#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_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
PDS5B	23047	broad.mit.edu	37	13	33315257	33315257	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr13:33315257G>A	ENST00000315596.10	+	22	2632	c.2446G>A	c.(2446-2448)Gaa>Aaa	p.E816K		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	816					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		GGTTCCAGATGAAGAAGTATC	0.289																																						uc010abf.3																			0				NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62						c.(2446-2448)Gaa>Aaa		Homo sapiens PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae) (PDS5B), mRNA.							101.0	93.0	96.0					13																	33315257		1807	4062	5869	SO:0001583	missense	23047				cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding	g.chr13:33315257G>A	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.2446G>A	13.37:g.33315257G>A	ENSP00000313851:p.Glu816Lys		Somatic				PDS5B_uc010abg.3_Non-coding_Transcript	p.E816K	NM_015032	NP_055847	WXS	Illumina GAIIx	Phase_I	Q9NTI5	PDS5B_HUMAN		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)	21	2632	+		Lung SC(185;0.0367)	816					Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	37	c.2446G>A	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.914279	0.92178	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	.	.	.	5.78	5.78	0.91487	Armadillo-like helical (1);Armadillo-type fold (1);	0.092724	0.85682	D	0.000000	T	0.54062	0.1835	L	0.38175	1.15	0.80722	D	1	P	0.37663	0.604	B	0.40066	0.318	T	0.51044	-0.8755	9	0.37606	T	0.19	-5.0161	19.0003	0.92830	0.0:0.0:1.0:0.0	.	816	Q9NTI5	PDS5B_HUMAN	K	816	.	ENSP00000313851:E816K	E	+	1	0	PDS5B	32213257	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.095000	0.94175	2.735000	0.93741	0.655000	0.94253	GAA		0.289	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		21	61	0	0	0	1	0	21	61				
PTGER4	5734	broad.mit.edu	37	5	40681232	40681232	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr5:40681232G>A	ENST00000302472.3	+	2	1161	c.137G>A	c.(136-138)cGc>cAc	p.R46H	PTGER4_ENST00000514343.1_3'UTR	NM_000958.2	NP_000949.1	P35408	PE2R4_HUMAN	prostaglandin E receptor 4 (subtype EP4)	46					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|bone development (GO:0060348)|cellular response to mechanical stimulus (GO:0071260)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|JNK cascade (GO:0007254)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of eosinophil extravasation (GO:2000420)|negative regulation of inflammatory response (GO:0050728)|negative regulation of integrin activation (GO:0033624)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|regulation of ossification (GO:0030278)|regulation of stress fiber assembly (GO:0051492)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|T-helper cell differentiation (GO:0042093)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)			breast(1)|endometrium(3)|liver(1)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23					Dinoprostone(DB00917)|Misoprostol(DB00929)	TGCAAGTCGCGCAAGGAGCAG	0.627											OREG0016588	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc003jlz.3																			0				breast(1)|endometrium(3)|liver(1)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						c.(136-138)cGc>cAc		Homo sapiens prostaglandin E receptor 4 (subtype EP4) (PTGER4), mRNA.							72.0	63.0	66.0					5																	40681232		2203	4300	6503	SO:0001583	missense	5734				G-protein signaling, coupled to cAMP nucleotide second messenger|immune response	integral to membrane|plasma membrane	prostaglandin E receptor activity	g.chr5:40681232G>A	L28175	CCDS3930.1	5p13.1	2012-08-08			ENSG00000171522	ENSG00000171522		"""GPCR / Class A : Prostanoid receptors"""	9596	protein-coding gene	gene with protein product		601586				7759114, 8661119	Standard	NM_000958		Approved	EP4	uc003jlz.3	P35408	OTTHUMG00000094769	ENST00000302472.3:c.137G>A	5.37:g.40681232G>A	ENSP00000302846:p.Arg46His		Somatic	OREG0016588	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	895		p.R46H	NM_000958	NP_000949	WXS	Illumina GAIIx	Phase_I	P35408	PE2R4_HUMAN			1	729	+			46					Q3MJ87	Missense_Mutation	SNP	ENST00000302472.3	37	c.137G>A	CCDS3930.1	.	.	.	.	.	.	.	.	.	.	G	36	5.603239	0.96614	.	.	ENSG00000171522	ENST00000302472	T	0.19669	2.13	5.37	5.37	0.77165	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.54382	0.1855	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.61686	-0.7012	10	0.66056	D	0.02	-25.0634	19.1085	0.93307	0.0:0.0:1.0:0.0	.	46	P35408	PE2R4_HUMAN	H	46	ENSP00000302846:R46H	ENSP00000302846:R46H	R	+	2	0	PTGER4	40716989	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.950000	0.87804	2.528000	0.85240	0.462000	0.41574	CGC		0.627	PTGER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211578.2	NM_000958		4	76	0	0	0	1	0	4	76				
TTLL4	9654	broad.mit.edu	37	2	219603432	219603432	+	Missense_Mutation	SNP	G	G	A	rs138326187	byFrequency	TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr2:219603432G>A	ENST00000392102.1	+	3	1373	c.1033G>A	c.(1033-1035)Gca>Aca	p.A345T	TTLL4_ENST00000258398.4_Missense_Mutation_p.A345T|TTLL4_ENST00000457313.1_Missense_Mutation_p.A180T|TTLL4_ENST00000442769.1_Missense_Mutation_p.A345T	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	345					protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		GAAATTGACCGCAAGAGGCTT	0.542																																					GBM(172;1818 2053 15407 20943 49753)	uc002viy.3																			0				endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39						c.(1033-1035)Gca>Aca		Homo sapiens tubulin tyrosine ligase-like family, member 4 (TTLL4), mRNA.							100.0	97.0	98.0					2																	219603432		2203	4300	6503	SO:0001583	missense	9654				protein polyglutamylation	cilium|microtubule basal body	ATP binding|tubulin binding|tubulin-tyrosine ligase activity	g.chr2:219603432G>A		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"""Tubulin tyrosine ligase-like family"""	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.1033G>A	2.37:g.219603432G>A	ENSP00000375951:p.Ala345Thr		Somatic				TTLL4_uc010zkl.1_Missense_Mutation_p.A180T|TTLL4_uc010fvx.3_Missense_Mutation_p.A345T	p.A345T	NM_014640	NP_055455	WXS	Illumina GAIIx	Phase_I	Q14679	TTLL4_HUMAN		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)	2	1403	+		Renal(207;0.0915)	345					A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	37	c.1033G>A	CCDS2422.1	.	.	.	.	.	.	.	.	.	.	G	4.815	0.151619	0.09185	.	.	ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000442769;ENST00000258398	T;T;T;T	0.04970	3.74;3.99;3.52;3.99	4.57	0.74	0.18330	.	0.607687	0.14727	N	0.301996	T	0.03263	0.0095	L	0.29908	0.895	0.09310	N	1	P;B;P	0.44006	0.824;0.016;0.824	B;B;B	0.30646	0.086;0.004;0.118	T	0.43196	-0.9406	10	0.41790	T	0.15	.	4.2768	0.10813	0.3392:0.0:0.5099:0.1509	.	180;345;345	E9PH58;E7EX20;Q14679	.;.;TTLL4_HUMAN	T	180;345;345;345	ENSP00000393332:A180T;ENSP00000375951:A345T;ENSP00000396555:A345T;ENSP00000258398:A345T	ENSP00000258398:A345T	A	+	1	0	TTLL4	219311676	0.408000	0.25360	0.177000	0.23020	0.013000	0.08279	1.559000	0.36320	-0.047000	0.13423	-1.114000	0.02060	GCA		0.542	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		4	109	0	0	0	1	0	4	109				
CRP	1401	broad.mit.edu	37	1	159683396	159683396	+	Silent	SNP	G	G	A			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr1:159683396G>A	ENST00000255030.5	-	2	697	c.594C>T	c.(592-594)ttC>ttT	p.F198F	CRP_ENST00000368111.1_Silent_p.F76F|CRP_ENST00000368112.1_Intron|CRP_ENST00000368110.1_Silent_p.F76F|CRP_ENST00000343919.2_Silent_p.F76F|CRP_ENST00000437342.1_Silent_p.F20F|CRP_ENST00000473196.1_5'UTR	NM_000567.2	NP_000558.2	P02741	CRP_HUMAN	C-reactive protein, pentraxin-related	198	Pentaxin.				acute-phase response (GO:0006953)|aging (GO:0007568)|cellular response to calcium ion (GO:0071277)|complement activation, classical pathway (GO:0006958)|defense response to Gram-positive bacterium (GO:0050830)|inflammatory response (GO:0006954)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|opsonization (GO:0008228)|positive regulation of dendrite development (GO:1900006)|protein polymerization (GO:0051258)|regulation of interleukin-8 secretion (GO:2000482)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to lead ion (GO:0010288)|wound healing (GO:0042060)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|growth cone (GO:0030426)	calcium ion binding (GO:0005509)|cholesterol binding (GO:0015485)|choline binding (GO:0033265)|complement component C1q binding (GO:0001849)|low-density lipoprotein particle binding (GO:0030169)			breast(1)|endometrium(3)|kidney(1)|lung(15)|ovary(1)|skin(1)	22	all_hematologic(112;0.0429)				inhaled insulin(DB05278)	CATTAGGACTGAAGGGCCCGC	0.542																																						uc001ftw.3																			0				breast(1)|endometrium(3)|kidney(1)|lung(15)|ovary(1)|skin(1)	22						c.(592-594)ttC>ttT		Homo sapiens C-reactive protein, pentraxin-related (CRP), mRNA.	Atorvastatin(DB01076)|Bezafibrate(DB01393)						76.0	78.0	77.0					1																	159683396		2203	4300	6503	SO:0001819	synonymous_variant	1401				acute-phase response|negative regulation of lipid storage|negative regulation of macrophage derived foam cell differentiation|opsonization		Gram-positive bacterial cell surface binding|choline binding|low-density lipoprotein particle binding|metal ion binding|protein binding	g.chr1:159683396G>A	M11725	CCDS30911.1	1q23.2	2013-05-13			ENSG00000132693	ENSG00000132693			2367	protein-coding gene	gene with protein product	"""pentraxin 1"""	123260				3840479, 6857266	Standard	NM_000567		Approved	PTX1	uc001ftw.3	P02741	OTTHUMG00000035344	ENST00000255030.5:c.594C>T	1.37:g.159683396G>A			Somatic				CRP_uc001ftx.1_Intron|CRP_uc001fty.1_Non-coding_Transcript	p.F198F	NM_000567	NP_000558	WXS	Illumina GAIIx	Phase_I	P02741	CRP_HUMAN			1	698	-	all_hematologic(112;0.0429)		198			Pentaxin.		A8K078|D3DVD9|D3DVE0|Q08AK3|Q8WW75	Silent	SNP	ENST00000255030.5	37	c.594C>T	CCDS30911.1																																																																																				0.542	CRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085553.1	NM_000567		31	101	0	0	0	1	0	31	101				
SNX3	8724	broad.mit.edu	37	6	108581972	108581972	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr6:108581972T>C	ENST00000230085.8	-	1	492	c.154A>G	c.(154-156)Agg>Ggg	p.R52G	SNX3_ENST00000426155.2_Missense_Mutation_p.R52G|SNX3_ENST00000368982.4_Missense_Mutation_p.R52G|SNX3_ENST00000349379.5_Intron	NM_003795.4	NP_003786.1	O60493	SNX3_HUMAN	sorting nexin 3	52	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				hemoglobin biosynthetic process (GO:0042541)|intracellular protein transport (GO:0006886)|intralumenal vesicle formation (GO:0070676)|membrane invagination (GO:0010324)|negative regulation of early endosome to late endosome transport (GO:2000642)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein transport (GO:0051224)|negative regulation of viral entry into host cell (GO:0046597)|regulation of cellular protein metabolic process (GO:0032268)|regulation of intracellular protein transport (GO:0033157)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein phosphatase binding (GO:0019903)			large_intestine(1)	1		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0136)|Epithelial(106;0.0564)|OV - Ovarian serous cystadenocarcinoma(136;0.0717)|all cancers(137;0.0743)		ACCTTGACCCTGATTTCGTAA	0.662																																						uc003psh.3																			0				large_intestine(1)	1						c.(154-156)Agg>Ggg		Homo sapiens sorting nexin 3 (SNX3), transcript variant 1, mRNA.							50.0	56.0	54.0					6																	108581972		2203	4300	6503	SO:0001583	missense	8724				cell communication|endocytosis|protein transport	early endosome|endosome membrane	phosphatidylinositol-3-phosphate binding|protein phosphatase binding	g.chr6:108581972T>C	AF034546	CCDS5064.1, CCDS5065.1, CCDS75501.1	6q21	2010-08-05			ENSG00000112335	ENSG00000112335		"""Sorting nexins"""	11174	protein-coding gene	gene with protein product		605930				9819414	Standard	XM_005267192		Approved	Grd19	uc003psh.3	O60493	OTTHUMG00000015323	ENST00000230085.8:c.154A>G	6.37:g.108581972T>C	ENSP00000230085:p.Arg52Gly		Somatic				SNX3_uc003psi.3_Missense_Mutation_p.R52G|SNX3_uc010kdi.3_Non-coding_Transcript	p.R52G	NM_003795	NP_003786	WXS	Illumina GAIIx	Phase_I	O60493	SNX3_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.0136)|Epithelial(106;0.0564)|OV - Ovarian serous cystadenocarcinoma(136;0.0717)|all cancers(137;0.0743)	0	493	-		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)	52			PX.		A8K0B1|E1P5E4|E1P5E5|O60718|Q4TT29|Q4TT31|Q5JXJ7|Q5JXJ8|Q96AP9|Q9C0J5|Q9NU45	Missense_Mutation	SNP	ENST00000230085.8	37	c.154A>G	CCDS5064.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.740230	0.49045	.	.	ENSG00000112335	ENST00000230085;ENST00000426155;ENST00000368982	T;T;T	0.40756	1.02;1.24;1.02	5.37	2.73	0.32206	Phox homologous domain (5);	0.213426	0.46145	D	0.000301	T	0.55481	0.1923	M	0.93328	3.405	0.53005	D	0.999965	P;B	0.34462	0.454;0.333	B;P	0.48901	0.22;0.594	T	0.64474	-0.6399	10	0.62326	D	0.03	-32.5525	12.6699	0.56862	0.0:0.0:0.4488:0.5512	.	52;52	O60493-2;O60493	.;SNX3_HUMAN	G	52	ENSP00000230085:R52G;ENSP00000401779:R52G;ENSP00000357978:R52G	ENSP00000230085:R52G	R	-	1	2	SNX3	108688665	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.664000	0.46783	0.827000	0.34685	0.459000	0.35465	AGG		0.662	SNX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041717.1			3	56	0	0	0	1	0	3	56				
ISOC2	79763	broad.mit.edu	37	19	55966378	55966378	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr19:55966378G>A	ENST00000425675.2	-	5	575	c.515C>T	c.(514-516)gCc>gTc	p.A172V	ISOC2_ENST00000085068.3_Missense_Mutation_p.A188V|ISOC2_ENST00000438389.2_Missense_Mutation_p.A102V			Q96AB3	ISOC2_HUMAN	isochorismatase domain containing 2	172					protein destabilization (GO:0031648)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			endometrium(1)|lung(4)|ovary(1)|stomach(1)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0535)		GGGGTGGACGGCATCGCCCAC	0.622											OREG0025682	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc002qla.3																			0				endometrium(1)|lung(4)|ovary(1)|stomach(1)	7						c.(562-564)gCc>gTc		Homo sapiens isochorismatase domain containing 2 (ISOC2), nuclear gene encoding mitochondrial protein, transcript variant 2, mRNA.							45.0	46.0	46.0					19																	55966378		2203	4300	6503	SO:0001583	missense	79763				protein destabilization	mitochondrion|nucleus	catalytic activity|protein binding	g.chr19:55966378G>A	AK027122	CCDS12925.1, CCDS46194.1, CCDS46195.1	19q13.42	2011-07-14			ENSG00000063241	ENSG00000063241			26278	protein-coding gene	gene with protein product		612928				17658461	Standard	NM_024710		Approved	FLJ23469	uc002qla.3	Q96AB3		ENST00000425675.2:c.515C>T	19.37:g.55966378G>A	ENSP00000401726:p.Ala172Val		Somatic	OREG0025682	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1011	ISOC2_uc002qlb.3_Missense_Mutation_p.A172V|ISOC2_uc002qlc.3_Missense_Mutation_p.A102V	p.A188V	NM_024710	NP_078986	WXS	Illumina GAIIx	Phase_I	Q96AB3	ISOC2_HUMAN	BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0535)	4	737	-	Breast(117;0.155)		172					Q6ZN91|Q9H5G0	Missense_Mutation	SNP	ENST00000425675.2	37	c.563C>T	CCDS46195.1	.	.	.	.	.	.	.	.	.	.	G	17.29	3.352378	0.61293	.	.	ENSG00000063241	ENST00000085068;ENST00000425675;ENST00000438389	.	.	.	3.88	3.88	0.44766	Isochorismatase-like (2);	0.000000	0.85682	D	0.000000	T	0.69369	0.3103	L	0.54323	1.7	0.58432	D	0.999998	D;D;D	0.71674	0.998;0.991;0.975	D;P;P	0.69142	0.962;0.884;0.848	T	0.73313	-0.4022	9	0.72032	D	0.01	-7.9387	13.7376	0.62827	0.0:0.0:1.0:0.0	.	102;172;188	Q96AB3-3;Q96AB3;Q96AB3-2	.;ISOC2_HUMAN;.	V	188;172;102	.	ENSP00000085068:A188V	A	-	2	0	ISOC2	60658190	1.000000	0.71417	0.810000	0.32431	0.070000	0.16714	8.272000	0.89885	1.891000	0.54761	0.491000	0.48974	GCC		0.622	ISOC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453179.1	NM_024710		3	47	0	0	0	1	0	3	47				
ICE1	23379	broad.mit.edu	37	5	5463854	5463854	+	Silent	SNP	G	G	A	rs201276348		TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr5:5463854G>A	ENST00000296564.7	+	13	4629	c.4407G>A	c.(4405-4407)aaG>aaA	p.K1469K		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1469					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						CTGCTGAGAAGTCCCCAGAGG	0.522																																						uc003jdm.4																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						c.(4405-4407)aaG>aaA		Homo sapiens KIAA0947 (KIAA0947), mRNA.							88.0	85.0	86.0					5																	5463854		1921	4129	6050	SO:0001819	synonymous_variant	23379							g.chr5:5463854G>A																												ENST00000296564.7:c.4407G>A	5.37:g.5463854G>A			Somatic					p.K1469K	NM_015325	NP_056140	WXS	Illumina GAIIx	Phase_I	Q9Y2F5	K0947_HUMAN			12	4629	+			1469					Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	37	c.4407G>A	CCDS47187.1																																																																																				0.522	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			4	112	0	0	0	1	0	4	112				
FRS3	10817	broad.mit.edu	37	6	41738433	41738433	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr6:41738433T>C	ENST00000373018.3	-	7	1654	c.1403A>G	c.(1402-1404)aAc>aGc	p.N468S	FRS3_ENST00000259748.2_Missense_Mutation_p.N468S	NM_006653.3	NP_006644.1	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3	468					fibroblast growth factor receptor signaling pathway (GO:0008543)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TCTCTGCAGGTTGGACATGGC	0.637																																						uc003orc.1																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						c.(1402-1404)aAc>aGc		Homo sapiens fibroblast growth factor receptor substrate 3 (FRS3), mRNA.							100.0	95.0	97.0					6																	41738433		2203	4300	6503	SO:0001583	missense	10817				fibroblast growth factor receptor signaling pathway	plasma membrane	fibroblast growth factor receptor binding|insulin receptor binding	g.chr6:41738433T>C	AF036718	CCDS4860.1	6p21.1	2010-08-05			ENSG00000137218	ENSG00000137218			16970	protein-coding gene	gene with protein product		607744				8761293, 9660748	Standard	NM_006653		Approved	SNT-2, FRS2beta, FRS2B	uc003orc.1	O43559	OTTHUMG00000014686	ENST00000373018.3:c.1403A>G	6.37:g.41738433T>C	ENSP00000362109:p.Asn468Ser		Somatic					p.N468S	NM_006653	NP_006644	WXS	Illumina GAIIx	Phase_I	O43559	FRS3_HUMAN	Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)		6	1647	-	Ovarian(28;0.0355)|Colorectal(47;0.121)		468					Q5T3D5	Missense_Mutation	SNP	ENST00000373018.3	37	c.1403A>G	CCDS4860.1	.	.	.	.	.	.	.	.	.	.	T	4.880	0.163576	0.09287	.	.	ENSG00000137218	ENST00000373018;ENST00000259748	T;T	0.22743	1.94;1.94	5.55	-0.326	0.12698	.	0.312847	0.42548	N	0.000700	T	0.01765	0.0056	N	0.02539	-0.55	0.37471	D	0.915624	B	0.02656	0.0	B	0.01281	0.0	T	0.35025	-0.9805	10	0.14252	T	0.57	-15.5291	4.7731	0.13166	0.1445:0.3987:0.0:0.4568	.	468	O43559	FRS3_HUMAN	S	468	ENSP00000362109:N468S;ENSP00000259748:N468S	ENSP00000259748:N468S	N	-	2	0	FRS3	41846411	0.996000	0.38824	1.000000	0.80357	0.995000	0.86356	0.369000	0.20416	0.394000	0.25230	0.529000	0.55759	AAC		0.637	FRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040532.2	NM_006653		6	99	0	0	0	1	0	6	99				
RALB	5899	broad.mit.edu	37	2	121050797	121050797	+	Silent	SNP	G	G	A			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr2:121050797G>A	ENST00000272519.5	+	5	852	c.582G>A	c.(580-582)aaG>aaA	p.K194K	RALB_ENST00000474855.2_Silent_p.K216K|RALB_ENST00000404963.3_Silent_p.K215K|RALB_ENST00000420510.1_Silent_p.K194K|RALB_ENST00000470417.1_3'UTR	NM_002881.2	NP_002872.1	P11234	RALB_HUMAN	v-ral simian leukemia viral oncogene homolog B	194					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of exocyst assembly (GO:0001928)|regulation of exocyst localization (GO:0060178)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(154;0.122)				AAAGCAGCAAGAACAAGAAAA	0.423																																						uc010yys.2																			0				endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15						c.(646-648)aaG>aaA		Homo sapiens v-ral simian leukemia viral oncogene homolog B (ras related; GTP binding protein) (RALB), mRNA.							111.0	109.0	109.0					2																	121050797		2203	4300	6503	SO:0001819	synonymous_variant	5899				Ras protein signal transduction|apoptosis|cell cycle|cytokinesis|nerve growth factor receptor signaling pathway|regulation of exocyst assembly|regulation of exocyst localization	cytosol|midbody|plasma membrane	GTP binding|GTPase activity|protein binding	g.chr2:121050797G>A		CCDS2131.1	2q14.2	2014-05-09	2013-07-09		ENSG00000144118	ENSG00000144118			9840	protein-coding gene	gene with protein product	"""ras related GTP binding protein B"""	179551					Standard	NM_002881		Approved		uc002tmk.3	P11234	OTTHUMG00000131435	ENST00000272519.5:c.582G>A	2.37:g.121050797G>A			Somatic				RALB_uc002tmk.3_Silent_p.K194K|RALB_uc002tml.3_Silent_p.K215K|RALB_uc010yyt.2_Non-coding_Transcript	p.K216K	NM_002881	NP_002872	WXS	Illumina GAIIx	Phase_I	P11234	RALB_HUMAN			4	691	+		Prostate(154;0.122)	194					B4E040|Q53T32|Q6ZS74	Silent	SNP	ENST00000272519.5	37	c.648G>A	CCDS2131.1																																																																																				0.423	RALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254232.3	NM_002881		5	38	0	0	0	1	0	5	38				
ARHGEF2	9181	broad.mit.edu	37	1	155927538	155927538	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr1:155927538T>C	ENST00000361247.4	-	13	1780	c.1681A>G	c.(1681-1683)Acc>Gcc	p.T561A	ARHGEF2_ENST00000313695.7_Missense_Mutation_p.T533A|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.T533A|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.T560A|ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000462460.2_Missense_Mutation_p.T606A|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.T562A	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	561	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					CGGATCCAGGTGCTCCGGTCA	0.582																																					Melanoma(178;35 2768 6610 28839)	uc001fmu.2																			0				breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40						c.(1813-1815)Acc>Gcc		Homo sapiens Rho/Rac guanine nucleotide exchange factor (GEF) 2 (ARHGEF2), transcript variant 3, mRNA.							104.0	75.0	85.0					1																	155927538		2203	4300	6503	SO:0001583	missense	9181				actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of Rho protein signal transduction|regulation of cell proliferation|small GTPase mediated signal transduction	Golgi apparatus|cytosol|microtubule|ruffle membrane|spindle|tight junction	Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|microtubule binding|zinc ion binding	g.chr1:155927538T>C	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	682	protein-coding gene	gene with protein product		607560	"""rho/rac guanine nucleotide exchange factor (GEF) 2"""			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.1681A>G	1.37:g.155927538T>C	ENSP00000354837:p.Thr561Ala		Somatic				ARHGEF2_uc001fmr.2_Missense_Mutation_p.T533A|ARHGEF2_uc001fms.2_Missense_Mutation_p.T560A|ARHGEF2_uc001fmt.2_Missense_Mutation_p.T561A	p.T605A	NM_004723	NP_004714	WXS	Illumina GAIIx	Phase_I	Q92974	ARHG2_HUMAN			16	2068	-	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		561					D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	37	c.1813A>G	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.336060	0.60963	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000313667	T;T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86;-0.86	5.28	5.28	0.74379	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.49916	D	0.000139	T	0.69133	0.3077	L	0.42245	1.32	0.40475	D	0.980385	B;P;B	0.52463	0.387;0.953;0.175	B;P;B	0.54759	0.262;0.76;0.171	T	0.70410	-0.4879	10	0.38643	T	0.18	-35.919	13.1991	0.59756	0.0:0.0:0.0:1.0	.	605;561;560	D3DVA5;Q92974;Q92974-2	.;ARHG2_HUMAN;.	A	533;561;562;533;560	ENSP00000315325:T533A;ENSP00000354837:T561A;ENSP00000357298:T562A;ENSP00000357299:T533A;ENSP00000314787:T560A	ENSP00000314787:T560A	T	-	1	0	ARHGEF2	154194162	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.389000	0.34453	2.213000	0.71641	0.528000	0.53228	ACC		0.582	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		5	57	0	0	0	1	0	5	57				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	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		Somatic					p.V600E	NM_004333	NP_004324	WXS	Illumina GAIIx	Phase_I	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		22	56	0	0	0	1	0	22	56				
APOB	338	broad.mit.edu	37	2	21229161	21229161	+	Missense_Mutation	SNP	G	G	A	rs144467873	byFrequency	TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr2:21229161G>A	ENST00000233242.1	-	26	10706	c.10579C>T	c.(10579-10581)Cgg>Tgg	p.R3527W		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3527			R -> Q (in FDB; dbSNP:rs5742904). {ECO:0000269|PubMed:21382890, ECO:0000269|PubMed:2563166, ECO:0000269|PubMed:9259199}.		artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACTGAAGACCGTGTGCTCTTG	0.433													G|||	2	0.000399361	0.0	0.0	5008	,	,		21124	0.001		0.0	False		,,,				2504	0.001					uc002red.3																			0				NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	GRCh37	CM950075	APOB	M	rs144467873	c.(10579-10581)Cgg>Tgg		Homo sapiens apolipoprotein B (including Ag(x) antigen) (APOB), mRNA.	Atorvastatin(DB01076)	G	TRP/ARG	0,4406		0,0,2203	132.0	135.0	134.0		10579	5.0	0.9	2	dbSNP_134	134	1,8599	1.2+/-3.3	0,1,4299	no	missense	APOB	NM_000384.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	3527/4564	21229161	1,13005	2203	4300	6503	SO:0001583	missense	338				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity	g.chr2:21229161G>A	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.10579C>T	2.37:g.21229161G>A	ENSP00000233242:p.Arg3527Trp		Somatic					p.R3527W	NM_000384	NP_000375	WXS	Illumina GAIIx	Phase_I	P04114	APOB_HUMAN			25	10707	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)		3527		R -> Q (in FDB; dbSNP:rs5742904).			O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	c.10579C>T	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.822054	0.50739	0.0	1.16E-4	ENSG00000084674	ENST00000233242;ENST00000535079	D	0.81499	-1.5	5.85	4.97	0.65823	.	0.000000	0.52532	D	0.000076	D	0.89220	0.6653	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90473	0.4454	10	0.87932	D	0	.	14.0194	0.64545	0.0:0.0:0.7246:0.2754	.	3527	P04114	APOB_HUMAN	W	3527	ENSP00000233242:R3527W	ENSP00000233242:R3527W	R	-	1	2	APOB	21082666	1.000000	0.71417	0.920000	0.36463	0.571000	0.35966	3.962000	0.56766	1.462000	0.47948	0.655000	0.94253	CGG		0.433	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			4	139	0	0	0	1	0	4	139				
DNASE2	1777	broad.mit.edu	37	19	12989328	12989328	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr19:12989328C>T	ENST00000222219.3	-	5	669	c.577G>A	c.(577-579)Gaa>Aaa	p.E193K	CTD-2265O21.7_ENST00000592400.1_RNA|DNASE2_ENST00000538460.1_Missense_Mutation_p.E138K	NM_001375.2	NP_001366.1	O00115	DNS2A_HUMAN	deoxyribonuclease II, lysosomal	193					apoptotic DNA fragmentation (GO:0006309)|DNA metabolic process (GO:0006259)|erythrocyte differentiation (GO:0030218)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)|DNA binding (GO:0003677)			breast(1)|large_intestine(1)|lung(4)|ovary(1)	7						TCGGGGAATTCCTGGGCAAAG	0.557																																						uc002mvn.1																			0				breast(1)|large_intestine(1)|lung(4)|ovary(1)	7						c.(577-579)Gaa>Aaa		Homo sapiens deoxyribonuclease II, lysosomal (DNASE2), mRNA.							104.0	100.0	101.0					19																	12989328		2203	4300	6503	SO:0001583	missense	1777				apoptosis	lysosome	DNA binding|deoxyribonuclease II activity|protein binding	g.chr19:12989328C>T	AF045937	CCDS12284.1	19p13.2	2012-10-02			ENSG00000105612	ENSG00000105612	3.1.22.1		2960	protein-coding gene	gene with protein product		126350		DNL, DNL2		1586130	Standard	NM_001375		Approved		uc002mvn.1	O00115		ENST00000222219.3:c.577G>A	19.37:g.12989328C>T	ENSP00000222219:p.Glu193Lys		Somatic				DNASE2_uc010xmr.1_Missense_Mutation_p.E138K	p.E193K	NM_001375	NP_001366	WXS	Illumina GAIIx	Phase_I	O00115	DNS2A_HUMAN			4	723	-			193					B2RD06|B7Z4K6|O43910	Missense_Mutation	SNP	ENST00000222219.3	37	c.577G>A	CCDS12284.1	.	.	.	.	.	.	.	.	.	.	C	2.025	-0.423723	0.04734	.	.	ENSG00000105612	ENST00000222219;ENST00000538460	T;T	0.13307	2.6;2.6	5.49	1.94	0.25998	.	0.817875	0.11465	N	0.561378	T	0.04227	0.0117	N	0.03948	-0.315	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.44003	-0.9356	10	0.06757	T	0.87	.	3.224	0.06725	0.0:0.3466:0.2261:0.4273	.	138;193	B7Z4K6;O00115	.;DNS2A_HUMAN	K	193;138	ENSP00000222219:E193K;ENSP00000445988:E138K	ENSP00000222219:E193K	E	-	1	0	DNASE2	12850328	0.997000	0.39634	0.043000	0.18650	0.144000	0.21451	1.859000	0.39418	0.372000	0.24591	-0.471000	0.05019	GAA		0.557	DNASE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451790.1			13	39	0	0	0	1	0	13	39				
RAB3IP	117177	broad.mit.edu	37	12	70149196	70149196	+	Missense_Mutation	SNP	A	A	G			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr12:70149196A>G	ENST00000247833.7	+	2	384	c.8A>G	c.(7-9)aAt>aGt	p.N3S	RAB3IP_ENST00000483530.2_Missense_Mutation_p.N3S|RAB3IP_ENST00000550536.1_Missense_Mutation_p.N19S|RAB3IP_ENST00000378815.6_Missense_Mutation_p.N3S|RAB3IP_ENST00000362025.5_Missense_Mutation_p.N19S|RAB3IP_ENST00000325555.9_5'UTR					RAB3A interacting protein											NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			GCTATGGCTAATGATCCCTTG	0.353																																						uc001svp.3																			0				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22						c.(55-57)aAt>aGt		Homo sapiens RAB3A interacting protein (rabin3) (RAB3IP), transcript variant alpha 2, mRNA.							97.0	88.0	91.0					12																	70149196		2203	4300	6503	SO:0001583	missense	117177				Golgi to plasma membrane transport|cilium assembly|protein localization to organelle|protein transport	actin cortical patch|centrosome|cytosol|lamellipodium|microtubule basal body|nucleus	guanyl-nucleotide exchange factor activity|protein binding	g.chr12:70149196A>G		CCDS8993.1, CCDS8995.1, CCDS8996.1, CCDS41811.1, CCDS44942.1	12q15	2013-01-22	2013-01-22		ENSG00000127328	ENSG00000127328			16508	protein-coding gene	gene with protein product	"""rabin3"""	608686					Standard	NM_175623		Approved	RABIN3	uc001svm.3	Q96QF0	OTTHUMG00000169437	ENST00000247833.7:c.8A>G	12.37:g.70149196A>G	ENSP00000247833:p.Asn3Ser		Somatic				RAB3IP_uc021rao.1_Missense_Mutation_p.N3S|RAB3IP_uc001svm.3_Missense_Mutation_p.N3S|RAB3IP_uc001svn.3_Missense_Mutation_p.N3S|RAB3IP_uc001svo.3_Non-coding_Transcript|RAB3IP_uc001svq.3_Missense_Mutation_p.N19S|RAB3IP_uc001svs.3_Non-coding_Transcript	p.N19S	NM_175623	NP_001019818	WXS	Illumina GAIIx	Phase_I	Q96QF0	RAB3I_HUMAN	Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)		1	503	+	Esophageal squamous(21;0.187)		19						Missense_Mutation	SNP	ENST00000247833.7	37	c.56A>G	CCDS8995.1	.	.	.	.	.	.	.	.	.	.	A	10.90	1.480955	0.26598	.	.	ENSG00000127328	ENST00000247833;ENST00000378815;ENST00000483530;ENST00000549760;ENST00000550536;ENST00000362025	T;T	0.41400	1.02;1.0	5.93	4.79	0.61399	.	0.296133	0.40064	N	0.001187	T	0.19805	0.0476	N	0.08118	0	0.80722	D	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.001	B;B;B;B	0.06405	0.001;0.001;0.002;0.002	T	0.06899	-1.0801	10	0.13470	T	0.59	.	7.8778	0.29603	0.7694:0.0:0.2306:0.0	.	19;19;3;3	Q96QF0-4;Q96QF0;Q96QF0-3;Q96QF0-7	.;RAB3I_HUMAN;.;.	S	3;3;3;3;19;19	ENSP00000247833:N3S;ENSP00000447300:N19S	ENSP00000247833:N3S	N	+	2	0	RAB3IP	68435463	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.418000	0.52721	1.077000	0.40990	0.533000	0.62120	AAT		0.353	RAB3IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280671.2	NM_022456		3	66	0	0	0	1	0	3	66				
KMT2C	58508	broad.mit.edu	37	7	151864343	151864343	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr7:151864343G>A	ENST00000262189.6	-	42	9856	c.9638C>T	c.(9637-9639)tCa>tTa	p.S3213L	KMT2C_ENST00000355193.2_Missense_Mutation_p.S3213L	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3213	Gln-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TTGTTTAGCTGAAAGGGCCTT	0.443																																						uc003wla.3										N							medulloblastoma		0				NS(6)|biliary_tract(9)|breast(24)|central_nervous_system(18)|cervix(6)|endometrium(31)|haematopoietic_and_lymphoid_tissue(1)|kidney(26)|large_intestine(52)|liver(1)|lung(102)|ovary(10)|pancreas(17)|prostate(15)|skin(20)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(8)|urinary_tract(15)	365						c.(9637-9639)tCa>tTa		Homo sapiens myeloid/lymphoid or mixed-lineage leukemia 3 (MLL3), mRNA.							140.0	132.0	135.0					7																	151864343		2203	4300	6503	SO:0001583	missense	58508				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding	g.chr7:151864343G>A	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.9638C>T	7.37:g.151864343G>A	ENSP00000262189:p.Ser3213Leu		Somatic				MLL3_uc003wkz.3_Missense_Mutation_p.S2274L|MLL3_uc003wky.3_Missense_Mutation_p.S722L	p.S3213L	NM_170606	NP_733751	WXS	Illumina GAIIx	Phase_I	Q8NEZ4	MLL3_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)	41	9857	-	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	3213			Gln-rich.		Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	c.9638C>T	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.594193	0.86953	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.84800	-1.89;-1.9	5.83	5.83	0.93111	.	0.000000	0.39407	N	0.001378	D	0.87188	0.6115	N	0.14661	0.345	0.80722	D	1	D;P;D	0.89917	0.994;0.773;1.0	D;P;D	0.85130	0.983;0.841;0.997	D	0.88386	0.3005	10	0.52906	T	0.07	.	20.115	0.97926	0.0:0.0:1.0:0.0	.	3213;2274;3213	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	MLL3_HUMAN;.;.	L	3213	ENSP00000262189:S3213L;ENSP00000347325:S3213L	ENSP00000262189:S3213L	S	-	2	0	MLL3	151495276	1.000000	0.71417	0.992000	0.48379	0.918000	0.54935	9.813000	0.99286	2.761000	0.94854	0.650000	0.86243	TCA		0.443	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			36	97	0	0	0	1	0	36	97				
ITGB3	3690	broad.mit.edu	37	17	45367119	45367119	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr17:45367119G>A	ENST00000559488.1	+	7	1028	c.1012G>A	c.(1012-1014)Gaa>Aaa	p.E338K	ITGB3_ENST00000435993.2_Missense_Mutation_p.E291K|ITGB3_ENST00000571680.1_Missense_Mutation_p.E338K|ITGB3_ENST00000560629.1_Silent_p.*326*	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	338	VWFA.				activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	TGCAGTGACTGAAAATGTAGT	0.483																																						uc002ilj.3																			0				breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39						c.(1012-1014)Gaa>Aaa		Homo sapiens integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61) (ITGB3), mRNA.	Abciximab(DB00054)|Tirofiban(DB00775)						143.0	126.0	132.0					17																	45367119		2203	4300	6503	SO:0001583	missense	3690				activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding	g.chr17:45367119G>A		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"""CD molecules"", ""Integrins"""	6156	protein-coding gene	gene with protein product	"""platelet glycoprotein IIIa"""	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.1012G>A	17.37:g.45367119G>A	ENSP00000452786:p.Glu338Lys		Somatic				ITGB3_uc002ili.1_Missense_Mutation_p.E338K|ITGB3_uc010wkr.1_Non-coding_Transcript	p.E338K	NM_000212	NP_000203	WXS	Illumina GAIIx	Phase_I	P05106	ITB3_HUMAN			6	1032	+			338			VWFA.		A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	37	c.1012G>A	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	G	7.382	0.629045	0.14257	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.97620	-4.46	5.3	-0.849	0.10723	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.516425	0.23556	N	0.046908	D	0.87601	0.6218	N	0.08118	0	0.22489	N	0.999052	B;B	0.28128	0.081;0.201	B;B	0.25884	0.04;0.064	T	0.80933	-0.1161	10	0.10902	T	0.67	.	5.4575	0.16598	0.3529:0.365:0.282:0.0	.	338;338	P05106;Q2YFE1	ITB3_HUMAN;.	K	338;291	ENSP00000407801:E291K	ENSP00000262017:E338K	E	+	1	0	C17orf57	42722118	0.003000	0.15002	0.998000	0.56505	0.996000	0.88848	0.543000	0.23237	0.208000	0.20626	0.462000	0.41574	GAA		0.483	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		21	35	0	0	0	1	0	21	35				
MKS1	54903	broad.mit.edu	37	17	56283864	56283864	+	Silent	SNP	G	G	A			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr17:56283864G>A	ENST00000393119.2	-	16	1526	c.1452C>T	c.(1450-1452)ggC>ggT	p.G484G	MKS1_ENST00000313863.6_Intron|MKS1_ENST00000337050.7_Splice_Site_p.A470V|MKS1_ENST00000546108.1_Silent_p.G281G|MKS1_ENST00000537529.2_Silent_p.G474G	NM_017777.3	NP_060247.2	Q9NXB0	MKS1_HUMAN	Meckel syndrome, type 1	484					branching morphogenesis of an epithelial tube (GO:0048754)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)				endometrium(5)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						AGGTGACAGTGCCTGTGGTCT	0.617																																						uc002ivr.2																			0				endometrium(5)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						c.(1450-1452)ggC>ggT		Homo sapiens Meckel syndrome, type 1 (MKS1), transcript variant 1, mRNA.							91.0	101.0	97.0					17																	56283864		2137	4249	6386	SO:0001819	synonymous_variant	54903				cilium assembly	centrosome|cilium|microtubule basal body	protein binding	g.chr17:56283864G>A	DQ185029	CCDS11603.2, CCDS54148.1	17q21-q24	2014-09-17			ENSG00000011143	ENSG00000011143			7121	protein-coding gene	gene with protein product	"""POC12 centriolar protein homolog (Chlamydomonas)"""	609883		MKS		7550354, 16415886, 18327255	Standard	NM_017777		Approved	FLJ20345, POC12, BBS13	uc002ivr.2	Q9NXB0	OTTHUMG00000133714	ENST00000393119.2:c.1452C>T	17.37:g.56283864G>A			Somatic				MKS1_uc010wnq.2_Silent_p.G281G|MKS1_uc021uam.1_Silent_p.G474G	p.G484G	NM_017777	NP_060247	WXS	Illumina GAIIx	Phase_I	Q9NXB0	MKS1_HUMAN			15	1527	-			484					B7WNX4|F5H885|Q284T0|Q96G13	Silent	SNP	ENST00000393119.2	37	c.1452C>T	CCDS11603.2	.	.	.	.	.	.	.	.	.	.	G	14.04	2.415337	0.42817	.	.	ENSG00000011143	ENST00000337050	T	0.69561	-0.41	5.22	-2.17	0.07059	.	.	.	.	.	T	0.62146	0.2404	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59804	-0.7385	6	0.66056	D	0.02	-32.7994	2.022	0.03511	0.3395:0.3439:0.2039:0.1126	.	.	.	.	V	470	ENSP00000338407:A470V	ENSP00000338407:A470V	A	-	2	0	MKS1	53638863	0.993000	0.37304	0.232000	0.24009	0.787000	0.44495	0.256000	0.18351	-0.521000	0.06426	-0.219000	0.12488	GCA		0.617	MKS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258015.2	NM_017777		4	71	0	0	0	1	0	4	71				
SNX13	23161	broad.mit.edu	37	7	17855871	17855872	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chr7:17855871_17855872insT	ENST00000409389.1	-	19	2091_2092	c.1919_1920insA	c.(1918-1920)aagfs	p.K640fs	SNX13_ENST00000496855.1_5'UTR|SNX13_ENST00000428135.3_Frame_Shift_Ins_p.K629fs			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	640	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					TATTAAAAGTCTTTTTTCCAGG	0.292																																						uc003stv.3																			0				breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38						c.(1885-1887)aagfs		Homo sapiens sorting nexin 13 (SNX13), mRNA.																																				SO:0001589	frameshift_variant	23161				cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity	g.chr7:17855871_17855872insT	AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"""Sorting nexins"""	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.1920dupA	7.37:g.17855877_17855877dupT	ENSP00000386705:p.Lys640fs		Somatic				SNX13_uc010kuc.3_Frame_Shift_Ins_p.K426fs|SNX13_uc003stw.1_Frame_Shift_Ins_p.K640fs|SNX13_uc010kub.3_Frame_Shift_Ins_p.K35fs	p.K629fs	NM_015132	NP_055947	WXS	Illumina GAIIx	Phase_I	Q9Y5W8	SNX13_HUMAN			18	2099_2100	-	Lung NSC(10;0.0261)|all_lung(11;0.0521)		640			PX.		B2RCI9|O94821|Q8WVZ2|Q8WXH8	Frame_Shift_Ins	INS	ENST00000409389.1	37	c.1886_1887insA																																																																																					0.292	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132		2	4						2	4	---	---	---	---
FUNDC1	139341	broad.mit.edu	37	X	44402059	44402059	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DJ-A2QA-01A-11D-A18F-08	TCGA-DJ-A2QA-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f8d67e6-5d90-447a-a421-2420df6fc47b	ab7884d1-54c7-49cd-86c9-93a0c0af8884	g.chrX:44402059delG	ENST00000378045.4	-	1	188	c.20delC	c.(19-21)cctfs	p.P8fs	FUNDC1_ENST00000483115.1_5'Flank	NM_173794.3	NP_776155.1	Q8IVP5	FUND1_HUMAN	FUN14 domain containing 1	8					mitochondrion degradation (GO:0000422)|response to hypoxia (GO:0001666)	integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane (GO:0005741)				breast(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	6						ACCTTGGGGAGGGGGGTTCCG	0.657																																						uc004dgc.3																			0				breast(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	6						c.(19-21)cctfs		Homo sapiens FUN14 domain containing 1 (FUNDC1), mRNA.							16.0	15.0	15.0					X																	44402059		2148	4199	6347	SO:0001589	frameshift_variant	139341							g.chrX:44402059delG	BC042813	CCDS14263.1	Xp11.4	2005-09-22			ENSG00000069509	ENSG00000069509			28746	protein-coding gene	gene with protein product		300871				12477932	Standard	NM_173794		Approved	MGC51029	uc004dgc.3	Q8IVP5	OTTHUMG00000021399	ENST00000378045.4:c.20delC	X.37:g.44402059delG	ENSP00000367284:p.Pro8fs		Somatic					p.P7fs	NM_173794	NP_776155	WXS	Illumina GAIIx	Phase_I	Q8IVP5	FUND1_HUMAN			0	163	-			7						Frame_Shift_Del	DEL	ENST00000378045.4	37	c.20delC	CCDS14263.1																																																																																				0.657	FUNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056320.1	NM_173794		2	4						2	4	---	---	---	---
