#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
PRAMEF1	65121	broad.mit.edu	37	1	12854545	12854545	+	Missense_Mutation	SNP	G	G	A	rs1063779	byFrequency	TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr1:12854545G>A	ENST00000332296.7	+	3	872	c.769G>A	c.(769-771)Gcc>Acc	p.A257T	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	257					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ACGGTTAGTTGCCAAATTCAG	0.453																																						uc001auj.2																			0				cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						c.(769-771)Gcc>Acc		Homo sapiens PRAME family member 1 (PRAMEF1), mRNA.							146.0	147.0	146.0					1																	12854545		2203	4299	6502	SO:0001583	missense	65121							g.chr1:12854545G>A	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"""-"""	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.769G>A	1.37:g.12854545G>A	ENSP00000332134:p.Ala257Thr						p.A257T	NM_023013	NP_075389	O95521	PRAM1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)	2	872	+	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)	257					Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	c.769G>A	CCDS148.1	.	.	.	.	.	.	.	.	.	.	.	0.554	-0.848251	0.02651	.	.	ENSG00000116721	ENST00000332296	T	0.15603	2.41	1.61	-3.22	0.05125	.	1.203370	0.05755	N	0.603963	T	0.07052	0.0179	N	0.17312	0.475	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.32241	-0.9914	10	0.02654	T	1	.	2.2209	0.03972	0.2882:0.0:0.2791:0.4327	rs1063779	257	O95521	PRAM1_HUMAN	T	257	ENSP00000332134:A257T	ENSP00000332134:A257T	A	+	1	0	PRAMEF1	12777132	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.491000	0.06474	-1.245000	0.02513	-0.694000	0.03704	GCC		0.453	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
LDLRAD2	401944	broad.mit.edu	37	1	22142439	22142439	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr1:22142439C>T	ENST00000344642.2	+	3	702	c.515C>T	c.(514-516)cCt>cTt	p.P172L	LDLRAD2_ENST00000543870.1_Missense_Mutation_p.P172L	NM_001013693.2	NP_001013715.2	Q5SZI1	LRAD2_HUMAN	low density lipoprotein receptor class A domain containing 2	172	LDL-receptor class A. {ECO:0000255|PROSITE-ProRule:PRU00124}.					integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(3)	6		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.00166)|all_lung(284;0.00172)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;5.2e-26)|COAD - Colon adenocarcinoma(152;1.13e-05)|GBM - Glioblastoma multiforme(114;1.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00598)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)		GCCTCAGGACCTTGTGGTGCC	0.627																																						uc001bfg.1																			0				endometrium(2)|large_intestine(1)|lung(3)	6						c.(514-516)cCt>cTt		Homo sapiens low density lipoprotein receptor class A domain containing 2 (LDLRAD2), mRNA.							86.0	79.0	81.0					1																	22142439		2203	4300	6503	SO:0001583	missense	401944					integral to membrane	receptor activity	g.chr1:22142439C>T	AL590103	CCDS30624.1	1p36.12	2008-02-05	2005-10-07		ENSG00000187942	ENSG00000187942			32071	protein-coding gene	gene with protein product			"""low density lipoprotein receptor A domain containing 2"""				Standard	NM_001013693		Approved		uc001bfg.1	Q5SZI1	OTTHUMG00000002675	ENST00000344642.2:c.515C>T	1.37:g.22142439C>T	ENSP00000340988:p.Pro172Leu						p.P172L	NM_001013693	NP_001013715	Q5SZI1	LRAD2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;5.2e-26)|COAD - Colon adenocarcinoma(152;1.13e-05)|GBM - Glioblastoma multiforme(114;1.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00598)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)	2	702	+		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.00166)|all_lung(284;0.00172)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)	172			LDL-receptor class A.		B9EJB3|Q6ZSN5	Missense_Mutation	SNP	ENST00000344642.2	37	c.515C>T	CCDS30624.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.675749	0.29783	.	.	ENSG00000187942	ENST00000344642;ENST00000543870	T;T	0.46451	0.87;0.87	3.99	0.859	0.19036	CUB (1);	1.308450	0.05309	N	0.524375	T	0.35770	0.0943	L	0.37800	1.135	0.19945	N	0.999947	B	0.22604	0.072	B	0.29077	0.098	T	0.40421	-0.9564	10	0.62326	D	0.03	-6.8496	5.9681	0.19336	0.0:0.5176:0.374:0.1084	.	172	Q5SZI1	LRAD2_HUMAN	L	172	ENSP00000340988:P172L;ENSP00000444097:P172L	ENSP00000340988:P172L	P	+	2	0	LDLRAD2	22015026	0.475000	0.25894	0.002000	0.10522	0.468000	0.32798	0.454000	0.21827	0.085000	0.17107	0.498000	0.49722	CCT		0.627	LDLRAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007601.1	NM_001013693	
GBP7	388646	broad.mit.edu	37	1	89618461	89618461	+	Splice_Site	SNP	C	C	G			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr1:89618461C>G	ENST00000294671.2	-	4	457		c.e4-1			NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7							membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		TAGGGTCACTCTAGTGTTAAA	0.438																																						uc001dna.2																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						c.e4-1		Homo sapiens guanylate binding protein 7 (GBP7), mRNA.							52.0	52.0	52.0					1																	89618461		2203	4300	6503	SO:0001630	splice_region_variant	388646					integral to membrane	GTP binding|GTPase activity	g.chr1:89618461C>G	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.319-1G>C	1.37:g.89618461C>G						GBP2_uc001dmy.1_5'Flank	p.S107_splice	NM_207398	NP_997281	Q8N8V2	GBP7_HUMAN		all cancers(265;0.00835)|Epithelial(280;0.0322)	4	458	-		Lung NSC(277;0.0908)	107						Splice_Site	SNP	ENST00000294671.2	37	c.319_splice	CCDS720.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.701659	0.30142	.	.	ENSG00000213512	ENST00000294671	.	.	.	3.41	3.41	0.39046	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3121	0.54933	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GBP7	89391049	1.000000	0.71417	0.010000	0.14722	0.078000	0.17371	5.303000	0.65738	1.757000	0.51966	0.205000	0.17691	.		0.438	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	Intron
RPL5	6125	broad.mit.edu	37	1	93299200	93299201	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr1:93299200_93299201delAG	ENST00000370321.3	+	3	262_263	c.172_173delAG	c.(172-174)agafs	p.R58fs		NM_000969.3	NP_000960.2	P46777	RL5_HUMAN	ribosomal protein L5	58					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	5S rRNA binding (GO:0008097)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)		TGTGACAAACAGAGATATCATT	0.371																																						uc001doz.3																			0				endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9	GRCh37	CD086185	RPL5	D		c.(172-174)agafs		Homo sapiens ribosomal protein L5 (RPL5), mRNA.																																				SO:0001589	frameshift_variant	6125				endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	5S rRNA binding|protein binding|structural constituent of ribosome	g.chr1:93299200_93299201delAG	U14966	CCDS741.1	1p22.1	2014-06-13			ENSG00000122406	ENSG00000122406		"""L ribosomal proteins"""	10360	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 135"""	603634				7937132, 7772601	Standard	NM_000969		Approved	L5, PPP1R135	uc001doz.3	P46777	OTTHUMG00000010899	ENST00000370321.3:c.172_173delAG	1.37:g.93299202_93299203delAG	ENSP00000359345:p.Arg58fs					FAM69A_uc001dpc.3_Intron|RPL5_uc001dpa.3_Non-coding_Transcript|RPL5_uc001dpb.3_Frame_Shift_Del_p.R8fs|RPL5_uc001dpd.3_5'Flank	p.R58fs	NM_000969	NP_000960	P46777	RL5_HUMAN		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)	2	250_251	+		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)	58					Q32LZ3|Q53HH6|Q9H3F4	Frame_Shift_Del	DEL	ENST00000370321.3	37	c.172_173delAG	CCDS741.1																																																																																				0.371	RPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030058.2	NM_000969	
HAO2	51179	broad.mit.edu	37	1	119923209	119923209	+	Intron	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr1:119923209G>A	ENST00000325945.3	+	2	65				HAO2_ENST00000361035.4_5'UTR	NM_001005783.1|NM_016527.2	NP_001005783.1|NP_057611.1	Q9NYQ3	HAOX2_HUMAN	hydroxyacid oxidase 2 (long chain)						fatty acid oxidation (GO:0019395)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)		TGGTGAGGCAGTGAAAATCCA	0.478																																						uc001ehr.1																			0				breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30								Homo sapiens hydroxyacid oxidase 2 (long chain) (HAO2), transcript variant 1, mRNA.																																				SO:0001627	intron_variant	51179				fatty acid alpha-oxidation	peroxisome	(S)-2-hydroxy-acid oxidase activity	g.chr1:119923209G>A	AF231917	CCDS901.1	1p13.3-p13.1	2008-07-18			ENSG00000116882	ENSG00000116882	1.1.3.15		4810	protein-coding gene	gene with protein product	"""(S)-2-hydroxy-acid oxidase"", ""glycolate oxidase"", ""long-chain L-2-hydroxy acid oxidase"", ""growth-inhibiting protein 16"""	605176				10777549	Standard	XM_005270913		Approved	HAOX2, GIG16	uc001ehr.1	Q9NYQ3	OTTHUMG00000012410	ENST00000325945.3:c.-8-492G>A	1.37:g.119923209G>A						HAO2_uc001ehq.1_5'UTR		NM_016527	NP_057611	Q9NYQ3	HAOX2_HUMAN		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)			+	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)						Q2TU86|Q5QP00|Q9UJS6	Translation_Start_Site	SNP	ENST00000325945.3	37		CCDS901.1																																																																																				0.478	HAO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034984.1	NM_001005783	
HSD3BP2	440606	broad.mit.edu	37	1	119985601	119985601	+	IGR	SNP	C	C	T	rs587710814	byFrequency	TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr1:119985601C>T								HSD3B2 (19943 upstream) : HSD3B1 (64224 downstream)																							TCATCCACACCGCCTGTATCA	0.507													C|||	11	0.00219649	0.0	0.0	5008	,	,		20454	0.001		0.0	False		,,,				2504	0.0102					uc001ehu.3																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(19)|ovary(2)|skin(1)	27						c.(406-408)acC>acT		Homo sapiens hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2 (HSD3B2), transcript variant 1, mRNA.	NADH(DB00157)|Trilostane(DB01108)																																			SO:0001628	intergenic_variant	3284				androgen biosynthetic process|glucocorticoid biosynthetic process|mineralocorticoid biosynthetic process	integral to membrane|microsome|mitochondrial inner membrane|mitochondrial intermembrane space|smooth endoplasmic reticulum membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|steroid delta-isomerase activity	g.chr1:119985601C>T																													1.37:g.119985601C>T							p.T136T			P26439	3BHS2_HUMAN		Lung(183;0.015)|LUSC - Lung squamous cell carcinoma(189;0.0836)	3	580	+	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)	0						Silent	SNP		37	c.408C>T																																																																																				0	0.507								
FAM63A	55793	broad.mit.edu	37	1	150974995	150974995	+	Silent	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr1:150974995C>T	ENST00000361936.5	-	3	1053	c.99G>A	c.(97-99)gaG>gaA	p.E33E	FAM63A_ENST00000312210.5_Intron|FAM63A_ENST00000470877.1_Intron|FAM63A_ENST00000361738.6_Silent_p.E81E|FAM63A_ENST00000493834.2_Intron	NM_018379.4	NP_060849	Q8N5J2	FA63A_HUMAN	family with sequence similarity 63, member A	33						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(3)|large_intestine(4)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CCTGAGGGTGCTCATCTGGGC	0.577																																						uc010pcn.2																			0				breast(1)|endometrium(3)|large_intestine(4)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						c.(241-243)gaG>gaA		Homo sapiens family with sequence similarity 63, member A (FAM63A), transcript variant 3, mRNA.							142.0	134.0	137.0					1																	150974995		2203	4300	6503	SO:0001819	synonymous_variant	55793						protein binding	g.chr1:150974995C>T	BC032321	CCDS976.1, CCDS30854.1, CCDS53361.1, CCDS55635.1	1q21.2	2008-02-05			ENSG00000143409	ENSG00000143409			25648	protein-coding gene	gene with protein product						10718198	Standard	NM_001040217		Approved	FLJ11280	uc010pcn.2	Q8N5J2	OTTHUMG00000035061	ENST00000361936.5:c.99G>A	1.37:g.150974995C>T						FAM63A_uc001ewc.3_Intron|FAM63A_uc010pcm.2_Intron|FAM63A_uc001ewd.3_Intron|FAM63A_uc001ewf.3_Silent_p.E33E|FAM63A_uc001ewg.3_Silent_p.E33E	p.E81E	NM_001163258	NP_001156730	Q8N5J2	FA63A_HUMAN	UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)		2	466	-	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		33					B3KWP4|B3KWV8|B4DXF2|B4E1S4|D3DV09|J3KP53|Q5SZF0|Q9NUL9|Q9P2F7	Silent	SNP	ENST00000361936.5	37	c.243G>A	CCDS976.1																																																																																				0.577	FAM63A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411753.1	NM_018379	
FLG	2312	broad.mit.edu	37	1	152284473	152284473	+	Silent	SNP	A	A	G			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr1:152284473A>G	ENST00000368799.1	-	3	2924	c.2889T>C	c.(2887-2889)tcT>tcC	p.S963S	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	963	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AAGCAGACCCAGACCACCTCT	0.582									Ichthyosis																													uc001ezu.1																			0				autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424						c.(2887-2889)tcT>tcC		Homo sapiens filaggrin (FLG), mRNA.							245.0	247.0	246.0					1																	152284473		2203	4297	6500	SO:0001819	synonymous_variant	2312	Ichthyosis	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity	g.chr1:152284473A>G	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2889T>C	1.37:g.152284473A>G						AK056431_uc001ezv.3_5'Flank	p.S963S	NM_002016	NP_002007	P20930	FILA_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		2	2925	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		963			Ser-rich.		Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	c.2889T>C	CCDS30860.1																																																																																				0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
DPT	1805	broad.mit.edu	37	1	168698174	168698174	+	Missense_Mutation	SNP	G	G	A	rs200956999		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr1:168698174G>A	ENST00000367817.3	-	1	328	c.239C>T	c.(238-240)aCg>aTg	p.T80M		NM_001937.4	NP_001928.2	Q07507	DERM_HUMAN	dermatopontin	80	2 X 53-55 AA tandem repeats.|3 X 6 AA repeats of D-R-[EQ]-W-[NQK]- [FY].				cell adhesion (GO:0007155)|collagen fibril organization (GO:0030199)|negative regulation of cell proliferation (GO:0008285)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.T80M(1)		kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)	12	all_hematologic(923;0.208)					GCTCTGTGGCGTGGGCATGCA	0.607													G|||	1	0.000199681	0.0	0.0014	5008	,	,		20980	0.0		0.0	False		,,,				2504	0.0					uc001gfp.3																			1	Substitution - Missense(1)	p.T80M(2)	prostate(1)	kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)	12						c.(238-240)aCg>aTg		Homo sapiens dermatopontin (DPT), mRNA.		G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	161.0	128.0	139.0		239	4.1	0.8	1		139	1,8599	1.2+/-3.3	0,1,4299	no	missense	DPT	NM_001937.4	81	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	80/202	168698174	2,13004	2203	4300	6503	SO:0001583	missense	1805				cell adhesion	extracellular space|proteinaceous extracellular matrix		g.chr1:168698174G>A	BC033736	CCDS1275.1	1q12-q23	2008-02-05			ENSG00000143196	ENSG00000143196			3011	protein-coding gene	gene with protein product		125597				8104875	Standard	NM_001937		Approved		uc001gfp.3	Q07507	OTTHUMG00000034554	ENST00000367817.3:c.239C>T	1.37:g.168698174G>A	ENSP00000356791:p.Thr80Met						p.T80M	NM_001937	NP_001928	Q07507	DERM_HUMAN			0	269	-	all_hematologic(923;0.208)		80			2 X 53-55 AA tandem repeats.|3 X 6 AA repeats of D-R-[EQ]-W-[NQK]- [FY].		A8K981|Q8N4R2|Q9UIX8	Missense_Mutation	SNP	ENST00000367817.3	37	c.239C>T	CCDS1275.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	22.2	4.264516	0.80358	2.27E-4	1.16E-4	ENSG00000143196	ENST00000367817	T	0.47869	0.83	5.0	4.06	0.47325	.	0.048107	0.85682	D	0.000000	T	0.47525	0.1450	L	0.58101	1.795	0.44366	D	0.997268	D	0.62365	0.991	P	0.56474	0.799	T	0.56805	-0.7918	9	0.72032	D	0.01	-9.9396	14.0368	0.64649	0.0:0.0:0.8474:0.1526	.	80	Q07507	DERM_HUMAN	M	80	ENSP00000356791:T80M	ENSP00000356791:T80M	T	-	2	0	DPT	166964798	1.000000	0.71417	0.752000	0.31206	0.970000	0.65996	7.492000	0.81482	1.024000	0.39682	0.655000	0.94253	ACG		0.607	DPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083618.1	NM_001937	
YOD1	55432	broad.mit.edu	37	1	207222900	207222900	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr1:207222900C>T	ENST00000315927.4	-	2	558	c.512G>A	c.(511-513)gGa>gAa	p.G171E	PFKFB2_ENST00000411990.2_5'UTR|YOD1_ENST00000367084.1_Missense_Mutation_p.G127E|YOD1_ENST00000391927.1_Missense_Mutation_p.G127E	NM_018566.3	NP_061036.3	Q5VVQ6	OTU1_HUMAN	YOD1 deubiquitinase	171	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				cellular amino acid metabolic process (GO:0006520)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein K11-linked deubiquitination (GO:0035871)|protein K27-linked deubiquitination (GO:1990167)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)		Lys48-specific deubiquitinase activity (GO:1990380)|metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			cervix(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(3)	11	Prostate(682;0.19)					CAAGACTCCTCCTTCGACGAC	0.483																																						uc001hfe.1																			0				cervix(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(3)	11						c.(511-513)gGa>gAa		Homo sapiens YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae) (YOD1), mRNA.							84.0	78.0	80.0					1																	207222900		2203	4300	6503	SO:0001583	missense	55432				cellular amino acid metabolic process|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|protein K48-linked deubiquitination|protein K63-linked deubiquitination	intracellular	protein binding|ubiquitin-specific protease activity|zinc ion binding	g.chr1:207222900C>T		CCDS31002.1, CCDS60402.1	1q32.2	2013-06-04	2013-06-04		ENSG00000180667	ENSG00000180667		"""OTU domain containing"""	25035	protein-coding gene	gene with protein product		612023	"""YOD1 OTU deubiquinating enzyme 1 homolog ( yeast)"", ""YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae)"""				Standard	NM_001276320		Approved	DKFZp451J1719, OTUD2, DUBA8	uc001hfe.1	Q5VVQ6	OTTHUMG00000036032	ENST00000315927.4:c.512G>A	1.37:g.207222900C>T	ENSP00000326813:p.Gly171Glu					PFKFB2_uc010psc.2_5'UTR|YOD1_uc001hff.1_Missense_Mutation_p.G127E	p.G171E	NM_018566	NP_061036	Q5VVQ6	OTU1_HUMAN			1	559	-	Prostate(682;0.19)		171			OTU.		B2RNX3|Q5VVQ5|Q6ZRS6|Q86T63|Q9P1L8	Missense_Mutation	SNP	ENST00000315927.4	37	c.512G>A	CCDS31002.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.737646	0.89573	.	.	ENSG00000180667	ENST00000367084;ENST00000315927;ENST00000391927	T;T;T	0.46819	0.86;0.86;0.86	5.97	5.97	0.96955	Ovarian tumour, otubain (2);	0.099239	0.64402	D	0.000002	T	0.68742	0.3034	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.91;1.0	T	0.64719	-0.6341	10	0.41790	T	0.15	0.176	19.4269	0.94746	0.0:1.0:0.0:0.0	.	127;171	Q5VVQ6-2;Q5VVQ6	.;OTU1_HUMAN	E	127;171;127	ENSP00000356051:G127E;ENSP00000326813:G171E;ENSP00000375793:G127E	ENSP00000326813:G171E	G	-	2	0	YOD1	205289523	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.724000	0.84798	2.836000	0.97738	0.655000	0.94253	GGA		0.483	YOD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087837.1	NM_018566	
PTER	9317	broad.mit.edu	37	10	16528558	16528558	+	Nonsense_Mutation	SNP	C	C	T	rs370033967		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr10:16528558C>T	ENST00000378000.1	+	4	886	c.640C>T	c.(640-642)Cga>Tga	p.R214*	PTER_ENST00000485788.1_3'UTR|PTER_ENST00000535784.2_Nonsense_Mutation_p.R214*|PTER_ENST00000298942.3_Nonsense_Mutation_p.R214*|PTER_ENST00000423462.2_Nonsense_Mutation_p.R214*	NM_001001484.2|NM_001261838.1|NM_030664.4	NP_001001484.1|NP_001248767.1|NP_109589.2	Q96BW5	PTER_HUMAN	phosphotriesterase related	214					catabolic process (GO:0009056)|epithelial cell differentiation (GO:0030855)	extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)	p.R214*(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)	15						TCAGATTATCCGAATATTGCA	0.478																																					Ovarian(2;46 150 15648 38137 47908)	uc001iog.1																			1	Substitution - Nonsense(1)	p.R214*(2)	large_intestine(1)	endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)	15						c.(640-642)Cga>Tga		Homo sapiens phosphotriesterase related (PTER), transcript variant 2, mRNA.		C	stop/ARG,stop/ARG	2,4404	4.2+/-10.8	0,2,2201	95.0	92.0	93.0		640,640	4.9	1.0	10		93	0,8600		0,0,4300	no	stop-gained,stop-gained	PTER	NM_001001484.1,NM_030664.3	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	214/350,214/350	16528558	2,13004	2203	4300	6503	SO:0001587	stop_gained	9317				catabolic process		hydrolase activity, acting on ester bonds|zinc ion binding	g.chr10:16528558C>T	BC015092	CCDS7111.1, CCDS58070.1, CCDS73070.1	10p12	2003-11-05			ENSG00000165983	ENSG00000165983			9590	protein-coding gene	gene with protein product		604446				9925913	Standard	NM_001001484		Approved		uc001ioi.2	Q96BW5	OTTHUMG00000017737	ENST00000378000.1:c.640C>T	10.37:g.16528558C>T	ENSP00000367239:p.Arg214*					PTER_uc001ioh.1_Nonsense_Mutation_p.R214*|PTER_uc001ioi.1_Nonsense_Mutation_p.R214*|PTER_uc009xjp.1_Nonsense_Mutation_p.R214*	p.R214*	NM_030664	NP_109589	Q96BW5	PTER_HUMAN			3	847	+			214					B0YJ77|B3KTF5|D3DRU0|Q9BY46	Nonsense_Mutation	SNP	ENST00000378000.1	37	c.640C>T	CCDS7111.1	.	.	.	.	.	.	.	.	.	.	C	37	6.037468	0.97226	4.54E-4	0.0	ENSG00000165983	ENST00000343656;ENST00000535784;ENST00000423462;ENST00000378000;ENST00000298942	.	.	.	5.83	4.92	0.64577	.	0.172230	0.52532	D	0.000071	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.1383	15.3267	0.74168	0.0:0.9321:0.0:0.0679	.	.	.	.	X	214	.	ENSP00000298942:R214X	R	+	1	2	PTER	16568564	1.000000	0.71417	0.988000	0.46212	0.982000	0.71751	4.858000	0.62947	2.775000	0.95449	0.650000	0.86243	CGA		0.478	PTER-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047001.2	NM_030664	
P2RX3	5024	broad.mit.edu	37	11	57106069	57106069	+	Silent	SNP	G	G	A	rs377236358		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr11:57106069G>A	ENST00000263314.2	+	1	79	c.45G>A	c.(43-45)tcG>tcA	p.S15S	P2RX3_ENST00000533436.1_3'UTR|SSRP1_ENST00000278412.2_5'Flank	NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	15					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						CCACCAAGTCGGTGGTTGTGA	0.532																																						uc001nju.3																			0		p.S15L(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						c.(43-45)tcG>tcA		Homo sapiens purinergic receptor P2X, ligand-gated ion channel, 3 (P2RX3), mRNA.		G		0,4402		0,0,2201	267.0	235.0	246.0		45	-7.4	0.9	11		246	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous	P2RX3	NM_002559.3		0,1,6496	AA,AG,GG		0.0116,0.0,0.0077		15/398	57106069	1,12993	2201	4296	6497	SO:0001819	synonymous_variant	5024				positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity	g.chr11:57106069G>A	Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.45G>A	11.37:g.57106069G>A						SSRP1_uc001njt.3_5'Flank	p.S15S	NM_002559	NP_002550	P56373	P2RX3_HUMAN			0	229	+			15					Q6DK37|Q9UQB6	Silent	SNP	ENST00000263314.2	37	c.45G>A	CCDS7953.1																																																																																				0.532	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559	
FOLR4	390243	broad.mit.edu	37	11	94040372	94040372	+	Silent	SNP	G	G	A	rs201258390		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr11:94040372G>A	ENST00000440961.2	+	3	413	c.369G>A	c.(367-369)ccG>ccA	p.P123P		NM_001199206.1	NP_001186135.1	A6ND01	JUNO_HUMAN	folate receptor 4, delta (putative)	130					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14						TGAATGTGCCGCTGTGCCAGG	0.542																																						uc021qou.1																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14						c.(388-390)ccG>ccA		Homo sapiens folate receptor 4 (delta) homolog (mouse) (FOLR4), mRNA.		G		0,4380		0,0,2190	98.0	105.0	102.0		390	-9.3	0.0	11		102	4,8572		0,4,4284	no	coding-synonymous	FOLR4	NM_001199206.1		0,4,6474	AA,AG,GG		0.0466,0.0,0.0309		130/251	94040372	4,12952	2190	4288	6478	SO:0001819	synonymous_variant	390243					extracellular region	folic acid binding|receptor activity	g.chr11:94040372G>A			11q14	2014-07-23	2012-12-07		ENSG00000183560	ENSG00000183560			32565	protein-coding gene	gene with protein product		615737	"""folate receptor 4 (delta) homolog (mouse)"""			11111049, 24739963	Standard	NM_001199206		Approved	Folbp3, JUNO	uc021qou.1	A6ND01		ENST00000440961.2:c.369G>A	11.37:g.94040372G>A							p.P130P	NM_001199206	NP_001186135	A6ND01	FOLR4_HUMAN			2	390	+			130						Silent	SNP	ENST00000440961.2	37	c.390G>A		.	.	.	.	.	.	.	.	.	.	G	10.68	1.417535	0.25552	0.0	4.66E-4	ENSG00000183560	ENST00000328458	.	.	.	4.67	-9.34	0.00636	.	.	.	.	.	T	0.36468	0.0968	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43278	-0.9401	4	.	.	.	-11.0741	3.953	0.09377	0.3474:0.4038:0.1639:0.0849	.	.	.	.	H	124	.	.	R	+	2	0	FOLR4	93680020	0.000000	0.05858	0.006000	0.13384	0.615000	0.37417	-4.885000	0.00174	-2.552000	0.00479	0.491000	0.48974	CGC		0.542	FOLR4-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000396420.1	NM_001080486	
MMP3	4314	broad.mit.edu	37	11	102709963	102709963	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr11:102709963C>T	ENST00000299855.5	-	7	1203	c.947G>A	c.(946-948)cGc>cAc	p.R316H	WTAPP1_ENST00000525739.2_RNA	NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	316					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	GAGGGATTTGCGCCAAAAGTG	0.403																																						uc001phj.1																			0		p.R316C(3)		endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						c.(946-948)cGc>cAc		Homo sapiens matrix metallopeptidase 3 (stromelysin 1, progelatinase) (MMP3), mRNA.	Marimastat(DB00786)|Simvastatin(DB00641)						78.0	86.0	83.0					11																	102709963		2203	4299	6502	SO:0001583	missense	4314				collagen catabolic process|proteolysis	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding	g.chr11:102709963C>T	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"""matrix metalloproteinase 3 (stromelysin 1, progelatinase)"""	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.947G>A	11.37:g.102709963C>T	ENSP00000299855:p.Arg316His					DD413629_uc021qpi.1_5'Flank	p.R316H	NM_002422	NP_002413	P08254	MMP3_HUMAN		BRCA - Breast invasive adenocarcinoma(274;0.0142)	6	1012	-		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	316			Hemopexin-like 1.		B2R8B8|Q3B7S0|Q6GRF8	Missense_Mutation	SNP	ENST00000299855.5	37	c.947G>A	CCDS8323.1	.	.	.	.	.	.	.	.	.	.	C	31	5.070674	0.93950	.	.	ENSG00000149968	ENST00000299855	T	0.04454	3.62	5.65	5.65	0.86999	Hemopexin/matrixin (2);	0.000000	0.36740	N	0.002424	T	0.34483	0.0899	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.42515	-0.9447	10	0.87932	D	0	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	316	P08254	MMP3_HUMAN	H	316	ENSP00000299855:R316H	ENSP00000299855:R316H	R	-	2	0	MMP3	102215173	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.869000	0.75521	2.941000	0.99782	0.655000	0.94253	CGC		0.403	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422	
TRIM29	23650	broad.mit.edu	37	11	120008271	120008271	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr11:120008271C>T	ENST00000341846.5	-	1	890	c.469G>A	c.(469-471)Gac>Aac	p.D157N		NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	157					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		AGGCCCGTGTCGGCCCGGGGG	0.642																																						uc001pwz.3																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						c.(469-471)Gac>Aac		Homo sapiens tripartite motif containing 29 (TRIM29), mRNA.							46.0	59.0	55.0					11																	120008271		2202	4299	6501	SO:0001583	missense	23650				transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr11:120008271C>T	AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"""Tripartite motif containing / Tripartite motif containing"""	17274	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM29"", ""ataxia-telangiectasia group D-associated protein"""	610658	"""tripartite motif-containing 29"""			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.469G>A	11.37:g.120008271C>T	ENSP00000343129:p.Asp157Asn					TRIM29_uc001pxa.3_Non-coding_Transcript	p.D157N	NM_012101	NP_036233	Q14134	TRI29_HUMAN		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)	0	593	-		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	157					Q96AA9|Q9BZY7	Missense_Mutation	SNP	ENST00000341846.5	37	c.469G>A	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.530181	0.45073	.	.	ENSG00000137699	ENST00000341846	T	0.38401	1.14	5.19	5.19	0.71726	.	0.178800	0.39274	N	0.001407	T	0.26629	0.0651	L	0.46157	1.445	0.80722	D	1	P	0.46020	0.871	B	0.33521	0.165	T	0.05733	-1.0867	9	.	.	.	.	11.3829	0.49768	0.0:0.9166:0.0:0.0834	.	157	Q14134	TRI29_HUMAN	N	157	ENSP00000343129:D157N	.	D	-	1	0	TRIM29	119513481	0.681000	0.27614	0.071000	0.20095	0.326000	0.28443	1.622000	0.36997	2.423000	0.82170	0.563000	0.77884	GAC		0.642	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101	
DDX11L8	100302090	broad.mit.edu	37	12	92920	92920	+	IGR	SNP	C	C	G	rs370608277		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr12:92920C>G								AC215219.1 (19598 upstream) : AC026369.1 (54131 downstream)																							ACTCACAAGACTGTGATCCAA	0.622																																						uc010sdi.1																			0											c.(70-72)aGt>aCt		SubName: Full=DEAD/H box polypeptide 11 like 11;																																				SO:0001628	intergenic_variant	100887824							g.chr12:92920C>G																													12.37:g.92920C>G						DDX11L11_uc010sdj.1_Non-coding_Transcript	p.S24T							0	99	-									Missense_Mutation	SNP		37	c.71G>C																																																																																				0	0.622								
IQSEC3	440073	broad.mit.edu	37	12	274924	274924	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr12:274924C>A	ENST00000538872.1	+	11	2957	c.2839C>A	c.(2839-2841)Ccg>Acg	p.P947T	IQSEC3_ENST00000382841.2_Missense_Mutation_p.P644T|IQSEC3_ENST00000326261.4_Missense_Mutation_p.P947T|RP11-598F7.6_ENST00000537295.1_lincRNA|RP11-598F7.5_ENST00000540136.1_RNA			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	947	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.P644T(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		ACTGGTGACCCCGCTCTCGGG	0.607																																						uc001qhw.2																			1	Substitution - Missense(1)	p.P644T(1)	central_nervous_system(1)	central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						c.(2839-2841)Ccg>Acg		Homo sapiens IQ motif and Sec7 domain 3 (IQSEC3), transcript variant 1, mRNA.							53.0	56.0	55.0					12																	274924		2203	4300	6503	SO:0001583	missense	440073				regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity	g.chr12:274924C>A	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2839C>A	12.37:g.274924C>A	ENSP00000437554:p.Pro947Thr					IQSEC3_uc001qhu.1_Missense_Mutation_p.P644T	p.P947T	NM_001170738	NP_001164209	Q9UPP2	IQEC3_HUMAN	OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)	10	2839	+	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		947			PH.		A6NIF2|A6NKV9|Q8TB43	Missense_Mutation	SNP	ENST00000538872.1	37	c.2839C>A	CCDS53728.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.468298	0.43839	.	.	ENSG00000120645	ENST00000538872;ENST00000326261;ENST00000382841	T;T;T	0.40225	1.04;1.04;1.04	5.39	4.51	0.55191	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.44477	0.1295	M	0.62016	1.91	0.58432	D	0.999999	B;B	0.29341	0.242;0.198	B;B	0.33846	0.113;0.171	T	0.41822	-0.9487	10	0.44086	T	0.13	.	14.3917	0.66983	0.0:0.9287:0.0:0.0713	.	947;644	Q9UPP2;Q9UPP2-2	IQEC3_HUMAN;.	T	947;947;644	ENSP00000437554:P947T;ENSP00000315662:P947T;ENSP00000372292:P644T	ENSP00000315662:P947T	P	+	1	0	IQSEC3	145185	0.998000	0.40836	0.852000	0.33557	0.003000	0.03518	3.963000	0.56773	1.415000	0.47037	-0.142000	0.14014	CCG		0.607	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902	
ZNF705A	440077	broad.mit.edu	37	12	8328517	8328517	+	Silent	SNP	C	C	T	rs375681214		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr12:8328517C>T	ENST00000359286.4	+	4	386	c.297C>T	c.(295-297)gaC>gaT	p.D99D		NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	99					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		CCAGAAAAGACGCATCCACCA	0.343																																						uc001qud.1																			0				NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18						c.(295-297)gaC>gaT		Homo sapiens zinc finger protein 705A (ZNF705A), mRNA.		C		0,4404		0,0,2202	77.0	73.0	75.0		297	-1.0	0.0	12		75	1,8563		0,1,4281	no	coding-synonymous	ZNF705A	NM_001004328.2		0,1,6483	TT,TC,CC		0.0117,0.0,0.0077		99/301	8328517	1,12967	2202	4282	6484	SO:0001819	synonymous_variant	440077				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr12:8328517C>T	AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"""Zinc fingers, C2H2-type"", ""-"""	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.297C>T	12.37:g.8328517C>T							p.D99D	NM_001004328	NP_001004328	Q6ZN79	Z705A_HUMAN		Kidney(36;0.0877)	3	369	+			99						Silent	SNP	ENST00000359286.4	37	c.297C>T	CCDS31737.1																																																																																				0.343	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328	
CYP27B1	1594	broad.mit.edu	37	12	58158830	58158830	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr12:58158830G>A	ENST00000228606.4	-	4	963	c.754C>T	c.(754-756)Cgc>Tgc	p.R252C	CYP27B1_ENST00000546496.1_5'Flank	NM_000785.3	NP_000776.1	O15528	CP27B_HUMAN	cytochrome P450, family 27, subfamily B, polypeptide 1	252					bone mineralization (GO:0030282)|calcitriol biosynthetic process from calciol (GO:0036378)|calcium ion homeostasis (GO:0055074)|calcium ion transport (GO:0006816)|decidualization (GO:0046697)|G1 to G0 transition (GO:0070314)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of bone mineralization (GO:0030500)|response to estrogen (GO:0043627)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	calcidiol 1-monooxygenase activity (GO:0004498)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.R252C(1)		central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|urinary_tract(1)	15	all_cancers(7;8.09e-80)|Lung NSC(6;2.26e-27)|all_lung(6;1.99e-25)|all_epithelial(6;3.62e-18)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;1.97e-113)|all cancers(5;1.54e-78)|BRCA - Breast invasive adenocarcinoma(9;0.0294)		Alfacalcidol(DB01436)|Calcidiol(DB00146)|Corticotropin(DB01285)|Ergocalciferol(DB00153)	CGGCAGAGGCGGCCCCAGGGC	0.607											OREG0021953	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc001spz.1																			1	Substitution - Missense(1)	p.R252C(2)	central_nervous_system(1)	central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|urinary_tract(1)	15						c.(754-756)Cgc>Tgc		Homo sapiens cytochrome P450, family 27, subfamily B, polypeptide 1 (CYP27B1), nuclear gene encoding mitochondrial protein, mRNA.	Calcidiol(DB00146)|Calcitriol(DB00136)|Ergocalciferol(DB00153)						49.0	52.0	51.0					12																	58158830		2201	4296	6497	SO:0001583	missense	1594				bone mineralization|calcium ion homeostasis|calcium ion transport|decidualization|G1 to G0 transition|hormone biosynthetic process|negative regulation of calcidiol 1-monooxygenase activity|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of keratinocyte differentiation|positive regulation of vitamin D 24-hydroxylase activity|positive regulation of vitamin D receptor signaling pathway|regulation of bone mineralization|response to estrogen stimulus|response to interferon-gamma|response to lipopolysaccharide|response to tumor necrosis factor|response to vitamin D|vitamin D biosynthetic process|xenobiotic metabolic process	mitochondrial outer membrane	calcidiol 1-monooxygenase activity|electron carrier activity|heme binding	g.chr12:58158830G>A	AB006987	CCDS8954.1	12q14.1	2013-11-13	2003-01-14		ENSG00000111012	ENSG00000111012		"""Cytochrome P450s"""	2606	protein-coding gene	gene with protein product	"""VDDR I"", ""1alpha(OH)ase"", ""25-Hydroxyvitamin D3 1alpha-hydroxylase"""	609506	"""cytochrome P450, subfamily XXVIIB (25-hydroxyvitamin D-1-alpha-hydroxylase), polypeptide 1"""	VDD1, PDDR		9295274, 9344864	Standard	NM_000785		Approved	CYP1, P450c1	uc001spz.1	O15528	OTTHUMG00000170457	ENST00000228606.4:c.754C>T	12.37:g.58158830G>A	ENSP00000228606:p.Arg252Cys		OREG0021953	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1028	CYP27B1_uc001sqa.1_Missense_Mutation_p.R17C|CYP27B1_uc001sqb.1_Missense_Mutation_p.P132L|CYP27B1_uc001sqc.1_Missense_Mutation_p.P132L	p.R252C	NM_000785	NP_000776	O15528	CP27B_HUMAN	GBM - Glioblastoma multiforme(5;1.97e-113)|all cancers(5;1.54e-78)|BRCA - Breast invasive adenocarcinoma(9;0.0294)		3	906	-	all_cancers(7;8.09e-80)|Lung NSC(6;2.26e-27)|all_lung(6;1.99e-25)|all_epithelial(6;3.62e-18)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		252					B2RC61|Q548T3	Missense_Mutation	SNP	ENST00000228606.4	37	c.754C>T	CCDS8954.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.511405	0.64522	.	.	ENSG00000111012	ENST00000228606;ENST00000546567	T;T	0.72167	-0.63;-0.63	4.89	4.89	0.63831	.	0.425571	0.27223	N	0.020353	T	0.80592	0.4652	M	0.66939	2.045	0.43242	D	0.99515	D	0.89917	1.0	D	0.75020	0.985	T	0.81688	-0.0819	10	0.72032	D	0.01	.	10.5846	0.45275	0.0:0.0:0.6989:0.3011	.	252	O15528	CP27B_HUMAN	C	252;17	ENSP00000228606:R252C;ENSP00000449472:R17C	ENSP00000228606:R252C	R	-	1	0	CYP27B1	56445097	0.865000	0.29922	1.000000	0.80357	0.997000	0.91878	1.798000	0.38814	2.543000	0.85770	0.561000	0.74099	CGC		0.607	CYP27B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409248.1	NM_000785	
AMDHD1	144193	broad.mit.edu	37	12	96348739	96348739	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr12:96348739G>A	ENST00000266736.2	+	3	401	c.295G>A	c.(295-297)Gaa>Aaa	p.E99K		NM_152435.2	NP_689648.2	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	99					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	imidazolonepropionase activity (GO:0050480)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|skin(1)	22						AAGAGTTCACGAATTTGCAAT	0.358																																						uc001tel.2																			0				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|skin(1)	22						c.(295-297)Gaa>Aaa		Homo sapiens amidohydrolase domain containing 1 (AMDHD1), mRNA.							146.0	132.0	137.0					12																	96348739		2203	4300	6503	SO:0001583	missense	144193				histidine catabolic process to glutamate and formamide	cytosol	imidazolonepropionase activity|metal ion binding	g.chr12:96348739G>A	AB075878	CCDS9057.1	12q23.1	2006-02-02				ENSG00000139344			28577	protein-coding gene	gene with protein product							Standard	NM_152435		Approved	MGC35366	uc001tel.2	Q96NU7	OTTHUMG00000170353	ENST00000266736.2:c.295G>A	12.37:g.96348739G>A	ENSP00000266736:p.Glu99Lys					AMDHD1_uc009zth.2_Intron	p.E99K	NM_152435	NP_689648	Q96NU7	HUTI_HUMAN			2	401	+			99					A8K463|Q68CI8	Missense_Mutation	SNP	ENST00000266736.2	37	c.295G>A	CCDS9057.1	.	.	.	.	.	.	.	.	.	.	G	36	5.609713	0.96637	.	.	ENSG00000139344	ENST00000266736	T	0.40225	1.04	5.91	5.91	0.95273	Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	T	0.79747	0.4499	H	0.98256	4.185	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.86588	0.1858	10	0.87932	D	0	-1.5331	20.2896	0.98541	0.0:0.0:1.0:0.0	.	99	Q96NU7	HUTI_HUMAN	K	99	ENSP00000266736:E99K	ENSP00000266736:E99K	E	+	1	0	AMDHD1	94872870	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.167000	0.94773	2.794000	0.96219	0.655000	0.94253	GAA		0.358	AMDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408640.1	NM_152435	
GLT8D2	83468	broad.mit.edu	37	12	104390580	104390580	+	Missense_Mutation	SNP	G	G	A	rs373952967		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr12:104390580G>A	ENST00000360814.4	-	8	938	c.533C>T	c.(532-534)gCg>gTg	p.A178V	GLT8D2_ENST00000548660.1_Missense_Mutation_p.A178V|GLT8D2_ENST00000546436.1_Missense_Mutation_p.A178V	NM_031302.3	NP_112592.1	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2	178						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			kidney(3)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	16						GAAAGCCGCCGCGTGGCCCAG	0.483																																						uc001tkh.1																			0				kidney(3)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	16						c.(532-534)gCg>gTg		Homo sapiens glycosyltransferase 8 domain containing 2 (GLT8D2), mRNA.		G	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	100.0	103.0	102.0		533	5.1	0.4	12		102	0,8600		0,0,4300	no	missense	GLT8D2	NM_031302.3	64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	178/350	104390580	1,13005	2203	4300	6503	SO:0001583	missense	83468					integral to membrane	transferase activity, transferring glycosyl groups	g.chr12:104390580G>A	BC022343	CCDS9096.1	12q23.3	2013-02-22			ENSG00000120820	ENSG00000120820		"""Glycosyltransferase family 8 domain containing"""	24890	protein-coding gene	gene with protein product							Standard	NM_031302		Approved	FLJ31494	uc001tkh.1	Q9H1C3	OTTHUMG00000170120	ENST00000360814.4:c.533C>T	12.37:g.104390580G>A	ENSP00000354053:p.Ala178Val					GLT8D2_uc001tki.1_Missense_Mutation_p.A178V	p.A178V	NM_031302	NP_112592	Q9H1C3	GL8D2_HUMAN			7	1090	-			178					Q96KA2	Missense_Mutation	SNP	ENST00000360814.4	37	c.533C>T	CCDS9096.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.371150	0.42003	2.27E-4	0.0	ENSG00000120820	ENST00000360814;ENST00000546436;ENST00000548660	T;T;T	0.36699	1.24;1.24;1.24	5.13	5.13	0.70059	.	0.052669	0.85682	D	0.000000	T	0.18045	0.0433	N	0.20483	0.58	0.80722	D	1	P	0.52692	0.955	B	0.38327	0.271	T	0.13980	-1.0489	10	0.02654	T	1	.	12.0178	0.53324	0.0791:0.0:0.9209:0.0	.	178	Q9H1C3	GL8D2_HUMAN	V	178	ENSP00000354053:A178V;ENSP00000449750:A178V;ENSP00000447450:A178V	ENSP00000354053:A178V	A	-	2	0	GLT8D2	102914710	1.000000	0.71417	0.428000	0.26697	0.778000	0.44026	7.962000	0.87912	2.385000	0.81259	0.563000	0.77884	GCG		0.483	GLT8D2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407371.1	NM_031302	
RFX4	5992	broad.mit.edu	37	12	107126727	107126727	+	Silent	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr12:107126727G>A	ENST00000392842.1	+	15	1911	c.1497G>A	c.(1495-1497)ttG>ttA	p.L499L	RFX4_ENST00000357881.4_Silent_p.L508L|RFX4_ENST00000229387.5_Silent_p.L405L|RP11-482D24.3_ENST00000552415.1_RNA|RP11-144F15.1_ENST00000551505.1_Intron	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	499					cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						AGATCATCTTGACAGAGGCTG	0.458																																						uc001tlt.3																			0				NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						c.(1522-1524)ttG>ttA		Homo sapiens regulatory factor X, 4 (influences HLA class II expression) (RFX4), transcript variant 4, mRNA.							132.0	129.0	130.0					12																	107126727		2203	4300	6503	SO:0001819	synonymous_variant	5992				transcription, DNA-dependent	nucleus	DNA binding	g.chr12:107126727G>A	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.1497G>A	12.37:g.107126727G>A						LOC100287944_uc021rdg.1_Intron|RFX4_uc001tlr.3_Silent_p.L499L|RFX4_uc001tls.3_Silent_p.L508L|RFX4_uc001tlv.3_Silent_p.L405L	p.L508L	NM_001206691	NP_001193620	Q33E94	RFX4_HUMAN			14	1664	+			499					A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	37	c.1524G>A	CCDS9106.1																																																																																				0.458	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491	
MMP17	4326	broad.mit.edu	37	12	132322758	132322758	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr12:132322758G>A	ENST00000360564.1	+	2	280	c.178G>A	c.(178-180)Ggt>Agt	p.G60S	MMP17_ENST00000535291.1_5'UTR	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	60					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	AAGCAGGTTCGGTTACCTGCC	0.647																																						uc001ujc.1																			0				endometrium(1)|large_intestine(3)|lung(1)	5						c.(178-180)Ggt>Agt		Homo sapiens matrix metallopeptidase 17 (membrane-inserted) (MMP17), mRNA.							24.0	27.0	26.0					12																	132322758		2202	4298	6500	SO:0001583	missense	4326				proteolysis	anchored to membrane|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding	g.chr12:132322758G>A	X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"""matrix metalloproteinase 17 (membrane-inserted)"""			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.178G>A	12.37:g.132322758G>A	ENSP00000353767:p.Gly60Ser					MMP17_uc001ujd.1_5'UTR	p.G60S	NM_016155	NP_057239	Q9ULZ9	MMP17_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	1	277	+	all_neural(191;0.0982)|Medulloblastoma(191;0.163)		60					Q14850	Missense_Mutation	SNP	ENST00000360564.1	37	c.178G>A	CCDS31927.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.037755	0.93630	.	.	ENSG00000198598	ENST00000360564	T	0.59083	0.29	4.78	4.78	0.61160	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84951	0.5586	H	0.97516	4.02	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90855	0.4734	10	0.87932	D	0	.	18.1642	0.89719	0.0:0.0:1.0:0.0	.	60	Q9ULZ9	MMP17_HUMAN	S	60	ENSP00000353767:G60S	ENSP00000353767:G60S	G	+	1	0	MMP17	130888711	1.000000	0.71417	0.986000	0.45419	0.754000	0.42855	9.580000	0.98207	2.367000	0.80283	0.561000	0.74099	GGT		0.647	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155	
TMTC4	84899	broad.mit.edu	37	13	101315357	101315357	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr13:101315357G>A	ENST00000376234.3	-	4	545	c.356C>T	c.(355-357)tCt>tTt	p.S119F	TMTC4_ENST00000328767.5_Intron|TMTC4_ENST00000342624.5_Missense_Mutation_p.S138F	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	119						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CATGAGGACAGAGATGCCACT	0.602																																						uc001vot.3																			0				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						c.(412-414)tCt>tTt		Homo sapiens transmembrane and tetratricopeptide repeat containing 4 (TMTC4), transcript variant 1, mRNA.							79.0	85.0	83.0					13																	101315357		2142	4245	6387	SO:0001583	missense	84899					integral to membrane	binding	g.chr13:101315357G>A		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.356C>T	13.37:g.101315357G>A	ENSP00000365408:p.Ser119Phe					TMTC4_uc001vou.3_Missense_Mutation_p.S119F|TMTC4_uc010tja.2_Intron	p.S138F	NM_032813	NP_001073137	Q5T4D3	TMTC4_HUMAN			4	726	-	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)		119					A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Missense_Mutation	SNP	ENST00000376234.3	37	c.413C>T	CCDS41904.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.142615	0.77888	.	.	ENSG00000125247	ENST00000376234;ENST00000342624	D;D	0.95238	-3.65;-3.65	4.91	4.05	0.47172	.	0.050842	0.85682	D	0.000000	D	0.94571	0.8251	M	0.69358	2.11	0.80722	D	1	P;B	0.36944	0.574;0.051	B;B	0.43728	0.429;0.171	D	0.94672	0.7857	10	0.72032	D	0.01	.	15.3371	0.74266	0.0:0.1402:0.8598:0.0	.	119;138	Q5T4D3;Q5T4D3-3	TMTC4_HUMAN;.	F	119;138	ENSP00000365408:S119F;ENSP00000343871:S138F	ENSP00000343871:S138F	S	-	2	0	TMTC4	100113358	1.000000	0.71417	0.621000	0.29145	0.839000	0.47603	6.185000	0.72013	1.289000	0.44618	0.561000	0.74099	TCT		0.602	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
SYT16	83851	broad.mit.edu	37	14	62547795	62547795	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr14:62547795G>A	ENST00000430451.2	+	4	1434	c.1237G>A	c.(1237-1239)Gtc>Atc	p.V413I	RP11-355I22.5_ENST00000553990.1_lincRNA	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	413	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		GCCCAACCCCGTCTTCAGGGA	0.582																																						uc001xfu.1																			0				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35						c.(1237-1239)Gtc>Atc		Homo sapiens synaptotagmin XVI (SYT16), mRNA.							39.0	43.0	41.0					14																	62547795		2150	4262	6412	SO:0001583	missense	83851							g.chr14:62547795G>A	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"""Synaptotagmins"""	23142	protein-coding gene	gene with protein product	"""synaptotagmin XIV-related"", "" chr14 synaptotagmin"""	610950	"""synaptotagmin XIV-like"""	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.1237G>A	14.37:g.62547795G>A	ENSP00000394700:p.Val413Ile					SYT16_uc010tsd.1_3'UTR|SYT16_uc010tse.1_5'UTR	p.V413I	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)	3	1434	+			413			C2 1.		B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	37	c.1237G>A	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.558571	0.27827	.	.	ENSG00000139973	ENST00000430451	T	0.71698	-0.59	5.27	-1.55	0.08558	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.513822	0.21864	N	0.068000	T	0.60637	0.2284	L	0.56124	1.755	0.42947	D	0.994361	B	0.15930	0.015	B	0.13407	0.009	T	0.51411	-0.8709	10	0.25751	T	0.34	-30.5872	12.5233	0.56072	0.4687:0.0:0.5313:0.0	.	413	Q17RD7	SYT16_HUMAN	I	413	ENSP00000394700:V413I	ENSP00000394700:V413I	V	+	1	0	SYT16	61617548	0.000000	0.05858	0.128000	0.21923	0.947000	0.59692	-1.244000	0.02902	-0.181000	0.10619	-0.119000	0.15052	GTC		0.582	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914	
RTL1	388015	broad.mit.edu	37	14	101349286	101349286	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr14:101349286C>T	ENST00000534062.1	-	1	1898	c.1840G>A	c.(1840-1842)Gcg>Acg	p.A614T	MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	614					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						TCCCAAGGCGCGGTGGAGGGA	0.552																																						uc010txj.1																			0				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						c.(1840-1842)Gcg>Acg		Homo sapiens retrotransposon-like 1 (RTL1), mRNA.							46.0	41.0	42.0					14																	101349286		1568	3582	5150	SO:0001583	missense	388015							g.chr14:101349286C>T		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.1840G>A	14.37:g.101349286C>T	ENSP00000435342:p.Ala614Thr					MIR127_uc001yig.3_5'Flank|MIR432_uc021sce.1_5'Flank|MIR136_uc010txk.1_5'Flank	p.A614T	NM_001134888	NP_001128360	E9PKS8	E9PKS8_HUMAN			0	1899	-			614					E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	37	c.1840G>A	CCDS53910.1	.	.	.	.	.	.	.	.	.	.	C	10.63	1.404047	0.25291	.	.	ENSG00000254656	ENST00000534062	T	0.23552	1.9	3.54	0.523	0.17060	.	0.641577	0.12040	N	0.505139	T	0.18551	0.0445	L	0.46157	1.445	0.09310	N	1	B	0.25955	0.138	B	0.17098	0.017	T	0.24835	-1.0149	10	0.72032	D	0.01	.	3.5938	0.07998	0.1698:0.5647:0.1652:0.1002	.	614	E9PKS8	.	T	614	ENSP00000435342:A614T	ENSP00000435342:A614T	A	-	1	0	RTL1	100419039	0.817000	0.29147	0.003000	0.11579	0.828000	0.46876	0.897000	0.28390	0.108000	0.17862	0.467000	0.42956	GCG		0.552	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
CKMT1A	548596	broad.mit.edu	37	15	43991229	43991229	+	Missense_Mutation	SNP	G	G	A	rs556793318		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr15:43991229G>A	ENST00000413453.2	+	9	1720	c.1196G>A	c.(1195-1197)cGt>cAt	p.R399H	STRC_ENST00000541030.1_Intron|CKMT1A_ENST00000434505.1_Missense_Mutation_p.R399H			P12532	KCRU_HUMAN	creatine kinase, mitochondrial 1A	399	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			lung(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)	Creatine(DB00148)	TGTGAACGGCGTCTGGAGAGA	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		19701	0.0		0.0	False		,,,				2504	0.001					uc001zsn.3																			0				lung(4)	4						c.(1195-1197)cGt>cAt		Homo sapiens creatine kinase, mitochondrial 1A (CKMT1A), nuclear gene encoding mitochondrial protein, mRNA.	Creatine(DB00148)						172.0	154.0	160.0					15																	43991229		2198	4294	6492	SO:0001583	missense	548596				creatine metabolic process	mitochondrial inner membrane	ATP binding|creatine kinase activity	g.chr15:43991229G>A	BC001926, BC006467	CCDS32217.1	15q15	2005-08-09			ENSG00000223572	ENSG00000223572	2.7.3.2		31736	protein-coding gene	gene with protein product		613415	"""creatine kinase, mitochondrial 1 (ubiquitous)"""	CKMT1			Standard	XM_005254498		Approved		uc001zsn.3	P12532	OTTHUMG00000059898	ENST00000413453.2:c.1196G>A	15.37:g.43991229G>A	ENSP00000406577:p.Arg399His					CKMT1A_uc010uea.2_Missense_Mutation_p.R430H	p.R399H	NM_001015001	NP_066270	P12532	KCRU_HUMAN		GBM - Glioblastoma multiforme(94;3.56e-07)	9	1588	+		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)	399			Phosphagen kinase C-terminal.		B4DIT8|B7ZA09|Q0VAM3|Q32NF6|Q53FC4	Missense_Mutation	SNP	ENST00000413453.2	37	c.1196G>A	CCDS32217.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.981894	0.34942	.	.	ENSG00000223572	ENST00000424065;ENST00000434505;ENST00000413453	T;T	0.11930	2.73;2.73	3.71	2.78	0.32641	.	0.156324	0.53938	D	0.000043	T	0.25382	0.0617	.	.	.	0.42354	D	0.992385	.	.	.	.	.	.	T	0.01305	-1.1390	7	0.72032	D	0.01	1.9794	9.9787	0.41800	0.103:0.0:0.897:0.0	.	.	.	.	H	430;399;399	ENSP00000413165:R399H;ENSP00000406577:R399H	ENSP00000406577:R399H	R	+	2	0	CKMT1A	41778521	1.000000	0.71417	0.992000	0.48379	0.990000	0.78478	3.443000	0.52907	0.520000	0.28426	0.393000	0.25936	CGT		0.493	CKMT1A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133136.1		
TMOD3	29766	broad.mit.edu	37	15	52155124	52155124	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr15:52155124C>A	ENST00000308580.7	+	2	324	c.43C>A	c.(43-45)Ctt>Att	p.L15I	TMOD3_ENST00000544199.1_Missense_Mutation_p.L15I	NM_014547.4	NP_055362.1	Q9NYL9	TMOD3_HUMAN	tropomodulin 3 (ubiquitous)	15						striated muscle thin filament (GO:0005865)	tropomyosin binding (GO:0005523)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|stomach(1)	14				all cancers(107;0.00194)		GTACAAAGACCTTGATGAAGA	0.443																																					Colon(122;1837 2251 18387 22826)	uc002abn.3																			0		p.D14H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|stomach(1)	14						c.(43-45)Ctt>Att		Homo sapiens tropomodulin 3 (ubiquitous) (TMOD3), mRNA.							121.0	108.0	112.0					15																	52155124		2195	4293	6488	SO:0001583	missense	29766					cytoplasm|cytoskeleton	actin binding|tropomyosin binding	g.chr15:52155124C>A	AF177171	CCDS10145.1	15q21.1-q21.2	2008-05-14			ENSG00000138594	ENSG00000138594			11873	protein-coding gene	gene with protein product		605112				10662549	Standard	NM_014547		Approved	UTMOD	uc002abn.3	Q9NYL9	OTTHUMG00000131803	ENST00000308580.7:c.43C>A	15.37:g.52155124C>A	ENSP00000308753:p.Leu15Ile						p.L15I	NM_014547	NP_055362	Q9NYL9	TMOD3_HUMAN		all cancers(107;0.00194)	1	326	+			15					B2R6G7|Q9NT43|Q9NZR0	Missense_Mutation	SNP	ENST00000308580.7	37	c.43C>A	CCDS10145.1	.	.	.	.	.	.	.	.	.	.	C	5.823	0.336163	0.11013	.	.	ENSG00000138594	ENST00000308580;ENST00000544199	T;T	0.27402	1.67;1.67	5.38	4.46	0.54185	.	0.138995	0.49305	D	0.000147	T	0.12944	0.0314	N	0.01640	-0.785	0.51767	D	0.999939	B	0.16396	0.017	B	0.29785	0.107	T	0.17653	-1.0362	10	0.02654	T	1	-4.9724	16.4675	0.84087	0.0:0.8687:0.1313:0.0	.	15	Q9NYL9	TMOD3_HUMAN	I	15	ENSP00000308753:L15I;ENSP00000438909:L15I	ENSP00000308753:L15I	L	+	1	0	TMOD3	49942416	0.196000	0.23350	1.000000	0.80357	0.997000	0.91878	0.390000	0.20768	1.397000	0.46682	0.655000	0.94253	CTT		0.443	TMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254740.3		
FRG2KP	102724018	broad.mit.edu	37	16	31580642	31580642	+	RNA	SNP	C	C	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr16:31580642C>A	ENST00000565692.1	-	0	0																											CTGCGGGGGCCCCGTCCCCAC	0.741																																						uc010vfr.1																			0											c.(175-177)ggG>ggT		Homo sapiens cold shock domain protein A pseudogene 1 (CSDAP1), non-coding RNA.																																						440359							g.chr16:31580642C>A																													16.37:g.31580642C>A							p.G59G							0	204	-									Silent	SNP	ENST00000565692.1	37	c.177G>T																																																																																					0.741	CTD-2014E2.5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000432903.1		
GLOD4	51031	broad.mit.edu	37	17	685869	685880	+	5'Flank	DEL	CCAGCACCTGGG	CCAGCACCTGGG	-	rs200285894		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr17:685869_685880delCCAGCACCTGGG	ENST00000301328.5	-	0	0				GLOD4_ENST00000536578.1_5'Flank|RNMTL1_ENST00000304478.4_In_Frame_Del_p.84_88PSTWE>Q|GLOD4_ENST00000301329.6_5'Flank			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4							extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TCCCGCGCTCCCAGCACCTGGGAAGAGTCTGG	0.608																																						uc002frw.3																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10						c.(250-264)cccagcacctgggaa>caa		Homo sapiens RNA methyltransferase like 1 (RNMTL1), mRNA.																																				SO:0001631	upstream_gene_variant	55178				RNA processing		protein binding|RNA binding|RNA methyltransferase activity	g.chr17:685869_685880delCCAGCACCTGGG	AF177342	CCDS32520.1	17p13.3	2008-02-05	2007-03-14	2007-03-14		ENSG00000167699			14111	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 25"""	C17orf25		11642406, 12528892	Standard	NM_016080		Approved	CGI-150, HC71	uc002fru.3	Q9HC38			17.37:g.685869_685880delCCAGCACCTGGG	Exception_encountered					GLOD4_uc002fru.3_5'Flank|GLOD4_uc010vqc.2_5'Flank|GLOD4_uc002frv.3_5'Flank	p.84_88PSTWE>Q	NM_018146	NP_060616	Q9HC36	RMTL1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (25;0.0219)	0	357_368	+			84					D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	In_Frame_Del	DEL	ENST00000301328.5	37	c.251_262delCCAGCACCTGGG																																																																																					0.608	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080	
OR1A1	8383	broad.mit.edu	37	17	3119408	3119408	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr17:3119408G>A	ENST00000304094.1	+	1	494	c.494G>A	c.(493-495)aGt>aAt	p.S165N		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	165						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						CTCACAGCTAGTCTGTCCTTC	0.483																																						uc010vrc.2																			0		p.A164D(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						c.(493-495)aGt>aAt		Homo sapiens olfactory receptor, family 1, subfamily A, member 1 (OR1A1), mRNA.							157.0	133.0	141.0					17																	3119408		2203	4300	6503	SO:0001583	missense	8383				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr17:3119408G>A	AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"""GPCR / Class A : Olfactory receptors"""	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.494G>A	17.37:g.3119408G>A	ENSP00000305207:p.Ser165Asn						p.S165N	NM_014565	NP_055380	Q9P1Q5	OR1A1_HUMAN			0	494	+			165					A5D914|Q6IFM1|Q6NTA9|Q96R87	Missense_Mutation	SNP	ENST00000304094.1	37	c.494G>A	CCDS11022.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.615320	0.28801	.	.	ENSG00000172146	ENST00000304094	T	0.00220	8.52	4.96	1.57	0.23409	GPCR, rhodopsin-like superfamily (1);	1.177080	0.05916	N	0.632579	T	0.00144	0.0004	N	0.16233	0.39	0.09310	N	1	B	0.26147	0.143	B	0.30943	0.122	T	0.25710	-1.0124	10	0.87932	D	0	.	4.4208	0.11479	0.3131:0.0:0.5261:0.1607	.	165	Q9P1Q5	OR1A1_HUMAN	N	165	ENSP00000305207:S165N	ENSP00000305207:S165N	S	+	2	0	OR1A1	3066158	0.000000	0.05858	0.051000	0.19133	0.975000	0.68041	-0.685000	0.05167	0.618000	0.30179	0.436000	0.28706	AGT		0.483	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565	
MYOCD	93649	broad.mit.edu	37	17	12649324	12649324	+	Missense_Mutation	SNP	T	T	G			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr17:12649324T>G	ENST00000343344.4	+	9	1060	c.1060T>G	c.(1060-1062)Tct>Gct	p.S354A	MYOCD_ENST00000425538.1_Missense_Mutation_p.S354A|MYOCD_ENST00000395988.1_3'UTR|AC005358.1_ENST00000609971.1_Missense_Mutation_p.S258A			Q8IZQ8	MYCD_HUMAN	myocardin	354					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		AAACAGTTTTTCTGGACAAAC	0.408																																						uc002gno.2																			0				breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70						c.(1060-1062)Tct>Gct		Homo sapiens myocardin (MYOCD), transcript variant 1, mRNA.							142.0	136.0	138.0					17																	12649324		2203	4300	6503	SO:0001583	missense	93649				cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation	nucleus	nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding	g.chr17:12649324T>G	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.1060T>G	17.37:g.12649324T>G	ENSP00000341835:p.Ser354Ala					MYOCD_uc002gnn.2_Missense_Mutation_p.S354A|MYOCD_uc002gnp.1_Missense_Mutation_p.S258A|MYOCD_uc002gnq.2_Missense_Mutation_p.S73A	p.S354A	NM_001146312	NP_001139784	Q8IZQ8	MYCD_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)	8	1359	+			354					Q5UBU5|Q8N7Q1	Missense_Mutation	SNP	ENST00000343344.4	37	c.1060T>G	CCDS11163.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.056695	0.36277	.	.	ENSG00000141052	ENST00000395982;ENST00000425538;ENST00000343344;ENST00000395988;ENST00000443061	T;T	0.44083	0.93;0.93	5.71	3.39	0.38822	.	0.219324	0.49305	D	0.000147	T	0.26195	0.0639	L	0.29908	0.895	0.39143	D	0.962087	B;B;B;B	0.21606	0.058;0.02;0.056;0.033	B;B;B;B	0.20184	0.008;0.009;0.028;0.012	T	0.07829	-1.0752	10	0.17369	T	0.5	-13.3387	7.3671	0.26779	0.0:0.0765:0.1445:0.7789	.	73;258;354;354	E9PEP9;Q8IZQ8-2;Q8IZQ8-3;Q8IZQ8	.;.;.;MYCD_HUMAN	A	73;354;354;258;59	ENSP00000341835:S354A;ENSP00000400148:S59A	ENSP00000341835:S354A	S	+	1	0	MYOCD	12590049	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.822000	0.39052	1.009000	0.39289	0.459000	0.35465	TCT		0.408	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604	
NCOR1	9611	broad.mit.edu	37	17	15967451	15967451	+	Missense_Mutation	SNP	G	G	A	rs373216507		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr17:15967451G>A	ENST00000268712.3	-	35	5409	c.5152C>T	c.(5152-5154)Cgg>Tgg	p.R1718W	NCOR1_ENST00000395857.3_Missense_Mutation_p.R302W|NCOR1_ENST00000395851.1_Missense_Mutation_p.R1734W	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1718	Interaction with C1D. {ECO:0000250}.|Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		tcccgctcccgttcccgttcc	0.537																																						uc002gpo.3																			0				NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107						c.(5152-5154)Cgg>Tgg		Homo sapiens nuclear receptor corepressor 1 (NCOR1), transcript variant 1, mRNA.		G	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	115.0	97.0	103.0		5200,5152	-5.5	0.0	17		103	0,8600		0,0,4300	no	missense,missense	NCOR1	NM_001190440.1,NM_006311.3	101,101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	1734/2338,1718/2441	15967451	1,13005	2203	4300	6503	SO:0001583	missense	9611				cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding	g.chr17:15967451G>A	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.5152C>T	17.37:g.15967451G>A	ENSP00000268712:p.Arg1718Trp					NCOR1_uc002gpn.3_Missense_Mutation_p.R1734W|NCOR1_uc002gpm.3_Missense_Mutation_p.R238W|NCOR1_uc010vwb.2_Missense_Mutation_p.R302W|NCOR1_uc010coy.3_Missense_Mutation_p.R626W|NCOR1_uc010vwc.2_Missense_Mutation_p.R528W	p.R1718W	NM_006311	NP_006302	O75376	NCOR1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)	34	5421	-			1718			Interaction with C1D (By similarity).|Interaction with ETO.		B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	c.5152C>T	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.946103	0.73672	2.27E-4	0.0	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	T;T;T	0.55588	2.63;2.63;0.51	5.24	-5.5	0.02576	.	0.299111	0.30920	N	0.008604	T	0.57431	0.2053	L	0.39898	1.24	0.09310	N	0.999999	D;D;D;D;D	0.89917	0.997;1.0;1.0;0.998;0.999	P;D;D;P;D	0.74023	0.736;0.937;0.982;0.861;0.929	T	0.61505	-0.7049	10	0.87932	D	0	-4.6897	15.2426	0.73482	0.0:0.0:0.7205:0.2795	.	528;1622;1718;1734;238	B4DZ48;E7EVK1;O75376;O75376-2;Q86YY1	.;.;NCOR1_HUMAN;.;.	W	1718;1734;1622;302	ENSP00000268712:R1718W;ENSP00000379192:R1734W;ENSP00000379198:R302W	ENSP00000268712:R1718W	R	-	1	2	NCOR1	15908176	0.881000	0.30235	0.009000	0.14445	0.939000	0.58152	0.659000	0.24994	-0.863000	0.04084	0.655000	0.94253	CGG		0.537	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
KRT24	192666	broad.mit.edu	37	17	38859722	38859722	+	Frame_Shift_Del	DEL	C	C	-			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr17:38859722delC	ENST00000264651.2	-	1	280	c.224delG	c.(223-225)ggtfs	p.G76fs		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	76	Gly-rich.|Head.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				CCCAAAACCACCCCCTACTGA	0.612																																					GBM(61;380 1051 14702 23642 31441)	uc002hvd.3																			0				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						c.(223-225)ggtfs		Homo sapiens keratin 24 (KRT24), mRNA.							46.0	60.0	55.0					17																	38859722		2203	4300	6503	SO:0001589	frameshift_variant	192666					cytoplasm|intermediate filament	structural molecule activity	g.chr17:38859722delC		CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.224delG	17.37:g.38859722delC	ENSP00000264651:p.Gly76fs						p.G75fs	NM_019016	NP_061889	Q2M2I5	K1C24_HUMAN			0	281	-		Breast(137;0.00526)	75			Gly-rich.|Head.		Q9NXG7	Frame_Shift_Del	DEL	ENST00000264651.2	37	c.224delG	CCDS11372.1																																																																																				0.612	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016	
ABI3	51225	broad.mit.edu	37	17	47297600	47297600	+	Silent	SNP	C	C	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr17:47297600C>A	ENST00000225941.1	+	6	1212	c.714C>A	c.(712-714)ccC>ccA	p.P238P	ABI3_ENST00000419580.2_Silent_p.P232P	NM_001135186.1|NM_016428.2	NP_001128658.1|NP_057512	Q9P2A4	ABI3_HUMAN	ABI family, member 3	238	Pro-rich.				cellular component movement (GO:0006928)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	12			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)			CACCTCTCCCCAGCTCCTTGG	0.701										HNSCC(55;0.14)																												uc002iop.1																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	12						c.(712-714)ccC>ccA		Homo sapiens ABI family, member 3 (ABI3), transcript variant 1, mRNA.							40.0	36.0	37.0					17																	47297600		2202	4300	6502	SO:0001819	synonymous_variant	51225				cellular component movement|regulation of cell migration	cytoplasm|lamellipodium	protein binding	g.chr17:47297600C>A	AB037886	CCDS11546.1, CCDS45725.1	17q21.3	2011-03-04	2008-09-12		ENSG00000108798	ENSG00000108798			29859	protein-coding gene	gene with protein product		606363				10978530, 11956071	Standard	NM_001135186		Approved	NESH, SSH3BP3	uc002iop.1	Q9P2A4	OTTHUMG00000161306	ENST00000225941.1:c.714C>A	17.37:g.47297600C>A		HNSCC(55;0.14)				ABI3_uc002ioq.1_Silent_p.P232P	p.P238P	NM_016428	NP_057512	Q9P2A4	ABI3_HUMAN	Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)		5	1212	+			238			Pro-rich.		C9IZN8|Q9H0P6	Silent	SNP	ENST00000225941.1	37	c.714C>A	CCDS11546.1																																																																																				0.701	ABI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364475.1	NM_016428	
MRPS7	51081	broad.mit.edu	37	17	73258761	73258761	+	Silent	SNP	A	A	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr17:73258761A>T	ENST00000245539.6	+	2	494	c.267A>T	c.(265-267)ccA>ccT	p.P89P	MRPS7_ENST00000579761.1_Silent_p.P89P|GGA3_ENST00000351904.7_5'Flank|GGA3_ENST00000579743.1_5'Flank|GGA3_ENST00000582717.1_5'Flank|GGA3_ENST00000582486.1_5'Flank|MRPS7_ENST00000579002.1_Silent_p.P118P|GGA3_ENST00000578348.1_5'Flank|GGA3_ENST00000537686.1_5'Flank|GGA3_ENST00000245541.6_5'Flank|GGA3_ENST00000538886.1_5'Flank	NM_015971.3	NP_057055.2	Q9Y2R9	RT07_HUMAN	mitochondrial ribosomal protein S7	89					translation (GO:0006412)	cytosolic small ribosomal subunit (GO:0022627)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)	6	all_cancers(13;1.25e-07)|all_epithelial(9;2.63e-08)|Breast(9;1.06e-07)		all cancers(21;3.02e-07)|Epithelial(20;2.92e-06)			TTGAAGACCCAGTCATCAGGT	0.473																																						uc002jnm.4																			0				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)	6						c.(265-267)ccA>ccT		Homo sapiens mitochondrial ribosomal protein S7 (MRPS7), nuclear gene encoding mitochondrial protein, mRNA.							110.0	114.0	113.0					17																	73258761		2203	4300	6503	SO:0001819	synonymous_variant	51081				translation	cytosolic small ribosomal subunit|mitochondrion	protein binding|RNA binding|structural constituent of ribosome	g.chr17:73258761A>T	AB051348	CCDS11718.1	17q25.1	2012-09-13				ENSG00000125445		"""Mitochondrial ribosomal proteins / small subunits"""	14499	protein-coding gene	gene with protein product		611974					Standard	NM_015971		Approved	MRP-S, RP-S7, RPMS7	uc002jnm.4	Q9Y2R9		ENST00000245539.6:c.267A>T	17.37:g.73258761A>T						GGA3_uc002jnk.2_5'Flank|GGA3_uc002jni.2_5'Flank|GGA3_uc002jnj.2_5'Flank|GGA3_uc010wry.2_5'Flank|GGA3_uc010wrw.2_5'Flank|GGA3_uc010wrx.2_5'Flank|GGA3_uc010wrz.2_5'Flank	p.P89P	NM_015971	NP_057055	Q9Y2R9	RT07_HUMAN	all cancers(21;3.02e-07)|Epithelial(20;2.92e-06)		1	500	+	all_cancers(13;1.25e-07)|all_epithelial(9;2.63e-08)|Breast(9;1.06e-07)		89					B2R9N5|Q53GD6	Silent	SNP	ENST00000245539.6	37	c.267A>T	CCDS11718.1																																																																																				0.473	MRPS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446666.1	NM_015971	
SETBP1	26040	broad.mit.edu	37	18	42530935	42530935	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr18:42530935C>T	ENST00000282030.5	+	4	1926	c.1630C>T	c.(1630-1632)Cga>Tga	p.R544*		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	544						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		CACCATGCTTCGAGAGGCAGT	0.507									Schinzel-Giedion syndrome																													uc010dni.3																			0				NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104						c.(1630-1632)Cga>Tga		Homo sapiens SET binding protein 1 (SETBP1), transcript variant 1, mRNA.							160.0	159.0	159.0					18																	42530935		2203	4300	6503	SO:0001587	stop_gained	26040	Schinzel-Giedion syndrome	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome		nucleus	DNA binding	g.chr18:42530935C>T	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.1630C>T	18.37:g.42530935C>T	ENSP00000282030:p.Arg544*						p.R544*	NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN		Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)	3	1926	+			544					A6H8W5|Q6P6C3|Q9UEF3	Nonsense_Mutation	SNP	ENST00000282030.5	37	c.1630C>T	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	C	39	7.567053	0.98361	.	.	ENSG00000152217	ENST00000282030	.	.	.	6.08	6.08	0.98989	.	0.183008	0.41001	D	0.000964	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.844	0.92196	0.0:1.0:0.0:0.0	.	.	.	.	X	544	.	ENSP00000282030:R544X	R	+	1	2	SETBP1	40784933	0.998000	0.40836	0.998000	0.56505	0.921000	0.55340	3.994000	0.56994	2.894000	0.99253	0.655000	0.94253	CGA		0.507	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
MUC16	94025	broad.mit.edu	37	19	8976821	8976821	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr19:8976821G>A	ENST00000397910.4	-	73	42448	c.42245C>T	c.(42244-42246)aCc>aTc	p.T14082I	MUC16_ENST00000596956.1_5'UTR|MUC16_ENST00000380951.5_Missense_Mutation_p.T723I	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	14112				Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATTGGAGATGGTGAAGTTGAG	0.567																																						uc002mkp.3																			0				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						c.(42244-42246)aCc>aTc		Homo sapiens mucin 16, cell surface associated (MUC16), mRNA.							116.0	118.0	117.0					19																	8976821		2007	4159	6166	SO:0001583	missense	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:8976821G>A	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.42245C>T	19.37:g.8976821G>A	ENSP00000381008:p.Thr14082Ile					MUC16_uc010dwi.3_Non-coding_Transcript|MUC16_uc010dwj.3_Missense_Mutation_p.T882I|MUC16_uc021uog.1_Intron	p.T14082I	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN			72	42449	-			14112	Missing (in Ref. 3; AAK74120).				Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	c.42245C>T	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	14.70|14.70	2.614110|2.614110	0.46631|0.46631	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000542240|ENST00000397910;ENST00000380951	.|T;T	.|0.51071	.|0.72;0.72	4.37|4.37	4.37|4.37	0.52481|0.52481	.|SEA (1);	.|0.000000	.|0.36444	.|N	.|0.002582	T|T	0.71617|0.71617	0.3361|0.3361	M|M	0.89287|0.89287	3.02|3.02	.|.	.|.	.|.	.|D;D	.|0.89917	.|1.0;0.99	.|D;D	.|0.91635	.|0.999;0.983	T|T	0.81516|0.81516	-0.0897|-0.0897	4|9	.|0.87932	.|D	.|0	.|.	12.6126|12.6126	0.56560|0.56560	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|21727;14082	.|Q8WXI7;B5ME49	.|MUC16_HUMAN;.	S|I	905|14082;723	.|ENSP00000381008:T14082I;ENSP00000370338:T723I	.|ENSP00000370338:T723I	P|T	-|-	1|2	0|0	MUC16|MUC16	8837821|8837821	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.281000|0.281000	0.26958|0.26958	5.290000|5.290000	0.65661|0.65661	2.430000|2.430000	0.82344|0.82344	0.457000|0.457000	0.33378|0.33378	CCA|ACC		0.567	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PODNL1	79883	broad.mit.edu	37	19	14046600	14046600	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr19:14046600G>A	ENST00000339560.5	-	5	722	c.449C>T	c.(448-450)gCg>gTg	p.A150V	PODNL1_ENST00000538371.2_Missense_Mutation_p.A148V|PODNL1_ENST00000254320.3_Missense_Mutation_p.A68V|PODNL1_ENST00000538517.2_Intron	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	150	Leu-rich.					proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			AGCCAGATCCGCGACACGGAG	0.667																																						uc002mxr.3																			0				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8						c.(448-450)gCg>gTg		Homo sapiens podocan-like 1 (PODNL1), transcript variant 1, mRNA.							26.0	29.0	28.0					19																	14046600		2203	4300	6503	SO:0001583	missense	79883					proteinaceous extracellular matrix		g.chr19:14046600G>A	AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05							26275	protein-coding gene	gene with protein product						12477932	Standard	NM_024825		Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000339560.5:c.449C>T	19.37:g.14046600G>A	ENSP00000345175:p.Ala150Val					PODNL1_uc010xni.2_Missense_Mutation_p.A68V|PODNL1_uc010xnj.2_Missense_Mutation_p.A148V|PODNL1_uc002mxs.3_Intron	p.A150V	NM_024825	NP_079101	Q6PEZ8	PONL1_HUMAN	OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)		4	723	-			150			Leu-rich.		B7Z564|Q9H5G9	Missense_Mutation	SNP	ENST00000339560.5	37	c.449C>T	CCDS12300.1	.	.	.	.	.	.	.	.	.	.	G	0.147	-1.096072	0.01843	.	.	ENSG00000132000	ENST00000538371;ENST00000339560;ENST00000254320	T;T;T	0.24538	1.95;5.64;1.85	4.97	2.83	0.33086	.	0.272209	0.25836	N	0.027983	T	0.12305	0.0299	N	0.16567	0.415	0.09310	N	1	P;B;P	0.44734	0.842;0.427;0.735	B;B;B	0.35931	0.214;0.065;0.184	T	0.11817	-1.0572	10	0.49607	T	0.09	.	7.0865	0.25259	0.283:0.0:0.717:0.0	.	148;68;150	F5H7F9;B7Z3M0;Q6PEZ8	.;.;PONL1_HUMAN	V	148;150;68	ENSP00000442553:A148V;ENSP00000345175:A150V;ENSP00000254320:A68V	ENSP00000254320:A68V	A	-	2	0	PODNL1	13907600	0.024000	0.19004	0.003000	0.11579	0.239000	0.25481	0.535000	0.23114	0.513000	0.28278	-0.354000	0.07668	GCG		0.667	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825	
NCAN	1463	broad.mit.edu	37	19	19351439	19351439	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr19:19351439G>A	ENST00000252575.6	+	12	3536	c.3437G>A	c.(3436-3438)gGc>gAc	p.G1146D	NCAN_ENST00000538881.1_Missense_Mutation_p.G597D	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	1146	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	ACGTGGATCGGCCTGAACGAC	0.632																																						uc002nlz.3																			0				breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64						c.(3436-3438)gGc>gAc		Homo sapiens neurocan (NCAN), mRNA.							152.0	107.0	122.0					19																	19351439		2203	4300	6503	SO:0001583	missense	1463				axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding	g.chr19:19351439G>A	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.3437G>A	19.37:g.19351439G>A	ENSP00000252575:p.Gly1146Asp					NCAN_uc002nma.3_5'UTR	p.G1146D	NM_004386	NP_004377	O14594	NCAN_HUMAN	Epithelial(12;0.00544)		11	3536	+			1146			C-type lectin.		Q9UPK6	Missense_Mutation	SNP	ENST00000252575.6	37	c.3437G>A	CCDS12397.1	.	.	.	.	.	.	.	.	.	.	g	23.5	4.422348	0.83559	.	.	ENSG00000130287	ENST00000539499;ENST00000252575;ENST00000538881	T;T	0.67345	-0.26;-0.26	3.98	3.98	0.46160	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.35555	N	0.003131	D	0.88496	0.6452	H	0.98802	4.335	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	D	0.92631	0.6116	10	0.87932	D	0	.	13.6121	0.62086	0.0:0.0:1.0:0.0	.	1146	O14594	NCAN_HUMAN	D	1160;1146;597	ENSP00000252575:G1146D;ENSP00000442202:G597D	ENSP00000252575:G1146D	G	+	2	0	NCAN	19212439	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	9.258000	0.95555	2.060000	0.61445	0.289000	0.19496	GGC		0.632	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386	
ZNF254	9534	broad.mit.edu	37	19	24310730	24310730	+	Missense_Mutation	SNP	C	C	G	rs144271497		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr19:24310730C>G	ENST00000357002.4	+	4	2043	c.1928C>G	c.(1927-1929)tCg>tGg	p.S643W	ZNF254_ENST00000342944.6_Missense_Mutation_p.S558W	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	643					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				AATCGGTCCTCGCACCTCACC	0.378																																						uc002nru.3																			0											c.(1927-1929)tCg>tGg		Homo sapiens zinc finger protein 254 (ZNF254), mRNA.							82.0	86.0	85.0					19																	24310730		2203	4295	6498	SO:0001583	missense	9534				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:24310730C>G	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"""Zinc fingers, C2H2-type"", ""-"""	13047	protein-coding gene	gene with protein product		604768	"""zinc finger protein 539"""	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.1928C>G	19.37:g.24310730C>G	ENSP00000349494:p.Ser643Trp					ZNF254_uc010xrk.2_Missense_Mutation_p.S558W	p.S643W	NM_203282	NP_975011	O75437	ZN254_HUMAN			3	2062	+		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)	643					A4QPC0|Q86XL7	Missense_Mutation	SNP	ENST00000357002.4	37	c.1928C>G	CCDS32983.1	.	.	.	.	.	.	.	.	.	.	C	1.918	-0.449151	0.04572	.	.	ENSG00000213096	ENST00000342944;ENST00000357002;ENST00000392281	T;T	0.63255	-0.03;3.27	0.427	-0.855	0.10700	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.74291	0.3697	M	0.90650	3.135	0.09310	N	1	D	0.61080	0.989	P	0.57425	0.82	T	0.64054	-0.6497	9	0.87932	D	0	.	5.2313	0.15424	0.0:0.731:0.0:0.269	.	643	O75437	ZN254_HUMAN	W	558;643;335	ENSP00000445527:S558W;ENSP00000349494:S643W	ENSP00000445527:S558W	S	+	2	0	ZNF254	24102570	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.326000	0.19646	-0.544000	0.06232	-0.763000	0.03452	TCG		0.378	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876	
SIGLEC10	89790	broad.mit.edu	37	19	51919181	51919181	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr19:51919181T>C	ENST00000339313.5	-	5	1111	c.995A>G	c.(994-996)cAg>cGg	p.Q332R	CTD-2616J11.2_ENST00000526996.1_RNA|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.Q249R|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.Q274R|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.Q332R|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.Q332R|SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.Q274R|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.Q284R			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	332	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		GGCTCGCTGCTGGGAGCCAAG	0.682																																						uc002pwo.3																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						c.(994-996)cAg>cGg		Homo sapiens sialic acid binding Ig-like lectin 10 (SIGLEC10), transcript variant 1, mRNA.							49.0	58.0	55.0					19																	51919181		2203	4299	6502	SO:0001583	missense	89790				cell adhesion	extracellular region|integral to membrane|plasma membrane	sugar binding	g.chr19:51919181T>C	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.995A>G	19.37:g.51919181T>C	ENSP00000345243:p.Gln332Arg					SIGLEC10_uc002pwp.3_Missense_Mutation_p.Q274R|SIGLEC10_uc021uyl.1_Missense_Mutation_p.Q249R|SIGLEC10_uc002pwq.3_Missense_Mutation_p.Q274R|SIGLEC10_uc010ycz.2_Missense_Mutation_p.Q284R|SIGLEC10_uc002pws.2_Intron|SIGLEC10_uc002pwr.3_Missense_Mutation_p.Q332R|SIGLEC10_uc010ycy.2_Intron|SIGLEC10_uc010eow.3_Missense_Mutation_p.Q144R|LOC100129083_uc021uym.1_Non-coding_Transcript	p.Q332R	NM_033130	NP_149121	Q96LC7	SIG10_HUMAN		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)	4	1217	-		all_neural(266;0.0199)	332			Ig-like C2-type 2.		A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	c.995A>G	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	11.11	1.541907	0.27563	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000441969;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;T;T;T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25;-0.25;-0.25;-0.25	4.37	-3.95	0.04118	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.505597	0.16564	N	0.208929	T	0.57636	0.2067	L	0.41961	1.31	0.09310	N	1	P;P;P;P;P;P	0.42456	0.624;0.78;0.739;0.739;0.753;0.624	B;P;P;P;B;B	0.51055	0.42;0.657;0.526;0.469;0.198;0.3	T	0.52586	-0.8556	10	0.31617	T	0.26	.	3.4014	0.07324	0.4209:0.2715:0.0:0.3077	.	284;332;332;274;274;332	C9JM10;B7ZL04;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;SIG10_HUMAN	R	332;249;332;274;274;284;332;146	ENSP00000342389:Q332R;ENSP00000396742:Q249R;ENSP00000348646:Q332R;ENSP00000408387:Q274R;ENSP00000389132:Q274R;ENSP00000414324:Q284R;ENSP00000345243:Q332R;ENSP00000435281:Q146R	ENSP00000345243:Q332R	Q	-	2	0	SIGLEC10	56610993	0.000000	0.05858	0.000000	0.03702	0.840000	0.47671	-1.653000	0.01986	-0.700000	0.05070	0.260000	0.18958	CAG		0.682	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
LILRB5	10990	broad.mit.edu	37	19	54759940	54759940	+	Silent	SNP	C	C	T	rs144716655	byFrequency	TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr19:54759940C>T	ENST00000316219.5	-	4	728	c.621G>A	c.(619-621)tcG>tcA	p.S207S	LILRB5_ENST00000450632.1_Silent_p.S198S|LILRB5_ENST00000449561.2_Silent_p.S207S|LILRB5_ENST00000345866.6_Intron	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	207	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CACTGGGGTTCGACCACACCT	0.522													.|||	3	0.000599042	0.0023	0.0	5008	,	,		17799	0.0		0.0	False		,,,				2504	0.0					uc010yer.1																			0				NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56						c.(592-594)tcG>tcA		Homo sapiens leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5 (LILRB5), transcript variant 1, mRNA.		C	,,	2,4404	4.2+/-10.8	0,2,2201	53.0	61.0	58.0		621,,621	-0.5	0.1	19	dbSNP_134	58	0,8600		0,0,4300	no	coding-synonymous,intron,coding-synonymous	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	,,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,,	207/592,,207/591	54759940	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	10990				cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity	g.chr19:54759940C>T	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.621G>A	19.37:g.54759940C>T						LILRB3_uc002qew.2_Intron|LILRB5_uc002qey.3_Silent_p.S207S|LILRB5_uc002qez.3_Intron|LILRB5_uc002qex.3_Silent_p.S207S|LILRB5_uc002qfa.1_Intron|LILRB5_uc010yes.1_Non-coding_Transcript	p.S198S			O75023	LIRB5_HUMAN		GBM - Glioblastoma multiforme(193;0.105)	3	705	-	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)		207			Ig-like C2-type 2.		Q8N760	Silent	SNP	ENST00000316219.5	37	c.594G>A	CCDS12885.1																																																																																				0.522	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
KIR3DL1	3811	broad.mit.edu	37	19	55325326	55325326	+	Intron	SNP	G	G	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr19:55325326G>T	ENST00000538269.1	+	2	61				KIR2DL4_ENST00000345540.5_Silent_p.V263V|KIR2DL4_ENST00000346587.4_Silent_p.V168V|KIR2DL4_ENST00000357494.4_Silent_p.V246V|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Silent_p.V318V|KIR3DL1_ENST00000358178.4_5'Flank|KIR3DL1_ENST00000391728.4_5'Flank|KIR2DL4_ENST00000396293.1_Silent_p.V151V|KIR2DL4_ENST00000463062.1_3'UTR|KIR2DL4_ENST00000359085.4_3'UTR|KIR3DL1_ENST00000326542.7_5'Flank			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		CTCAGGAGGTGACATACGCAC	0.473																																						uc010yfl.2																			0				breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	23						c.(952-954)gtG>gtT		Homo sapiens killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 4 (KIR2DL4), transcript variant 1, mRNA.							23.0	37.0	32.0					19																	55325326		1858	3894	5752	SO:0001627	intron_variant	3805				cellular defense response|regulation of immune response	integral to plasma membrane	receptor activity	g.chr19:55325326G>T	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.35-3663G>T	19.37:g.55325326G>T						KIR3DL2_uc010yfj.2_Intron|KIR3DL2_uc010yfk.1_Intron|KIR3DL2_uc021vbm.1_Intron|KIR3DL2_uc002qhf.3_Silent_p.V151V|KIR3DL2_uc002qhg.3_Silent_p.V263V|KIR3DL2_uc002qhi.3_3'UTR|KIR3DL2_uc021vbn.1_3'UTR|KIR3DL2_uc002qhh.3_Silent_p.V168V|KIR3DL2_uc002qhj.3_Silent_p.V246V|KIR3DL2_uc010esd.3_3'UTR|KIR3DL2_uc010ese.3_Non-coding_Transcript|KIR3DL2_uc010esf.3_5'Flank|KIR3DL2_uc021vbo.1_5'Flank|KIR3DL2_uc002qhk.4_5'Flank|KIR3DL2_uc002qhl.4_5'Flank	p.V318V	NM_002255	NP_002246	P43630	KI3L2_HUMAN		GBM - Glioblastoma multiforme(193;0.0192)	7	987	+			396					O43473|Q14946|Q16541	Silent	SNP	ENST00000538269.1	37	c.954G>T																																																																																					0.473	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289	
NLRP13	126204	broad.mit.edu	37	19	56424570	56424570	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr19:56424570G>A	ENST00000342929.3	-	5	612	c.613C>T	c.(613-615)Cgt>Tgt	p.R205C	NLRP13_ENST00000588751.1_Missense_Mutation_p.R205C	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	205							ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		GATGTATTACGGATATATACG	0.498																																						uc010ygg.2																			0				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109						c.(613-615)Cgt>Tgt		Homo sapiens NLR family, pyrin domain containing 13 (NLRP13), mRNA.							170.0	180.0	176.0					19																	56424570		2203	4300	6503	SO:0001583	missense	126204						ATP binding	g.chr19:56424570G>A	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.613C>T	19.37:g.56424570G>A	ENSP00000343891:p.Arg205Cys						p.R205C	NM_176810	NP_789780	Q86W25	NAL13_HUMAN		GBM - Glioblastoma multiforme(193;0.0642)	4	638	-		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)	205					Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	c.613C>T	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.551680	0.27739	.	.	ENSG00000173572	ENST00000342929	T	0.73575	-0.76	2.13	-3.22	0.05125	.	.	.	.	.	T	0.67988	0.2952	N	0.19112	0.55	0.09310	N	1	D	0.89917	1.0	D	0.67231	0.95	T	0.57728	-0.7761	9	0.40728	T	0.16	.	3.3866	0.07274	0.4418:0.2118:0.3463:0.0	.	205	Q86W25	NAL13_HUMAN	C	205	ENSP00000343891:R205C	ENSP00000343891:R205C	R	-	1	0	NLRP13	61116382	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.477000	0.06583	-0.640000	0.05495	-1.031000	0.02408	CGT		0.498	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
RAD51AP2	729475	broad.mit.edu	37	2	17699042	17699042	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr2:17699042G>T	ENST00000399080.2	-	1	664	c.641C>A	c.(640-642)gCt>gAt	p.A214D		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	214										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AACACTGTTAGCTTTACATCT	0.313																																						uc002rcl.1																			0				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						c.(640-642)gCt>gAt		Homo sapiens RAD51 associated protein 2 (RAD51AP2), mRNA.							75.0	72.0	73.0					2																	17699042		1841	4096	5937	SO:0001583	missense	729475							g.chr2:17699042G>T	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.641C>A	2.37:g.17699042G>T	ENSP00000382030:p.Ala214Asp					RAD51AP2_uc010exn.1_Missense_Mutation_p.A205D	p.A214D	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN			0	665	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)		214						Missense_Mutation	SNP	ENST00000399080.2	37	c.641C>A	CCDS42656.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.700037	0.48307	.	.	ENSG00000214842	ENST00000399080	T	0.34275	1.37	3.91	2.93	0.34026	.	.	.	.	.	T	0.25865	0.0630	N	0.24115	0.695	0.09310	N	1	P	0.52061	0.95	P	0.48227	0.571	T	0.17319	-1.0373	9	0.62326	D	0.03	-0.0927	0.6798	0.00873	0.1579:0.1916:0.2833:0.3672	.	214	Q09MP3	R51A2_HUMAN	D	214	ENSP00000382030:A214D	ENSP00000382030:A214D	A	-	2	0	RAD51AP2	17562523	0.000000	0.05858	0.827000	0.32855	0.991000	0.79684	-0.249000	0.08842	1.038000	0.40049	0.655000	0.94253	GCT		0.313	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218	
REG1B	5968	broad.mit.edu	37	2	79314050	79314050	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr2:79314050T>C	ENST00000305089.3	-	3	151	c.71A>G	c.(70-72)gAg>gGg	p.E24G		NM_006507.3	NP_006498.1	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta	24					cell proliferation (GO:0008283)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)	p.E24A(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(40)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	51						TGTCTGGGACTCCTGGCCTGG	0.488																																						uc002sny.2																			1	Substitution - Missense(1)	p.E24A(2)|p.E24D(1)	lung(1)	central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(40)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	51						c.(70-72)gAg>gGg		Homo sapiens regenerating islet-derived 1 beta (REG1B), mRNA.							98.0	104.0	102.0					2																	79314050		2203	4300	6503	SO:0001583	missense	5968				cell proliferation	extracellular region	sugar binding	g.chr2:79314050T>C		CCDS1963.1	2p12	2008-06-04	2008-06-04		ENSG00000172023	ENSG00000172023			9952	protein-coding gene	gene with protein product	"""lithostathine 1 beta"", ""secretory pancreatic stone protein 2"""	167771	"""regenerating islet-derived 1 beta (pancreatic stone protein, pancreatic thread protein)"""			8110835	Standard	NM_006507		Approved	REGL, PSPS2, REGH, REGI-BETA	uc002sny.2	P48304	OTTHUMG00000130019	ENST00000305089.3:c.71A>G	2.37:g.79314050T>C	ENSP00000303206:p.Glu24Gly					REG1B_uc010ffv.1_Missense_Mutation_p.E24G|REG1B_uc010ffw.3_Missense_Mutation_p.E24G	p.E24G	NM_006507	NP_006498	P48304	REG1B_HUMAN			2	183	-			24						Missense_Mutation	SNP	ENST00000305089.3	37	c.71A>G	CCDS1963.1	.	.	.	.	.	.	.	.	.	.	t	10.97	1.501857	0.26949	.	.	ENSG00000172023	ENST00000305089	T	0.04406	3.63	3.58	2.36	0.29203	.	0.817704	0.10012	N	0.727077	T	0.07007	0.0178	M	0.70275	2.135	0.09310	N	1	D;P	0.61697	0.99;0.942	B;B	0.42462	0.388;0.253	T	0.35699	-0.9778	10	0.23891	T	0.37	.	5.9934	0.19480	0.2309:0.0:0.0:0.7691	.	24;24	Q6ICS1;P48304	.;REG1B_HUMAN	G	24	ENSP00000303206:E24G	ENSP00000303206:E24G	E	-	2	0	REG1B	79167558	0.002000	0.14202	0.011000	0.14972	0.090000	0.18270	0.499000	0.22546	0.525000	0.28522	0.459000	0.35465	GAG		0.488	REG1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252292.2	NM_006507	
WASH2P	375260	broad.mit.edu	37	2	114355998	114355998	+	RNA	SNP	C	C	G	rs17857355	byFrequency	TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr2:114355998C>G	ENST00000538033.2	+	0	2178							Q6VEQ5	WASH2_HUMAN	WAS protein family homolog 2 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)										CCAAGGTGGGCACTTGATGTC	0.612																																						uc002tkh.3																			0											c.(616-618)Cac>Gac		Homo sapiens WAS protein family homolog 2 pseudogene (WASH2P), non-coding RNA.																																						375260							g.chr2:114355998C>G			2q13	2010-07-08	2008-01-16	2008-01-16	ENSG00000146556	ENSG00000146556		"""WAS protein homologs"""	33145	pseudogene	pseudogene			"""family with sequence similarity 39, member B"""	FAM39B		18159949	Standard	NR_024077		Approved	MGC52000	uc002tkh.3	Q6VEQ5	OTTHUMG00000047822		2.37:g.114355998C>G						WASH2P_uc002tka.3_Non-coding_Transcript|WASH2P_uc002tkd.3_Non-coding_Transcript	p.H206D							4	674	+									Missense_Mutation	SNP	ENST00000538033.2	37	c.616C>G																																																																																					0.612	WASH2P-002	KNOWN	mRNA_end_NF|basic	retained_intron	pseudogene	OTTHUMT00000467782.1	NM_198943	
DPP10	57628	broad.mit.edu	37	2	116573266	116573266	+	Silent	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr2:116573266G>A	ENST00000410059.1	+	21	2391	c.1911G>A	c.(1909-1911)ctG>ctA	p.L637L	DPP10_ENST00000393147.2_Silent_p.L641L|DPP10_ENST00000409163.1_Silent_p.L587L|DPP10_ENST00000310323.8_Silent_p.L630L	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	637						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						TGCTGAAACTGCCTTACATTG	0.279																																						uc002tle.3																			0				breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						c.(1921-1923)ctG>ctA		Homo sapiens dipeptidyl-peptidase 10 (non-functional) (DPP10), transcript variant 3, mRNA.							105.0	99.0	101.0					2																	116573266		2202	4298	6500	SO:0001819	synonymous_variant	57628				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity	g.chr2:116573266G>A	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"""dipeptidylpeptidase 10"", ""dipeptidyl-peptidase 10"""			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1911G>A	2.37:g.116573266G>A						DPP10_uc002tla.2_Silent_p.L637L|DPP10_uc002tlb.2_Silent_p.L587L|DPP10_uc002tlc.2_Silent_p.L633L|DPP10_uc002tlf.2_Silent_p.L630L	p.L641L	NM_001178034	NP_001171505	Q8N608	DPP10_HUMAN			20	1944	+			637					A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Silent	SNP	ENST00000410059.1	37	c.1923G>A	CCDS46400.1																																																																																				0.279	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
LRP2	4036	broad.mit.edu	37	2	170058265	170058265	+	Silent	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr2:170058265G>A	ENST00000263816.3	-	44	8610	c.8325C>T	c.(8323-8325)tgC>tgT	p.C2775C		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2775	LDL-receptor class A 17. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	CCCTGAACAGGCACCCTGCCT	0.498																																						uc002ues.3																			0				biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315						c.(8323-8325)tgC>tgT		Homo sapiens low density lipoprotein receptor-related protein 2 (LRP2), mRNA.	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)						176.0	149.0	158.0					2																	170058265		2203	4300	6503	SO:0001819	synonymous_variant	4036				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding	g.chr2:170058265G>A		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.8325C>T	2.37:g.170058265G>A							p.C2775C	NM_004525	NP_004516	P98164	LRP2_HUMAN		STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	43	8538	-			2775			LDL-receptor class A 17.		O00711|Q16215	Silent	SNP	ENST00000263816.3	37	c.8325C>T	CCDS2232.1																																																																																				0.498	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
UGT1A1	54658	broad.mit.edu	37	2	234668958	234668958	+	Missense_Mutation	SNP	C	C	T	rs386656374|rs370790922		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr2:234668958C>T	ENST00000608383.1	+	1	25	c.25C>T	c.(25-27)Cgc>Tgc	p.R9C	UGT1A7_ENST00000373426.3_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A3_ENST00000482026.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A8_ENST00000305208.5_Missense_Mutation_p.R9C|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000360418.3_Missense_Mutation_p.R9C|UGT1A6_ENST00000406651.1_Intron			P22309	UD11_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A1	9					acute-phase response (GO:0006953)|bilirubin conjugation (GO:0006789)|biphenyl catabolic process (GO:0070980)|cellular glucuronidation (GO:0052695)|cellular response to ethanol (GO:0071361)|cellular response to glucocorticoid stimulus (GO:0071385)|digestion (GO:0007586)|drug metabolic process (GO:0017144)|estrogen metabolic process (GO:0008210)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|heme catabolic process (GO:0042167)|heterocycle metabolic process (GO:0046483)|liver development (GO:0001889)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of steroid metabolic process (GO:0045939)|organ regeneration (GO:0031100)|porphyrin-containing compound metabolic process (GO:0006778)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	cytochrome complex (GO:0070069)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(2)|endometrium(7)|large_intestine(5)|lung(9)|skin(4)|urinary_tract(2)	30		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Acetaminophen(DB00316)|Adenine(DB00173)|Atorvastatin(DB01076)|Axitinib(DB06626)|Diclofenac(DB00586)|Dolutegravir(DB08930)|Eltrombopag(DB06210)|Erlotinib(DB00530)|Estradiol(DB00783)|Etoposide(DB00773)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indacaterol(DB05039)|Indomethacin(DB00328)|Irinotecan(DB00762)|Losartan(DB00678)|Lovastatin(DB00227)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naltrexone(DB00704)|Naproxen(DB00788)|Nilotinib(DB04868)|Pazopanib(DB06589)|Propofol(DB00818)|Raltegravir(DB06817)|Regorafenib(DB08896)|Rifampicin(DB01045)|Simvastatin(DB00641)|Sorafenib(DB00398)|Suprofen(DB00870)|Testosterone Propionate(DB01420)	CCAGGGCGGACGCCCACTTGT	0.567											OREG0003837	type=REGULATORY REGION|Gene=UGT1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																										uc002vuw.3																			0				breast(1)|central_nervous_system(2)|endometrium(7)|large_intestine(5)|lung(9)|skin(4)|urinary_tract(2)	30								Homo sapiens UDP glucuronosyltransferase 1 family, polypeptide A5 (UGT1A5), mRNA.	Abacavir(DB01048)|Adenine(DB00173)|Diclofenac(DB00586)|Estradiol(DB00783)|Ezetimibe(DB00973)|Irinotecan(DB00762)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Rifampin(DB01045)|Troglitazone(DB00197)	C	CYS/ARG,,,,,,,,,	0,4406		0,0,2203	35.0	32.0	33.0		25,,,,,,,,,	-0.3	0.0	2		33	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A1,UGT1A3	NM_000463.2,NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	180,,,,,,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,,,,,,,,,	9/534,,,,,,,,,	234668958	1,13005	2203	4300	6503	SO:0001583	missense	54658				bilirubin conjugation|digestion|estrogen metabolic process|flavone metabolic process|heme catabolic process	endoplasmic reticulum membrane|microsome	enzyme binding|enzyme inhibitor activity|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|retinoic acid binding|steroid binding	g.chr2:234668958C>T	M57899	CCDS2510.1	2q37.1	2014-09-17	2005-07-20		ENSG00000242366	ENSG00000242366	2.4.1.17	"""UDP glucuronosyltransferases"""	12530	other	complex locus constituent		191740	"""UDP glycosyltransferase 1 family, polypeptide A1"""	UGT1, GNT1		9295054, 9535849	Standard	NM_000463		Approved	UGT1A		P22309	OTTHUMG00000059117	ENST00000608383.1:c.25C>T	2.37:g.234668958C>T	ENSP00000476741:p.Arg9Cys		OREG0003837	type=REGULATORY REGION|Gene=UGT1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	2375	UGT1A1_uc010zmv.1_Intron|UGT1A1_uc002vup.3_Intron|UGT1A1_uc002vuq.3_Intron|UGT1A1_uc002vur.3_Intron|UGT1A1_uc010zmw.1_Intron|UGT1A1_uc002vus.3_Intron|UGT1A1_uc010zmx.1_Intron|UGT1A1_uc002vut.3_Intron|UGT1A1_uc002vuu.3_Intron|UGT1A1_uc010zmy.1_Intron|UGT1A1_uc002vuv.4_Intron|UGT1A1_uc010zmz.1_Intron|UGT1A1_uc010zna.1_Intron|UGT1A1_uc002vux.3_Intron|UGT1A1_uc010znb.1_Intron|UGT1A1_uc002vuy.3_Intron|UGT1A1_uc002vva.3_Intron|UGT1A1_uc010znc.1_Missense_Mutation_p.R9C|UGT1A1_uc002vvb.3_Missense_Mutation_p.R9C		NM_019078	NP_061951	P22309	UD11_HUMAN		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)			+		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)						A6NJC3|B8K286	Missense_Mutation	SNP	ENST00000608383.1	37		CCDS2510.1	.	.	.	.	.	.	.	.	.	.	C	9.649	1.140937	0.21205	0.0	1.16E-4	ENSG00000241635	ENST00000305208;ENST00000360418	T;T	0.61274	0.12;0.18	5.32	-0.272	0.12919	.	.	.	.	.	T	0.42675	0.1213	L	0.40543	1.245	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.0	T	0.30031	-0.9992	9	0.38643	T	0.18	.	4.9903	0.14211	0.1355:0.4554:0.0:0.4091	.	9;9	A6NJC3;P22309	.;UD11_HUMAN	C	9	ENSP00000304845:R9C;ENSP00000353593:R9C	ENSP00000304845:R9C	R	+	1	0	UGT1A1	234333697	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.619000	0.05572	0.014000	0.14944	0.650000	0.86243	CGC		0.567	UGT1A1-203	KNOWN	basic|CCDS	protein_coding	protein_coding			
L3MBTL1	26013	broad.mit.edu	37	20	42168804	42168804	+	Missense_Mutation	SNP	T	T	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr20:42168804T>A	ENST00000427442.2	+	20	2280	c.2121T>A	c.(2119-2121)gaT>gaA	p.D707E	L3MBTL1_ENST00000444063.1_Missense_Mutation_p.D639E|L3MBTL1_ENST00000418998.1_Missense_Mutation_p.D707E|L3MBTL1_ENST00000373134.1_Missense_Mutation_p.D644E|L3MBTL1_ENST00000373135.3_Missense_Mutation_p.D639E			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	639	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						TCACGCCCGATGTCGTGCACC	0.612																																						uc002xkn.1																			0				breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						c.(1192-1194)gaT>gaA		Homo sapiens l(3)mbt-like 1 (Drosophila) (L3MBTL1), transcript variant I, mRNA.							90.0	64.0	73.0					20																	42168804		2203	4300	6503	SO:0001583	missense	26013				chromatin modification|hemopoiesis|negative regulation of transcription, DNA-dependent|regulation of megakaryocyte differentiation|regulation of mitosis	chromatin|condensed chromosome|nucleoplasm	identical protein binding|methylated histone residue binding|nucleosomal histone binding|SAM domain binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr20:42168804T>A	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"""Zinc fingers, C2HC-type containing"", ""Sterile alpha motif (SAM) domain containing"""	15905	protein-coding gene	gene with protein product	"""lethal (3) malignant brain tumor l(3)"""	608802	"""l(3)mbt (Drosophila)-like"", ""l(3)mbt-like (Drosophila)"""	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.2121T>A	20.37:g.42168804T>A	ENSP00000402107:p.Asp707Glu					L3MBTL1_uc010zwh.2_Missense_Mutation_p.D707E|L3MBTL1_uc002xkm.3_Missense_Mutation_p.D639E|L3MBTL1_uc010ggl.3_Missense_Mutation_p.D644E|L3MBTL1_uc002xkl.3_Missense_Mutation_p.D639E|L3MBTL1_uc002xko.3_Missense_Mutation_p.D291E|L3MBTL1_uc002xkp.3_Missense_Mutation_p.D27E|SGK2_uc002xkq.1_5'UTR	p.D398E	NM_015478	NP_056293	Q9Y468	LMBL1_HUMAN			12	1325	+			639					B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Missense_Mutation	SNP	ENST00000427442.2	37	c.1194T>A	CCDS46602.2	.	.	.	.	.	.	.	.	.	.	T	13.30	2.195776	0.38806	.	.	ENSG00000185513	ENST00000427442;ENST00000418998;ENST00000373135;ENST00000444063;ENST00000373134;ENST00000422861;ENST00000373133	T;T;T;T;T;T	0.21031	2.31;2.31;2.28;2.31;2.29;2.03	5.55	-2.98	0.05513	.	0.312336	0.32952	N	0.005450	T	0.09992	0.0245	N	0.21583	0.68	0.20563	N	0.999885	B;B;B;B;B	0.28233	0.022;0.004;0.204;0.008;0.013	B;B;B;B;B	0.24006	0.01;0.008;0.05;0.011;0.036	T	0.15578	-1.0432	10	0.38643	T	0.18	.	6.8704	0.24117	0.1591:0.5601:0.0:0.2808	.	707;291;27;639;639	Q9Y468-5;Q9Y468-3;Q6ZWF5;Q9Y468-2;Q9Y468-1	.;.;.;.;.	E	707;707;639;639;644;425;291	ENSP00000402107:D707E;ENSP00000398516:D707E;ENSP00000362227:D639E;ENSP00000403316:D639E;ENSP00000362226:D644E;ENSP00000410139:D425E	ENSP00000362225:D291E	D	+	3	2	L3MBTL1	41602218	0.078000	0.21339	0.001000	0.08648	0.046000	0.14306	-0.413000	0.07123	-0.469000	0.06911	0.533000	0.62120	GAT		0.612	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107	
ITSN1	6453	broad.mit.edu	37	21	35174748	35174748	+	Splice_Site	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr21:35174748G>A	ENST00000381318.3	+	20	2607	c.2319G>A	c.(2317-2319)tgG>tgA	p.W773*	ITSN1_ENST00000379960.5_Intron|ITSN1_ENST00000399326.3_Intron|ITSN1_ENST00000381285.4_Intron|ITSN1_ENST00000381291.4_Splice_Site_p.W773*|ITSN1_ENST00000399352.1_Intron|ITSN1_ENST00000399355.2_Splice_Site_p.W773*|ITSN1_ENST00000399353.1_Intron|ITSN1_ENST00000437442.2_Intron|ITSN1_ENST00000399349.1_Intron|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399338.4_Intron|ITSN1_ENST00000399367.3_Intron	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	773	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						AAGGGGAATGGGTAAGTGTTG	0.378																																						uc002yta.1																			0				breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						c.e20+1		Homo sapiens intersectin 1 (SH3 domain protein) (ITSN1), transcript variant 1, mRNA.							427.0	389.0	402.0					21																	35174748		2203	4300	6503	SO:0001630	splice_region_variant	6453				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity	g.chr21:35174748G>A	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.2319+1G>A	21.37:g.35174748G>A						DONSON_uc002ysn.1_Intron|ITSN1_uc010gmj.3_Intron|ITSN1_uc002ysy.3_Intron|ITSN1_uc002ysx.3_Intron|ITSN1_uc002yth.4_Intron|ITSN1_uc002ysz.3_Intron|ITSN1_uc010gmg.3_Intron|ITSN1_uc010gmh.3_Intron|ITSN1_uc002ysw.3_Splice_Site_p.W773_splice|ITSN1_uc010gmi.3_Splice_Site_p.W736_splice|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytc.1_Intron|ITSN1_uc010gmk.3_Splice_Site_p.W736_splice|ITSN1_uc010gml.3_Intron|ITSN1_uc002ytd.3_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron|ITSN1_uc002yte.3_Splice_Site_p.W707_splice|ITSN1_uc021wip.1_Intron|ITSN1_uc002ytf.1_Splice_Site	p.W773_splice	NM_003024	NP_003015	Q15811	ITSN1_HUMAN			20	2587	+			773			SH3 1.		A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Nonsense_Mutation	SNP	ENST00000381318.3	37	c.2319_splice	CCDS33545.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	43|43	10.149627|10.149627	0.99348|0.99348	.|.	.|.	ENSG00000205726|ENSG00000205726	ENST00000440794|ENST00000381318;ENST00000381291;ENST00000399355	.|.	.|.	.|.	5.32|5.32	5.32|5.32	0.75619|0.75619	.|.	.|0.177976	.|0.39544	.|N	.|0.001321	T|.	0.43942|.	0.1270|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.32025|.	-0.9922|.	4|.	.|0.02654	.|T	.|1	.|.	16.5349|16.5349	0.84370|0.84370	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	S|X	8|773	.|.	.|ENSP00000370691:W773X	G|W	+|+	1|3	0|0	ITSN1|ITSN1	34096618|34096618	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.860000|7.860000	0.86993|0.86993	2.634000|2.634000	0.89283|0.89283	0.655000|0.655000	0.94253|0.94253	GGT|TGG		0.378	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024	Nonsense_Mutation
TAB1	10454	broad.mit.edu	37	22	39822903	39822903	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr22:39822903A>G	ENST00000216160.6	+	9	1179	c.1117A>G	c.(1117-1119)Agc>Ggc	p.S373G	TAB1_ENST00000331454.3_Missense_Mutation_p.S373G	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	373					activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart morphogenesis (GO:0003007)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lung development (GO:0030324)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|protein complex (GO:0043234)	catalytic activity (GO:0003824)|enzyme activator activity (GO:0008047)|kinase activator activity (GO:0019209)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						GGGCGAAATGAGCCAGCCCAC	0.667																																						uc003axt.3																			0				breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						c.(1117-1119)Agc>Ggc		Homo sapiens TGF-beta activated kinase 1/MAP3K7 binding protein 1 (TAB1), transcript variant alpha, mRNA.							55.0	50.0	52.0					22																	39822903		2203	4300	6503	SO:0001583	missense	10454				activation of MAPK activity|activation of MAPKKK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane	catalytic activity|protein binding	g.chr22:39822903A>G	U49928	CCDS13992.1, CCDS13993.1	22q13.1	2010-02-05	2010-02-05	2010-02-05	ENSG00000100324	ENSG00000100324			18157	protein-coding gene	gene with protein product	"""TAK1-binding protein 1"", ""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	602615	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	MAP3K7IP1		8638164, 10187861	Standard	NM_153497		Approved		uc003axt.3	Q15750	OTTHUMG00000151102	ENST00000216160.6:c.1117A>G	22.37:g.39822903A>G	ENSP00000216160:p.Ser373Gly					TAB1_uc003axr.3_Missense_Mutation_p.S449G|TAB1_uc011aok.2_Missense_Mutation_p.S207G|TAB1_uc003axu.1_Missense_Mutation_p.S373G	p.S373G	NM_006116	NP_006107	Q15750	TAB1_HUMAN			8	1166	+			373					Q2PP09|Q8IZW2	Missense_Mutation	SNP	ENST00000216160.6	37	c.1117A>G	CCDS13993.1	.	.	.	.	.	.	.	.	.	.	A	13.23	2.175856	0.38413	.	.	ENSG00000100324	ENST00000216160;ENST00000331454	T;T	0.47177	0.87;0.85	5.45	5.45	0.79879	.	0.223501	0.45126	D	0.000388	T	0.32496	0.0831	L	0.29908	0.895	0.39315	D	0.965148	B;B;P	0.38922	0.001;0.001;0.651	B;B;B	0.29598	0.003;0.003;0.104	T	0.18398	-1.0338	10	0.22706	T	0.39	.	15.5136	0.75806	1.0:0.0:0.0:0.0	.	373;373;517	Q15750-2;Q15750;Q59FT7	.;TAB1_HUMAN;.	G	373	ENSP00000216160:S373G;ENSP00000333049:S373G	ENSP00000216160:S373G	S	+	1	0	TAB1	38152849	1.000000	0.71417	1.000000	0.80357	0.501000	0.33797	4.786000	0.62425	2.067000	0.61834	0.383000	0.25322	AGC		0.667	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497	
SETD2	29072	broad.mit.edu	37	3	47058654	47058654	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr3:47058654C>T	ENST00000409792.3	-	21	7666	c.7624G>A	c.(7624-7626)Gag>Aag	p.E2542K		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2542	Interaction with POLR2A.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TTAATGTACTCCTTGGTTTTG	0.473			"""N, F, S, Mis"""		clear cell renal carcinoma																																	uc003cqv.3				Rec	yes		3	3p21.31	29072	"""N, F, S, Mis"""	SET domain containing 2			E			clear cell renal carcinoma		0				breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141						c.(7825-7827)Gag>Aag		Homo sapiens SET domain containing 2 (SETD2), mRNA.							281.0	265.0	271.0					3																	47058654		2203	4300	6503	SO:0001583	missense	29072				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding	g.chr3:47058654C>T	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.7624G>A	3.37:g.47058654C>T	ENSP00000386759:p.Glu2542Lys					SETD2_uc003cqs.3_Missense_Mutation_p.E2542K|SETD2_uc003cqr.3_Missense_Mutation_p.E141K	p.E2609K	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)	21	7911	-		Acute lymphoblastic leukemia(5;0.0169)	2542					O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	c.7825G>A	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	31	5.066646	0.93898	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	D	0.89415	-2.51	4.88	4.88	0.63580	SRI, Set2 Rpb1 interacting (1);	0.000000	0.53938	D	0.000050	D	0.93739	0.7999	M	0.65498	2.005	0.80722	D	1	D;D	0.63880	0.968;0.993	P;D	0.78314	0.898;0.991	D	0.93961	0.7240	10	0.59425	D	0.04	.	18.2365	0.89951	0.0:1.0:0.0:0.0	.	2542;2542	F2Z317;Q9BYW2	.;SETD2_HUMAN	K	2542	ENSP00000386759:E2542K	ENSP00000386759:E2542K	E	-	1	0	SETD2	47033658	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.562000	0.82300	2.543000	0.85770	0.655000	0.94253	GAG		0.473	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
UGT2B4	7363	broad.mit.edu	37	4	70361046	70361046	+	Silent	SNP	G	G	A	rs370531105		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr4:70361046G>A	ENST00000305107.6	-	1	580	c.534C>T	c.(532-534)taC>taT	p.Y178Y	UGT2B4_ENST00000381096.3_Silent_p.Y42Y|UGT2B4_ENST00000512583.1_Silent_p.Y178Y|UGT2B4_ENST00000506580.1_Intron	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	178					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	TTTCAATTGCGTAGCCAGGAG	0.453																																						uc003hek.4																			0				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47						c.(532-534)taC>taT		Homo sapiens UDP glucuronosyltransferase 2 family, polypeptide B4 (UGT2B4), mRNA.		G		1,4361	2.1+/-5.4	0,1,2180	64.0	64.0	64.0		534	-4.8	0.0	4		64	0,8588		0,0,4294	no	coding-synonymous	UGT2B4	NM_021139.2		0,1,6474	AA,AG,GG		0.0,0.0229,0.0077		178/529	70361046	1,12949	2181	4294	6475	SO:0001819	synonymous_variant	7363				estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity	g.chr4:70361046G>A	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"""UDP glucuronosyltransferases"""	12553	protein-coding gene	gene with protein product		600067	"""UDP glycosyltransferase 2 family, polypeptide B4"""			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.534C>T	4.37:g.70361046G>A						UGT2B4_uc011cap.2_Silent_p.Y42Y|UGT2B4_uc003hel.4_Silent_p.Y178Y	p.Y178Y	NM_021139	NP_066962	P06133	UD2B4_HUMAN			0	581	-			178					A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Silent	SNP	ENST00000305107.6	37	c.534C>T	CCDS43234.1																																																																																				0.453	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139	
ADH7	131	broad.mit.edu	37	4	100349278	100349278	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr4:100349278G>A	ENST00000209665.4	-	4	589	c.349C>T	c.(349-351)Cgc>Tgc	p.R117C	ADH7_ENST00000482593.1_Missense_Mutation_p.R48C|ADH7_ENST00000476959.1_Missense_Mutation_p.R125C|ADH7_ENST00000437033.2_Missense_Mutation_p.R105C	NM_000673.4	NP_000664.2	P40394	ADH7_HUMAN	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	117					ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|extracellular negative regulation of signal transduction (GO:1900116)|fatty acid omega-oxidation (GO:0010430)|oxidation-reduction process (GO:0055114)|response to bacterium (GO:0009617)|response to ethanol (GO:0045471)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular region (GO:0005576)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|aldehyde oxidase activity (GO:0004031)|ethanol binding (GO:0035276)|receptor antagonist activity (GO:0048019)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)	19				OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)		TCTGGGTTGCGACAAGCATTG	0.343																																						uc003huv.2																			0				breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)	19						c.(349-351)Cgc>Tgc		Homo sapiens alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide (ADH7), transcript variant 2, mRNA.	NADH(DB00157)						146.0	146.0	146.0					4																	100349278		2203	4300	6503	SO:0001583	missense	131				ethanol oxidation|fatty acid omega-oxidation|response to bacterium|response to ethanol|xenobiotic metabolic process	cytosol|soluble fraction	alcohol dehydrogenase activity, zinc-dependent|aldehyde oxidase activity|ethanol binding|receptor antagonist activity|retinol binding|retinol dehydrogenase activity	g.chr4:100349278G>A	X76342	CCDS34034.1, CCDS54781.1	4q23-q24	2008-02-05			ENSG00000196344	ENSG00000196344	1.1.1.1	"""Alcohol dehydrogenases"""	256	protein-coding gene	gene with protein product		600086				8195208	Standard	NM_000673		Approved	ADH-4	uc021xqj.1	P40394	OTTHUMG00000159318	ENST00000209665.4:c.349C>T	4.37:g.100349278G>A	ENSP00000209665:p.Arg117Cys					ADH7_uc021xqj.1_Missense_Mutation_p.R125C	p.R117C	NM_000673	NP_000664	P40394	ADH7_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)	3	590	-			117					A2RRB6|A8MVN9|B2R760|B4DWV6|Q13713	Missense_Mutation	SNP	ENST00000209665.4	37	c.349C>T	CCDS34034.1	.	.	.	.	.	.	.	.	.	.	G	16.32	3.091407	0.55968	.	.	ENSG00000196344	ENST00000437033;ENST00000209665;ENST00000482593;ENST00000476959;ENST00000474027	T;T;T;T;T	0.05580	3.42;3.42;3.42;3.42;3.42	4.91	-4.26	0.03755	GroES-like (1);Alcohol dehydrogenase GroES-like (1);	0.515963	0.19924	N	0.103003	T	0.06781	0.0173	M	0.75150	2.29	0.09310	N	1	B	0.17268	0.021	B	0.15870	0.014	T	0.28170	-1.0052	10	0.72032	D	0.01	-4.2334	4.6986	0.12816	0.4511:0.0:0.2356:0.3133	.	117	P40394	ADH7_HUMAN	C	105;117;48;125;48	ENSP00000414254:R105C;ENSP00000209665:R117C;ENSP00000420613:R48C;ENSP00000420269:R125C;ENSP00000420300:R48C	ENSP00000209665:R117C	R	-	1	0	ADH7	100568301	0.000000	0.05858	0.000000	0.03702	0.679000	0.39708	-0.998000	0.03701	-0.461000	0.06993	0.655000	0.94253	CGC		0.343	ADH7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000673	
COL25A1	84570	broad.mit.edu	37	4	109780829	109780829	+	Missense_Mutation	SNP	G	G	C	rs369025098		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr4:109780829G>C	ENST00000399132.1	-	24	1833	c.1303C>G	c.(1303-1305)Ctc>Gtc	p.L435V	COL25A1_ENST00000399126.1_Missense_Mutation_p.L435V|COL25A1_ENST00000399127.1_Missense_Mutation_p.L416V	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1											NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		GCTTCGTGGAGGTTGCCGTTG	0.493																																						uc021xqo.1																			0				NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49						c.(1303-1305)Ctc>Gtc		Homo sapiens collagen, type XXV, alpha 1 (COL25A1), transcript variant 1, mRNA.							178.0	180.0	179.0					4																	109780829		2013	4163	6176	SO:0001583	missense	84570					collagen|extracellular space	beta-amyloid binding|heparin binding	g.chr4:109780829G>C	AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517		"""Collagens"""	18603	protein-coding gene	gene with protein product		610004				11927537	Standard	NM_001256074		Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.1303C>G	4.37:g.109780829G>C	ENSP00000382083:p.Leu435Val					COL25A1_uc003hze.1_Missense_Mutation_p.L435V|COL25A1_uc021xqp.1_Missense_Mutation_p.L435V|COL25A1_uc003hzg.3_Missense_Mutation_p.L435V|COL25A1_uc003hzd.3_Non-coding_Transcript|COL25A1_uc003hzf.3_Missense_Mutation_p.L201V	p.L435V	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.000173)	22	1359	-		Hepatocellular(203;0.217)	435						Missense_Mutation	SNP	ENST00000399132.1	37	c.1303C>G	CCDS43258.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.514143	0.44763	.	.	ENSG00000188517	ENST00000399132;ENST00000333642;ENST00000401873;ENST00000399127;ENST00000399126;ENST00000443653	D;D;D	0.93189	-3.18;-2.71;-3.18	5.82	3.93	0.45458	.	0.050245	0.85682	D	0.000000	D	0.85957	0.5818	N	0.13098	0.295	0.32485	N	0.541037	B;B	0.21821	0.061;0.014	B;B	0.27715	0.082;0.009	T	0.82147	-0.0601	9	.	.	.	-5.4108	13.0823	0.59121	0.0:0.0:0.6591:0.3409	.	435;435	Q9BXS0-2;Q9BXS0	.;COPA1_HUMAN	V	435;437;416;416;435;365	ENSP00000382083:L435V;ENSP00000382078:L416V;ENSP00000382077:L435V	.	L	-	1	0	COL25A1	110000278	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	4.309000	0.59135	2.749000	0.94314	0.650000	0.86243	CTC		0.493	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315938.2	NM_032518	
CARD6	84674	broad.mit.edu	37	5	40852581	40852581	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr5:40852581A>G	ENST00000254691.5	+	3	1346	c.1147A>G	c.(1147-1149)Atg>Gtg	p.M383V	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	383					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						TTGTGCCACCATGCTGTGTTC	0.458																																						uc003jmg.3																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						c.(1147-1149)Atg>Gtg		Homo sapiens caspase recruitment domain family, member 6 (CARD6), mRNA.							82.0	78.0	79.0					5																	40852581		2203	4300	6503	SO:0001583	missense	84674				apoptosis|regulation of apoptosis	intracellular		g.chr5:40852581A>G	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.1147A>G	5.37:g.40852581A>G	ENSP00000254691:p.Met383Val						p.M383V	NM_032587	NP_115976	Q9BX69	CARD6_HUMAN			2	1222	+			383					Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	37	c.1147A>G	CCDS3935.1	.	.	.	.	.	.	.	.	.	.	A	7.459	0.644323	0.14451	.	.	ENSG00000132357	ENST00000254691;ENST00000509771	T	0.39787	1.06	5.49	-3.81	0.04294	.	0.276497	0.32134	N	0.006527	T	0.28896	0.0717	L	0.54323	1.7	0.80722	D	1	B	0.17852	0.024	B	0.10450	0.005	T	0.01587	-1.1318	10	0.54805	T	0.06	-0.8806	4.6342	0.12516	0.2045:0.51:0.0707:0.2147	.	383	Q9BX69	CARD6_HUMAN	V	383	ENSP00000254691:M383V	ENSP00000254691:M383V	M	+	1	0	CARD6	40888338	0.253000	0.23982	0.171000	0.22900	0.072000	0.16883	0.509000	0.22707	-0.803000	0.04415	0.533000	0.62120	ATG		0.458	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3		
MROH2B	133558	broad.mit.edu	37	5	41061746	41061746	+	Nonsense_Mutation	SNP	G	G	A	rs200958096		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr5:41061746G>A	ENST00000399564.4	-	6	991	c.541C>T	c.(541-543)Cga>Tga	p.R181*		NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	181																	TCAGACAGTCGGTTGGCATCC	0.483																																						uc003jmj.4																			0				breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|liver(1)|lung(81)|ovary(6)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(4)	133						c.(541-543)Cga>Tga		Homo sapiens HEAT repeat family member 7B2 (HEATR7B2), mRNA.							155.0	151.0	152.0					5																	41061746		1926	4119	6045	SO:0001587	stop_gained	133558						binding	g.chr5:41061746G>A		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.541C>T	5.37:g.41061746G>A	ENSP00000382476:p.Arg181*					HEATR7B2_uc021xxt.1_Nonsense_Mutation_p.R181*	p.R181*	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN			5	1031	-			181					Q68DM1|Q7Z4U4|Q8N7X3	Nonsense_Mutation	SNP	ENST00000399564.4	37	c.541C>T	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	G	41	9.103516	0.99066	.	.	ENSG00000171495	ENST00000399564	.	.	.	5.81	5.81	0.92471	.	0.000000	0.47455	D	0.000234	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	15.5834	0.76462	0.0:0.0:1.0:0.0	.	.	.	.	X	181	.	ENSP00000382476:R181X	R	-	1	2	HEATR7B2	41097503	1.000000	0.71417	0.983000	0.44433	0.987000	0.75469	2.941000	0.49011	2.756000	0.94617	0.655000	0.94253	CGA		0.483	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
HCN1	348980	broad.mit.edu	37	5	45267351	45267351	+	Silent	SNP	A	A	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr5:45267351A>T	ENST00000303230.4	-	7	1680	c.1623T>A	c.(1621-1623)atT>atA	p.I541I		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	541					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						TCAGCAGGCAAATCTCTATAA	0.403																																						uc003jok.3																			0		p.E540E(1)		NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						c.(1621-1623)atT>atA		Homo sapiens hyperpolarization activated cyclic nucleotide-gated potassium channel 1 (HCN1), mRNA.							88.0	83.0	84.0					5																	45267351		2203	4300	6503	SO:0001819	synonymous_variant	348980					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity	g.chr5:45267351A>T	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.1623T>A	5.37:g.45267351A>T							p.I541I	NM_021072	NP_066550	O60741	HCN1_HUMAN			6	1648	-			541						Silent	SNP	ENST00000303230.4	37	c.1623T>A	CCDS3952.1																																																																																				0.403	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072	
LYSMD3	116068	broad.mit.edu	37	5	89814725	89814725	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr5:89814725G>A	ENST00000315948.6	-	3	976	c.832C>T	c.(832-834)Cca>Tca	p.P278S	LYSMD3_ENST00000500869.2_Silent_p.C119C|LYSMD3_ENST00000509384.1_3'UTR	NM_198273.1	NP_938014.1	Q7Z3D4	LYSM3_HUMAN	LysM, putative peptidoglycan-binding, domain containing 3	278						integral component of membrane (GO:0016021)				breast(2)|large_intestine(1)|lung(2)|prostate(1)|urinary_tract(1)	7		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-31)|Epithelial(54;5.22e-26)|all cancers(79;2.42e-22)		CCTTTAGTTGGCACAATTCCA	0.388																																						uc003kjr.3																			0				breast(2)|large_intestine(1)|lung(2)|prostate(1)|urinary_tract(1)	7						c.(832-834)Cca>Tca		Homo sapiens LysM, putative peptidoglycan-binding, domain containing 3 (LYSMD3), mRNA.							136.0	126.0	129.0					5																	89814725		1933	4139	6072	SO:0001583	missense	116068				cell wall macromolecule catabolic process	integral to membrane		g.chr5:89814725G>A	BX537972	CCDS43338.1, CCDS68911.1	5q14.3	2010-12-09			ENSG00000176018	ENSG00000176018			26969	protein-coding gene	gene with protein product							Standard	NM_001286812		Approved	FLJ13542	uc003kjr.3	Q7Z3D4	OTTHUMG00000162667	ENST00000315948.6:c.832C>T	5.37:g.89814725G>A	ENSP00000314518:p.Pro278Ser					LYSMD3_uc010jaz.2_Silent_p.C119C|LYSMD3_uc003kjs.1_3'UTR	p.P278S	NM_198273	NP_938014	Q7Z3D4	LYSM3_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;1.94e-31)|Epithelial(54;5.22e-26)|all cancers(79;2.42e-22)	2	980	-		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)	278					Q5H9U0|Q6PEK0|Q9NTE9	Missense_Mutation	SNP	ENST00000315948.6	37	c.832C>T	CCDS43338.1	.	.	.	.	.	.	.	.	.	.	G	11.26	1.586611	0.28268	.	.	ENSG00000176018;ENSG00000259141	ENST00000315948;ENST00000554351	T	0.23552	1.9	5.84	5.84	0.93424	.	0.211716	0.39759	N	0.001278	T	0.25680	0.0625	M	0.64997	1.995	0.40023	D	0.975438	B	0.25772	0.134	B	0.18561	0.022	T	0.04961	-1.0915	10	0.17369	T	0.5	-20.3809	13.3556	0.60625	0.0719:0.0:0.9281:0.0	.	278	Q7Z3D4	LYSM3_HUMAN	S	278	ENSP00000314518:P278S	ENSP00000314518:P278S	P	-	1	0	AC027323.1;LYSMD3	89850481	1.000000	0.71417	0.969000	0.41365	0.522000	0.34438	4.650000	0.61440	2.751000	0.94390	0.591000	0.81541	CCA		0.388	LYSMD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369987.2	XM_371760	
BRD8	10902	broad.mit.edu	37	5	137502312	137502312	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr5:137502312G>A	ENST00000254900.5	-	10	1263	c.892C>T	c.(892-894)Cca>Tca	p.P298S	BRD8_ENST00000411594.2_Intron|BRD8_ENST00000515014.1_5'Flank|BRD8_ENST00000230901.5_Missense_Mutation_p.P371S|BRD8_ENST00000402931.1_Missense_Mutation_p.P298S|BRD8_ENST00000455658.2_Missense_Mutation_p.P257S	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	298					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			ACAGGGGGTGGCACAAGTTTA	0.537																																						uc003lcf.1																			0				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35						c.(892-894)Cca>Tca		Homo sapiens bromodomain containing 8 (BRD8), transcript variant 2, mRNA.							74.0	68.0	70.0					5																	137502312		2203	4300	6503	SO:0001583	missense	10902				cell surface receptor linked signaling pathway|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription from RNA polymerase II promoter	mitochondrion|NuA4 histone acetyltransferase complex	sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity	g.chr5:137502312G>A	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.892C>T	5.37:g.137502312G>A	ENSP00000254900:p.Pro298Ser					BRD8_uc011cyl.2_Missense_Mutation_p.P77S|BRD8_uc021yea.1_Intron|BRD8_uc003lcg.3_Missense_Mutation_p.P371S|BRD8_uc003lci.3_Intron|BRD8_uc011cym.2_Missense_Mutation_p.P282S|BRD8_uc011cyn.1_Missense_Mutation_p.P257S	p.P298S	NM_139199	NP_631938	Q9H0E9	BRD8_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)		9	947	-			298					O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Missense_Mutation	SNP	ENST00000254900.5	37	c.892C>T	CCDS4198.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.001210	0.54254	.	.	ENSG00000112983	ENST00000254900;ENST00000230901;ENST00000402931;ENST00000455658	T;T;T;T	0.31247	1.84;1.5;1.63;1.62	5.65	4.77	0.60923	.	0.169147	0.53938	D	0.000056	T	0.28632	0.0709	N	0.24115	0.695	0.52501	D	0.999958	P;P;D;P;B	0.59767	0.617;0.483;0.986;0.939;0.191	B;B;P;B;B	0.50825	0.173;0.084;0.651;0.426;0.073	T	0.02743	-1.1116	10	0.12766	T	0.61	-4.4126	15.8662	0.79067	0.0:0.1356:0.8644:0.0	.	257;282;77;371;298	F8W820;B4DN43;B4DMS9;Q9H0E9-2;Q9H0E9	.;.;.;.;BRD8_HUMAN	S	298;371;298;257	ENSP00000254900:P298S;ENSP00000230901:P371S;ENSP00000384845:P298S;ENSP00000408396:P257S	ENSP00000230901:P371S	P	-	1	0	BRD8	137530211	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	5.588000	0.67517	1.612000	0.50221	0.655000	0.94253	CCA		0.537	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696	
PCDHB17	54661	broad.mit.edu	37	5	140536602	140536602	+	Silent	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr5:140536602C>T	ENST00000539533.1	+	1	1026	c.1026C>T	c.(1024-1026)aaC>aaT	p.N342N						protocadherin beta 17 pseudogene																		TGGATATAAACGACAACGCAC	0.443																																						uc003lis.3																			0											c.(1021-1023)aaC>aaT		Homo sapiens protocadherin beta 17 pseudogene (PCDHB17), non-coding RNA.																																				SO:0001819	synonymous_variant	54661							g.chr5:140536602C>T	AF152527		5q31	2010-01-26				ENSG00000255622		"""Cadherins / Protocadherins : Clustered"""	14547	pseudogene	pseudogene						10380929	Standard	NR_001280		Approved	PCDH-psi1	uc003lis.3			ENST00000539533.1:c.1026C>T	5.37:g.140536602C>T							p.N341N							0	1023	+									Silent	SNP	ENST00000539533.1	37	c.1023C>T																																																																																					0.443	PCDHB17-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
PCDHGB3	56102	broad.mit.edu	37	5	140751057	140751057	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr5:140751057G>A	ENST00000576222.1	+	1	1227	c.1096G>A	c.(1096-1098)Gtt>Att	p.V366I	PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	366	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGGACTGCCGTTGCCCTGAT	0.408																																						uc003ljw.2																			0		p.V365V(1)		breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35						c.(1096-1098)Gtt>Att		Homo sapiens protocadherin gamma subfamily B, 3 (PCDHGB3), transcript variant 1, mRNA.							42.0	43.0	43.0					5																	140751057		1928	4137	6065	SO:0001583	missense	56102				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:140751057G>A	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1096G>A	5.37:g.140751057G>A	ENSP00000461862:p.Val366Ile					PCDHGC5_uc003lji.2_Intron|PCDHGC5_uc003ljk.2_Intron|PCDHGC5_uc003ljm.2_Intron|PCDHGC5_uc003ljo.2_Intron|PCDHGC5_uc003ljq.2_Intron|PCDHGC5_uc003ljs.2_Intron|PCDHGC5_uc003lju.2_Intron|PCDHGC5_uc003ljy.2_5'Flank|PCDHGC5_uc011dat.2_Missense_Mutation_p.V366I|PCDHGC5_uc011dau.2_5'Flank	p.V366I	NM_018924	NP_061747	Q9Y5F6	PCDGM_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		0	1096	+			369			Cadherin 4.		A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	c.1096G>A	CCDS58980.1																																																																																				0.408	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924	
SLIT3	6586	broad.mit.edu	37	5	168180912	168180912	+	Missense_Mutation	SNP	C	C	T	rs562240210	byFrequency	TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr5:168180912C>T	ENST00000519560.1	-	17	2205	c.1786G>A	c.(1786-1788)Gtg>Atg	p.V596M	SLIT3_ENST00000404867.3_Missense_Mutation_p.V596M|SLIT3_ENST00000332966.8_Missense_Mutation_p.V596M	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	596					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.V596M(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGCCCGTGCACGGTCTCCAGC	0.617													C|||	3	0.000599042	0.0015	0.0014	5008	,	,		19792	0.0		0.0	False		,,,				2504	0.0				Ovarian(29;311 847 10864 17279 24903)	uc010jjg.3																			1	Substitution - Missense(1)	p.V596M(2)	endometrium(1)	endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100						c.(1786-1788)Gtg>Atg		Homo sapiens slit homolog 3 (Drosophila) (SLIT3), mRNA.							50.0	47.0	48.0					5																	168180912		2203	4300	6503	SO:0001583	missense	6586				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding	g.chr5:168180912C>T	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.1786G>A	5.37:g.168180912C>T	ENSP00000430333:p.Val596Met					SLIT3_uc003mab.3_Missense_Mutation_p.V596M	p.V596M	NM_003062	NP_003053	O75094	SLIT3_HUMAN	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		16	2206	-	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	596					A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	37	c.1786G>A	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	C	10.42	1.344413	0.24339	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.80480	-1.38;-1.38;-1.38	5.27	1.51	0.23008	.	0.462046	0.24247	N	0.040202	T	0.75280	0.3828	M	0.62723	1.935	0.36921	D	0.891391	P	0.35745	0.518	B	0.35727	0.209	T	0.73017	-0.4115	10	0.54805	T	0.06	.	9.4068	0.38466	0.0:0.7088:0.0:0.2912	.	596	O75094	SLIT3_HUMAN	M	596	ENSP00000430333:V596M;ENSP00000332164:V596M;ENSP00000384890:V596M	ENSP00000332164:V596M	V	-	1	0	SLIT3	168113490	0.076000	0.21285	0.051000	0.19133	0.313000	0.28021	0.562000	0.23531	0.003000	0.14656	-0.781000	0.03364	GTG		0.617	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
GRM6	2916	broad.mit.edu	37	5	178413868	178413868	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr5:178413868C>G	ENST00000517717.1	-	8	1509	c.1471G>C	c.(1471-1473)Ggc>Cgc	p.G491R	GRM6_ENST00000231188.5_Missense_Mutation_p.G491R|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	491					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		GCCCACTGGCCCACTGCCTGG	0.642																																						uc003mjr.3																			0		p.V490M(1)		NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55						c.(1471-1473)Ggc>Cgc		Homo sapiens glutamate receptor, metabotropic 6 (GRM6), mRNA.							68.0	57.0	61.0					5																	178413868		2203	4300	6503	SO:0001583	missense	2916				detection of visible light|visual perception	integral to plasma membrane		g.chr5:178413868C>G	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1471G>C	5.37:g.178413868C>G	ENSP00000430767:p.Gly491Arg					GRM6_uc003mjq.3_5'Flank|GRM6_uc010jla.1_Missense_Mutation_p.G74R|GRM6_uc003mjs.1_Missense_Mutation_p.G111R	p.G491R	NM_000843	NP_000834	O15303	GRM6_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)	6	1650	-	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	491						Missense_Mutation	SNP	ENST00000517717.1	37	c.1471G>C	CCDS4442.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.515740	0.85495	.	.	ENSG00000113262	ENST00000319065;ENST00000231188;ENST00000517717	D;D	0.95447	-3.71;-3.71	4.74	4.74	0.60224	.	.	.	.	.	D	0.97253	0.9102	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.91635	0.999;0.958	D	0.97902	1.0303	9	0.87932	D	0	.	15.5896	0.76517	0.0:1.0:0.0:0.0	.	619;491	E7EX65;O15303	.;GRM6_HUMAN	R	619;491;491	ENSP00000231188:G491R;ENSP00000430767:G491R	ENSP00000231188:G491R	G	-	1	0	GRM6	178346474	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.787000	0.62432	2.339000	0.79563	0.462000	0.41574	GGC		0.642	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
OR14J1	442191	broad.mit.edu	37	6	29274611	29274611	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr6:29274611G>A	ENST00000377160.2	+	1	209	c.145G>A	c.(145-147)Gtg>Atg	p.V49M		NM_030946.1	NP_112208.1	Q9UGF5	O14J1_HUMAN	olfactory receptor, family 14, subfamily J, member 1	49						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(2)	17						CATCATTACCGTGGACCGTCG	0.468																																						uc011dln.2																			0				endometrium(2)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(2)	17						c.(145-147)Gtg>Atg		Homo sapiens olfactory receptor, family 14, subfamily J, member 1 (OR14J1), mRNA.							213.0	196.0	202.0					6																	29274611		1511	2709	4220	SO:0001583	missense	442191				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr6:29274611G>A		CCDS34362.1	6p21.3	2012-08-09	2008-04-02	2008-04-02	ENSG00000204695	ENSG00000204695		"""GPCR / Class A : Olfactory receptors"""	13971	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily U, member 1"""	OR5U1			Standard	NM_030946		Approved	hs6M1-28	uc011dln.2	Q9UGF5	OTTHUMG00000031184	ENST00000377160.2:c.145G>A	6.37:g.29274611G>A	ENSP00000366365:p.Val49Met						p.V49M	NM_030946	NP_112208	Q9UGF5	O14J1_HUMAN			0	145	+			49					A2BEC2|B0V078|Q5ST27	Missense_Mutation	SNP	ENST00000377160.2	37	c.145G>A	CCDS34362.1	.	.	.	.	.	.	.	.	.	.	G	10.58	1.390025	0.25118	.	.	ENSG00000204695	ENST00000377160	T	0.03094	4.05	4.86	-2.06	0.07298	GPCR, rhodopsin-like superfamily (1);	1.121790	0.06954	N	0.815154	T	0.00608	0.0020	N	0.05259	-0.085	0.09310	N	1	B	0.23058	0.079	B	0.10450	0.005	T	0.48186	-0.9057	10	0.56958	D	0.05	.	5.2367	0.15450	0.0:0.3101:0.2788:0.4111	.	49	Q9UGF5	O14J1_HUMAN	M	49	ENSP00000366365:V49M	ENSP00000366365:V49M	V	+	1	0	OR14J1	29382590	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	-2.621000	0.00878	-0.408000	0.07565	-0.272000	0.10252	GTG		0.468	OR14J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076362.2		
CLIC5	53405	broad.mit.edu	37	6	45917082	45917082	+	Silent	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr6:45917082C>T	ENST00000185206.6	-	3	839	c.687G>A	c.(685-687)acG>acA	p.T229T	CLIC5_ENST00000544153.1_Silent_p.T70T|CLIC5_ENST00000339561.6_Silent_p.T70T	NM_001114086.1	NP_001107558.1	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5	229					auditory receptor cell stereocilium organization (GO:0060088)|chloride transport (GO:0006821)|diet induced thermogenesis (GO:0002024)|female pregnancy (GO:0007565)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|sensory perception of sound (GO:0007605)|transport (GO:0006810)	actin cytoskeleton (GO:0015629)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|stereocilium (GO:0032420)	voltage-gated chloride channel activity (GO:0005247)	p.T70T(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	13						AGGGCGGGTGCGTGCCGGGGG	0.547																																						uc003oxv.3																			1	Substitution - coding silent(1)	p.T70T(1)	upper_aerodigestive_tract(1)	endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	13						c.(685-687)acG>acA		Homo sapiens chloride intracellular channel 5 (CLIC5), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.							140.0	133.0	135.0					6																	45917082		2203	4300	6503	SO:0001819	synonymous_variant	53405				female pregnancy	actin cytoskeleton|cell cortex|chloride channel complex|Golgi apparatus|insoluble fraction|microtubule organizing center	protein binding|voltage-gated chloride channel activity	g.chr6:45917082C>T	AF216941	CCDS4914.1, CCDS47438.1, CCDS59022.1	6p12.3	2014-03-14			ENSG00000112782	ENSG00000112782		"""Ion channels / Chloride channels : Intracellular"""	13517	protein-coding gene	gene with protein product		607293				10793131	Standard	NM_001114086		Approved		uc003oxv.3	Q9NZA1	OTTHUMG00000014775	ENST00000185206.6:c.687G>A	6.37:g.45917082C>T						CLIC5_uc003oxu.3_Silent_p.T70T|CLIC5_uc003oxx.3_Silent_p.T70T	p.T229T	NM_001114086	NP_001107558	Q9NZA1	CLIC5_HUMAN			2	793	-			229					B3KUF1|Q5T4Z0|Q8NBY3|Q96JT5|Q9BWZ0	Silent	SNP	ENST00000185206.6	37	c.687G>A	CCDS47438.1																																																																																				0.547	CLIC5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040761.1		
COL19A1	1310	broad.mit.edu	37	6	70642699	70642699	+	Missense_Mutation	SNP	T	T	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr6:70642699T>A	ENST00000322773.4	+	7	793	c.691T>A	c.(691-693)Tac>Aac	p.Y231N		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	231	Laminin G-like.				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						ACTTAAAATCTACTGCAGTGC	0.303																																						uc003pfc.1																			0				breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						c.(691-693)Tac>Aac		Homo sapiens collagen, type XIX, alpha 1 (COL19A1), mRNA.							58.0	58.0	58.0					6																	70642699		2201	4299	6500	SO:0001583	missense	1310				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging	g.chr6:70642699T>A		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.691T>A	6.37:g.70642699T>A	ENSP00000316030:p.Tyr231Asn					COL19A1_uc010kam.2_Missense_Mutation_p.Y127N	p.Y231N	NM_001858	NP_001849	Q14993	COJA1_HUMAN			6	808	+			231			TSP N-terminal.		Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	37	c.691T>A	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	T	12.58	1.982072	0.34942	.	.	ENSG00000082293	ENST00000322773	T	0.02552	4.25	5.68	3.29	0.37713	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.074661	0.53938	D	0.000047	T	0.03220	0.0094	M	0.77313	2.365	0.80722	D	1	D	0.53619	0.961	P	0.47744	0.556	T	0.37430	-0.9706	10	0.59425	D	0.04	.	9.7951	0.40731	0.0:0.1389:0.0:0.8611	.	231	Q14993	COJA1_HUMAN	N	231	ENSP00000316030:Y231N	ENSP00000316030:Y231N	Y	+	1	0	COL19A1	70699420	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.270000	0.78493	0.443000	0.26582	0.533000	0.62120	TAC		0.303	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		
KCNQ5	56479	broad.mit.edu	37	6	73904675	73904675	+	Silent	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr6:73904675C>T	ENST00000370398.1	+	14	2446	c.2337C>T	c.(2335-2337)gaC>gaT	p.D779D	KCNQ5_ENST00000355194.4_Silent_p.D779D|KCNQ5_ENST00000414165.2_Silent_p.D669D|KCNQ5_ENST00000403813.2_Silent_p.D770D|KCNQ5_ENST00000342056.2_Silent_p.D798D|KCNQ5_ENST00000402622.2_Silent_p.D789D|KCNQ5_ENST00000355635.3_Silent_p.D780D	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	779					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	GCATTTCTGACGTCACCACCT	0.512																																					GBM(142;1375 1859 14391 23261 44706)	uc011dyh.2																			0				breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						c.(2392-2394)gaC>gaT		Homo sapiens potassium voltage-gated channel, KQT-like subfamily, member 5 (KCNQ5), transcript variant 4, mRNA.							113.0	99.0	104.0					6																	73904675		2203	4300	6503	SO:0001819	synonymous_variant	56479				protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity	g.chr6:73904675C>T	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.2337C>T	6.37:g.73904675C>T						KCNQ5_uc011dyi.2_Silent_p.D789D|KCNQ5_uc010kat.3_Silent_p.D770D|KCNQ5_uc003pgk.3_Silent_p.D779D|KCNQ5_uc011dyj.2_Silent_p.D669D|KCNQ5_uc011dyk.2_Silent_p.D529D	p.D798D	NM_001160133	NP_001153605	Q9NR82	KCNQ5_HUMAN		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	14	2741	+		all_epithelial(107;0.116)|Lung NSC(302;0.219)	779					A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Silent	SNP	ENST00000370398.1	37	c.2394C>T	CCDS4976.1																																																																																				0.512	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842	
RSPH10B	222967	broad.mit.edu	37	7	5967958	5967958	+	Silent	SNP	G	G	C			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr7:5967958G>C	ENST00000405415.1	-	19	2687	c.2301C>G	c.(2299-2301)gtC>gtG	p.V767V	RSPH10B_ENST00000539903.1_3'UTR|RSPH10B_ENST00000404406.1_Silent_p.V767V|RSPH10B_ENST00000535104.1_5'UTR|RSPH10B_ENST00000337579.3_Silent_p.V767V|RSPH10B_ENST00000441023.2_Silent_p.V767V			P0C881	R10B1_HUMAN	radial spoke head 10 homolog B (Chlamydomonas)	767										breast(1)|kidney(1)|lung(4)|ovary(1)|skin(4)	11		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)		TCACAAAGAAGACGTACATAT	0.438																																						uc011jwk.2																			0				breast(1)|kidney(1)|lung(4)|ovary(1)|skin(4)	11						c.(1165-1167)tCt>tGt		Homo sapiens radial spoke head 10 homolog B2 (Chlamydomonas) (RSPH10B2), mRNA.							429.0	394.0	406.0					7																	5967958		2203	4300	6503	SO:0001819	synonymous_variant	728194							g.chr7:5967958G>C		CCDS34598.1	7p22.2	2008-07-04			ENSG00000155026	ENSG00000155026			27362	protein-coding gene	gene with protein product						16507594	Standard	NM_173565		Approved		uc003sph.1	P0C881	OTTHUMG00000152378	ENST00000405415.1:c.2301C>G	7.37:g.5967958G>C						RSPH10B_uc003spg.1_Intron|RSPH10B_uc003sph.1_Silent_p.V767V|RSPH10B_uc010ktd.1_Silent_p.V767V	p.S389C			B2RC85	R10B2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)	10	1437	-		Ovarian(82;0.0694)	0					A6NMW7|Q86ST9|Q8NE68	Silent	SNP	ENST00000405415.1	37	c.1166C>G	CCDS34598.1																																																																																				0.438	RSPH10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325465.2	NM_173565	
HDAC9	9734	broad.mit.edu	37	7	18868807	18868807	+	Silent	SNP	C	C	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr7:18868807C>A	ENST00000432645.2	+	17	2337	c.2337C>A	c.(2335-2337)ccC>ccA	p.P779P	HDAC9_ENST00000441542.2_Silent_p.P782P|HDAC9_ENST00000406451.4_Silent_p.P779P|HDAC9_ENST00000401921.1_Silent_p.P738P	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	779	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	TTGTGAGGCCCCCTGGCCATC	0.537																																						uc003sui.3																			0				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82						c.(2344-2346)ccC>ccA		Homo sapiens histone deacetylase 9 (HDAC9), transcript variant 5, mRNA.	Valproic Acid(DB00313)						145.0	137.0	139.0					7																	18868807		1984	4158	6142	SO:0001819	synonymous_variant	9734				B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity	g.chr7:18868807C>A	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.2337C>A	7.37:g.18868807C>A						HDAC9_uc003sue.3_Silent_p.P779P|HDAC9_uc011jyd.2_Silent_p.P779P|HDAC9_uc003suh.3_Silent_p.P779P|HDAC9_uc003suj.3_Silent_p.P738P|HDAC9_uc003suk.3_Silent_p.P27P|HDAC9_uc003sua.1_Silent_p.P757P	p.P782P	NM_178425	NP_848512	Q9UKV0	HDAC9_HUMAN			16	2387	+	all_lung(11;0.187)		779			Histone deacetylase.		A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	c.2346C>A	CCDS47555.1																																																																																				0.537	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
STARD3NL	83930	broad.mit.edu	37	7	38247143	38247143	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr7:38247143C>A	ENST00000009041.7	+	2	295	c.38C>A	c.(37-39)aCc>aAc	p.T13N	STARD3NL_ENST00000396013.1_Missense_Mutation_p.T13N|STARD3NL_ENST00000544203.1_Missense_Mutation_p.T6N|STARD3NL_ENST00000434197.1_Missense_Mutation_p.T13N	NM_032016.3	NP_114405.1	O95772	MENTO_HUMAN	STARD3 N-terminal like	13						endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10						AACGCTCTCACCGGGAGCCAG	0.512																																						uc003tfr.3																			0				endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10						c.(37-39)aCc>aAc		Homo sapiens STARD3 N-terminal like (STARD3NL), mRNA.							85.0	79.0	81.0					7																	38247143		2203	4300	6503	SO:0001583	missense	83930					integral to membrane|late endosome membrane		g.chr7:38247143C>A	AJ492267	CCDS5455.1	7p14-p13	2003-02-06			ENSG00000010270	ENSG00000010270			19169	protein-coding gene	gene with protein product		611759				12393907	Standard	NM_032016		Approved	MENTHO, MGC3251	uc003tfr.3	O95772	OTTHUMG00000023659	ENST00000009041.7:c.38C>A	7.37:g.38247143C>A	ENSP00000009041:p.Thr13Asn						p.T13N	NM_032016	NP_114405	O95772	MENTO_HUMAN			1	311	+			13					A4D1X0	Missense_Mutation	SNP	ENST00000009041.7	37	c.38C>A	CCDS5455.1	.	.	.	.	.	.	.	.	.	.	C	8.441	0.850871	0.17034	.	.	ENSG00000010270	ENST00000009041;ENST00000544203;ENST00000434197;ENST00000396013;ENST00000440144;ENST00000453225;ENST00000429075	T;T;T;T;T;T;T	0.42513	1.55;1.54;1.55;1.55;0.97;0.97;0.97	6.17	2.18	0.27775	.	0.536174	0.22494	N	0.059334	T	0.19287	0.0463	N	0.08118	0	0.23282	N	0.997982	B;B	0.12630	0.006;0.006	B;B	0.14023	0.01;0.005	T	0.15752	-1.0426	10	0.27082	T	0.32	-4.8272	6.505	0.22190	0.1118:0.3197:0.4912:0.0774	.	13;13	C9JKL2;O95772	.;MENTO_HUMAN	N	13;6;13;13;13;13;13	ENSP00000009041:T13N;ENSP00000439436:T6N;ENSP00000394000:T13N;ENSP00000379334:T13N;ENSP00000411933:T13N;ENSP00000395455:T13N;ENSP00000402028:T13N	ENSP00000009041:T13N	T	+	2	0	STARD3NL	38213668	0.906000	0.30813	0.329000	0.25429	0.960000	0.62799	1.379000	0.34340	0.457000	0.26962	0.655000	0.94253	ACC		0.512	STARD3NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226929.2		
EGFR	1956	broad.mit.edu	37	7	55221782	55221782	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr7:55221782C>T	ENST00000275493.2	+	7	1003	c.826C>T	c.(826-828)Cag>Tag	p.Q276*	EGFR_ENST00000420316.2_Nonsense_Mutation_p.Q276*|EGFR_ENST00000344576.2_Nonsense_Mutation_p.Q276*|EGFR_ENST00000442591.1_Nonsense_Mutation_p.Q276*|EGFR_ENST00000455089.1_Nonsense_Mutation_p.Q231*|EGFR_ENST00000342916.3_Nonsense_Mutation_p.Q276*|EGFR_ENST00000454757.2_Nonsense_Mutation_p.Q223*	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	276			Missing (variant EGFR vIII; found in a lung cancer sample; somatic mutation; induces lung cancer when exogenously expressed). {ECO:0000269|PubMed:16672372}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CACCACGTACCAGATGGATGT	0.592		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												uc003tqk.3		8	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""A, O, Mis"""	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""			"""E, O"""		NSCLC	"""glioma, NSCLC"""		0		p.V30_R297>G(5)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110						c.(826-828)Cag>Tag		Homo sapiens epidermal growth factor receptor (EGFR), transcript variant 1, mRNA.	Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)						197.0	156.0	169.0					7																	55221782		2203	4300	6503	SO:0001587	stop_gained	1956	Lung Cancer, Familial Clustering of	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	g.chr7:55221782C>T		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.826C>T	7.37:g.55221782C>T	ENSP00000275493:p.Gln276*	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)				EGFR_uc003tqh.3_Nonsense_Mutation_p.Q276*|EGFR_uc003tqi.3_Nonsense_Mutation_p.Q276*|EGFR_uc003tqj.3_Nonsense_Mutation_p.Q276*|EGFR_uc022adm.1_Nonsense_Mutation_p.Q276*|EGFR_uc010kzg.2_Nonsense_Mutation_p.Q231*|EGFR_uc022adn.1_Nonsense_Mutation_p.Q231*|EGFR_uc011kco.2_Nonsense_Mutation_p.Q223*|EGFR_uc011kcp.1_5'Flank|EGFR_uc011kcq.1_5'Flank	p.Q276*	NM_005228	NP_005219	P00533	EGFR_HUMAN	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		6	1072	+	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		276					O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Nonsense_Mutation	SNP	ENST00000275493.2	37	c.826C>T	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	C	37	6.577314	0.97676	.	.	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000420316;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	.	.	.	5.94	4.12	0.48240	.	0.107102	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	15.5778	0.76408	0.0:0.7275:0.2725:0.0	.	.	.	.	X	231;276;146;276;276;276;276;223;70	.	ENSP00000275493:Q276X	Q	+	1	0	EGFR	55189276	1.000000	0.71417	0.997000	0.53966	0.749000	0.42624	2.590000	0.46154	0.826000	0.34661	0.563000	0.77884	CAG		0.592	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
COL1A2	1278	broad.mit.edu	37	7	94040216	94040216	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr7:94040216C>T	ENST00000297268.6	+	22	1684	c.1213C>T	c.(1213-1215)Cgt>Tgt	p.R405C		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	405					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TCCTGGTTCTCGTGGTCTTCC	0.448										HNSCC(75;0.22)																												uc003ung.1																		COL1A2/PLAG1(3)	0				NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115						c.(1213-1215)Cgt>Tgt		Homo sapiens collagen, type I, alpha 2 (COL1A2), mRNA.	Collagenase(DB00048)						152.0	150.0	150.0					7																	94040216		2203	4300	6503	SO:0001583	missense	1278				axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging	g.chr7:94040216C>T	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.1213C>T	7.37:g.94040216C>T	ENSP00000297268:p.Arg405Cys	HNSCC(75;0.22)				COL1A2_uc011kib.1_Intron	p.R405C	NM_000089	NP_000080	P08123	CO1A2_HUMAN	STAD - Stomach adenocarcinoma(171;0.0031)		21	1684	+	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		405					P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	c.1213C>T	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.367345	0.82463	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.96168	-3.93	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.98213	0.9409	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.98376	1.0556	10	0.87932	D	0	.	20.5276	0.99231	0.0:1.0:0.0:0.0	.	405	P08123	CO1A2_HUMAN	C	405;406	ENSP00000297268:R405C	ENSP00000297268:R405C	R	+	1	0	COL1A2	93878152	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.937000	0.99478	0.650000	0.86243	CGT		0.448	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
REPIN1	29803	broad.mit.edu	37	7	150069659	150069659	+	Silent	SNP	C	C	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr7:150069659C>A	ENST00000425389.2	+	1	1407	c.1329C>A	c.(1327-1329)ggC>ggA	p.G443G	REPIN1_ENST00000397281.2_Silent_p.G443G|REPIN1_ENST00000540729.1_Silent_p.G443G|REPIN1_ENST00000479668.1_3'UTR|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000444957.1_Silent_p.G443G|REPIN1_ENST00000489432.2_Silent_p.G500G	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	443					DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			TCTCCCAGGGCAGCCATCTGG	0.716																																						uc022apt.1																			0				cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14						c.(7-9)Gcc>Tcc		Homo sapiens mRNA; cDNA DKFZp762K135 (from clone DKFZp762K135).							8.0	12.0	11.0					7																	150069659		1958	4036	5994	SO:0001819	synonymous_variant	29803				DNA replication	nuclear origin of replication recognition complex	DNA binding|zinc ion binding	g.chr7:150069659C>A	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"""Zinc fingers, C2H2-type"""	17922	protein-coding gene	gene with protein product	"""replication initiation region protein (60kD)"", ""zinc finger protein AP4"", ""zinc finger protein 464 (RIP60)"""		"""zinc finger protein 464 (RIP60)"""	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.1329C>A	7.37:g.150069659C>A						REPIN1_uc003whd.2_Silent_p.G432G|REPIN1_uc010lpq.1_Silent_p.G443G|REPIN1_uc010lpr.1_Silent_p.G500G|REPIN1_uc003whc.2_Silent_p.G443G|REPIN1_uc003whe.2_Silent_p.G443G	p.A3S			Q9BWE0	REPI1_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.011)		0	375	-	Ovarian(565;0.183)|Melanoma(164;0.226)		11					C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Silent	SNP	ENST00000425389.2	37	c.7G>T	CCDS43677.1																																																																																				0.716	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
CSMD1	64478	broad.mit.edu	37	8	3889525	3889525	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr8:3889525C>T	ENST00000520002.1	-	4	1067	c.512G>A	c.(511-513)tGc>tAc	p.C171Y	CSMD1_ENST00000542608.1_Missense_Mutation_p.C171Y|CSMD1_ENST00000602557.1_Missense_Mutation_p.C171Y|CSMD1_ENST00000539096.1_Missense_Mutation_p.C171Y|CSMD1_ENST00000602723.1_Missense_Mutation_p.C171Y|CSMD1_ENST00000400186.3_Missense_Mutation_p.C171Y|CSMD1_ENST00000537824.1_Missense_Mutation_p.C171Y			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	171	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GCCAGGGAGGCAGCTGTACCG	0.512																																						uc022aqr.1																			0				breast(20)|large_intestine(5)	25						c.(511-513)tGc>tAc		Homo sapiens CUB and Sushi multiple domains 1 (CSMD1), mRNA.							119.0	130.0	126.0					8																	3889525		2118	4247	6365	SO:0001583	missense	64478					integral to membrane		g.chr8:3889525C>T			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.512G>A	8.37:g.3889525C>T	ENSP00000430733:p.Cys171Tyr						p.C171Y	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)	3	902	-		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)	171			Sushi 1.		Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37	c.512G>A		.	.	.	.	.	.	.	.	.	.	C	23.7	4.443977	0.83993	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	D;D;D;D;D	0.99784	-6.74;-6.74;-6.74;-6.74;-6.74	5.52	5.52	0.82312	.	0.000000	0.53938	U	0.000052	D	0.99900	0.9952	H	0.99117	4.435	0.54753	D	0.999989	D	0.89917	1.0	D	0.91635	0.999	D	0.96202	0.9146	10	0.87932	D	0	.	18.4147	0.90565	0.0:1.0:0.0:0.0	.	171	E5RIG2	.	Y	171;171;33;171;171;171	ENSP00000383047:C171Y;ENSP00000430733:C171Y;ENSP00000441462:C171Y;ENSP00000446243:C171Y;ENSP00000441675:C171Y	ENSP00000320445:C33Y	C	-	2	0	CSMD1	3876933	1.000000	0.71417	0.962000	0.40283	0.796000	0.44982	7.558000	0.82253	2.612000	0.88384	0.655000	0.94253	TGC		0.512	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
OPRK1	4986	broad.mit.edu	37	8	54163342	54163342	+	Splice_Site	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr8:54163342G>A	ENST00000265572.3	-	2	553	c.256C>T	c.(256-258)Cga>Tga	p.R86*	OPRK1_ENST00000520287.1_Splice_Site_p.R86*	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	86					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-inhibiting opioid receptor signaling pathway (GO:0031635)|behavior (GO:0007610)|defense response to virus (GO:0051607)|immune response (GO:0006955)|locomotory behavior (GO:0007626)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of saliva secretion (GO:0046877)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dynorphin receptor activity (GO:0038048)|opioid receptor activity (GO:0004985)			NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	43		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CGCGCTCACCGGATGATCACG	0.687																																						uc003xrh.1																			0				NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	43						c.e1+1		Homo sapiens opioid receptor, kappa 1 (OPRK1), mRNA.	Buprenorphine(DB00921)|Butorphanol(DB00611)|Cocaine(DB00907)|Codeine(DB00318)|Dezocine(DB01209)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Meperidine(DB00454)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Tramadol(DB00193)						37.0	31.0	33.0					8																	54163342		2202	4299	6501	SO:0001630	splice_region_variant	4986				behavior|immune response|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception|synaptic transmission|viral genome replication	integral to plasma membrane	kappa-opioid receptor activity|protein binding	g.chr8:54163342G>A		CCDS6152.1, CCDS64895.1	8q11.2	2014-05-21			ENSG00000082556	ENSG00000082556		"""GPCR / Class A : Opioid receptors"""	8154	protein-coding gene	gene with protein product		165196				8188308	Standard	XM_005251252		Approved	KOR, OPRK	uc003xri.1	P41145	OTTHUMG00000164276	ENST00000265572.3:c.257+1C>T	8.37:g.54163342G>A						OPRK1_uc022aup.1_Splice_Site|OPRK1_uc003xri.1_Splice_Site_p.R86_splice|OPRK1_uc010lyc.1_Splice_Site	p.R86_splice	NM_000912	NP_000903	P41145	OPRK_HUMAN			1	632	-		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)	86					E5RHC9|Q499G4	Nonsense_Mutation	SNP	ENST00000265572.3	37	c.257_splice	CCDS6152.1	.	.	.	.	.	.	.	.	.	.	G	41	8.916862	0.99002	.	.	ENSG00000082556	ENST00000265572;ENST00000520287;ENST00000396798	.	.	.	5.07	1.98	0.26296	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.1852	0.20493	0.093:0.0:0.4567:0.4504	.	.	.	.	X	86;86;72	.	ENSP00000265572:R86X	R	-	1	2	OPRK1	54325895	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.659000	0.46741	0.694000	0.31654	0.462000	0.41574	CGA		0.687	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1		Nonsense_Mutation
CHD7	55636	broad.mit.edu	37	8	61769443	61769443	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr8:61769443G>A	ENST00000423902.2	+	34	8083	c.7604G>A	c.(7603-7605)aGt>aAt	p.S2535N	CHD7_ENST00000529472.1_3'UTR|CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2535					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			ACGTCATTGAGTGCAGTAAGT	0.542																																						uc003xue.3																			0				NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123						c.(7603-7605)aGt>aAt		Homo sapiens chromodomain helicase DNA binding protein 7 (CHD7), mRNA.							56.0	59.0	58.0					8																	61769443		2134	4244	6378	SO:0001583	missense	55636				central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity	g.chr8:61769443G>A	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.7604G>A	8.37:g.61769443G>A	ENSP00000392028:p.Ser2535Asn					CHD7_uc022aux.1_Intron	p.S2535N	NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	BRCA - Breast invasive adenocarcinoma(89;0.143)		33	8096	+		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	2535					D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	37	c.7604G>A	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.267481	0.40095	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	T	0.81163	-1.46	5.62	4.74	0.60224	.	0.239554	0.39083	N	0.001471	T	0.71358	0.3330	L	0.29908	0.895	0.35001	D	0.755936	B	0.17667	0.023	B	0.18263	0.021	T	0.71361	-0.4616	10	0.27785	T	0.31	-11.8586	15.103	0.72296	0.0:0.4329:0.567:0.0	.	2535	Q9P2D1	CHD7_HUMAN	N	2535	ENSP00000392028:S2535N	ENSP00000307304:S2535N	S	+	2	0	CHD7	61931997	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.375000	0.44283	1.348000	0.45733	0.655000	0.94253	AGT		0.542	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
UBAP2	55833	broad.mit.edu	37	9	33923830	33923830	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr9:33923830C>T	ENST00000379238.1	-	24	2876	c.2759G>A	c.(2758-2760)gGc>gAc	p.G920D	UBAP2_ENST00000379239.4_Missense_Mutation_p.G653D|UBAP2_ENST00000539807.1_Missense_Mutation_p.G675D|UBAP2_ENST00000449054.1_Missense_Mutation_p.G920D|UBAP2_ENST00000360802.1_Missense_Mutation_p.G920D|UBAP2_ENST00000379235.1_Missense_Mutation_p.G159D					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		ACTGGGCATGCCTGTGTAGTA	0.567																																						uc003ztq.1																			0		p.T919I(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32						c.(2758-2760)gGc>gAc		Homo sapiens ubiquitin associated protein 2 (UBAP2), mRNA.							210.0	166.0	181.0					9																	33923830		2203	4300	6503	SO:0001583	missense	55833							g.chr9:33923830C>T	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.2759G>A	9.37:g.33923830C>T	ENSP00000368540:p.Gly920Asp					UBAP2_uc011loc.1_Missense_Mutation_p.G829D|UBAP2_uc011lod.1_Missense_Mutation_p.G653D|UBAP2_uc011loe.1_Missense_Mutation_p.G675D|UBAP2_uc011lof.1_Missense_Mutation_p.G845D|UBAP2_uc003ztn.1_Missense_Mutation_p.G159D|UBAP2_uc003zto.1_Missense_Mutation_p.G159D|UBAP2_uc003ztp.2_Missense_Mutation_p.G159D	p.G920D	NM_018449	NP_060919	Q5T6F2	UBAP2_HUMAN	LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)	23	2872	-			920						Missense_Mutation	SNP	ENST00000379238.1	37	c.2759G>A	CCDS6547.1	.	.	.	.	.	.	.	.	.	.	C	16.75	3.208603	0.58343	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379235;ENST00000379239;ENST00000539807;ENST00000351580	T;T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39;1.39	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.65026	0.2652	M	0.81942	2.565	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.998;0.998;0.999;0.999	D;D;D;D;D	0.71656	0.974;0.939;0.939;0.964;0.941	T	0.66799	-0.5832	10	0.72032	D	0.01	-13.1121	20.3214	0.98679	0.0:1.0:0.0:0.0	.	845;675;653;829;920	F5H4D5;F5H2U4;A6NCA8;F5H2C8;Q5T6F2	.;.;.;.;UBAP2_HUMAN	D	920;920;920;829;159;653;675;354	ENSP00000368540:G920D;ENSP00000416932:G920D;ENSP00000354039:G920D;ENSP00000368537:G159D;ENSP00000368541:G653D;ENSP00000439329:G675D	ENSP00000259602:G354D	G	-	2	0	UBAP2	33913830	1.000000	0.71417	0.536000	0.28039	0.252000	0.25951	7.456000	0.80751	2.804000	0.96469	0.655000	0.94253	GGC		0.567	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
GABBR2	9568	broad.mit.edu	37	9	101148021	101148021	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr9:101148021G>C	ENST00000259455.2	-	11	2022	c.1563C>G	c.(1561-1563)aaC>aaG	p.N521K		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	521					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	GGATGATAAGGTTGTTCATGT	0.388																																						uc004ays.3																		NOTCH1_ENST00000277541/GABBR2(2)	0				breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49						c.(1561-1563)aaC>aaG		Homo sapiens gamma-aminobutyric acid (GABA) B receptor, 2 (GABBR2), mRNA.	Baclofen(DB00181)						157.0	142.0	147.0					9																	101148021		2203	4300	6503	SO:0001583	missense	9568				negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity	g.chr9:101148021G>C	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.1563C>G	9.37:g.101148021G>C	ENSP00000259455:p.Asn521Lys						p.N521K	NM_005458	NP_005449	O75899	GABR2_HUMAN			10	2023	-		Acute lymphoblastic leukemia(62;0.0527)	521					O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	c.1563C>G	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.815049	0.70912	.	.	ENSG00000136928	ENST00000259455	D	0.88046	-2.33	5.74	1.83	0.25207	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.93585	0.7952	M	0.93062	3.375	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.92184	0.5754	10	0.87932	D	0	-40.0009	8.3973	0.32564	0.3944:0.0:0.6056:0.0	.	521	O75899	GABR2_HUMAN	K	521	ENSP00000259455:N521K	ENSP00000259455:N521K	N	-	3	2	GABBR2	100187842	1.000000	0.71417	0.996000	0.52242	0.959000	0.62525	3.020000	0.49643	0.361000	0.24292	0.563000	0.77884	AAC		0.388	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
TLR4	7099	broad.mit.edu	37	9	120475663	120475663	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chr9:120475663G>C	ENST00000355622.6	+	3	1358	c.1257G>C	c.(1255-1257)ttG>ttC	p.L419F	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.L379F	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	419					activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	CAAACTTCTTGGGCTTAGAAC	0.373																																						uc004bjz.3																			0		p.F418L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103						c.(1255-1257)ttG>ttC		Homo sapiens toll-like receptor 4 (TLR4), transcript variant 1, mRNA.							63.0	64.0	64.0					9																	120475663		2203	4300	6503	SO:0001583	missense	7099				activation of MAPK activity|cellular response to mechanical stimulus|detection of fungus|detection of lipopolysaccharide|I-kappaB phosphorylation|innate immune response|intestinal epithelial structure maintenance|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-23 production|negative regulation of interleukin-6 production|negative regulation of osteoclast differentiation|negative regulation of tumor necrosis factor production|positive regulation of chemokine production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interferon-gamma production|positive regulation of interleukin-1 production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 biosynthetic process|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of platelet activation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor biosynthetic process|positive regulation of tumor necrosis factor production|T-helper 1 type immune response|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	external side of plasma membrane|integral to plasma membrane|lipopolysaccharide receptor complex|perinuclear region of cytoplasm	lipopolysaccharide receptor activity|transmembrane receptor activity	g.chr9:120475663G>C	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"""CD molecules"""	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.1257G>C	9.37:g.120475663G>C	ENSP00000363089:p.Leu419Phe					TLR4_uc004bkb.3_Missense_Mutation_p.L219F|TLR4_uc004bka.3_Missense_Mutation_p.L379F	p.L419F	NM_138554	NP_612564	O00206	TLR4_HUMAN			2	1548	+			419					A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	37	c.1257G>C	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.654523	0.29425	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.00966	5.49;5.49	5.7	2.89	0.33648	.	1.576350	0.03494	N	0.216991	T	0.01156	0.0038	N	0.12961	0.28	0.09310	N	1	P	0.51537	0.946	P	0.47118	0.538	T	0.47355	-0.9124	10	0.51188	T	0.08	.	4.4431	0.11584	0.3073:0.0:0.5129:0.1798	.	419	O00206	TLR4_HUMAN	F	379;419	ENSP00000377997:L379F;ENSP00000363089:L419F	ENSP00000363089:L419F	L	+	3	2	TLR4	119515484	0.253000	0.23982	0.453000	0.27007	0.703000	0.40648	0.791000	0.26915	0.353000	0.24079	0.650000	0.86243	TTG		0.373	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554	
MAGEB1	4112	broad.mit.edu	37	X	30268639	30268639	+	Missense_Mutation	SNP	G	G	A	rs113819941		TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chrX:30268639G>A	ENST00000378981.3	+	4	350	c.29G>A	c.(28-30)cGt>cAt	p.R10H	MAGEB1_ENST00000397550.1_Missense_Mutation_p.R10H|MAGEB1_ENST00000397548.2_Missense_Mutation_p.R10H	NM_002363.4	NP_002354.2	P43366	MAGB1_HUMAN	melanoma antigen family B, 1	10										NS(2)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	32						AGTAAGCTCCGTGCTCGTGAG	0.587																																						uc022buh.1																			0				NS(2)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	32						c.(28-30)cGt>cAt		Homo sapiens melanoma antigen family B, 1 (MAGEB1), transcript variant 3, mRNA.							42.0	33.0	36.0					X																	30268639		2202	4300	6502	SO:0001583	missense	4112							g.chrX:30268639G>A		CCDS14222.1	Xp21.3	2009-03-17			ENSG00000214107	ENSG00000214107			6808	protein-coding gene	gene with protein product	"""DSS/AHC critical interval MAGE superfamily 10"", ""cancer/testis antigen family 3, member 1"""	300097				7761436, 9441743	Standard	NM_002363		Approved	MAGEL1, MAGE-Xp, DAM10, MGC9322, CT3.1	uc004dce.3	P43366	OTTHUMG00000021322	ENST00000378981.3:c.29G>A	X.37:g.30268639G>A	ENSP00000368264:p.Arg10His					MAGEB1_uc004dcc.3_Missense_Mutation_p.R10H|MAGEB1_uc004dcd.3_Missense_Mutation_p.R10H|MAGEB1_uc004dce.3_Missense_Mutation_p.R10H	p.R10H	NM_177415	NP_803134	P43366	MAGB1_HUMAN			0	29	+			10					B2RC79|O00601|O75862|Q6FHJ0|Q96CW8	Missense_Mutation	SNP	ENST00000378981.3	37	c.29G>A	CCDS14222.1	.	.	.	.	.	.	.	.	.	.	G	13.58	2.278517	0.40294	.	.	ENSG00000214107	ENST00000378981;ENST00000397550;ENST00000397548	T;T;T	0.06294	3.32;3.32;3.32	3.99	3.99	0.46301	Melanoma associated antigen, MAGE, N-terminal (1);	0.251113	0.27981	N	0.017071	T	0.23014	0.0556	M	0.81341	2.54	0.22968	N	0.998498	D	0.89917	1.0	D	0.91635	0.999	T	0.01956	-1.1240	10	0.42905	T	0.14	.	10.4831	0.44706	0.0:0.0:1.0:0.0	.	10	P43366	MAGB1_HUMAN	H	10	ENSP00000368264:R10H;ENSP00000380683:R10H;ENSP00000380681:R10H	ENSP00000368264:R10H	R	+	2	0	MAGEB1	30178560	0.174000	0.23070	0.563000	0.28383	0.044000	0.14063	1.373000	0.34272	2.232000	0.73038	0.600000	0.82982	CGT		0.587	MAGEB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056160.1	NM_002363	
CXorf22	170063	broad.mit.edu	37	X	35970005	35970005	+	Missense_Mutation	SNP	T	T	A			TCGA-06-0211-02A-02D-2280-08	TCGA-06-0211-10A-01D-1491-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3914c02e-44ad-4c96-8464-61aa95b42c49	ebf97220-6d4d-4016-bae3-ec279144c19d	g.chrX:35970005T>A	ENST00000297866.5	+	6	1037	c.971T>A	c.(970-972)aTt>aAt	p.I324N		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	324										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						ACTACTATCATTATCTCCTGT	0.289																																						uc004ddj.3																			0				breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						c.(970-972)aTt>aAt		Homo sapiens chromosome X open reading frame 22 (CXorf22), mRNA.							55.0	54.0	54.0					X																	35970005		2193	4244	6437	SO:0001583	missense	170063							g.chrX:35970005T>A	BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.971T>A	X.37:g.35970005T>A	ENSP00000297866:p.Ile324Asn					CXorf22_uc010ngv.3_Non-coding_Transcript	p.I324N	NM_152632	NP_689845	Q6ZTR5	CX022_HUMAN			5	1037	+			324					Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	37	c.971T>A	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	T	14.55	2.567985	0.45798	.	.	ENSG00000165164	ENST00000297866	T	0.60171	0.21	5.76	5.76	0.90799	.	0.966245	0.08655	N	0.913391	T	0.58764	0.2145	L	0.47716	1.5	0.28568	N	0.91077	D	0.56287	0.975	P	0.46543	0.52	T	0.50440	-0.8828	10	0.25751	T	0.34	-21.2532	14.1133	0.65137	0.0:0.0:0.0:1.0	.	324	Q6ZTR5	CX022_HUMAN	N	324	ENSP00000297866:I324N	ENSP00000297866:I324N	I	+	2	0	CXorf22	35879926	1.000000	0.71417	0.820000	0.32676	0.233000	0.25261	5.415000	0.66411	1.931000	0.55961	0.417000	0.27973	ATT		0.289	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632	
