18	88	0	0	0	1	0	18	88				
PTENP1	11191	broad.mit.edu	37	9	33676262	33676262	+	RNA	SNP	G	G	A	rs184983613		TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr9:33676262G>A	ENST00000532280.1	-	0	1235					NR_023917.1				phosphatase and tensin homolog pseudogene 1 (functional)																		ATACCAGTTCGTCCCTTTCCA	0.393																																						uc003zth.4																			0											c.(286-288)Cga>Tga		Homo sapiens phosphatase and tensin homolog pseudogene 1 (PTENP1), non-coding RNA.																																						11191							g.chr9:33676262G>A	AF023139, BC038293, BY797336		9p13.3	2014-09-11	2014-01-16		ENSG00000237984	ENSG00000237984		"""-"""	9589	pseudogene	pseudogene		613531	"""phosphatase and tensin homolog pseudogene 1"""			9393738, 9620558	Standard	NR_023917		Approved	PTEN2, psiPTEN, PTH2, PTEN-rs, PTENpg1	uc003zth.4		OTTHUMG00000000410		9.37:g.33676262G>A							p.R96*							0	1157	-									Nonsense_Mutation	SNP	ENST00000532280.1	37	c.286C>T																																																																																					0.393	PTENP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000395145.1	NR_023917		24	99	0	0	0	1	0	24	99				
SRPK2	6733	broad.mit.edu	37	7	104782687	104782687	+	Silent	SNP	T	T	C			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr7:104782687T>C	ENST00000393651.3	-	11	1398	c.1311A>G	c.(1309-1311)acA>acG	p.T437T	SRPK2_ENST00000357311.3_Silent_p.T426T|SRPK2_ENST00000489828.1_Silent_p.T426T	NM_182692.1	NP_872634.1			SRSF protein kinase 2											NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						AGCTGCTATATGTGTAATCAC	0.428																																						uc003vcv.3																			0				NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						c.(1309-1311)acA>acG		Homo sapiens SRSF protein kinase 2 (SRPK2), transcript variant 1, mRNA.							196.0	186.0	189.0					7																	104782687		2203	4300	6503	SO:0001819	synonymous_variant	6733				angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity	g.chr7:104782687T>C	U88666	CCDS5735.1, CCDS34724.1	7q22-q31.1	2010-06-23	2010-06-23		ENSG00000135250	ENSG00000135250			11306	protein-coding gene	gene with protein product	"""SR protein kinase 2"", ""serine/arginine-rich splicing factor kinase 2"""	602980	"""SFRS protein kinase 2"""			8208298, 9472028	Standard	NM_182692		Approved	SFRSK2	uc003vcv.4	P78362	OTTHUMG00000157405	ENST00000393651.3:c.1311A>G	7.37:g.104782687T>C						SRPK2_uc003vct.3_Silent_p.T426T|SRPK2_uc003vcu.3_Silent_p.T426T|SRPK2_uc003vcw.1_Silent_p.T426T	p.T437T	NM_182692	NP_872634	P78362	SRPK2_HUMAN			10	1399	-			426			Protein kinase.			Silent	SNP	ENST00000393651.3	37	c.1311A>G	CCDS34724.1	.	.	.	.	.	.	.	.	.	.	T	8.959	0.970114	0.18659	.	.	ENSG00000135250	ENST00000477925	.	.	.	5.32	-9.6	0.00553	.	.	.	.	.	T	0.43765	0.1262	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	T	0.51309	-0.8722	4	.	.	.	-11.4267	6.6801	0.23115	0.1911:0.5414:0.0771:0.1904	.	.	.	.	V	33	.	.	I	-	1	0	SRPK2	104569923	0.104000	0.21937	0.654000	0.29608	0.991000	0.79684	-0.743000	0.04845	-1.880000	0.01125	-0.375000	0.07067	ATA		0.428	SRPK2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348723.1	NM_182691		8	139	0	0	0	1	0	8	139				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	uc003vwc.4	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333	NP_004324	P15056	BRAF_HUMAN			14	1860	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		30	45	0	0	0	1	0	30	45				
ANGPTL1	9068	broad.mit.edu	37	1	178834453	178834453	+	Silent	SNP	T	T	C			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr1:178834453T>C	ENST00000234816.2	-	3	906	c.459A>G	c.(457-459)caA>caG	p.Q153Q	ANGPTL1_ENST00000367629.1_Silent_p.Q153Q|RALGPS2_ENST00000367635.3_Intron|RALGPS2_ENST00000367634.2_Intron	NM_004673.3	NP_004664.1	O95841	ANGL1_HUMAN	angiopoietin-like 1	153					transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(2)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	14						TGTTTTCCAGTTGGGAAAGTT	0.388																																						uc001gma.3																			0				breast(2)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	14						c.(457-459)caA>caG		Homo sapiens angiopoietin-like 1 (ANGPTL1), mRNA.							104.0	97.0	99.0					1																	178834453		2203	4300	6503	SO:0001819	synonymous_variant	9068					extracellular space	receptor binding	g.chr1:178834453T>C	AF107253	CCDS1327.1	1q25.2	2013-02-06			ENSG00000116194	ENSG00000116194		"""Fibrinogen C domain containing"""	489	protein-coding gene	gene with protein product	"""angioarrestin"""	603874		ANGPT3		10025962, 9286704	Standard	NM_004673		Approved	ANG3, AngY, ARP1	uc001gma.3	O95841	OTTHUMG00000035075	ENST00000234816.2:c.459A>G	1.37:g.178834453T>C						RALGPS2_uc001gly.1_Intron|RALGPS2_uc010pnb.2_Intron|RALGPS2_uc001glz.3_Intron|ANGPTL1_uc001gmb.3_Silent_p.Q153Q|ANGPTL1_uc010pnc.1_Silent_p.Q75Q	p.Q153Q	NM_004673	NP_004664	O95841	ANGL1_HUMAN			2	935	-			153					Q5T5Z5	Silent	SNP	ENST00000234816.2	37	c.459A>G	CCDS1327.1																																																																																				0.388	ANGPTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084924.1	NM_004673		11	26	0	0	0	1	0	11	26				
AFF2	2334	broad.mit.edu	37	X	148044403	148044403	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chrX:148044403C>T	ENST00000370460.2	+	13	3328	c.2849C>T	c.(2848-2850)aCa>aTa	p.T950I	AFF2_ENST00000342251.3_Missense_Mutation_p.T917I|AFF2_ENST00000370457.5_Missense_Mutation_p.T917I|AFF2_ENST00000286437.5_Missense_Mutation_p.T591I	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	950					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GGACAAATCACATCTACCAAA	0.433																																						uc004fcp.3																			0				breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109						c.(2848-2850)aCa>aTa		Homo sapiens AF4/FMR2 family, member 2 (AFF2), transcript variant 1, mRNA.							107.0	92.0	97.0					X																	148044403		2203	4300	6503	SO:0001583	missense	2334				RNA splicing|brain development|mRNA processing|regulation of RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding	g.chrX:148044403C>T	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.2849C>T	X.37:g.148044403C>T	ENSP00000359489:p.Thr950Ile					AFF2_uc004fcq.3_Missense_Mutation_p.T940I|AFF2_uc004fcr.3_Missense_Mutation_p.T911I|AFF2_uc011mxb.2_Missense_Mutation_p.T915I|AFF2_uc004fcs.3_Missense_Mutation_p.T917I|AFF2_uc011mxc.2_Missense_Mutation_p.T591I	p.T950I	NM_002025	NP_002016	P51816	AFF2_HUMAN			12	3328	+	Acute lymphoblastic leukemia(192;6.56e-05)		950					A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	c.2849C>T	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.963430	0.34659	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	5.78	3.0	0.34707	.	0.699047	0.14048	N	0.344921	T	0.48857	0.1523	L	0.47716	1.5	0.31331	N	0.684775	B;B;B;B;B;B	0.17667	0.023;0.004;0.004;0.004;0.019;0.023	B;B;B;B;B;B	0.17433	0.012;0.011;0.011;0.011;0.011;0.018	T	0.48399	-0.9039	10	0.33940	T	0.23	.	2.9128	0.05743	0.1478:0.554:0.1401:0.1581	.	591;915;917;911;940;950	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	I	950;917;917;591	ENSP00000359489:T950I;ENSP00000359486:T917I;ENSP00000345459:T917I;ENSP00000286437:T591I	ENSP00000286437:T591I	T	+	2	0	AFF2	147852099	0.978000	0.34361	0.621000	0.29145	0.137000	0.21094	0.905000	0.28504	0.665000	0.31066	0.600000	0.82982	ACA		0.433	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		6	52	0	0	0	1	0	6	52				
STC2	8614	broad.mit.edu	37	5	172755126	172755126	+	Missense_Mutation	SNP	C	C	G			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr5:172755126C>G	ENST00000265087.4	-	1	1380	c.71G>C	c.(70-72)gGg>gCg	p.G24A		NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	24					cellular calcium ion homeostasis (GO:0006874)|cellular response to hypoxia (GO:0071456)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|regulation of hormone biosynthetic process (GO:0046885)|regulation of store-operated calcium entry (GO:2001256)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGCGTCGGTCCCCCGCGCCGG	0.637																																						uc003mco.1																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25						c.(70-72)gGg>gCg		Homo sapiens stanniocalcin 2 (STC2), mRNA.							102.0	105.0	104.0					5																	172755126		2203	4300	6503	SO:0001583	missense	8614				cell surface receptor linked signaling pathway|cell-cell signaling	extracellular region	hormone activity	g.chr5:172755126C>G	AB012664	CCDS4388.1	5q35.2	2004-05-17			ENSG00000113739	ENSG00000113739			11374	protein-coding gene	gene with protein product		603665				9723890, 9753616	Standard	NM_003714		Approved	STC-2	uc003mco.1	O76061	OTTHUMG00000130542	ENST00000265087.4:c.71G>C	5.37:g.172755126C>G	ENSP00000265087:p.Gly24Ala					STC2_uc003mcn.1_5'Flank	p.G24A	NM_003714	NP_003705	O76061	STC2_HUMAN	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		0	1381	-	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	24						Missense_Mutation	SNP	ENST00000265087.4	37	c.71G>C	CCDS4388.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.948269	0.73787	.	.	ENSG00000113739	ENST00000265087	.	.	.	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.75199	0.3817	L	0.57536	1.79	0.80722	D	1	D	0.67145	0.996	D	0.67548	0.952	T	0.76705	-0.2861	9	0.56958	D	0.05	-33.512	17.0331	0.86466	0.0:1.0:0.0:0.0	.	24	O76061	STC2_HUMAN	A	24	.	ENSP00000265087:G24A	G	-	2	0	STC2	172687732	1.000000	0.71417	0.991000	0.47740	0.236000	0.25371	6.509000	0.73725	2.554000	0.86153	0.655000	0.94253	GGG		0.637	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252965.1	NM_003714		22	101	0	0	0	1	0	22	101				
GALNT1	2589	broad.mit.edu	37	18	33271056	33271056	+	Silent	SNP	G	G	A			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr18:33271056G>A	ENST00000269195.5	+	7	1162	c.1059G>A	c.(1057-1059)acG>acA	p.T353T	GALNT1_ENST00000537549.1_Silent_p.T293T	NM_020474.3	NP_065207.2	Q10472	GALT1_HUMAN	polypeptide N-acetylgalactosaminyltransferase 1	353					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.T353T(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(4)|stomach(1)	21						CACCTTACACGTTTCCAGGAG	0.403																																						uc010dmu.3																			1	Substitution - coding silent(1)	p.T353T(2)	lung(1)	autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(4)|stomach(1)	21						c.(1057-1059)acG>acA		Homo sapiens UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1) (GALNT1), mRNA.							175.0	170.0	172.0					18																	33271056		2203	4299	6502	SO:0001819	synonymous_variant	2589				protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	Golgi cisterna membrane|extracellular region|integral to membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding	g.chr18:33271056G>A		CCDS11915.1	18q12.1	2014-03-13	2014-03-13		ENSG00000141429	ENSG00000141429	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4123	protein-coding gene	gene with protein product	"""protein-UDP acetylgalactosaminyltransferase 1"", ""polypeptide GalNAc transferase 1"""	602273	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1)"""			7592619, 12199709	Standard	NM_020474		Approved	GalNAc-T1	uc002kzb.3	Q10472	OTTHUMG00000132567	ENST00000269195.5:c.1059G>A	18.37:g.33271056G>A						GALNT1_uc002kyz.4_Silent_p.T293T|GALNT1_uc002kzb.3_Silent_p.T353T	p.T353T	NM_020474	NP_065207	Q10472	GALT1_HUMAN			7	1112	+			353					Q86TJ7|Q9UM86	Silent	SNP	ENST00000269195.5	37	c.1059G>A	CCDS11915.1																																																																																				0.403	GALNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255771.2	NM_020474		9	158	0	0	0	1	0	9	158				
WDR45B	56270	broad.mit.edu	37	17	80579584	80579584	+	Silent	SNP	G	G	A			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr17:80579584G>A	ENST00000392325.4	-	6	713	c.519C>T	c.(517-519)agC>agT	p.S173S	WDR45B_ENST00000571835.1_5'UTR	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	173																	GCTTCTCCGTGCTGGCCAGGT	0.582																																						uc002kfq.3																			0				breast(2)|central_nervous_system(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	12						c.(517-519)agC>agT		Homo sapiens WDR45-like (WDR45L), mRNA.							85.0	67.0	73.0					17																	80579584		2203	4300	6503	SO:0001819	synonymous_variant	56270				autophagy|response to starvation	organelle membrane	phosphatidylinositol-3,5-bisphosphate binding	g.chr17:80579584G>A	AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580		"""WD repeat domain containing"""	25072	protein-coding gene	gene with protein product		609226	"""WDR45-like"""	WDR45L		12477932	Standard	NM_019613		Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.519C>T	17.37:g.80579584G>A						WDR45L_uc002kfr.3_Non-coding_Transcript	p.S173S	NM_019613	NP_062559	Q5MNZ6	WIPI3_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.0835)		5	714	-	Breast(20;0.00106)|all_neural(118;0.0952)	all_cancers(8;0.101)|all_epithelial(8;0.198)	173					O95328|Q2MCP6|Q6IBN2	Silent	SNP	ENST00000392325.4	37	c.519C>T	CCDS11815.2																																																																																				0.582	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613		7	35	0	0	0	1	0	7	35				
KIAA0141	9812	broad.mit.edu	37	5	141307808	141307808	+	Silent	SNP	C	C	A			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr5:141307808C>A	ENST00000432126.2	+	4	491	c.357C>A	c.(355-357)tcC>tcA	p.S119S	KIAA0141_ENST00000194118.4_Silent_p.S119S	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	119					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACACTGCTCCTGGCACAGTC	0.627																																						uc003lls.3																			0		p.C118*(1)		endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16						c.(355-357)tcC>tcA		Homo sapiens KIAA0141 (KIAA0141), nuclear gene encoding mitochondrial protein, transcript variant 2, mRNA.							108.0	99.0	102.0					5																	141307808		2203	4300	6503	SO:0001819	synonymous_variant	9812				apoptosis|regulation of caspase activity	mitochondrion	protein binding	g.chr5:141307808C>A	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"""death ligand signal enhancer"""	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.357C>A	5.37:g.141307808C>A						KIAA0141_uc003llt.3_Silent_p.S119S	p.S119S	NM_001142603	NP_055588	Q14154	DELE_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		3	479	+		all_hematologic(541;0.118)	119					Q969R4|Q96EU9	Silent	SNP	ENST00000432126.2	37	c.357C>A	CCDS4268.1																																																																																				0.627	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773		6	58	0	0	0	1	0	6	58				
PARPBP	55010	broad.mit.edu	37	12	102559570	102559570	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr12:102559570G>A	ENST00000358383.5	+	6	775	c.730G>A	c.(730-732)Gat>Aat	p.D244N	PARPBP_ENST00000543784.1_Missense_Mutation_p.D130N|PARPBP_ENST00000378128.3_Missense_Mutation_p.D244N|PARPBP_ENST00000327680.2_Missense_Mutation_p.D163N|PARPBP_ENST00000535811.1_Intron|PARPBP_ENST00000541394.1_Missense_Mutation_p.D321N|PARPBP_ENST00000392911.2_Missense_Mutation_p.D163N			Q9NWS1	PARI_HUMAN	PARP1 binding protein	244					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(8)|urinary_tract(2)	11						ACCACCATCAGATCCTTTAAG	0.363																																						uc010swa.2																			0				endometrium(1)|lung(8)|urinary_tract(2)	11						c.(961-963)Gat>Aat		Homo sapiens PARP1 binding protein (PARPBP), mRNA.							131.0	131.0	131.0					12																	102559570		2203	4300	6503	SO:0001583	missense	55010				response to DNA damage stimulus	cytoplasm|nucleus	DNA binding	g.chr12:102559570G>A	AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"""PARP-1 binding protein"""	613687	"""chromosome 12 open reading frame 48"""	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.730G>A	12.37:g.102559570G>A	ENSP00000351153:p.Asp244Asn					PARPBP_uc001tjf.3_Missense_Mutation_p.D244N|PARPBP_uc001tjg.3_Missense_Mutation_p.D163N|PARPBP_uc001tjh.3_Missense_Mutation_p.D163N|PARPBP_uc010swb.2_Missense_Mutation_p.D130N|PARPBP_uc009zuc.3_Intron|PARPBP_uc001tjj.3_5'UTR|PARPBP_uc001tjk.3_Missense_Mutation_p.D244N|PARPBP_uc009zud.3_Missense_Mutation_p.D244N	p.D321N	NM_017915	NP_060385	Q9NWS1	PR1BP_HUMAN			6	1073	+			244					B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Missense_Mutation	SNP	ENST00000358383.5	37	c.961G>A	CCDS9090.2	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934873	0.73442	.	.	ENSG00000185480	ENST00000378128;ENST00000327680;ENST00000541394;ENST00000543784;ENST00000358383;ENST00000392911;ENST00000417507;ENST00000412715	T;T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98	6.08	5.19	0.71726	.	0.129506	0.64402	N	0.000001	T	0.58308	0.2113	L	0.50333	1.59	0.52501	D	0.999953	D;P;B;D;B	0.89917	0.998;0.617;0.36;1.0;0.36	D;B;B;D;B	0.77004	0.958;0.403;0.181;0.989;0.181	T	0.57177	-0.7856	10	0.40728	T	0.16	-11.7195	15.2802	0.73778	0.0669:0.0:0.9331:0.0	.	130;321;244;244;244	B4DT40;B4DZ31;Q9NWS1-6;Q9NWS1-7;Q9NWS1	.;.;.;.;PR1BP_HUMAN	N	244;163;321;130;244;163;211;211	ENSP00000367368:D244N;ENSP00000332915:D163N;ENSP00000440850:D321N;ENSP00000444576:D130N;ENSP00000351153:D244N;ENSP00000376643:D163N;ENSP00000411313:D211N;ENSP00000393867:D211N	ENSP00000332915:D163N	D	+	1	0	C12orf48	101083700	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	5.750000	0.68712	1.575000	0.49775	0.591000	0.81541	GAT		0.363	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915		7	126	0	0	0	1	0	7	126				
MUC16	94025	broad.mit.edu	37	19	9074483	9074483	+	Silent	SNP	A	A	G			TCGA-DJ-A1QF-01A-12D-A14W-08	TCGA-DJ-A1QF-10A-01D-A14W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b21fe815-1958-4e1f-ad92-ae5c83303c82	6c5b9e0f-d833-440a-89ff-a5fb5f8b7579	g.chr19:9074483A>G	ENST00000397910.4	-	3	13166	c.12963T>C	c.(12961-12963)gcT>gcC	p.A4321A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4323	Ser-rich.|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						TTGTCTCTGTAGCAGAGCTGG	0.502																																						uc002mkp.3																			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.(12961-12963)gcT>gcC		Homo sapiens mucin 16, cell surface associated (MUC16), mRNA.							99.0	99.0	99.0					19																	9074483		2108	4221	6329	SO:0001819	synonymous_variant	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:9074483A>G	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.12963T>C	19.37:g.9074483A>G							p.A4321A	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN			2	13167	-			4323			Ser-rich.|Thr-rich.		Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	c.12963T>C	CCDS54212.1																																																																																				0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		14	20	0	0	0	1	0	14	20				
