#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
TIE1	7075	broad.mit.edu	37	1	43783609	43783609	+	Missense_Mutation	SNP	C	C	T			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr1:43783609C>T	ENST00000372476.3	+	17	2867	c.2788C>T	c.(2788-2790)Cgg>Tgg	p.R930W	TIE1_ENST00000473014.1_3'UTR|TIE1_ENST00000433781.2_Missense_Mutation_p.R575W	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	930	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|peptidyl-tyrosine phosphorylation (GO:0018108)|plasma membrane fusion (GO:0045026)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R930W(2)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				AGATTTTCTGCGGAAAAGCCG	0.527																																						ENST00000372476.3																			2	Substitution - Missense(2)	p.R930W(2)	prostate(2)	breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70						c.(2788-2790)Cgg>Tgg		tyrosine kinase with immunoglobulin-like and EGF-like domains 1							196.0	210.0	205.0					1																	43783609		2203	4300	6503	SO:0001583	missense	7075				mesoderm development	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	g.chr1:43783609C>T	BC038239	CCDS482.1	1p34-p33	2013-02-11	2004-12-13	2004-12-14	ENSG00000066056	ENSG00000066056	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11809	protein-coding gene	gene with protein product		600222	"""tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1"""	TIE		1312667	Standard	NM_005424		Approved	JTK14	uc001ciu.3	P35590	OTTHUMG00000007282	ENST00000372476.3:c.2788C>T	1.37:g.43783609C>T	ENSP00000361554:p.Arg930Trp					TIE1_ENST00000433781.2_Missense_Mutation_p.R575W|TIE1_ENST00000473014.1_3'UTR	p.R930W	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN			17	2867	+	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)	930			Protein kinase.		B5A949|B5A950	Missense_Mutation	SNP	ENST00000372476.3	37	c.2788C>T	CCDS482.1	.	.	.	.	.	.	.	.	.	.	C	18.43	3.623112	0.66901	.	.	ENSG00000066056	ENST00000372476;ENST00000372475;ENST00000536913;ENST00000433781	D;D	0.84589	-1.87;-1.87	6.06	0.713	0.18173	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.205040	0.23809	N	0.044351	D	0.91758	0.7393	M	0.85197	2.74	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.90931	0.4790	10	0.87932	D	0	.	12.4715	0.55790	0.4527:0.4427:0.1046:0.0	.	885;575;930	B4DTW8;B4DKW0;P35590	.;.;TIE1_HUMAN	W	930;333;213;575	ENSP00000361554:R930W;ENSP00000411728:R575W	ENSP00000361553:R333W	R	+	1	2	TIE1	43556196	0.995000	0.38212	0.492000	0.27490	0.873000	0.50193	2.601000	0.46249	-0.106000	0.12110	0.655000	0.94253	CGG		0.527	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424		28	298	28	298	---	---	---	---
ETV3L	440695	broad.mit.edu	37	1	157069117	157069117	+	Missense_Mutation	SNP	G	G	T			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr1:157069117G>T	ENST00000454449.2	-	2	396	c.112C>A	c.(112-114)Cag>Aag	p.Q38K		NM_001004341.2	NP_001004341.1	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	38					cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.Q38K(2)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Hepatocellular(266;0.158)	Prostate(1639;0.184)				AGCTGGATCTGCCGGGAGCCT	0.617																																						ENST00000454449.2																			2	Substitution - Missense(2)	p.Q38K(2)	prostate(2)	breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24						c.(112-114)Cag>Aag		ets variant 3-like							48.0	48.0	48.0					1																	157069117		2203	4300	6503	SO:0001583	missense	440695					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr1:157069117G>T	AK131392	CCDS30893.1	1q23.1	2013-09-24	2008-09-12		ENSG00000253831	ENSG00000253831			33834	protein-coding gene	gene with protein product			"""ets variant gene 3-like"""				Standard	NM_001004341		Approved	FLJ16478	uc001fqq.2	Q6ZN32	OTTHUMG00000041325	ENST00000454449.2:c.112C>A	1.37:g.157069117G>T	ENSP00000430271:p.Gln38Lys						p.Q38K	NM_001004341.2	NP_001004341.1	Q6ZN32	ETV3L_HUMAN			2	396	-	Hepatocellular(266;0.158)	Prostate(1639;0.184)	38						Missense_Mutation	SNP	ENST00000454449.2	37	c.112C>A	CCDS30893.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.041346	0.93685	.	.	ENSG00000253831	ENST00000454449	T	0.53423	0.62	4.96	4.96	0.65561	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (2);	0.000000	0.36200	N	0.002737	T	0.66066	0.2752	M	0.80508	2.5	0.47153	D	0.999338	D	0.76494	0.999	D	0.91635	0.999	T	0.70699	-0.4800	10	0.72032	D	0.01	.	17.1432	0.86759	0.0:0.0:1.0:0.0	.	38	Q6ZN32	ETV3L_HUMAN	K	38	ENSP00000430271:Q38K	ENSP00000430271:Q38K	Q	-	1	0	ETV3L	155335741	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.557000	0.98129	2.556000	0.86216	0.655000	0.94253	CAG		0.617	ETV3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099024.2	NM_001004341		3	56	3	56	---	---	---	---
ZNF678	339500	broad.mit.edu	37	1	227842075	227842075	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr1:227842075C>T	ENST00000343776.5	+	4	469	c.124C>T	c.(124-126)Cag>Tag	p.Q42*	ZNF678_ENST00000397097.3_Nonsense_Mutation_p.Q97*|ZNF678_ENST00000608949.1_Nonsense_Mutation_p.Q42*	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	42					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q42*(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				TTTGCCAGAGCAGGATATGAA	0.333																																						ENST00000343776.5																			1	Substitution - Nonsense(1)	p.Q42*(1)	prostate(1)	central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24						c.(124-126)Cag>Tag		zinc finger protein 678							96.0	105.0	102.0					1																	227842075		2202	4299	6501	SO:0001587	stop_gained	339500				regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding	g.chr1:227842075C>T	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"""Zinc fingers, C2H2-type"", ""-"""	28652	protein-coding gene	gene with protein product	"""hypothetical protein MGC42493"""					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.124C>T	1.37:g.227842075C>T	ENSP00000344828:p.Gln42*					ZNF678_ENST00000608949.1_Nonsense_Mutation_p.Q42*|ZNF678_ENST00000397097.3_Nonsense_Mutation_p.Q97*	p.Q42*	NM_178549.3	NP_848644.2	F5GXA7	F5GXA7_HUMAN			4	469	+		Prostate(94;0.0885)						Q8IVQ9	Nonsense_Mutation	SNP	ENST00000343776.5	37	c.124C>T		.	.	.	.	.	.	.	.	.	.	C	8.368	0.834578	0.16820	.	.	ENSG00000181450	ENST00000343776;ENST00000397097;ENST00000440339	.	.	.	1.5	1.5	0.22942	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	6.0899	0.19989	0.0:0.6739:0.3261:0.0	.	.	.	.	X	42;97;97	.	ENSP00000344828:Q42X	Q	+	1	0	ZNF678	225908698	0.034000	0.19679	0.058000	0.19502	0.101000	0.19017	0.746000	0.26275	0.708000	0.31955	0.514000	0.50259	CAG		0.333	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		11	134	11	134	---	---	---	---
LPIN1	23175	broad.mit.edu	37	2	11943067	11943067	+	Missense_Mutation	SNP	C	C	T			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr2:11943067C>T	ENST00000256720.2	+	14	1906	c.1813C>T	c.(1813-1815)Cgc>Tgc	p.R605C	LPIN1_ENST00000449576.2_Missense_Mutation_p.R690C|LPIN1_ENST00000425416.2_Missense_Mutation_p.R611C|LPIN1_ENST00000396097.1_Missense_Mutation_p.R335C|LPIN1_ENST00000396099.1_Missense_Mutation_p.R647C|LPIN1_ENST00000404113.2_Missense_Mutation_p.R106C	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	605					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.R605C(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TGATGAGGAGCGCGCAGCTGC	0.498																																						ENST00000256720.2																			1	Substitution - Missense(1)	p.R605C(1)	prostate(1)	autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45						c.(1813-1815)Cgc>Tgc		lipin 1							180.0	163.0	169.0					2																	11943067		2203	4300	6503	SO:0001583	missense	23175				fatty acid catabolic process|transcription, DNA-dependent|triglyceride biosynthetic process|triglyceride mobilization	cytosol|endoplasmic reticulum membrane	phosphatidate phosphatase activity	g.chr2:11943067C>T	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.1813C>T	2.37:g.11943067C>T	ENSP00000256720:p.Arg605Cys					LPIN1_ENST00000425416.2_Missense_Mutation_p.R611C|LPIN1_ENST00000404113.2_Missense_Mutation_p.R106C|LPIN1_ENST00000396097.1_Missense_Mutation_p.R335C|LPIN1_ENST00000396099.1_Missense_Mutation_p.R647C|LPIN1_ENST00000449576.2_Missense_Mutation_p.R690C	p.R605C	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN		Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)	14	1906	+	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)		605					A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	c.1813C>T	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.723847	0.48728	.	.	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113;ENST00000454151	T;T;T;T;T;T;T	0.80909	-1.43;-1.42;-1.42;-1.42;-1.27;-0.42;0.5	4.69	3.75	0.43078	.	0.426017	0.27673	N	0.018326	T	0.73393	0.3581	N	0.19112	0.55	0.35483	D	0.798341	B;P;P	0.49559	0.41;0.925;0.84	B;P;B	0.46758	0.039;0.526;0.039	T	0.82244	-0.0553	10	0.56958	D	0.05	-21.0422	15.3509	0.74384	0.0:0.8602:0.1398:0.0	.	106;690;605	B4DET9;F5GY24;Q14693	.;.;LPIN1_HUMAN	C	690;647;611;605;335;106;132	ENSP00000397908:R690C;ENSP00000379406:R647C;ENSP00000401522:R611C;ENSP00000256720:R605C;ENSP00000379404:R335C;ENSP00000386120:R106C;ENSP00000413714:R132C	ENSP00000256720:R605C	R	+	1	0	LPIN1	11860518	0.995000	0.38212	0.938000	0.37757	0.331000	0.28603	3.478000	0.53158	2.310000	0.77875	0.561000	0.74099	CGC		0.498	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		19	172	19	172	---	---	---	---
SNRNP27	11017	broad.mit.edu	37	2	70130361	70130361	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr2:70130361C>T	ENST00000244227.3	+	5	822	c.397C>T	c.(397-399)Cag>Tag	p.Q133*	SNRNP27_ENST00000409116.1_Intron|AC019206.1_ENST00000599032.1_5'Flank|SNRNP27_ENST00000488986.1_3'UTR	NM_006857.2	NP_006848.1	Q8WVK2	SNR27_HUMAN	small nuclear ribonucleoprotein 27kDa (U4/U6.U5)	133					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.Q133*(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	11						AAATGTCTCTCAGAAGAGGAA	0.328																																						ENST00000244227.3																			1	Substitution - Nonsense(1)	p.Q133*(1)	prostate(1)	cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	11						c.(397-399)Cag>Tag		small nuclear ribonucleoprotein 27kDa (U4/U6.U5)							190.0	175.0	180.0					2																	70130361		2203	4300	6503	SO:0001587	stop_gained	11017				mRNA processing|RNA splicing	nucleus	nucleic acid binding	g.chr2:70130361C>T	X76302	CCDS33219.1	2p14	2011-10-11			ENSG00000124380	ENSG00000124380			30240	protein-coding gene	gene with protein product	"""nucleic acid binding protein RY 1"""					7931148	Standard	NM_006857		Approved	RY1	uc002sfw.3	Q8WVK2	OTTHUMG00000152689	ENST00000244227.3:c.397C>T	2.37:g.70130361C>T	ENSP00000244227:p.Gln133*					SNRNP27_ENST00000409116.1_Intron|SNRNP27_ENST00000488986.1_3'UTR	p.Q133*	NM_006857.2	NP_006848.1	Q8WVK2	SNR27_HUMAN			5	822	+			133					Q15410	Nonsense_Mutation	SNP	ENST00000244227.3	37	c.397C>T	CCDS33219.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.397334	0.62177	.	.	ENSG00000124380	ENST00000244227	.	.	.	4.72	4.72	0.59763	.	0.179024	0.49305	D	0.000160	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.2166	0.73270	0.0:1.0:0.0:0.0	.	.	.	.	X	133	.	ENSP00000244227:Q133X	Q	+	1	0	SNRNP27	69983865	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.320000	0.59203	2.436000	0.82500	0.462000	0.41574	CAG		0.328	SNRNP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327369.1	NM_006857		10	117	10	117	---	---	---	---
ABCF3	55324	broad.mit.edu	37	3	183908945	183908945	+	Missense_Mutation	SNP	A	A	C	rs140615216		TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr3:183908945A>C	ENST00000429586.2	+	16	1656	c.1471A>C	c.(1471-1473)Att>Ctt	p.I491L	EIF2B5_ENST00000444495.1_Intron|ABCF3_ENST00000292808.5_Missense_Mutation_p.I485L	NM_018358.2	NP_060828.2	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 3	491					defense response to virus (GO:0051607)	membrane (GO:0016020)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.I491L(1)		breast(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(20)|ovary(3)|prostate(5)|upper_aerodigestive_tract(1)	39	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTCGCCGCCAATTCTGCAGCT	0.557																																						ENST00000429586.2																			1	Substitution - Missense(1)	p.I491L(1)	prostate(1)	breast(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(20)|ovary(3)|prostate(5)|upper_aerodigestive_tract(1)	39						c.(1471-1473)Att>Ctt		ATP-binding cassette, sub-family F (GCN20), member 3							160.0	150.0	153.0					3																	183908945		2203	4300	6503	SO:0001583	missense	55324						ATP binding|ATPase activity	g.chr3:183908945A>C	U66685	CCDS3254.1	3q27.1	2012-05-16			ENSG00000161204	ENSG00000161204		"""ATP binding cassette transporters / subfamily F"""	72	protein-coding gene	gene with protein product						8894702	Standard	NM_018358		Approved	EST201864	uc003fmz.2	Q9NUQ8	OTTHUMG00000156824	ENST00000429586.2:c.1471A>C	3.37:g.183908945A>C	ENSP00000411471:p.Ile491Leu					EIF2B5_ENST00000444495.1_Intron|ABCF3_ENST00000292808.5_Missense_Mutation_p.I485L	p.I491L	NM_018358.2	NP_060828.2	Q9NUQ8	ABCF3_HUMAN	Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		16	1656	+	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		491					A8K241|Q86UA2|Q8NAN1|Q96GS8|Q9H7A8	Missense_Mutation	SNP	ENST00000429586.2	37	c.1471A>C	CCDS3254.1	.	.	.	.	.	.	.	.	.	.	A	13.94	2.386190	0.42308	.	.	ENSG00000161204	ENST00000429586;ENST00000292808	D;D	0.91521	-2.86;-2.86	5.74	0.507	0.16967	.	0.165681	0.52532	D	0.000065	T	0.78104	0.4231	N	0.11106	0.095	0.49299	D	0.999778	B;B	0.11235	0.004;0.001	B;B	0.15870	0.014;0.002	T	0.65274	-0.6208	10	0.30078	T	0.28	-7.5428	9.5878	0.39528	0.7082:0.0:0.2918:0.0	.	485;491	Q9NUQ8-2;Q9NUQ8	.;ABCF3_HUMAN	L	491;485	ENSP00000411471:I491L;ENSP00000292808:I485L	ENSP00000292808:I485L	I	+	1	0	ABCF3	185391639	0.566000	0.26618	0.131000	0.22000	0.996000	0.88848	1.404000	0.34623	0.364000	0.24374	0.533000	0.62120	ATT		0.557	ABCF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346047.1	NM_018358		8	119	8	119	---	---	---	---
MSH3	4437	broad.mit.edu	37	5	79952234	79952234	+	Missense_Mutation	SNP	C	C	A			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr5:79952234C>A	ENST00000265081.6	+	2	322	c.242C>A	c.(241-243)aCa>aAa	p.T81K	DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000439211.2_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	81	Interaction with EXO1.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)	p.T81K(1)|p.T72K(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		ATATAGGCTACAGAAATTGAC	0.388								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)	ENST00000265081.6																			2	Substitution - Missense(2)	p.T81K(1)|p.T72K(1)	prostate(2)	NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						c.(241-243)aCa>aAa	Mismatch excision repair (MMR)	mutS homolog 3							123.0	129.0	127.0					5																	79952234		2203	4300	6503	SO:0001583	missense	4437				maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding	g.chr5:79952234C>A	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.242C>A	5.37:g.79952234C>A	ENSP00000265081:p.Thr81Lys						p.T81K	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)	2	322	+		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)	81			Interaction with EXO1.		A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	c.242C>A	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	C	6.044	0.376486	0.11466	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.86497	-2.13	4.83	3.96	0.45880	.	1.366250	0.04763	N	0.426604	D	0.83073	0.5175	L	0.40543	1.245	0.09310	N	1	B	0.19817	0.039	B	0.16722	0.016	T	0.65944	-0.6045	9	.	.	.	0.0722	9.5204	0.39131	0.0:0.9004:0.0:0.0996	.	81	P20585	MSH3_HUMAN	K	81;72	ENSP00000265081:T81K	.	T	+	2	0	MSH3	79987990	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	1.251000	0.32862	1.153000	0.42468	0.563000	0.77884	ACA		0.388	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		10	140	10	140	---	---	---	---
HLA-F	3134	broad.mit.edu	37	6	29694720	29694720	+	IGR	SNP	G	G	A			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr6:29694720G>A	ENST00000376861.1	+	0	1544				HLA-F_ENST00000440587.2_Missense_Mutation_p.G237E|HLA-F_ENST00000259951.7_Missense_Mutation_p.G366E|HLA-F_ENST00000475996.1_Intron			P30511	HLAF_HUMAN	major histocompatibility complex, class I, F						antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)	p.G366E(1)		cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						TTTCTCCTGGGGGTGCTCTTC	0.498																																						ENST00000440587.2																			1	Substitution - Missense(1)	p.G366E(1)	prostate(1)	cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						c.(709-711)gGg>gAg		major histocompatibility complex, class I, F							121.0	141.0	134.0					6																	29694720		1426	2661	4087	SO:0001628	intergenic_variant	3134				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity	g.chr6:29694720G>A	AY253269	CCDS43437.1, CCDS43438.1, CCDS43439.1	6p21.3	2013-01-11			ENSG00000204642	ENSG00000204642		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4963	protein-coding gene	gene with protein product		143110				1688605	Standard	NM_018950		Approved		uc003nno.4	P30511	OTTHUMG00000031156		6.37:g.29694720G>A						HLA-F_ENST00000259951.7_Missense_Mutation_p.G366E|HLA-F_ENST00000475996.1_Intron	p.G237E			P30511	HLAF_HUMAN			6	1069	+			0			Alpha-3.|Ig-like C1-type.		Q5JQI8|Q5JQJ1|Q5SPT5|Q860R0|Q8MGQ1|Q8WLP5|Q95HC0|Q9TP68	Missense_Mutation	SNP	ENST00000376861.1	37	c.710G>A	CCDS43438.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	10.02|10.02	1.237245|1.237245	0.22711|0.22711	.|.	.|.	ENSG00000204642|ENSG00000204642	ENST00000449921;ENST00000259951;ENST00000399258;ENST00000440587|ENST00000444621	T;T|.	0.01025|.	5.43;5.59|.	0.62|0.62	-0.344|-0.344	0.12628|0.12628	.|.	.|.	.|.	.|.	.|.	T|T	0.16685|0.16685	0.0401|0.0401	L|L	0.36672|0.36672	1.1|1.1	0.25609|0.25609	N|N	0.986519|0.986519	D;B|.	0.64830|.	0.994;0.068|.	D;B|.	0.65010|.	0.931;0.017|.	T|T	0.29610|0.29610	-1.0006|-1.0006	9|6	0.87932|0.87932	D|D	0|0	.|.	4.9559|4.9559	0.14038|0.14038	0.2561:0.0:0.7439:0.0|0.2561:0.0:0.7439:0.0	.|.	366;366|.	A8MVU7;P30511-3|.	.;.|.	E|R	343;366;280;237|48	ENSP00000259951:G366E;ENSP00000404130:G237E|.	ENSP00000259951:G366E|ENSP00000392251:G48R	G|G	+|+	2|1	0|0	HLA-F|HLA-F	29802699|29802699	1.000000|1.000000	0.71417|0.71417	0.427000|0.427000	0.26684|0.26684	0.030000|0.030000	0.12068|0.12068	4.802000|4.802000	0.62539|0.62539	-0.212000|-0.212000	0.10109|0.10109	-0.462000|-0.462000	0.05337|0.05337	GGG|GGG		0.498	HLA-F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195083.1	NM_018950		11	132	11	132	---	---	---	---
CEP85L	387119	broad.mit.edu	37	6	118790443	118790443	+	Silent	SNP	T	T	G			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr6:118790443T>G	ENST00000368491.3	-	12	2667	c.2046A>C	c.(2044-2046)acA>acC	p.T682T	CEP85L_ENST00000368488.5_Silent_p.T685T	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	682						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.T682T(1)									ATAAAGAGCATGTCTCATCTG	0.413																																						ENST00000368491.3																			1	Substitution - coding silent(1)	p.T682T(1)	prostate(1)								c.(2044-2046)acA>acC		centrosomal protein 85kDa-like							149.0	138.0	142.0					6																	118790443		1876	4123	5999	SO:0001819	synonymous_variant	387119					centrosome		g.chr6:118790443T>G	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.2046A>C	6.37:g.118790443T>G						CEP85L_ENST00000368488.5_Silent_p.T685T	p.T682T	NM_001042475.2	NP_001035940.1	Q5SZL2	CF204_HUMAN			12	2667	-			682					A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Silent	SNP	ENST00000368491.3	37	c.2046A>C	CCDS43498.1																																																																																				0.413	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		10	123	10	123	---	---	---	---
GSDMD	79792	broad.mit.edu	37	8	144643931	144643931	+	Missense_Mutation	SNP	C	C	A			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr8:144643931C>A	ENST00000526406.1	+	10	1639	c.756C>A	c.(754-756)agC>agA	p.S252R	GSDMD_ENST00000262580.4_Missense_Mutation_p.S252R|GSDMD_ENST00000533063.1_Missense_Mutation_p.S300R	NM_001166237.1	NP_001159709.1	P57764	GSDMD_HUMAN	gasdermin D	252					cellular response to extracellular stimulus (GO:0031668)			p.S252R(1)		breast(1)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	12						GTTCCACGAGCGAAGGCGCCT	0.672																																						ENST00000526406.1																			1	Substitution - Missense(1)	p.S252R(1)	prostate(1)	breast(1)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	12						c.(754-756)agC>agA		gasdermin D							31.0	29.0	30.0					8																	144643931		2189	4295	6484	SO:0001583	missense	79792							g.chr8:144643931C>A	AK096216	CCDS34956.1	8q24.3	2008-07-31	2008-07-31	2008-07-31		ENSG00000104518			25697	protein-coding gene	gene with protein product			"""gasdermin domain containing 1"""	GSDMDC1		15289881, 17350798	Standard	NM_024736		Approved	FLJ12150, DF5L	uc003yyg.3	P57764		ENST00000526406.1:c.756C>A	8.37:g.144643931C>A	ENSP00000433209:p.Ser252Arg					GSDMD_ENST00000533063.1_Missense_Mutation_p.S300R|GSDMD_ENST00000262580.4_Missense_Mutation_p.S252R	p.S252R	NM_001166237.1	NP_001159709.1	P57764	GSDMD_HUMAN			10	1639	+			252					D3DWJ9|Q96Q98	Missense_Mutation	SNP	ENST00000526406.1	37	c.756C>A	CCDS34956.1	.	.	.	.	.	.	.	.	.	.	C	11.30	1.596932	0.28445	.	.	ENSG00000104518	ENST00000526406;ENST00000533063;ENST00000262580;ENST00000534018	T;T;T;T	0.22945	1.93;1.93;1.93;1.93	4.35	-8.71	0.00848	.	6.940960	0.00166	N	0.000000	T	0.13543	0.0328	L	0.27053	0.805	0.09310	N	1	B;B;B	0.16166	0.016;0.016;0.013	B;B;B	0.11329	0.006;0.006;0.006	T	0.13791	-1.0496	10	0.21014	T	0.42	20.479	3.5413	0.07812	0.0802:0.3542:0.2765:0.2891	.	252;252;300	A8K702;P57764;G3V1A6	.;GSDMD_HUMAN;.	R	252;300;252;268	ENSP00000433209:S252R;ENSP00000433958:S300R;ENSP00000262580:S252R;ENSP00000436684:S268R	ENSP00000262580:S252R	S	+	3	2	GSDMD	144715074	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.849000	0.00733	-3.130000	0.00236	-1.328000	0.01277	AGC		0.672	GSDMD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382046.3	NM_024736		3	15	3	15	---	---	---	---
LHX3	8022	broad.mit.edu	37	9	139091593	139091593	+	Missense_Mutation	SNP	C	C	A	rs142521088		TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr9:139091593C>A	ENST00000371748.5	-	3	481	c.385G>T	c.(385-387)Gac>Tac	p.D129Y	LHX3_ENST00000371746.3_Missense_Mutation_p.D134Y	NM_178138.4	NP_835258.1	Q9UBR4	LHX3_HUMAN	LIM homeobox 3	129	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				inner ear development (GO:0048839)|lung development (GO:0030324)|medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|placenta development (GO:0001890)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron cell fate specification (GO:0021520)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.D134Y(1)		large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Myeloproliferative disorder(178;0.0511)		Epithelial(140;8.43e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.26e-07)		TAGAACTCGTCGCCCGTGGCC	0.672																																						ENST00000371746.3																			1	Substitution - Missense(1)	p.D134Y(1)	prostate(1)	large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8						c.(400-402)Gac>Tac		LIM homeobox 3							30.0	29.0	30.0					9																	139091593		2198	4300	6498	SO:0001583	missense	8022				inner ear development|organ morphogenesis|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr9:139091593C>A	AF096169	CCDS6994.1, CCDS6995.1	9q34.3	2011-06-20			ENSG00000107187	ENSG00000107187		"""Homeoboxes / LIM class"""	6595	protein-coding gene	gene with protein product		600577				10598593, 10717474	Standard	NM_178138		Approved		uc004cgz.3	Q9UBR4	OTTHUMG00000020924	ENST00000371748.5:c.385G>T	9.37:g.139091593C>A	ENSP00000360813:p.Asp129Tyr					LHX3_ENST00000371748.5_Missense_Mutation_p.D129Y	p.D134Y	NM_014564.3	NP_055379.1	Q9UBR4	LHX3_HUMAN		Epithelial(140;8.43e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.26e-07)	3	518	-		Myeloproliferative disorder(178;0.0511)	129			LIM zinc-binding 2.		Q5TB39|Q5TB40|Q9NZB5|Q9P0I8|Q9P0I9	Missense_Mutation	SNP	ENST00000371748.5	37	c.400G>T	CCDS6994.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.647555	0.87958	.	.	ENSG00000107187	ENST00000371748;ENST00000371746;ENST00000325195	D;D	0.87650	-2.28;-2.28	4.35	4.35	0.52113	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.95868	0.8655	H	0.97415	4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	D	0.97549	1.0091	10	0.87932	D	0	.	16.0484	0.80735	0.0:1.0:0.0:0.0	.	129;134	Q9UBR4;F1T0D9	LHX3_HUMAN;.	Y	129;134;132	ENSP00000360813:D129Y;ENSP00000360811:D134Y	ENSP00000319224:D132Y	D	-	1	0	LHX3	138231414	1.000000	0.71417	0.956000	0.39512	0.806000	0.45545	7.314000	0.78988	2.256000	0.74724	0.561000	0.74099	GAC		0.672	LHX3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055048.3			9	38	9	38	---	---	---	---
WT1-AS	51352	broad.mit.edu	37	11	32460593	32460593	+	RNA	SNP	T	T	C			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr11:32460593T>C	ENST00000395900.1	+	0	1471				WT1-AS_ENST00000525436.1_RNA|WT1-AS_ENST00000478367.1_RNA|WT1-AS_ENST00000442957.1_RNA|WT1-AS_ENST00000494911.1_RNA|WT1-AS_ENST00000426618.2_RNA|WT1-AS_ENST00000459866.1_RNA	NR_023920.1		Q06250	WIT1_HUMAN	WT1 antisense RNA									p.C56R(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(1)	6						ACCCCGGCGCTGTCCACTGCA	0.617																																						ENST00000395900.1																			1	Substitution - Missense(1)	p.C56R(1)	prostate(1)	endometrium(1)|large_intestine(2)|lung(2)|prostate(1)	6															37.0	35.0	36.0					11																	32460593		2202	4299	6501			51352							g.chr11:32460593T>C	BC002734		11p13	2012-10-19	2012-08-15	2012-01-25	ENSG00000183242	ENSG00000183242		"""Long non-coding RNAs"", ""-"""	18135	non-coding RNA	RNA, long non-coding	"""Wilms tumor associated protein"""	607899	"""Wilms tumor upstream neighbor 1"", ""WT1 antisense RNA (non-protein coding)"""	WIT1		2173145, 8406502, 17210670	Standard	NR_120546		Approved	WIT-1, WT1AS, WT1-AS1	uc010red.2	Q06250	OTTHUMG00000039557		11.37:g.32460593T>C						WT1-AS_ENST00000442957.1_RNA|WT1-AS_ENST00000525436.1_RNA|WT1-AS_ENST00000426618.2_RNA		NR_023920.1						0	1471	+								Q4KMY0|Q96A27	RNA	SNP	ENST00000395900.1	37																																																																																						0.617	WT1-AS-001	KNOWN	basic	antisense	antisense	OTTHUMT00000095437.1	NR_023920		3	54	3	54	---	---	---	---
NTM	50863	broad.mit.edu	37	11	132081914	132081914	+	Splice_Site	SNP	A	A	C			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr11:132081914A>C	ENST00000374786.1	+	3	879		c.e3-1		NTM_ENST00000474900.1_Splice_Site|NTM_ENST00000425719.2_Splice_Site|NTM_ENST00000427481.2_Splice_Site|NTM_ENST00000539799.1_Splice_Site|NTM_ENST00000374791.3_Splice_Site|NTM_ENST00000374784.1_Splice_Site	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin						cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.?(2)		breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						TTGTTTCCACAGTATCTCCCA	0.383																																						ENST00000374786.1																			2	Unknown(2)	p.?(2)	prostate(2)	breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						c.e3-1		neurotrimin							59.0	60.0	60.0					11																	132081914		2201	4297	6498	SO:0001630	splice_region_variant	50863				cell adhesion|neuron recognition	anchored to membrane|plasma membrane		g.chr11:132081914A>C	AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"""Immunoglobulin superfamily / I-set domain containing"""	17941	protein-coding gene	gene with protein product	"""neurotrimin"", ""IgLON family member 2"""	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.401-1A>C	11.37:g.132081914A>C						NTM_ENST00000374784.1_Splice_Site|NTM_ENST00000539799.1_Splice_Site|NTM_ENST00000425719.2_Splice_Site|NTM_ENST00000474900.1_Splice_Site|NTM_ENST00000374791.3_Splice_Site|NTM_ENST00000427481.2_Splice_Site		NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN			3	879	+								A0MTT2|Q6UXJ3|Q86VJ9	Splice_Site	SNP	ENST00000374786.1	37		CCDS8491.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.954948	0.73902	.	.	ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000550167;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5764	0.84681	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NTM	131587124	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.420000	0.90256	2.371000	0.80710	0.533000	0.62120	.		0.383	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522	Intron	4	35	4	35	---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6686950	6686950	+	Splice_Site	SNP	C	C	T	rs529117126		TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr12:6686950C>T	ENST00000357008.2	-	37	5525		c.e37+1		RP5-940J5.6_ENST00000501075.2_RNA|CHD4_ENST00000544040.1_Splice_Site|CHD4_ENST00000544484.1_Splice_Site|CHD4_ENST00000309577.6_Splice_Site	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4						ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.?(3)		central_nervous_system(2)	2						CAACCGCTCACCTTAAACCTT	0.463																																					Colon(32;586 792 4568 16848 45314)	ENST00000309577.6																			3	Unknown(3)	p.?(3)	prostate(3)	central_nervous_system(2)	2						c.e36+1		chromodomain helicase DNA binding protein 4							103.0	102.0	102.0					12																	6686950		2203	4300	6503	SO:0001630	splice_region_variant	1108				chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding	g.chr12:6686950C>T	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.5361+1G>A	12.37:g.6686950C>T						CHD4_ENST00000544484.1_Splice_Site|CHD4_ENST00000544040.1_Splice_Site|CHD4_ENST00000357008.2_Splice_Site				Q14839	CHD4_HUMAN			36	5609	-								Q8IXZ5	Splice_Site	SNP	ENST00000357008.2	37		CCDS8552.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.616076	0.87359	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7859	0.96437	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CHD4	6557211	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.464000	0.80887	2.746000	0.94184	0.655000	0.94253	.		0.463	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273	Intron	4	84	4	84	---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19511256	19511256	+	Missense_Mutation	SNP	A	A	G			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr12:19511256A>G	ENST00000299275.6	+	21	2741	c.2735A>G	c.(2734-2736)cAt>cGt	p.H912R	PLEKHA5_ENST00000539256.1_Missense_Mutation_p.H670R|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.H856R|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.H901R|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.H975R|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.H970R|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.H1078R|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.H894R|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.H970R	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	912					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)	p.H912R(2)|p.H1073R(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					ATAAGAAGACATCAACAAGCG	0.433																																					Pancreas(196;329 2193 11246 14234 19524)	ENST00000538714.1																			3	Substitution - Missense(3)	p.H912R(2)|p.H1073R(1)	prostate(3)	autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						c.(2908-2910)cAt>cGt		pleckstrin homology domain containing, family A member 5							109.0	91.0	97.0					12																	19511256		2203	4300	6503	SO:0001583	missense	54477						1-phosphatidylinositol binding|protein binding	g.chr12:19511256A>G	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.2735A>G	12.37:g.19511256A>G	ENSP00000299275:p.His912Arg					PLEKHA5_ENST00000355397.3_Missense_Mutation_p.H970R|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.H670R|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.H894R|PLEKHA5_ENST00000299275.6_Missense_Mutation_p.H912R|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.H901R|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.H975R|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.H856R|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.H1078R	p.H970R	NM_001143821.2	NP_001137293.2	Q9HAU0	PKHA5_HUMAN			23	2913	+	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)		912	P -> S (in Ref. 6; BAA91742).				A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	37	c.2909A>G	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	12.79	2.044801	0.36085	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974;ENST00000538972	T;T;T;T;T;T;T;T;T;T;T	0.52057	2.24;1.95;2.16;2.2;2.06;1.74;1.95;2.19;2.19;2.27;0.68	5.36	4.2	0.49525	.	0.150024	0.64402	D	0.000016	T	0.44265	0.1285	L	0.58810	1.83	0.39025	D	0.95982	B;B;B;B;B;B;B;B	0.23249	0.01;0.008;0.024;0.007;0.082;0.009;0.005;0.016	B;B;B;B;B;B;B;B	0.25140	0.013;0.023;0.014;0.005;0.058;0.006;0.01;0.033	T	0.49021	-0.8982	10	0.48119	T	0.1	-23.6537	11.4842	0.50344	0.9203:0.0:0.0797:0.0	.	975;894;901;1073;856;1078;912;970	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;Q9HAU0-5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;.;PKHA5_HUMAN;.	R	975;970;856;1074;1078;912;670;970;901;894;867;193	ENSP00000325155:H975R;ENSP00000347560:H970R;ENSP00000352104:H856R;ENSP00000404296:H1078R;ENSP00000299275:H912R;ENSP00000440611:H670R;ENSP00000439673:H970R;ENSP00000400411:H901R;ENSP00000439837:H894R;ENSP00000440371:H867R;ENSP00000443553:H193R	ENSP00000299275:H912R	H	+	2	0	PLEKHA5	19402523	1.000000	0.71417	0.814000	0.32528	0.777000	0.43975	4.775000	0.62346	2.263000	0.75096	0.451000	0.29950	CAT		0.433	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		4	36	4	36	---	---	---	---
PFKM	5213	broad.mit.edu	37	12	48533667	48533667	+	Missense_Mutation	SNP	T	T	C			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr12:48533667T>C	ENST00000312352.7	+	13	1202	c.1163T>C	c.(1162-1164)cTa>cCa	p.L388P	PFKM_ENST00000359794.5_Missense_Mutation_p.L388P|PFKM_ENST00000551804.1_Missense_Mutation_p.L357P|PFKM_ENST00000340802.6_Missense_Mutation_p.L459P|PFKM_ENST00000395233.2_Missense_Mutation_p.L357P|PFKM_ENST00000547587.1_Missense_Mutation_p.L388P	NM_001166687.1	NP_001160159.1	P08237	PFKAM_HUMAN	phosphofructokinase, muscle	388	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of insulin secretion (GO:0032024)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.L388P(1)		NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						TACAAGCTTCTAGCTCATGTC	0.512																																						ENST00000340802.6																			1	Substitution - Missense(1)	p.L388P(1)	prostate(1)	NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						c.(1375-1377)cTa>cCa		phosphofructokinase, muscle							113.0	95.0	101.0					12																	48533667		2203	4300	6503	SO:0001583	missense	5213				fructose 6-phosphate metabolic process|glycolysis|muscle cell homeostasis	6-phosphofructokinase complex|apical plasma membrane	6-phosphofructokinase activity|ATP binding|identical protein binding|kinase binding|metal ion binding|protein C-terminus binding	g.chr12:48533667T>C	M26066	CCDS8760.1, CCDS53786.1	12q13.11	2014-06-13					2.7.1.11		8877	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 122"""	610681	"""phosphofructokinase, polypeptide X"""	PFKX			Standard	NM_001166686		Approved	PFK-1, PPP1R122	uc001rrb.2	P08237		ENST00000312352.7:c.1163T>C	12.37:g.48533667T>C	ENSP00000309438:p.Leu388Pro					PFKM_ENST00000551804.1_Missense_Mutation_p.L357P|PFKM_ENST00000395233.2_Missense_Mutation_p.L357P|PFKM_ENST00000547587.1_Missense_Mutation_p.L388P|PFKM_ENST00000359794.5_Missense_Mutation_p.L388P|PFKM_ENST00000312352.7_Missense_Mutation_p.L388P	p.L459P	NM_001166686.1	NP_001160158.1	P08237	K6PF_HUMAN			15	1600	+			388					J3KNX3|Q16814|Q16815|Q6ZTT1	Missense_Mutation	SNP	ENST00000312352.7	37	c.1376T>C	CCDS8760.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.219666	0.79464	.	.	ENSG00000152556	ENST00000340802;ENST00000359794;ENST00000395233;ENST00000551804;ENST00000547587;ENST00000312352	T;T;T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35;-1.35;-1.35	5.03	5.03	0.67393	Phosphofructokinase domain (1);	0.000000	0.64402	D	0.000003	D	0.90872	0.7132	M	0.89840	3.065	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.91833	0.5477	10	0.49607	T	0.09	-2.9809	14.1886	0.65623	0.0:0.0:0.0:1.0	.	357;388;459	P08237-2;P08237;Q6ZTT1	.;K6PF_HUMAN;.	P	459;388;357;357;388;388	ENSP00000345771:L459P;ENSP00000352842:L388P;ENSP00000378656:L357P;ENSP00000448177:L357P;ENSP00000449426:L388P;ENSP00000309438:L388P	ENSP00000309438:L388P	L	+	2	0	PFKM	46819934	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.619000	0.83057	2.239000	0.73571	0.533000	0.62120	CTA		0.512	PFKM-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406490.1	NM_000289		4	37	4	37	---	---	---	---
LRIG3	121227	broad.mit.edu	37	12	59282122	59282122	+	Missense_Mutation	SNP	C	C	G			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr12:59282122C>G	ENST00000320743.3	-	7	1222	c.936G>C	c.(934-936)aaG>aaC	p.K312N	LRIG3_ENST00000379141.4_Missense_Mutation_p.K252N	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	312					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.K312N(2)	LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			GCTCACTGAGCTTCTGGCAGA	0.493			T	ROS1	NSCLC																																	ENST00000320743.3				Dom	yes		12	12q14.1	121227	T	leucine-rich repeats and immunoglobulin-like domains 3			E	ROS1		NSCLC	LRIG3/ROS1(2)	2	Substitution - Missense(2)	p.K312N(2)	prostate(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						c.(934-936)aaG>aaC		leucine-rich repeats and immunoglobulin-like domains 3							90.0	85.0	87.0					12																	59282122		2203	4300	6503	SO:0001583	missense	121227					integral to membrane		g.chr12:59282122C>G	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"""Immunoglobulin superfamily / I-set domain containing"""	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.936G>C	12.37:g.59282122C>G	ENSP00000326759:p.Lys312Asn					LRIG3_ENST00000379141.4_Missense_Mutation_p.K252N	p.K312N	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	GBM - Glioblastoma multiforme(1;1.17e-18)		7	1222	-			312					Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	37	c.936G>C	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.189165	0.38707	.	.	ENSG00000139263	ENST00000379141;ENST00000320743	T;T	0.54479	0.57;0.57	5.76	0.592	0.17471	.	0.000000	0.39407	N	0.001379	T	0.40979	0.1139	N	0.04320	-0.23	0.54753	D	0.999987	B;D	0.89917	0.22;1.0	B;D	0.74348	0.198;0.983	T	0.30268	-0.9984	9	.	.	.	.	5.4682	0.16656	0.0:0.3235:0.1397:0.5369	.	252;312	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	N	252;312	ENSP00000368436:K252N;ENSP00000326759:K312N	.	K	-	3	2	LRIG3	57568389	0.993000	0.37304	0.998000	0.56505	0.983000	0.72400	0.259000	0.18405	-0.068000	0.12953	-0.182000	0.12963	AAG		0.493	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		8	77	8	77	---	---	---	---
ZFC3H1	196441	broad.mit.edu	37	12	72036214	72036214	+	Splice_Site	SNP	A	A	C			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr12:72036214A>C	ENST00000378743.3	-	6	1986		c.e6+1		SNORA17_ENST00000391159.1_RNA	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing						RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.?(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						TTTGGCTCATACCTGGAGAAC	0.343																																						ENST00000378743.3																			1	Unknown(1)	p.?(1)	prostate(1)	NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						c.e6+1		zinc finger, C3H1-type containing							149.0	135.0	139.0					12																	72036214		1844	4097	5941	SO:0001630	splice_region_variant	196441				RNA processing	intracellular	metal ion binding	g.chr12:72036214A>C	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.1627+1T>G	12.37:g.72036214A>C								NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN			6	1986	-								Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Splice_Site	SNP	ENST00000378743.3	37		CCDS41813.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.237221	0.79800	.	.	ENSG00000133858	ENST00000378743	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5877	0.76499	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZFC3H1	70322481	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	8.281000	0.89905	2.099000	0.63709	0.454000	0.30748	.		0.343	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982	Intron	7	68	7	68	---	---	---	---
ANAPC5	51433	broad.mit.edu	37	12	121746472	121746472	+	Missense_Mutation	SNP	G	G	T			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr12:121746472G>T	ENST00000261819.3	-	17	2200	c.2079C>A	c.(2077-2079)aaC>aaA	p.N693K	ANAPC5_ENST00000541887.1_Missense_Mutation_p.N680K|ANAPC5_ENST00000535482.1_Missense_Mutation_p.N359K|ANAPC5_ENST00000544314.1_5'UTR|ANAPC5_ENST00000344395.4_Missense_Mutation_p.N581K|ANAPC5_ENST00000441917.2_Missense_Mutation_p.N581K	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN	anaphase promoting complex subunit 5	693					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)	p.N693K(2)		breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CTTCATTGAGGTTCTCGATGG	0.453																																						ENST00000261819.3																			2	Substitution - Missense(2)	p.N693K(2)	prostate(2)	breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31						c.(2077-2079)aaC>aaA		anaphase promoting complex subunit 5							117.0	102.0	108.0					12																	121746472		2203	4300	6503	SO:0001583	missense	51433				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	protein phosphatase binding|ubiquitin-protein ligase activity	g.chr12:121746472G>T	AF191339	CCDS9220.1, CCDS45000.1	12q24.31	2014-08-12			ENSG00000089053	ENSG00000089053		"""Anaphase promoting complex subunits"""	15713	protein-coding gene	gene with protein product		606948				9469815	Standard	NM_016237		Approved	APC5	uc001uag.3	Q9UJX4	OTTHUMG00000169157	ENST00000261819.3:c.2079C>A	12.37:g.121746472G>T	ENSP00000261819:p.Asn693Lys					ANAPC5_ENST00000344395.4_Missense_Mutation_p.N581K|ANAPC5_ENST00000544314.1_5'UTR|ANAPC5_ENST00000441917.2_Missense_Mutation_p.N581K|ANAPC5_ENST00000541887.1_Missense_Mutation_p.N680K|ANAPC5_ENST00000535482.1_Missense_Mutation_p.N359K	p.N693K	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN			17	2200	-	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)		693					E9PFB2|Q8N4H7|Q9BQD4	Missense_Mutation	SNP	ENST00000261819.3	37	c.2079C>A	CCDS9220.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.390882	0.42410	.	.	ENSG00000089053	ENST00000441917;ENST00000541887;ENST00000261819;ENST00000535482;ENST00000544314;ENST00000344395	T;T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93;-0.93	5.74	3.88	0.44766	Tetratricopeptide-like helical (1);	0.156175	0.56097	D	0.000035	T	0.61085	0.2319	L	0.44542	1.39	0.80722	D	1	P;B;B	0.38370	0.628;0.118;0.255	B;B;B	0.34489	0.184;0.037;0.053	T	0.56986	-0.7888	10	0.40728	T	0.16	.	6.5596	0.22479	0.1613:0.0:0.6909:0.1478	.	359;581;693	F5H0N1;E9PFB2;Q9UJX4	.;.;APC5_HUMAN	K	581;680;693;359;295;581	ENSP00000415061:N581K;ENSP00000439875:N680K;ENSP00000261819:N693K;ENSP00000438754:N359K;ENSP00000343787:N581K	ENSP00000261819:N693K	N	-	3	2	ANAPC5	120230855	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	0.928000	0.28831	0.741000	0.32674	0.563000	0.77884	AAC		0.453	ANAPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402582.1			7	103	7	103	---	---	---	---
COG3	83548	broad.mit.edu	37	13	46066301	46066301	+	Missense_Mutation	SNP	G	G	T			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr13:46066301G>T	ENST00000349995.5	+	11	1215	c.1103G>T	c.(1102-1104)aGt>aTt	p.S368I	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	368					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)	p.S368I(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		CAGGTTCGTAGTGGCTGTGCC	0.383																																					Ovarian(150;1048 1859 18083 21577 42700)	ENST00000349995.5																			1	Substitution - Missense(1)	p.S368I(1)	prostate(1)	breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24						c.(1102-1104)aGt>aTt		component of oligomeric golgi complex 3							217.0	175.0	189.0					13																	46066301		2203	4300	6503	SO:0001583	missense	83548				ER to Golgi vesicle-mediated transport|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein glycosylation|protein localization to organelle|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	cis-Golgi network|Golgi cisterna membrane|Golgi transport complex	protein binding|protein transporter activity	g.chr13:46066301G>T	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"""Components of oligomeric golgi complex"""	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1103G>T	13.37:g.46066301G>T	ENSP00000258654:p.Ser368Ile					COG3_ENST00000465942.1_3'UTR	p.S368I	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)	11	1215	+		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	368					B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	37	c.1103G>T	CCDS9398.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.962017	0.92791	.	.	ENSG00000136152	ENST00000349995	T	0.48836	0.8	5.87	5.87	0.94306	.	0.040815	0.85682	D	0.000000	T	0.64227	0.2579	L	0.58583	1.82	0.80722	D	1	D;D;D	0.69078	0.985;0.997;0.967	P;D;P	0.63597	0.901;0.916;0.491	T	0.56998	-0.7886	10	0.30854	T	0.27	-7.337	19.1915	0.93669	0.0:0.0:1.0:0.0	.	205;368;368	B4E2F3;Q96JB2;Q96JB2-2	.;COG3_HUMAN;.	I	368	ENSP00000258654:S368I	ENSP00000258654:S368I	S	+	2	0	COG3	44964302	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.615000	0.98356	2.779000	0.95612	0.655000	0.94253	AGT		0.383	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			3	34	3	34	---	---	---	---
PLA2G4F	255189	broad.mit.edu	37	15	42446634	42446634	+	Silent	SNP	C	C	T			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr15:42446634C>T	ENST00000382396.4	-	3	293	c.207G>A	c.(205-207)gtG>gtA	p.V69V	PLA2G4F_ENST00000397272.3_Silent_p.V69V			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	69	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)	p.V69V(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		GCCACAGTTGCACATAGCAGT	0.597																																						ENST00000397272.3																			1	Substitution - coding silent(1)	p.V69V(1)	prostate(1)	breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						c.(205-207)gtG>gtA		phospholipase A2, group IVF							42.0	37.0	38.0					15																	42446634		2203	4299	6502	SO:0001819	synonymous_variant	255189				phospholipid catabolic process	cytosol|lysosomal membrane	metal ion binding|phospholipase A2 activity	g.chr15:42446634C>T		CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.207G>A	15.37:g.42446634C>T						PLA2G4F_ENST00000382396.4_Silent_p.V69V	p.V69V	NM_213600.3	NP_998765.3	Q68DD2	PA24F_HUMAN		GBM - Glioblastoma multiforme(94;8.97e-07)	3	298	-		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)	69			C2.		Q6ZMC8	Silent	SNP	ENST00000382396.4	37	c.207G>A	CCDS32204.1																																																																																				0.597	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600		5	32	5	32	---	---	---	---
USH1G	124590	broad.mit.edu	37	17	72915904	72915904	+	Missense_Mutation	SNP	G	G	A			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr17:72915904G>A	ENST00000319642.1	-	2	1209	c.1027C>T	c.(1027-1029)Cgg>Tgg	p.R343W		NM_001282489.1|NM_173477.2	NP_001269418.1|NP_775748.2	Q495M9	USH1G_HUMAN	Usher syndrome 1G (autosomal recessive)	343					equilibrioception (GO:0050957)|inner ear morphogenesis (GO:0042472)|inner ear receptor cell differentiation (GO:0060113)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	spectrin binding (GO:0030507)	p.R343W(1)	HN1/USH1G(2)	endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(3)	14	all_lung(278;0.172)|Lung NSC(278;0.207)					AGCCGACCCCGCGGCGCTCCC	0.687																																						ENST00000319642.1																		HN1/USH1G(2)	1	Substitution - Missense(1)	p.R343W(1)	prostate(1)	endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(3)	14						c.(1027-1029)Cgg>Tgg		Usher syndrome 1G (autosomal recessive)							37.0	46.0	43.0					17																	72915904		2201	4293	6494	SO:0001583	missense	124590				equilibrioception|photoreceptor cell maintenance|sensory perception of sound	actin cytoskeleton		g.chr17:72915904G>A	AK091243	CCDS32725.1	17q25.1	2013-01-10			ENSG00000182040	ENSG00000182040		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	16356	protein-coding gene	gene with protein product		607696				12588794	Standard	NM_001282489		Approved	Sans, FLJ33924, ANKS4A	uc002jme.1	Q495M9	OTTHUMG00000178864	ENST00000319642.1:c.1027C>T	17.37:g.72915904G>A	ENSP00000320076:p.Arg343Trp						p.R343W	NM_001282489.1|NM_173477.2	NP_001269418.1|NP_775748.2	Q495M9	USH1G_HUMAN			2	1209	-	all_lung(278;0.172)|Lung NSC(278;0.207)		343					Q8N251	Missense_Mutation	SNP	ENST00000319642.1	37	c.1027C>T	CCDS32725.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.424552	0.43020	.	.	ENSG00000182040	ENST00000319642	T	0.71341	-0.56	4.34	3.36	0.38483	.	0.353403	0.29900	N	0.010915	T	0.64929	0.2643	L	0.32530	0.975	0.45194	D	0.998209	D	0.69078	0.997	P	0.47299	0.543	T	0.69468	-0.5137	10	0.72032	D	0.01	-21.4193	13.7601	0.62961	0.0:0.0:0.8452:0.1548	.	343	Q495M9	USH1G_HUMAN	W	343	ENSP00000320076:R343W	ENSP00000320076:R343W	R	-	1	2	USH1G	70427499	1.000000	0.71417	0.930000	0.37139	0.300000	0.27592	4.464000	0.60134	1.061000	0.40601	-0.276000	0.10085	CGG		0.687	USH1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443676.1	NM_173477		4	84	4	84	---	---	---	---
DNAH17	8632	broad.mit.edu	37	17	76459153	76459153	+	Missense_Mutation	SNP	C	C	T			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr17:76459153C>T	ENST00000585328.1	-	57	9056	c.8932G>A	c.(8932-8934)Gtc>Atc	p.V2978I	DNAH17_ENST00000389840.5_Missense_Mutation_p.V2969I|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2969	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V2978I(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			GAGGCCTTGACTTCCCACTAC	0.562																																						ENST00000389840.5																			1	Substitution - Missense(1)	p.V2978I(1)	prostate(1)	NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116						c.(8905-8907)Gtc>Atc		dynein, axonemal, heavy chain 17							108.0	83.0	91.0					17																	76459153		2203	4300	6503	SO:0001583	missense	8632							g.chr17:76459153C>T	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.8932G>A	17.37:g.76459153C>T	ENSP00000465516:p.Val2978Ile					DNAH17_ENST00000585328.1_Missense_Mutation_p.V2978I|DNAH17_ENST00000586052.1_5'UTR	p.V2969I					BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)		57	9029	-								O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37	c.8905G>A		.	.	.	.	.	.	.	.	.	.	C	14.99	2.698846	0.48307	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.46451	0.87	4.91	4.91	0.64330	.	.	.	.	.	T	0.34571	0.0902	N	0.16130	0.375	0.42825	D	0.994008	.	.	.	.	.	.	T	0.11842	-1.0571	7	0.15952	T	0.53	.	17.6869	0.88258	0.0:1.0:0.0:0.0	.	.	.	.	I	2978;2969	ENSP00000374490:V2969I	ENSP00000300671:V2978I	V	-	1	0	DNAH17	73970748	1.000000	0.71417	0.979000	0.43373	0.780000	0.44128	5.676000	0.68131	2.277000	0.76020	0.555000	0.69702	GTC		0.562	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		3	27	3	27	---	---	---	---
PSG1	5669	broad.mit.edu	37	19	43372318	43372318	+	Missense_Mutation	SNP	A	A	G	rs1058795	byFrequency	TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr19:43372318A>G	ENST00000436291.2	-	5	1294	c.1178T>C	c.(1177-1179)gTt>gCt	p.V393A	PSG1_ENST00000312439.6_Missense_Mutation_p.V393A|PSG1_ENST00000403380.3_Missense_Mutation_p.V300A|PSG1_ENST00000595356.1_Missense_Mutation_p.V393A|PSG1_ENST00000595124.1_Missense_Mutation_p.V300A|PSG1_ENST00000244296.2_Missense_Mutation_p.V393A	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	393	Ig-like C2-type 3.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				AACAGAGCAAACATAGAGCCC	0.458													.|||	2	0.000399361	0.0008	0.0	5008	,	,		19000	0.001		0.0	False		,,,				2504	0.0					ENST00000244296.2																			0				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						c.(1177-1179)gTt>gCt		pregnancy specific beta-1-glycoprotein 1		A	ALA/VAL,ALA/VAL,ALA/VAL	1,4403		0,1,2201	203.0	206.0	205.0		1178,1178,1178	-3.0	0.0	19	dbSNP_86	205	3,8593		0,3,4295	no	missense,missense,missense	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	64,64,64	0,4,6496	GG,GA,AA		0.0349,0.0227,0.0308	,,	393/420,393/418,393/427	43372318	4,12996	2202	4298	6500	SO:0001583	missense	5669							g.chr19:43372318A>G		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.1178T>C	19.37:g.43372318A>G	ENSP00000413041:p.Val393Ala					PSG1_ENST00000436291.2_Missense_Mutation_p.V393A|PSG1_ENST00000403380.3_Missense_Mutation_p.V300A|PSG1_ENST00000595356.1_Missense_Mutation_p.V393A|PSG1_ENST00000595124.1_Missense_Mutation_p.V300A|PSG1_ENST00000312439.6_Missense_Mutation_p.V393A	p.V393A	NM_006905.2	NP_008836.2					5	1315	-		Prostate(69;0.00682)						O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	37	c.1178T>C	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	0.001	-2.890596	0.00060	2.27E-4	3.49E-4	ENSG00000231924	ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.11495	2.77;2.77;2.77;2.77	1.51	-3.02	0.05446	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.03783	0.0107	N	0.16567	0.415	0.09310	N	1	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.06405	0.001;0.001;0.001;0.001;0.001;0.002;0.002	T	0.43114	-0.9411	9	0.02654	T	1	.	0.553	0.00666	0.3393:0.1796:0.3032:0.1779	rs1058795	393;300;393;300;393;300;265	P11464-4;G5E9F7;P11464;Q8NBY8;P11464-3;Q9UPK8;B4DTG5	.;.;PSG1_HUMAN;.;.;.;.	A	393;300;393;393	ENSP00000413041:V393A;ENSP00000385386:V300A;ENSP00000308970:V393A;ENSP00000244296:V393A	ENSP00000244296:V393A	V	-	2	0	PSG1	48064158	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.213000	0.02991	-3.027000	0.00267	-1.266000	0.01441	GTT		0.458	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1			6	242	6	242	---	---	---	---
LILRA4	23547	broad.mit.edu	37	19	54849889	54849889	+	Missense_Mutation	SNP	C	C	T			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr19:54849889C>T	ENST00000291759.4	-	3	189	c.133G>A	c.(133-135)Gtg>Atg	p.V45M	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	45	Ig-like C2-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.V45M(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		CAGATGGTCACGGGGTTATGC	0.537											OREG0003656	type=REGULATORY REGION|Gene=LILRA4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																										ENST00000291759.4																			1	Substitution - Missense(1)	p.V45M(1)	prostate(1)	NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32						c.(133-135)Gtg>Atg		leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4							103.0	92.0	96.0					19																	54849889		2203	4300	6503	SO:0001583	missense	23547					integral to membrane	receptor activity	g.chr19:54849889C>T	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.133G>A	19.37:g.54849889C>T	ENSP00000291759:p.Val45Met		OREG0003656	type=REGULATORY REGION|Gene=LILRA4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	1003		p.V45M	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN		GBM - Glioblastoma multiforme(193;0.0565)	3	189	-	Ovarian(34;0.19)		45			Ig-like C2-type 1.		Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	c.133G>A	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	11.48	1.651589	0.29336	.	.	ENSG00000239961	ENST00000291759	T	0.16897	2.31	2.5	0.302	0.15786	Immunoglobulin-like fold (1);	0.135368	0.33610	N	0.004727	T	0.36799	0.0980	M	0.88377	2.95	0.09310	N	0.999999	D	0.89917	1.0	D	0.68483	0.958	T	0.11397	-1.0589	10	0.38643	T	0.18	.	4.4673	0.11696	0.0:0.6605:0.0:0.3395	.	45	P59901	LIRA4_HUMAN	M	45	ENSP00000291759:V45M	ENSP00000291759:V45M	V	-	1	0	LILRA4	59541701	0.097000	0.21791	0.196000	0.23383	0.040000	0.13550	0.539000	0.23175	0.140000	0.18849	0.557000	0.71058	GTG		0.537	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276		7	98	7	98	---	---	---	---
ZNF134	7693	broad.mit.edu	37	19	58132430	58132430	+	Missense_Mutation	SNP	C	C	T			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr19:58132430C>T	ENST00000396161.5	+	3	1253	c.943C>T	c.(943-945)Cct>Tct	p.P315S		NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P315S(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		TGGAGAAAATCCTTATGATTG	0.418																																						ENST00000396161.5																			2	Substitution - Missense(2)	p.P315S(2)	prostate(2)	endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11						c.(943-945)Cct>Tct		zinc finger protein 134							132.0	135.0	134.0					19																	58132430		2201	4300	6501	SO:0001583	missense	7693					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr19:58132430C>T	U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"""Zinc fingers, C2H2-type"""	12918	protein-coding gene	gene with protein product		604076	"""zinc finger protein 134 (clone pHZ-15)"""			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.943C>T	19.37:g.58132430C>T	ENSP00000379464:p.Pro315Ser						p.P315S	NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)	3	1253	+		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)	315					Q9Y4B2	Missense_Mutation	SNP	ENST00000396161.5	37	c.943C>T	CCDS42638.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.148501	0.78001	.	.	ENSG00000213762	ENST00000418193;ENST00000541849;ENST00000396161	T	0.28454	1.61	4.45	4.45	0.53987	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.45458	0.1343	L	0.41027	1.25	0.39501	D	0.968204	D	0.76494	0.999	D	0.64687	0.928	T	0.49652	-0.8917	9	0.87932	D	0	.	16.3388	0.83075	0.0:1.0:0.0:0.0	.	315	P52741	ZN134_HUMAN	S	382;235;315	ENSP00000379464:P315S	ENSP00000379464:P315S	P	+	1	0	ZNF134	62824242	0.476000	0.25901	0.999000	0.59377	0.994000	0.84299	3.294000	0.51787	2.458000	0.83093	0.561000	0.74099	CCT		0.418	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	NM_003435		4	104	4	104	---	---	---	---
GART	2618	broad.mit.edu	37	21	34903824	34903824	+	Nonsense_Mutation	SNP	C	C	A			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr21:34903824C>A	ENST00000381831.3	-	6	831	c.568G>T	c.(568-570)Gaa>Taa	p.E190*	GART_ENST00000381815.4_Nonsense_Mutation_p.E190*|GART_ENST00000361093.5_Nonsense_Mutation_p.E190*|GART_ENST00000381839.3_Nonsense_Mutation_p.E190*|GART_ENST00000497313.1_5'UTR	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	190	ATP-grasp.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)	p.E190*(1)		NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	AGAAGTTCTTCAATGACAATT	0.353																																						ENST00000381831.3																			1	Substitution - Nonsense(1)	p.E190*(1)	prostate(1)	NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31						c.(568-570)Gaa>Taa		phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	Pemetrexed(DB00642)						143.0	144.0	144.0					21																	34903824		2203	4300	6503	SO:0001587	stop_gained	2618				'de novo' IMP biosynthetic process|purine base biosynthetic process	cytosol	ATP binding|metal ion binding|methyltransferase activity|phosphoribosylamine-glycine ligase activity|phosphoribosylformylglycinamidine cyclo-ligase activity|phosphoribosylglycinamide formyltransferase activity|protein binding	g.chr21:34903824C>A	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.568G>T	21.37:g.34903824C>A	ENSP00000371253:p.Glu190*					GART_ENST00000381815.4_Nonsense_Mutation_p.E190*|GART_ENST00000361093.5_Nonsense_Mutation_p.E190*|GART_ENST00000381839.3_Nonsense_Mutation_p.E190*|GART_ENST00000497313.1_5'UTR	p.E190*	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN			6	831	-			190			ATP-grasp.		A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Nonsense_Mutation	SNP	ENST00000381831.3	37	c.568G>T	CCDS13627.1	.	.	.	.	.	.	.	.	.	.	C	39	7.378762	0.98248	.	.	ENSG00000159131	ENST00000381815;ENST00000381831;ENST00000381839;ENST00000361093;ENST00000430874;ENST00000426819	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-33.5951	20.6439	0.99570	0.0:1.0:0.0:0.0	.	.	.	.	X	190	.	ENSP00000354388:E190X	E	-	1	0	GART	33825694	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	6.786000	0.75094	2.890000	0.99128	0.650000	0.86243	GAA		0.353	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819		16	168	16	168	---	---	---	---
MUC3A	4584	broad.mit.edu	37	7	100552898	100552898	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr7:100552898delG	ENST00000319509.7	+	2	1543	c.1543delG	c.(1543-1545)ggcfs	p.G515fs				Q02505	MUC3A_HUMAN	mucin 3A, cell surface associated	2180	Ser-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|extracellular matrix structural constituent (GO:0005201)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(32)|prostate(3)	44						TGACAATGGTGGCACCTGGGA	0.567																																						ENST00000319509.7																			0				breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(32)|prostate(3)	44						c.(1543-1545)ggcfs		mucin 3A, cell surface associated							175.0	163.0	167.0					7																	100552898		876	1991	2867	SO:0001589	frameshift_variant	4584							g.chr7:100552898delG	AF113616		7q22.1	2012-04-20	2006-03-14		ENSG00000169894	ENSG00000169894		"""Mucins"""	7513	protein-coding gene	gene with protein product		158371	"""mucin 3A, intestinal"""	MUC3		2393399, 10973822	Standard	XM_006710192		Approved		uc003uxl.1	Q02505	OTTHUMG00000157038	ENST00000319509.7:c.1543delG	7.37:g.100552898delG	ENSP00000324834:p.Gly515fs						p.G515fs							2	1543	+								O14650|O14651|O43418|O43421|Q02506|Q6W763|Q9H3Q7|Q9UKW9|Q9UN93|Q9UN94|Q9UN95	Frame_Shift_Del	DEL	ENST00000319509.7	37	c.1543delG																																																																																					0.567	MUC3A-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347215.1	XM_001725354		9	157	9	157	---	---	---	---
GSE1	23199	broad.mit.edu	37	16	85701839	85701840	+	Frame_Shift_Ins	INS	-	-	T	rs200204743		TCGA-G9-6356-01A-11D-1786-08	TCGA-G9-6356-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2bdbfc0-d13e-4d0f-904b-05c033a72b77	56d3cf13-362a-4701-850e-bd8cf98ac9a4	g.chr16:85701839_85701840insT	ENST00000253458.7	+	14	3400_3401	c.3224_3225insT	c.(3223-3228)cctccafs	p.P1076fs	GSE1_ENST00000405402.2_Frame_Shift_Ins_p.P972fs|GSE1_ENST00000393243.1_Frame_Shift_Ins_p.P1003fs	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	1076																	AGCCGCGCCCCTCCACCCCAGC	0.639																																						ENST00000253458.7																			0											c.(3223-3228)cctccafs		Gse1 coiled-coil protein																																				SO:0001589	frameshift_variant	23199							g.chr16:85701839_85701840insT	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"""genetic suppressor element 1"""		"""KIAA0182"", ""Gse1 coiled-coil protein homolog (mouse)"""	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.3225dupT	16.37:g.85701840_85701840dupT	ENSP00000253458:p.Pro1076fs					GSE1_ENST00000405402.2_Frame_Shift_Ins_p.P972fs|GSE1_ENST00000393243.1_Frame_Shift_Ins_p.P1003fs	p.P1076fs	NM_014615.2	NP_055430.1					14	3400_3401	+								D3DUM4|Q8IY61|Q96GA4|Q9BW09	Frame_Shift_Ins	INS	ENST00000253458.7	37	c.3224_3225insT	CCDS10952.1																																																																																				0.639	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		14	123	14	123	---	---	---	---
