#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_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
MYCL	4610	genome.wustl.edu	37	1	40363614	40363614	+	Silent	SNP	T	T	A			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	T	T	T	A	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	c6bf38cf-18b1-46e2-99b5-e0b6a0fc7592	47f0907e-96b3-46c2-9acb-198105f451e7	g.chr1:40363614T>A	ENST00000372816.2	-	2	972	c.525A>T	c.(523-525)gtA>gtT	p.V175V	RP1-118J21.5_ENST00000418255.1_RNA|MYCL_ENST00000397332.2_Silent_p.V205V			P12524	MYCL_HUMAN	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived homolog	175						nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GCCTCTTCTCTACTGTCACAA	0.478																																						dbGAP											0			1											76.0	79.0	78.0					1																	40363614		2203	4300	6503	40136201	SO:0001819	synonymous_variant	0				CCDS30682.1, CCDS44117.1, CCDS44117.2, CCDS53300.1	1p34.3	2013-07-09	2013-07-09	2013-07-09	ENSG00000116990	ENSG00000116990		"""Basic helix-loop-helix proteins"""	7555	protein-coding gene	gene with protein product	"""l-myc protein"", ""myc-related gene from lung cancer"", ""oncogene lmyc"""	164850	"""v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived"""	MYCL1		8978772	Standard	NM_001033082		Approved	LMYC, bHLHe38	uc001cer.2	P12524	OTTHUMG00000009243	ENST00000372816.2:c.525A>T	1.37:g.40363614T>A		Somatic	195	1.01	2		2	60.00	3	WXS	Illumina HiSeq	Phase_IV	40136201	57	37.36	34	A2A2C9|B4DJH2|Q14897|Q5QPL0|Q5QPL1|Q9NUE9	Silent	SNP	HMMPfam_HLH,HMMSmart_SM00353,superfamily_HLH helix-loop-helix DNA-binding domain,HMMPfam_Myc_N	p.V175	ENST00000372816.2	37	c.525	CCDS30682.1	1																																																																																			-	HMMPfam_Myc_N		0.478	MYCL-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	MYCL1	protein_coding	OTTHUMT00000277004.1	T	NM_001033082		40136201	-1	no_errors	NM_001033081.1	genbank	human	validated	54_36p	silent	SNP	1.000	A
CNGA3	1261	genome.wustl.edu	37	2	99012373	99012373	+	Missense_Mutation	SNP	C	C	T	rs148616345	byFrequency	TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	c6bf38cf-18b1-46e2-99b5-e0b6a0fc7592	47f0907e-96b3-46c2-9acb-198105f451e7	g.chr2:99012373C>T	ENST00000272602.2	+	7	779	c.740C>T	c.(739-741)aCg>aTg	p.T247M	CNGA3_ENST00000393504.1_Missense_Mutation_p.T247M|CNGA3_ENST00000436404.2_Missense_Mutation_p.T229M|CNGA3_ENST00000409937.1_Missense_Mutation_p.T251M			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	247			T -> M. {ECO:0000269|PubMed:24903488}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						AAGACGACCACGCAGTTCAAG	0.507													C|||	7	0.00139776	0.0015	0.0	5008	,	,		16960	0.005		0.0	False		,,,				2504	0.0					dbGAP											0			2						C	MET/THR,MET/THR	8,4398	14.3+/-33.2	0,8,2195	120.0	116.0	118.0		686,740	1.4	0.5	2	dbSNP_134	118	14,8586	11.2+/-40.8	0,14,4286	yes	missense,missense	CNGA3	NM_001079878.1,NM_001298.2	81,81	0,22,6481	TT,TC,CC		0.1628,0.1816,0.1692	benign,benign	229/677,247/695	99012373	22,12984	2203	4300	6503	98378805	SO:0001583	missense	0			S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.740C>T	2.37:g.99012373C>T	ENSP00000272602:p.Thr247Met	Somatic	268	0.74	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	98378805	53	44.21	42	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	HMMPfam_cNMP_binding,HMMSmart_cNMP,HMMPfam_Ion_trans,PatternScan_CNMP_BINDING_1,PatternScan_CNMP_BINDING_2,superfamily_cNMP_binding,superfamily_SSF81324	p.T247M	ENST00000272602.2	37	c.740	CCDS2034.1	2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	0.027	-1.366459	0.01235	0.001816	0.001628	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.97505	-4.41;-4.41;-4.41;-4.41	5.28	1.43	0.22495	Ion transport (1);	1.870490	0.01894	N	0.038783	D	0.92031	0.7475	N	0.04805	-0.155	0.09310	N	1	B;B;B	0.16166	0.016;0.001;0.005	B;B;B	0.19391	0.025;0.006;0.019	D	0.84915	0.0850	10	0.33940	T	0.23	.	8.5107	0.33215	0.0:0.0781:0.5349:0.387	.	251;229;247	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	M	247;229;247;251	ENSP00000377140:T247M;ENSP00000410070:T229M;ENSP00000272602:T247M;ENSP00000386761:T251M	ENSP00000272602:T247M	T	+	2	0	CNGA3	98378805	0.000000	0.05858	0.511000	0.27724	0.044000	0.14063	0.296000	0.19083	0.099000	0.17552	-0.505000	0.04504	ACG	-	HMMPfam_Ion_trans,superfamily_SSF81324		0.507	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CNGA3	protein_coding	OTTHUMT00000252986.1	C	NM_001298		98378805	+1	no_errors	NM_001298.1	genbank	human	reviewed	54_36p	missense	SNP	0.001	T
KIT	3815	genome.wustl.edu	37	4	55564702	55564702	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	c6bf38cf-18b1-46e2-99b5-e0b6a0fc7592	47f0907e-96b3-46c2-9acb-198105f451e7	g.chr4:55564702C>T	ENST00000288135.5	+	3	687	c.590C>T	c.(589-591)tCg>tTg	p.S197L		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	197	Ig-like C2-type 2.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCAGTGCTGTCGGAAAAATTC	0.498		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													dbGAP	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	0			4											104.0	94.0	98.0					4																	55564702		2203	4300	6503	55259459	SO:0001583	missense	0	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.590C>T	4.37:g.55564702C>T	ENSP00000288135:p.Ser197Leu	Somatic	44	0.00	0		15	57.14	20	WXS	Illumina HiSeq	Phase_IV	55259459	32	37.25	19	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	p.S197L	ENST00000288135.5	37	c.590	CCDS3496.1	4	.	.	.	.	.	.	.	.	.	.	C	15.45	2.836686	0.50951	.	.	ENSG00000157404	ENST00000288135;ENST00000412167;ENST00000536403	D;D	0.81659	-1.52;-1.51	5.75	4.91	0.64330	Immunoglobulin-like fold (1);	0.113900	0.39834	N	0.001251	D	0.86548	0.5959	M	0.78637	2.42	0.53005	D	0.999969	D;D	0.71674	0.982;0.998	P;P	0.56216	0.674;0.794	D	0.88178	0.2869	10	0.87932	D	0	.	12.9428	0.58354	0.0:0.9253:0.0:0.0747	.	197;197	P10721-2;P10721	.;KIT_HUMAN	L	197	ENSP00000288135:S197L;ENSP00000390987:S197L	ENSP00000288135:S197L	S	+	2	0	KIT	55259459	0.999000	0.42202	0.062000	0.19696	0.022000	0.10575	5.295000	0.65692	1.440000	0.47531	0.643000	0.83706	TCG	-	NULL		0.498	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KIT	protein_coding	OTTHUMT00000250618.1	C			55259459	+1	no_errors	NM_000222.2	genbank	human	reviewed	54_36p	missense	SNP	0.086	T
KIT	3815	genome.wustl.edu	37	4	55599321	55599321	+	Missense_Mutation	SNP	A	A	T	rs121913507		TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	c6bf38cf-18b1-46e2-99b5-e0b6a0fc7592	47f0907e-96b3-46c2-9acb-198105f451e7	g.chr4:55599321A>T	ENST00000288135.5	+	17	2544	c.2447A>T	c.(2446-2448)gAc>gTc	p.D816V		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	816	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> F (in mastocytosis; requires 2 nucleotide substitutions; somatic mutation; constitutively activated and is much more rapidly autophosphorylated than wild type). {ECO:0000269|PubMed:9990072}.|D -> H (in a testicular tumor; seminoma; somatic mutation; constitutively activated; dbSNP:rs28933969). {ECO:0000269|PubMed:10362788}.|D -> V (in mast cell leukemia and mastocytosis; somatic mutation; constitutively activated; loss of interaction with MPDZ). {ECO:0000269|PubMed:7691885, ECO:0000269|PubMed:9990072}.|D -> Y (in acute myeloid leukemia, mastocytosis and a germ cell tumor of the testis; somatic mutation; constitutively activated). {ECO:0000269|PubMed:16175573, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9657776, ECO:0000269|PubMed:9990072}.		actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.D816V(758)|p.D816F(6)|p.D816I(2)|p.D816G(2)|p.D816>VVA(1)|p.D816A(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTAGCCAGAGACATCAAGAAT	0.393		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													dbGAP	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	770	Substitution - Missense(769)|Complex - insertion inframe(1)	haematopoietic_and_lymphoid_tissue(745)|testis(16)|ovary(5)|skin(2)|soft_tissue(1)|genital_tract(1)	4	GRCh37	CM952169	KIT	M	rs121913507						145.0	146.0	145.0					4																	55599321		2203	4300	6503	55294078	SO:0001583	missense	0	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2447A>T	4.37:g.55599321A>T	ENSP00000288135:p.Asp816Val	Somatic	59	6.35	4		35	55.13	43	WXS	Illumina HiSeq	Phase_IV	55294078	24	51.02	25	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	p.D816V	ENST00000288135.5	37	c.2447	CCDS3496.1	4	.	.	.	.	.	.	.	.	.	.	A	27.4	4.831107	0.91036	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.83591	-1.74;-1.74	5.62	5.62	0.85841	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000011	D	0.85093	0.5618	N	0.21097	0.63	0.80722	A	1	D;D	0.71674	0.998;0.991	D;D	0.68943	0.961;0.933	D	0.88419	0.3027	9	0.87932	D	0	.	15.8126	0.78576	1.0:0.0:0.0:0.0	.	812;816	P10721-2;P10721	.;KIT_HUMAN	V	816;812	ENSP00000288135:D816V;ENSP00000390987:D812V	ENSP00000288135:D816V	D	+	2	0	KIT	55294078	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.181000	0.94874	2.148000	0.66965	0.477000	0.44152	GAC	-	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like		0.393	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KIT	protein_coding	OTTHUMT00000250618.1	A			55294078	+1	no_errors	NM_000222.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
LRRTM2	26045	genome.wustl.edu	37	5	138209820	138209820	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	c6bf38cf-18b1-46e2-99b5-e0b6a0fc7592	47f0907e-96b3-46c2-9acb-198105f451e7	g.chr5:138209820G>C	ENST00000274711.6	-	2	808	c.430C>G	c.(430-432)Cag>Gag	p.Q144E	CTNNA1_ENST00000355078.5_Intron|CTNNA1_ENST00000518825.1_Intron|LRRTM2_ENST00000523537.1_Intron|CTNNA1_ENST00000540387.1_5'Flank|LRRTM2_ENST00000518785.1_Intron|CTNNA1_ENST00000302763.7_Intron|CTNNA1_ENST00000520400.1_Intron|LRRTM2_ENST00000521094.2_Intron	NM_015564.2	NP_056379.1	O43300	LRRT2_HUMAN	leucine rich repeat transmembrane neuronal 2	144					long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|synapse organization (GO:0050808)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|urinary_tract(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GATGACAGCTGATTAAAAGAC	0.423																																						dbGAP											0			5											53.0	55.0	54.0					5																	138209820		1875	4113	5988	138237719	SO:0001583	missense	0			AB007876	CCDS47272.1	5q31	2008-02-05				ENSG00000146006			19409	protein-coding gene	gene with protein product		610868				12676565	Standard	NM_015564		Approved	KIAA0416	uc011cyz.1	O43300		ENST00000274711.6:c.430C>G	5.37:g.138209820G>C	ENSP00000274711:p.Gln144Glu	Somatic	203	0.00	0		0	0.00	0	WXS	Illumina HiSeq	Phase_IV	138237719	98	30.00	42	A0AVL3|A8K4U9|B7ZLN8|Q7L770	Missense_Mutation	SNP	HMMPfam_LRR_1,HMMSmart_SM00369,superfamily_L domain-like	p.Q144E	ENST00000274711.6	37	c.430	CCDS47272.1	5	.	.	.	.	.	.	.	.	.	.	G	9.057	0.993466	0.19043	.	.	ENSG00000146006	ENST00000274711	T	0.55588	0.51	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.42108	0.1188	L	0.48935	1.535	0.58432	D	0.99999	P	0.38922	0.651	B	0.30401	0.115	T	0.30446	-0.9978	10	0.28530	T	0.3	.	14.0608	0.64800	0.0:0.0:0.8493:0.1507	.	144	O43300	LRRT2_HUMAN	E	144	ENSP00000274711:Q144E	ENSP00000274711:Q144E	Q	-	1	0	LRRTM2	138237719	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.459000	0.66685	2.865000	0.98341	0.655000	0.94253	CAG	-	HMMPfam_LRR_1,HMMSmart_SM00369,superfamily_L domain-like		0.423	LRRTM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRRTM2	protein_coding	OTTHUMT00000374043.2	G			138237719	-1	no_errors	NM_015564.2	genbank	human	validated	54_36p	missense	SNP	1.000	C
CD74	972	genome.wustl.edu	37	5	149792285	149792285	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	c6bf38cf-18b1-46e2-99b5-e0b6a0fc7592	47f0907e-96b3-46c2-9acb-198105f451e7	g.chr5:149792285G>A	ENST00000009530.7	-	1	29	c.28C>T	c.(28-30)Cgg>Tgg	p.R10W	CD74_ENST00000524315.1_Missense_Mutation_p.R10W|CD74_ENST00000377795.3_Missense_Mutation_p.R10W|CD74_ENST00000353334.6_Missense_Mutation_p.R10W			P04233	HG2A_HUMAN	CD74 molecule, major histocompatibility complex, class II invariant chain	10					activation of MAPK activity (GO:0000187)|antigen processing and presentation of endogenous antigen (GO:0019883)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|chaperone mediated protein folding requiring cofactor (GO:0051085)|defense response (GO:0006952)|immunoglobulin mediated immune response (GO:0016064)|intracellular protein transport (GO:0006886)|macrophage migration inhibitory factor signaling pathway (GO:0035691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of peptide secretion (GO:0002792)|negative regulation of T cell differentiation (GO:0045581)|negative thymic T cell selection (GO:0045060)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type 2 immune response (GO:0002830)|positive thymic T cell selection (GO:0045059)|prostaglandin biosynthetic process (GO:0001516)|protein complex assembly (GO:0006461)|regulation of macrophage activation (GO:0043030)|signal transduction (GO:0007165)|T cell selection (GO:0045058)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|macrophage migration inhibitory factor receptor complex (GO:0035692)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|NOS2-CD74 complex (GO:0035693)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)|vacuole (GO:0005773)	beta-amyloid binding (GO:0001540)|cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|macrophage migration inhibitory factor binding (GO:0035718)|MHC class II protein binding (GO:0042289)|MHC class II protein binding, via antigen binding groove (GO:0042658)|MHC class II protein complex binding (GO:0023026)|protein binding involved in protein folding (GO:0044183)	p.R10W(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)	5		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGATCTTCCCGACAGCTCCTG	0.612			T	ROS1	NSCLC																																	dbGAP		Dom	yes		5	5q32	972	"""CD74 molecule, major histocompatibility complex, class II invariant chain"""		E	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	5											152.0	153.0	153.0					5																	149792285		2203	4300	6503	149772478	SO:0001583	missense	0				CCDS34276.1, CCDS47308.1, CCDS47309.1	5q32	2012-09-20	2006-03-28		ENSG00000019582	ENSG00000019582		"""CD molecules"""	1697	protein-coding gene	gene with protein product	"""HLA-DR-gamma"", ""Ia-associated invariant chain"", ""gamma chain of class II antigens"", ""MHC HLA-DR gamma chain"""	142790	"""CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)"""	DHLAG		6324166, 3001652	Standard	NM_004355		Approved		uc003lsc.3	P04233	OTTHUMG00000163559	ENST00000009530.7:c.28C>T	5.37:g.149792285G>A	ENSP00000009530:p.Arg10Trp	Somatic	266	0.37	1		4335	45.83	3678	WXS	Illumina HiSeq	Phase_IV	149772478	51	41.38	36	A8K7R1|B4DNE8|D3DQG3|D3DQG4|Q14597|Q29832|Q5U0J8|Q8SNA0|Q8WLP6	Missense_Mutation	SNP	HMMPfam_Thyroglobulin_1,HMMSmart_SM00211,PatternScan_THYROGLOBULIN_1_1,superfamily_Thyroglobulin type-1 domain,HMMPfam_MHCassoc_trimer,superfamily_Class II MHC-associated invariant chain ectoplasmic trimerization domain,HMMPfam_MHC2-interact	p.R10W	ENST00000009530.7	37	c.28	CCDS47309.1	5	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.496|5.496	0.276441|0.276441	0.10403|0.10403	.|.	.|.	ENSG00000019582|ENSG00000019582	ENST00000377795;ENST00000353334;ENST00000524315;ENST00000009530|ENST00000518797	T|.	0.59638|.	0.25|.	5.09|5.09	-0.158|-0.158	0.13383|0.13383	.|.	1.523410|.	0.04231|.	N|.	0.335207|.	T|T	0.08313|0.08313	0.0207|0.0207	N|N	0.02011|0.02011	-0.69|-0.69	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0|.	T|T	0.28870|0.28870	-1.0030|-1.0030	10|5	0.72032|.	D|.	0.01|.	1.0452|1.0452	0.8313|0.8313	0.01131|0.01131	0.3006:0.3515:0.1527:0.1953|0.3006:0.3515:0.1527:0.1953	.|.	10;10;10;10|.	A9YLN4;P04233-3;P04233-2;P04233|.	.;.;.;HG2A_HUMAN|.	W|L	10|4	ENSP00000009530:R10W|.	ENSP00000009530:R10W|.	R|S	-|-	1|2	2|0	CD74|CD74	149772478|149772478	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.474000|-0.474000	0.06607|0.06607	-0.356000|-0.356000	0.08187|0.08187	-2.070000|-2.070000	0.00385|0.00385	CGG|TCG	-	NULL		0.612	CD74-003	KNOWN	basic|appris_principal|CCDS	protein_coding	CD74	protein_coding	OTTHUMT00000374178.1	G	NM_004355		149772478	-1	no_errors	NM_001025159.1	genbank	human	validated	54_36p	missense	SNP	0.002	A
SPAM1	6677	genome.wustl.edu	37	7	123599598	123599598	+	Missense_Mutation	SNP	G	G	A	rs200074039	byFrequency	TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	c6bf38cf-18b1-46e2-99b5-e0b6a0fc7592	47f0907e-96b3-46c2-9acb-198105f451e7	g.chr7:123599598G>A	ENST00000439500.1	+	6	1718	c.1105G>A	c.(1105-1107)Gtc>Atc	p.V369I	SPAM1_ENST00000223028.7_Missense_Mutation_p.V369I|SPAM1_ENST00000340011.5_Missense_Mutation_p.V369I|SPAM1_ENST00000460182.1_Missense_Mutation_p.V369I|SPAM1_ENST00000402183.2_Missense_Mutation_p.V369I	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	369					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)			breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CATAATCAACGTCACACTAGC	0.388													G|||	2	0.000399361	0.0	0.0	5008	,	,		18274	0.002		0.0	False		,,,				2504	0.0					dbGAP											0			7											101.0	93.0	96.0					7																	123599598		2203	4300	6503	123386834	SO:0001583	missense	0			L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.1105G>A	7.37:g.123599598G>A	ENSP00000402123:p.Val369Ile	Somatic	228	0.87	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	123386834	67	37.96	41	Q8TC30	Missense_Mutation	SNP	HMMPfam_Glyco_hydro_56,superfamily_Glyco_hydro_cat	p.V369I	ENST00000439500.1	37	c.1105	CCDS5791.1	7	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	13.84	2.356231	0.41700	.	.	ENSG00000106304	ENST00000402183;ENST00000460182;ENST00000340011;ENST00000439500;ENST00000223028	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.87	0.6	0.17524	.	0.195589	0.43919	N	0.000520	T	0.41949	0.1181	M	0.84511	2.7	0.36154	D	0.847674	P;D	0.56287	0.94;0.975	P;P	0.50378	0.518;0.639	T	0.51513	-0.8696	10	0.72032	D	0.01	-14.2531	6.8597	0.24060	0.2781:0.1135:0.6084:0.0	.	369;369	Q8TC30;P38567	.;HYALP_HUMAN	I	369	ENSP00000386028:V369I;ENSP00000417934:V369I;ENSP00000345849:V369I;ENSP00000402123:V369I;ENSP00000223028:V369I	ENSP00000223028:V369I	V	+	1	0	SPAM1	123386834	1.000000	0.71417	0.083000	0.20561	0.007000	0.05969	3.726000	0.54977	-0.093000	0.12396	-0.880000	0.02959	GTC	-	HMMPfam_Glyco_hydro_56		0.388	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SPAM1	protein_coding	OTTHUMT00000348309.1	G			123386834	+1	no_errors	NM_003117.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
PLCE1	51196	genome.wustl.edu	37	10	95931194	95931194	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	c6bf38cf-18b1-46e2-99b5-e0b6a0fc7592	47f0907e-96b3-46c2-9acb-198105f451e7	g.chr10:95931194C>A	ENST00000371380.3	+	3	1985	c.1750C>A	c.(1750-1752)Ctt>Att	p.L584I	PLCE1_ENST00000371375.1_Missense_Mutation_p.L276I|PLCE1_ENST00000371385.3_Missense_Mutation_p.L276I|PLCE1_ENST00000260766.3_Missense_Mutation_p.L584I			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	584	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				AGCGTCGATTCTTACCACTCA	0.488																																						dbGAP											0			10											122.0	120.0	121.0					10																	95931194		2031	4197	6228	95921184	SO:0001583	missense	0				CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"""nephrosis type 3"""	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.1750C>A	10.37:g.95931194C>A	ENSP00000360431:p.Leu584Ile	Somatic	470	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	95921184	206	19.46	50	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	HMMPfam_C2,HMMSmart_SM00239,HMMPfam_RA,HMMSmart_SM00314,HMMPfam_PI-PLC-X,HMMSmart_SM00148,HMMPfam_PI-PLC-Y,HMMSmart_SM00149,HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_efhand_like,superfamily_PLC-like phosphodiesterases,superfamily_EF-hand	p.L584I	ENST00000371380.3	37	c.1750	CCDS41552.1	10	.	.	.	.	.	.	.	.	.	.	C	9.413	1.080928	0.20309	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.26223	1.75;1.75;1.77;1.77	5.84	4.94	0.65067	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.228496	0.37530	N	0.002050	T	0.18923	0.0454	N	0.19112	0.55	0.30581	N	0.762557	B;B;B	0.25667	0.064;0.052;0.131	B;B;B	0.32980	0.156;0.05;0.11	T	0.16100	-1.0414	10	0.23891	T	0.37	.	12.0712	0.53618	0.1363:0.7329:0.1308:0.0	.	584;276;584	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	I	584;584;276;276	ENSP00000260766:L584I;ENSP00000360431:L584I;ENSP00000360438:L276I;ENSP00000360426:L276I	ENSP00000260766:L584I	L	+	1	0	PLCE1	95921184	1.000000	0.71417	0.528000	0.27938	0.024000	0.10985	4.224000	0.58593	1.482000	0.48325	-0.127000	0.14921	CTT	-	HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF		0.488	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PLCE1	protein_coding	OTTHUMT00000049469.3	C	NM_016341		95921184	+1	no_errors	NM_016341.3	genbank	human	validated	54_36p	missense	SNP	0.239	A
SYT1	6857	genome.wustl.edu	37	12	79611354	79611354	+	Missense_Mutation	SNP	G	G	A	rs144005237		TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	c6bf38cf-18b1-46e2-99b5-e0b6a0fc7592	47f0907e-96b3-46c2-9acb-198105f451e7	g.chr12:79611354G>A	ENST00000261205.4	+	4	712	c.55G>A	c.(55-57)Gcg>Acg	p.A19T	SYT1_ENST00000552744.1_Missense_Mutation_p.A19T|SYT1_ENST00000393240.3_Missense_Mutation_p.A19T|SYT1_ENST00000457153.2_Missense_Mutation_p.A19T	NM_005639.2	NP_005630.1	P21579	SYT1_HUMAN	synaptotagmin I	19					calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|detection of calcium ion (GO:0005513)|glutamate secretion (GO:0014047)|neurotransmitter secretion (GO:0007269)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of vesicle fusion (GO:0031340)|protein homooligomerization (GO:0051260)|regulation of exocytosis (GO:0017157)|regulation of regulated secretory pathway (GO:1903305)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|vesicle docking (GO:0048278)	cell junction (GO:0030054)|clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|endocytic vesicle membrane (GO:0030666)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol binding (GO:0005545)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|pancreas(2)|skin(6)	25						CACCACTGTCGCGACTGTTCT	0.532																																						dbGAP											0			12						G	THR/ALA,THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	56.0	56.0	56.0		55,55,55	4.6	0.1	12	dbSNP_134	56	0,8600		0,0,4300	no	missense,missense,missense	SYT1	NM_001135805.1,NM_001135806.1,NM_005639.2	58,58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign	19/423,19/423,19/423	79611354	1,13005	2203	4300	6503	78135485	SO:0001583	missense	0				CCDS9017.1	12q21.2	2013-09-20			ENSG00000067715	ENSG00000067715		"""Synaptotagmins"""	11509	protein-coding gene	gene with protein product		185605		SYT, SVP65		1840599	Standard	NM_001135805		Approved	P65	uc001syv.3	P21579	OTTHUMG00000134326	ENST00000261205.4:c.55G>A	12.37:g.79611354G>A	ENSP00000261205:p.Ala19Thr	Somatic	71	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	78135485	54	37.21	32	Q6AI31	Missense_Mutation	SNP	HMMPfam_C2,HMMSmart_SM00239,superfamily_C2 domain (Calcium/lipid-binding domain CaLB)	p.A19T	ENST00000261205.4	37	c.55	CCDS9017.1	12	.	.	.	.	.	.	.	.	.	.	G	10.65	1.408521	0.25378	2.27E-4	0.0	ENSG00000067715	ENST00000393240;ENST00000261205;ENST00000457153;ENST00000552074;ENST00000547046;ENST00000549671;ENST00000551304;ENST00000552744;ENST00000552624;ENST00000446242	T;T;T;T;T;T	0.59906	0.25;0.25;0.23;0.25;1.89;2.48	5.51	4.62	0.57501	.	0.303302	0.37095	N	0.002258	T	0.44477	0.1295	L	0.36672	1.1	0.54753	D	0.999981	B;B	0.12630	0.006;0.006	B;B	0.04013	0.001;0.001	T	0.28681	-1.0036	10	0.18710	T	0.47	.	11.2104	0.48795	0.1472:0.0:0.8528:0.0	.	19;19	Q6AI31;P21579	.;SYT1_HUMAN	T	19	ENSP00000376932:A19T;ENSP00000261205:A19T;ENSP00000391056:A19T;ENSP00000447575:A19T;ENSP00000448861:A19T;ENSP00000401559:A19T	ENSP00000261205:A19T	A	+	1	0	SYT1	78135485	0.939000	0.31865	0.063000	0.19743	0.137000	0.21094	2.024000	0.41049	1.321000	0.45227	0.643000	0.83706	GCG	-	NULL		0.532	SYT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SYT1	protein_coding	OTTHUMT00000259415.1	G	NM_005639		78135485	+1	no_errors	NM_005639.1	genbank	human	validated	54_36p	missense	SNP	0.964	A
U2AF1	7307	genome.wustl.edu	37	21	44524456	44524456	+	Missense_Mutation	SNP	G	G	A	rs371769427		TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	c6bf38cf-18b1-46e2-99b5-e0b6a0fc7592	47f0907e-96b3-46c2-9acb-198105f451e7	g.chr21:44524456G>A	ENST00000291552.4	-	2	193	c.101C>T	c.(100-102)tCt>tTt	p.S34F	U2AF1_ENST00000486519.1_5'UTR|U2AF1_ENST00000459639.1_5'UTR|U2AF1_ENST00000398137.1_5'UTR|U2AF1_ENST00000380276.2_Missense_Mutation_p.S34F	NM_006758.2	NP_006749.1	Q01081	U2AF1_HUMAN	U2 small nuclear RNA auxiliary factor 1	34					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S34F(45)|p.S34Y(12)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(111)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	126						GTGCAACCGAGAGCACCTGTC	0.358			Mis		"""CLL, MDS"""																																	dbGAP		Dom	yes		21	21q22.3	7307	U2 small nuclear RNA auxiliary factor 1		L	57	Substitution - Missense(57)	haematopoietic_and_lymphoid_tissue(43)|lung(12)|endometrium(2)	21						G	PHE/SER,PHE/SER,	1,4405		0,1,2202	67.0	64.0	65.0		101,101,	5.5	1.0	21		65	0,8600		0,0,4300	no	missense,missense,utr-5	U2AF1	NM_001025203.1,NM_006758.2,NM_001025204.1	155,155,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,	34/241,34/241,	44524456	1,13005	2203	4300	6503	43397525	SO:0001583	missense	0			BC001177	CCDS13694.1, CCDS33574.1, CCDS42948.1	21q22.3	2014-09-17	2006-04-11		ENSG00000160201	ENSG00000160201		"""RNA binding motif (RRM) containing"""	12453	protein-coding gene	gene with protein product		191317	"""U2(RNU2) small nuclear RNA auxiliary factor binding protein"", ""U2(RNU2) small nuclear RNA auxiliary factor 1"""	U2AFBP		8660980, 7956352	Standard	NM_006758		Approved	U2AF35, RNU2AF1, RN	uc002zdb.1	Q01081	OTTHUMG00000086836	ENST00000291552.4:c.101C>T	21.37:g.44524456G>A	ENSP00000291552:p.Ser34Phe	Somatic	69	0.00	0		48	55.96	61	WXS	Illumina HiSeq	Phase_IV	43397525	12	52.00	13	Q701P4|Q71RF1	Missense_Mutation	SNP	HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928	p.S34F	ENST00000291552.4	37	c.101	CCDS13694.1	21	.	.	.	.	.	.	.	.	.	.	G	29.7	5.025187	0.93518	2.27E-4	0.0	ENSG00000160201	ENST00000380276;ENST00000291552	T;T	0.46063	0.88;0.88	5.47	5.47	0.80525	Zinc finger, CCCH-type (3);	0.000000	0.85682	D	0.000000	T	0.77239	0.4101	H	0.96430	3.82	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.997	D	0.84864	0.0821	10	0.87932	D	0	-15.7954	19.3169	0.94218	0.0:0.0:1.0:0.0	.	34;34;34	Q69YM7;Q01081;Q701P4	.;U2AF1_HUMAN;.	F	34	ENSP00000369629:S34F;ENSP00000291552:S34F	ENSP00000291552:S34F	S	-	2	0	U2AF1	43397525	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.864000	0.92294	2.560000	0.86352	0.563000	0.77884	TCT	-	HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1		0.358	U2AF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	U2AF1	protein_coding	OTTHUMT00000195541.1	G	NM_006758		43397525	-1	no_errors	NM_001025203.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
POLDIP3	84271	genome.wustl.edu	37	22	42998992	42998992	+	Silent	SNP	A	A	G			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	c6bf38cf-18b1-46e2-99b5-e0b6a0fc7592	47f0907e-96b3-46c2-9acb-198105f451e7	g.chr22:42998992A>G	ENST00000252115.5	-	2	338	c.234T>C	c.(232-234)ctT>ctC	p.L78L	POLDIP3_ENST00000339677.6_Silent_p.L78L|POLDIP3_ENST00000451060.2_5'Flank|POLDIP3_ENST00000491021.1_5'UTR|POLDIP3_ENST00000348657.2_Silent_p.L78L	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	78					poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						CTTTCTGCAAAAGCTTCTCCC	0.562																																					Ovarian(52;967 1128 5875 19997 42537)	dbGAP											0			22											95.0	93.0	94.0					22																	42998992		2203	4300	6503	41328936	SO:0001819	synonymous_variant	0				CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"""RNA binding motif (RRM) containing"""	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.234T>C	22.37:g.42998992A>G		Somatic	269	2.18	6		35	42.62	26	WXS	Illumina HiSeq	Phase_IV	41328936	32	58.44	45	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Silent	SNP	HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD	p.L78	ENST00000252115.5	37	c.234	CCDS14038.1	22																																																																																			-	NULL		0.562	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLDIP3	protein_coding	OTTHUMT00000320433.1	A	NM_032311		41328936	-1	no_errors	NM_032311.3	genbank	human	reviewed	54_36p	silent	SNP	1.000	G
TLR4	7099	genome.wustl.edu	37	9	120475317	120475320	+	Frame_Shift_Del	DEL	TTAA	TTAA	-			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	TTAA	TTAA	TTAA	-	TTAA	TTAA	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	c6bf38cf-18b1-46e2-99b5-e0b6a0fc7592	47f0907e-96b3-46c2-9acb-198105f451e7	g.chr9:120475317_120475320delTTAA	ENST00000355622.6	+	3	1012_1015	c.911_914delTTAA	c.(910-915)tttaatfs	p.FN304fs	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Frame_Shift_Del_p.FN264fs	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	304					activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	ATTGACTTATTTAATTGTTTGACA	0.338																																						dbGAP											0			9																																								119515141	SO:0001589	frameshift_variant	0			U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"""CD molecules"""	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.911_914delTTAA	9.37:g.120475317_120475320delTTAA	ENSP00000363089:p.Phe304fs	Somatic	NA	NA	NA		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	119515138	NA	NA	NA	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Frame_Shift_Del	DEL	HMMPfam_TIR,HMMSmart_SM00255,superfamily_Toll/Interleukin receptor TIR domain,HMMPfam_LRRCT,HMMSmart_SM00082,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00365,superfamily_L domain-like	p.N305fs	ENST00000355622.6	37	c.911_914	CCDS6818.1	9																																																																																			-	superfamily_L domain-like		0.338	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TLR4	protein_coding	OTTHUMT00000055549.3	TTAA	NM_138554		119515141	+1	no_errors	NM_138554.3	genbank	human	reviewed	54_36p	frame_shift_del	DEL	0.040:0.049:0.060:0.352	-
