#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
KRTAP10-12	386685	broad.mit.edu	37	21	46117516	46117516	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr21:46117516C>T	ENST00000400365.3	+	1	430	c.400C>T	c.(400-402)Cag>Tag	p.Q134*	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	134	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						ATGCTGCCAGCAGTCTAGCTG	0.617																																						ENST00000400365.3																			0				large_intestine(1)|lung(8)	9						c.(400-402)Cag>Tag		keratin associated protein 10-12							140.0	142.0	141.0					21																	46117516		2203	4300	6503	SO:0001587	stop_gained	386685					keratin filament		g.chr21:46117516C>T	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"""Keratin associated proteins"""	20533	protein-coding gene	gene with protein product			"""keratin associated protein 18-12"""	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.400C>T	21.37:g.46117516C>T	ENSP00000383216:p.Gln134*					TSPEAR_ENST00000323084.4_Intron	p.Q134*	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN			1	430	+			134			19 X 5 AA repeats of C-C-X(3).		B2RPA3	Nonsense_Mutation	SNP	ENST00000400365.3	37	c.400C>T	CCDS42967.1	.	.	.	.	.	.	.	.	.	.	c	10.77	1.443271	0.25987	.	.	ENSG00000189169	ENST00000400365	.	.	.	2.75	1.81	0.25067	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	6.9112	0.24336	0.0:0.8464:0.0:0.1536	.	.	.	.	X	134	.	ENSP00000383216:Q134X	Q	+	1	0	KRTAP10-12	44941944	0.000000	0.05858	0.814000	0.32528	0.061000	0.15899	-0.511000	0.06321	1.248000	0.43934	0.298000	0.19748	CAG		0.617	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699		6	122	0	0	0	1	0	6	122				
IGFBP7	3490	broad.mit.edu	37	4	57898634	57898634	+	Missense_Mutation	SNP	T	T	C			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr4:57898634T>C	ENST00000295666.4	-	4	820	c.787A>G	c.(787-789)Att>Gtt	p.I263V	IGFBP7_ENST00000537922.1_Missense_Mutation_p.I263V|IGFBP7_ENST00000512512.1_5'UTR	NM_001553.2	NP_001544.1	Q16270	IBP7_HUMAN	insulin-like growth factor binding protein 7	263	Ig-like C2-type.				cell adhesion (GO:0007155)|cellular response to hormone stimulus (GO:0032870)|embryo implantation (GO:0007566)|inner ear development (GO:0048839)|negative regulation of cell proliferation (GO:0008285)|regulation of cell growth (GO:0001558)|regulation of steroid biosynthetic process (GO:0050810)|response to cortisol (GO:0051414)|response to heat (GO:0009408)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|lung(3)	5	Glioma(25;0.08)|all_neural(26;0.181)				"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	ACCACTGTAATTTTTGCTGAT	0.368																																						ENST00000295666.4																			0				central_nervous_system(1)|endometrium(1)|lung(3)	5						c.(787-789)Att>Gtt		insulin-like growth factor binding protein 7	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)						141.0	131.0	134.0					4																	57898634		2203	4300	6503	SO:0001583	missense	3490				cell adhesion|negative regulation of cell proliferation|regulation of cell growth	extracellular space	insulin-like growth factor binding	g.chr4:57898634T>C	S75725	CCDS3512.1	4q12	2013-01-11			ENSG00000163453	ENSG00000163453		"""Immunoglobulin superfamily / I-set domain containing"""	5476	protein-coding gene	gene with protein product		602867				7694637, 7980422	Standard	NM_001553		Approved	MAC25, IGFBP-7, PSF, FSTL2	uc003hcn.3	Q16270	OTTHUMG00000128772	ENST00000295666.4:c.787A>G	4.37:g.57898634T>C	ENSP00000295666:p.Ile263Val					IGFBP7_ENST00000537922.1_Missense_Mutation_p.I263V|IGFBP7_ENST00000512512.1_5'UTR	p.I263V	NM_001553.2	NP_001544.1	Q16270	IBP7_HUMAN			4	820	-	Glioma(25;0.08)|all_neural(26;0.181)		263			Ig-like C2-type.		B4E1N2|B7Z9W7|Q07822|Q53YE6|Q9UCA8	Missense_Mutation	SNP	ENST00000295666.4	37	c.787A>G	CCDS3512.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.947232	0.53186	.	.	ENSG00000163453	ENST00000295666;ENST00000537922	T;T	0.38240	1.15;1.15	5.71	5.71	0.89125	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.34658	0.0905	N	0.03115	-0.41	0.47009	D	0.999289	D;D	0.63880	0.958;0.993	D;D	0.76071	0.97;0.987	T	0.40194	-0.9576	10	0.18710	T	0.47	-5.5568	14.5594	0.68126	0.0:0.0:0.0:1.0	.	263;263	B4E1N2;Q16270	.;IBP7_HUMAN	V	263	ENSP00000295666:I263V;ENSP00000444146:I263V	ENSP00000295666:I263V	I	-	1	0	IGFBP7	57593391	1.000000	0.71417	0.926000	0.36857	0.916000	0.54674	6.820000	0.75267	2.172000	0.68678	0.533000	0.62120	ATT		0.368	IGFBP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250693.1			6	35	0	0	0	1	0	6	35				
TRMT1	55621	broad.mit.edu	37	19	13220604	13220604	+	Silent	SNP	T	T	C			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr19:13220604T>C	ENST00000592062.1	-	11	1725	c.1155A>G	c.(1153-1155)gaA>gaG	p.E385E	TRMT1_ENST00000437766.1_Silent_p.E385E|TRMT1_ENST00000357720.4_Silent_p.E385E|TRMT1_ENST00000221504.8_Silent_p.E356E			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	385	Trm1 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00958}.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)		GCCCACAGTGTTCACACTCGG	0.627																																						ENST00000592062.1																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14						c.(1153-1155)gaA>gaG		tRNA methyltransferase 1 homolog (S. cerevisiae)							76.0	78.0	77.0					19																	13220604		2203	4300	6503	SO:0001819	synonymous_variant	55621						RNA binding|tRNA (guanine-N2-)-methyltransferase activity|zinc ion binding	g.chr19:13220604T>C	AF196479	CCDS12293.1, CCDS45997.1	19p13.13	2012-06-12	2012-06-12						25980	protein-coding gene	gene with protein product		611669				10982862	Standard	NM_001142554		Approved	FLJ20244, TRM1	uc002mwl.3	Q9NXH9		ENST00000592062.1:c.1155A>G	19.37:g.13220604T>C						TRMT1_ENST00000357720.4_Silent_p.E385E|TRMT1_ENST00000437766.1_Silent_p.E385E|TRMT1_ENST00000221504.8_Silent_p.E356E	p.E385E			Q9NXH9	TRM1_HUMAN	OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)	11	1725	-			385					O76103|Q548Y5|Q8WVA6	Silent	SNP	ENST00000592062.1	37	c.1155A>G	CCDS12293.1																																																																																				0.627	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722		10	26	0	0	0	1	0	10	26				
B3GNT3	10331	broad.mit.edu	37	19	17922809	17922809	+	Missense_Mutation	SNP	G	G	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr19:17922809G>T	ENST00000318683.6	+	3	1144	c.997G>T	c.(997-999)Gac>Tac	p.D333Y	B3GNT3_ENST00000595387.1_Missense_Mutation_p.D333Y	NM_014256.3	NP_055071.2	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	333					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)|galactosyltransferase activity (GO:0008378)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	21						GTCCTCCTTTGACCCCTGCTT	0.622																																						ENST00000318683.6																			0				breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	21						c.(997-999)Gac>Tac		UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3							130.0	119.0	123.0					19																	17922809		2203	4300	6503	SO:0001583	missense	10331				protein glycosylation	Golgi membrane|integral to plasma membrane	galactosyltransferase activity	g.chr19:17922809G>T	AB015630	CCDS12364.1	19p13.1	2013-02-19				ENSG00000179913		"""Beta 3-glycosyltransferases"""	13528	protein-coding gene	gene with protein product	"""putative type II membrane protein"", ""beta-1,3-N-acetylglucosaminyltransferase bGnT-3"", ""transmembrane protein 3"""	605863		TMEM3		10072769, 11042166	Standard	NM_014256		Approved	B3GN-T3, beta3Gn-T3, HP10328, B3GNT-3	uc002nhl.1	Q9Y2A9		ENST00000318683.6:c.997G>T	19.37:g.17922809G>T	ENSP00000321874:p.Asp333Tyr					B3GNT3_ENST00000595387.1_Missense_Mutation_p.D333Y	p.D333Y	NM_014256.3	NP_055071.2	Q9Y2A9	B3GN3_HUMAN			3	1144	+			333					B2RAS4|Q6NWU9|Q6NXU9|Q8WWR6|Q9C0J2	Missense_Mutation	SNP	ENST00000318683.6	37	c.997G>T	CCDS12364.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.577846	0.65878	.	.	ENSG00000179913	ENST00000318683	T	0.57107	0.42	5.23	5.23	0.72850	.	0.055773	0.64402	D	0.000002	T	0.78317	0.4264	M	0.91818	3.245	0.58432	D	0.99999	D	0.89917	1.0	D	0.78314	0.991	D	0.83673	0.0167	10	0.87932	D	0	.	16.2661	0.82579	0.0:0.0:1.0:0.0	.	333	Q9Y2A9	B3GN3_HUMAN	Y	333	ENSP00000321874:D333Y	ENSP00000321874:D333Y	D	+	1	0	B3GNT3	17783809	1.000000	0.71417	0.999000	0.59377	0.560000	0.35617	4.537000	0.60643	2.452000	0.82932	0.561000	0.74099	GAC		0.622	B3GNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466877.1	NM_014256		13	114	1	0	2.32078e-09	1	2.32078e-09	13	114				
NPR1	4881	broad.mit.edu	37	1	153660685	153660685	+	Missense_Mutation	SNP	G	G	A	rs148747309		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr1:153660685G>A	ENST00000368680.3	+	15	2877	c.2405G>A	c.(2404-2406)cGc>cAc	p.R802H		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	802	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CTGACGTTGCGCAAATTTAAC	0.582																																					Pancreas(141;1349 1870 15144 15830 40702)	ENST00000368680.3																			0				NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42						c.(2404-2406)cGc>cAc		natriuretic peptide receptor A/guanylate cyclase A (atrionatriuretic peptide receptor A)	Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)		HIS/ARG	0,4406		0,0,2203	107.0	96.0	100.0		2405	3.4	1.0	1	dbSNP_134	100	1,8599	1.2+/-3.3	0,1,4299	no	missense	NPR1	NM_000906.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	802/1062	153660685	1,13005	2203	4300	6503	SO:0001583	missense	4881				body fluid secretion|intracellular signal transduction|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation		ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity	g.chr1:153660685G>A	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.2405G>A	1.37:g.153660685G>A	ENSP00000357669:p.Arg802His						p.R802H	NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.151)		15	2877	+	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		802			Protein kinase.		B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	37	c.2405G>A	CCDS1051.1	.	.	.	.	.	.	.	.	.	.	g	19.14	3.769733	0.69992	0.0	1.16E-4	ENSG00000169418	ENST00000368680;ENST00000428723	T	0.62498	0.02	4.45	3.44	0.39384	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000005	T	0.63141	0.2486	M	0.82716	2.605	0.80722	D	1	P;D	0.56521	0.801;0.976	B;P	0.50082	0.199;0.63	T	0.70539	-0.4844	10	0.72032	D	0.01	.	11.267	0.49116	0.0:0.0:0.8168:0.1832	.	281;802	B7Z4Y7;P16066	.;ANPRA_HUMAN	H	802;281	ENSP00000357669:R802H	ENSP00000357669:R802H	R	+	2	0	NPR1	151927309	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	2.788000	0.47806	2.438000	0.82558	0.457000	0.33378	CGC		0.582	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906		5	36	0	0	0	1	0	5	36				
FOXP4	116113	broad.mit.edu	37	6	41555115	41555115	+	Missense_Mutation	SNP	A	A	T	rs200305782	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr6:41555115A>T	ENST00000307972.4	+	6	749	c.737A>T	c.(736-738)aAg>aTg	p.K246M	FOXP4_ENST00000409208.1_Missense_Mutation_p.K246M|FOXP4_ENST00000373057.3_Missense_Mutation_p.K244M|FOXP4_ENST00000373060.1_Missense_Mutation_p.K246M|FOXP4_ENST00000373063.3_Missense_Mutation_p.K245M			Q8IVH2	FOXP4_HUMAN	forkhead box P4	246					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GACAGCGTCAAGCAGGAGGGG	0.692											OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	A|||	5	0.000998403	0.0	0.0	5008	,	,		14662	0.005		0.0	False		,,,				2504	0.0					ENST00000373060.1																			0				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16						c.(736-738)aAg>aTg		forkhead box P4							63.0	66.0	65.0					6																	41555115		2203	4299	6502	SO:0001583	missense	116113				embryonic foregut morphogenesis|heart development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr6:41555115A>T	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.737A>T	6.37:g.41555115A>T	ENSP00000309823:p.Lys246Met		OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	902	FOXP4_ENST00000307972.4_Missense_Mutation_p.K246M|FOXP4_ENST00000373063.3_Missense_Mutation_p.K245M|FOXP4_ENST00000409208.1_Missense_Mutation_p.K246M|FOXP4_ENST00000373057.3_Missense_Mutation_p.K244M	p.K246M	NM_001012426.1|NM_001012427.1	NP_001012426.1|NP_001012427.1	Q8IVH2	FOXP4_HUMAN			7	1195	+	Ovarian(28;0.0327)|Colorectal(47;0.196)		246					Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	37	c.737A>T	CCDS34447.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	A	15.07	2.725393	0.48833	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95	4.92	3.52	0.40303	.	0.119501	0.56097	D	0.000027	T	0.33089	0.0851	M	0.69823	2.125	0.46317	D	0.998982	P;P;B	0.46621	0.881;0.881;0.06	P;P;B	0.46718	0.525;0.525;0.09	T	0.21109	-1.0255	10	0.66056	D	0.02	.	8.6657	0.34118	0.8811:0.0:0.1189:0.0	.	245;244;246	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	M	246;245;246;244;246	ENSP00000362151:K246M;ENSP00000362154:K245M;ENSP00000386958:K246M;ENSP00000362148:K244M;ENSP00000309823:K246M	ENSP00000309823:K246M	K	+	2	0	FOXP4	41663093	1.000000	0.71417	1.000000	0.80357	0.140000	0.21249	5.542000	0.67218	0.695000	0.31675	0.533000	0.62120	AAG		0.692	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		4	71	0	0	0	1	0	4	71				
FAM111A	63901	broad.mit.edu	37	11	58920619	58920619	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr11:58920619G>A	ENST00000528737.1	+	5	4296	c.1478G>A	c.(1477-1479)cGa>cAa	p.R493Q	FAM111A_ENST00000531147.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000533703.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000420244.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000361723.3_Missense_Mutation_p.R493Q			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	493	Interaction with SV40 large T antigen.				defense response to virus (GO:0051607)|DNA replication (GO:0006260)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_epithelial(135;0.139)				CAGGGTCAGCGAGCAAAGAAA	0.403																																						ENST00000528737.1																			0				breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22						c.(1477-1479)cGa>cAa		family with sequence similarity 111, member A							96.0	98.0	97.0					11																	58920619		2201	4295	6496	SO:0001583	missense	63901				proteolysis		serine-type endopeptidase activity	g.chr11:58920619G>A	AK092953	CCDS7973.1	11q12.1	2014-03-13				ENSG00000166801			24725	protein-coding gene	gene with protein product		615292				11572484, 23996431, 23684011	Standard	NM_022074		Approved	FLJ22794, KIAA1895	uc001nnq.3	Q96PZ2		ENST00000528737.1:c.1478G>A	11.37:g.58920619G>A	ENSP00000434435:p.Arg493Gln					FAM111A_ENST00000420244.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000533703.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000361723.3_Missense_Mutation_p.R493Q|FAM111A_ENST00000531147.1_Missense_Mutation_p.R493Q	p.R493Q			Q96PZ2	F111A_HUMAN			5	4296	+		all_epithelial(135;0.139)	493					A8K5Y8|Q5RKS9|Q5XKM2|Q68DK9|Q6IPR7|Q9H5Y1	Missense_Mutation	SNP	ENST00000528737.1	37	c.1478G>A	CCDS7973.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.211715	0.58452	.	.	ENSG00000166801	ENST00000528737;ENST00000420244;ENST00000361723;ENST00000533703;ENST00000531147	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	4.67	2.66	0.31614	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.413349	0.21534	N	0.073015	T	0.58278	0.2111	M	0.83953	2.67	0.09310	N	1	D	0.69078	0.997	P	0.54629	0.757	T	0.49808	-0.8900	10	0.42905	T	0.14	-0.2031	7.2558	0.26175	0.0929:0.0:0.739:0.1681	.	493	Q96PZ2	F111A_HUMAN	Q	493	ENSP00000434435:R493Q;ENSP00000406683:R493Q;ENSP00000355264:R493Q;ENSP00000433154:R493Q;ENSP00000431631:R493Q	ENSP00000355264:R493Q	R	+	2	0	FAM111A	58677195	0.002000	0.14202	0.091000	0.20842	0.014000	0.08584	0.942000	0.29017	1.340000	0.45581	-0.136000	0.14681	CGA		0.403	FAM111A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393975.1	NM_022074		7	89	0	0	0	1	0	7	89				
ANO8	57719	broad.mit.edu	37	19	17435806	17435806	+	Silent	SNP	G	G	A	rs540938848		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr19:17435806G>A	ENST00000159087.4	-	17	3209	c.3051C>T	c.(3049-3051)agC>agT	p.S1017S		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	1017					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						GGCGGGTGTCGCTGCCTGTGG	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		12103	0.001		0.0	False		,,,				2504	0.0					ENST00000159087.4																			0				autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						c.(3049-3051)agC>agT		anoctamin 8							62.0	79.0	73.0					19																	17435806		2202	4299	6501	SO:0001819	synonymous_variant	57719					chloride channel complex	chloride channel activity	g.chr19:17435806G>A	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	29329	protein-coding gene	gene with protein product		610216	"""KIAA1623"", ""transmembrane protein 16H"""	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.3051C>T	19.37:g.17435806G>A							p.S1017S	NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN			17	3209	-			1017					A6NIJ0	Silent	SNP	ENST00000159087.4	37	c.3051C>T	CCDS32949.1																																																																																				0.667	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644		6	104	0	0	0	1	0	6	104				
NRAS	4893	broad.mit.edu	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	rs11554290	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACTCTTCTTGTCCAGCTGT	0.458	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												ENST00000369535.4	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50		Dom	yes		1	1p13.2	4893	Mis	neuroblastoma RAS viral (v-ras) oncogene homolog			"""L, E"""			"""melanoma, MM, AML, thyroid"""		1016	Substitution - Missense(1016)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)	skin(466)|thyroid(279)|haematopoietic_and_lymphoid_tissue(124)|NS(50)|large_intestine(27)|lung(17)|urinary_tract(11)|adrenal_gland(7)|liver(7)|breast(7)|soft_tissue(4)|testis(3)|endometrium(3)|ovary(3)|central_nervous_system(2)|pancreas(2)|eye(1)|prostate(1)|meninges(1)|autonomic_ganglia(1)	NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085						c.(181-183)cAa>cGa		neuroblastoma RAS viral (v-ras) oncogene homolog							180.0	156.0	164.0					1																	115256529		2203	4300	6503	SO:0001583	missense	4893	Noonan syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity	g.chr1:115256529T>C	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.182A>G	1.37:g.115256529T>C	ENSP00000358548:p.Gln61Arg	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)					p.Q61R	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	3	435	-	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)	61		Q -> K (in neuroblastoma cell).|Q -> R (in lung carcinoma cell and melanoma; dbSNP:rs11554290).			Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	c.182A>G	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.004139	0.74932	.	.	ENSG00000213281	ENST00000369535	D	0.83673	-1.75	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.86489	0.5945	M	0.92604	3.325	0.80722	D	1	B	0.28512	0.214	B	0.39590	0.304	D	0.88255	0.2919	10	0.66056	D	0.02	.	15.0132	0.71565	0.0:0.0:0.0:1.0	rs11554290;rs11554290	61	P01111	RASN_HUMAN	R	61	ENSP00000358548:Q61R	ENSP00000358548:Q61R	Q	-	2	0	NRAS	115058052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	CAA		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		52	62	0	0	0	1	0	52	62				
NODAL	4838	broad.mit.edu	37	10	72195326	72195326	+	Missense_Mutation	SNP	C	C	T	rs10999334	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr10:72195326C>T	ENST00000287139.3	-	2	606	c.607G>A	c.(607-609)Gag>Aag	p.E203K	AC022532.1_ENST00000420338.2_Silent_p.L91L	NM_018055.4	NP_060525.3	Q96S42	NODAL_HUMAN	nodal growth differentiation factor	203			E -> K (in HTX5; decrease in signal transduction; dbSNP:rs10999334). {ECO:0000269|PubMed:19064609}.		axial mesodermal cell fate specification (GO:0048327)|brain development (GO:0007420)|cell migration involved in gastrulation (GO:0042074)|digestive tract morphogenesis (GO:0048546)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic pattern specification (GO:0009880)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endodermal cell differentiation (GO:0035987)|epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification (GO:0060802)|floor plate morphogenesis (GO:0033505)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|heart looping (GO:0001947)|inhibition of neuroepithelial cell differentiation (GO:0002085)|left lung morphogenesis (GO:0060460)|liver development (GO:0001889)|maternal placenta development (GO:0001893)|maternal process involved in parturition (GO:0060137)|mesendoderm development (GO:0048382)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of chorionic trophoblast cell proliferation (GO:1901383)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of trophoblast cell migration (GO:1901164)|neural fold formation (GO:0001842)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|placenta development (GO:0001890)|polarity specification of proximal/distal axis (GO:0010085)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gastrulation (GO:0010470)|regulation of stem cell maintenance (GO:2000036)|SMAD protein signal transduction (GO:0060395)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway involved in primitive streak formation (GO:0090010)|trophectodermal cellular morphogenesis (GO:0001831)|vasculature development (GO:0001944)	extracellular space (GO:0005615)	morphogen activity (GO:0016015)|type I activin receptor binding (GO:0070698)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	15						TGCCTCTGCTCCTGCGAGAGG	0.662													C|||	13	0.00259585	0.0	0.0	5008	,	,		18479	0.0119		0.0	False		,,,				2504	0.001					ENST00000287139.3																			0				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	15						c.(607-609)Gag>Aag		nodal growth differentiation factor							32.0	34.0	33.0					10																	72195326		2203	4300	6503	SO:0001583	missense	4838				growth	extracellular space	cytokine activity|growth factor activity	g.chr10:72195326C>T	BC033585	CCDS7304.1	10q22.1	2012-12-07	2012-12-07		ENSG00000156574	ENSG00000156574			7865	protein-coding gene	gene with protein product		601265	"""nodal, mouse, homolog"", ""nodal homolog (mouse)"""			9354794	Standard	NM_018055		Approved		uc001jrc.2	Q96S42	OTTHUMG00000018408	ENST00000287139.3:c.607G>A	10.37:g.72195326C>T	ENSP00000287139:p.Glu203Lys					AC022532.1_ENST00000420338.2_Silent_p.L91L	p.E203K	NM_018055.4	NP_060525.3	Q96S42	NODAL_HUMAN			2	606	-			203		E -> K (in HTX5; decrease in signal transduction; dbSNP:rs10999334).			Q2M3A5|Q8N4V3	Missense_Mutation	SNP	ENST00000287139.3	37	c.607G>A	CCDS7304.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	C	6.904	0.536390	0.13188	.	.	ENSG00000156574	ENST00000287139;ENST00000414871	D;D	0.84944	-1.92;-1.9	5.88	4.99	0.66335	.	0.414253	0.29172	N	0.012930	T	0.69602	0.3129	L	0.32530	0.975	0.32354	N	0.558023	B	0.06786	0.001	B	0.04013	0.001	T	0.70439	-0.4871	10	0.19590	T	0.45	.	10.3912	0.44168	0.0:0.8488:0.0:0.1512	rs10999334;rs52824892;rs10999334	203	Q96S42	NODAL_HUMAN	K	203;148	ENSP00000287139:E203K;ENSP00000394468:E148K	ENSP00000287139:E203K	E	-	1	0	NODAL	71865332	0.963000	0.33076	0.882000	0.34594	0.014000	0.08584	2.126000	0.42026	1.497000	0.48584	-0.137000	0.14449	GAG		0.662	NODAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048511.1	NM_018055		3	32	0	0	0	1	0	3	32				
NPAS4	266743	broad.mit.edu	37	11	66189993	66189993	+	Silent	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr11:66189993G>A	ENST00000311034.2	+	3	575	c.399G>A	c.(397-399)caG>caA	p.Q133Q		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	133	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						CTGTGCGCCAGCAACTCACCC	0.582																																						ENST00000311034.2																			0				breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						c.(397-399)caG>caA		neuronal PAS domain protein 4							147.0	125.0	133.0					11																	66189993		2200	4295	6495	SO:0001819	synonymous_variant	266743				transcription, DNA-dependent		DNA binding|signal transducer activity	g.chr11:66189993G>A	AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"""Basic helix-loop-helix proteins"""	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.399G>A	11.37:g.66189993G>A							p.Q133Q	NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN			3	575	+			133			PAS 1.		B7ZL81|Q8N8S5|Q8N9Q9	Silent	SNP	ENST00000311034.2	37	c.399G>A	CCDS8138.1																																																																																				0.582	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		3	45	0	0	0	1	0	3	45				
ACAN	176	broad.mit.edu	37	15	89391161	89391161	+	Missense_Mutation	SNP	C	C	T	rs143697605		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr15:89391161C>T	ENST00000561243.1	+	8	1624	c.1624C>T	c.(1624-1626)Cgg>Tgg	p.R542W	ACAN_ENST00000559004.1_Missense_Mutation_p.R542W|ACAN_ENST00000352105.7_Missense_Mutation_p.R542W|ACAN_ENST00000439576.2_Missense_Mutation_p.R542W|ACAN_ENST00000558207.1_Missense_Mutation_p.R542W			P16112	PGCA_HUMAN	aggrecan	542	G2-B.|Link 3. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)	p.R542W(1)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TGTGAGCCCCCGGACCCCATG	0.607													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11533	0.0		0.0	False		,,,				2504	0.0					ENST00000439576.2																			1	Substitution - Missense(1)	p.R542W(1)	large_intestine(1)	NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93						c.(1624-1626)Cgg>Tgg		aggrecan							72.0	75.0	74.0					15																	89391161		1949	4147	6096	SO:0001583	missense	176				cell adhesion		hyaluronic acid binding|sugar binding	g.chr15:89391161C>T	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.1624C>T	15.37:g.89391161C>T	ENSP00000453342:p.Arg542Trp					ACAN_ENST00000352105.7_Missense_Mutation_p.R542W|ACAN_ENST00000559004.1_Missense_Mutation_p.R542W|ACAN_ENST00000561243.1_Missense_Mutation_p.R542W|ACAN_ENST00000558207.1_Missense_Mutation_p.R542W	p.R542W	NM_013227.3	NP_037359.3	E7EX88	E7EX88_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.146)		9	1998	+	Lung NSC(78;0.0392)|all_lung(78;0.077)		542					Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	c.1624C>T	CCDS53970.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	15.01	2.707015	0.48412	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.13901	2.55;2.55	5.35	3.4	0.38934	.	.	.	.	.	T	0.49541	0.1563	H	0.97103	3.94	0.40088	D	0.976221	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.63817	-0.6551	9	0.87932	D	0	-18.098	11.6973	0.51551	0.3215:0.6785:0.0:0.0	.	542;542;542	E7ENV9;E7EX88;Q6PID9	.;.;.	W	542	ENSP00000387356:R542W;ENSP00000341615:R542W	ENSP00000268134:R542W	R	+	1	2	ACAN	87192165	0.202000	0.23423	0.676000	0.29932	0.976000	0.68499	0.725000	0.25970	0.581000	0.29539	0.563000	0.77884	CGG		0.607	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		4	56	0	0	0	1	0	4	56				
COG7	91949	broad.mit.edu	37	16	23428325	23428325	+	Missense_Mutation	SNP	A	A	G			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr16:23428325A>G	ENST00000307149.5	-	9	1440	c.1255T>C	c.(1255-1257)Tgc>Cgc	p.C419R		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	419					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		AACAGGCCGCAGGTCCCCAGG	0.567																																						ENST00000307149.5																			0				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27						c.(1255-1257)Tgc>Cgc		component of oligomeric golgi complex 7							85.0	67.0	73.0					16																	23428325		2197	4300	6497	SO:0001583	missense	91949				intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding	g.chr16:23428325A>G	AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"""Components of oligomeric golgi complex"""	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.1255T>C	16.37:g.23428325A>G	ENSP00000305442:p.Cys419Arg						p.C419R	NM_153603.3	NP_705831.1	P83436	COG7_HUMAN		GBM - Glioblastoma multiforme(48;0.0401)	9	1440	-			419					Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	37	c.1255T>C	CCDS10610.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.246237	0.80024	.	.	ENSG00000168434	ENST00000307149	T	0.44482	0.92	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.59783	0.2219	M	0.66939	2.045	0.80722	D	1	D	0.71674	0.998	D	0.68353	0.957	T	0.56159	-0.8025	10	0.21540	T	0.41	-8.1377	14.9498	0.71064	1.0:0.0:0.0:0.0	.	419	P83436	COG7_HUMAN	R	419	ENSP00000305442:C419R	ENSP00000305442:C419R	C	-	1	0	COG7	23335826	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	4.920000	0.63390	2.135000	0.66039	0.533000	0.62120	TGC		0.567	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1			3	37	0	0	0	1	0	3	37				
MT1A	4489	broad.mit.edu	37	16	56670827	56670827	+	5'Flank	SNP	C	C	T	rs11076159	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr16:56670827C>T	ENST00000290705.8	+	0	0				MT1JP_ENST00000564564.1_RNA	NM_005946.2	NP_005937.2	P04731	MT1A_HUMAN	metallothionein 1A						cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(1)	3					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGCAAAGGGACGTCGGAGAAG	0.537													.|||	439	0.0876597	0.1982	0.0432	5008	,	,		18660	0.1052		0.0229	False		,,,				2504	0.0184					ENST00000564564.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr16:56670827C>T	BC029475	CCDS32454.1	16q13	2012-10-02	2007-03-02			ENSG00000205362		"""Metallothioneins"""	7393	protein-coding gene	gene with protein product		156350	"""metallothionein 1S"""	MT1, MT1S		6089206, 6327055	Standard	NM_005946		Approved		uc002ejq.3	P04731			16.37:g.56670827C>T	Exception_encountered													0	806	+								Q86YX5	RNA	SNP	ENST00000290705.8	37		CCDS32454.1																																																																																				0.537	MT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434324.1	NM_005946		3	47	0	0	0	1	0	3	47				
OR4M1	441670	broad.mit.edu	37	14	20248797	20248797	+	Missense_Mutation	SNP	T	T	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr14:20248797T>A	ENST00000315957.4	+	1	397	c.316T>A	c.(316-318)Ttt>Att	p.F106I		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	106						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CTTCTTACACTTTGTTGGGGC	0.473																																						ENST00000315957.4																			0				NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42						c.(316-318)Ttt>Att		olfactory receptor, family 4, subfamily M, member 1							234.0	253.0	246.0					14																	20248797		2203	4300	6503	SO:0001583	missense	441670				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr14:20248797T>A		CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"""GPCR / Class A : Olfactory receptors"""	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.316T>A	14.37:g.20248797T>A	ENSP00000319654:p.Phe106Ile						p.F106I	NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)	1	397	+	all_cancers(95;0.00108)		106					B9EH18|Q6IFA3	Missense_Mutation	SNP	ENST00000315957.4	37	c.316T>A	CCDS32021.1	.	.	.	.	.	.	.	.	.	.	.	13.79	2.343637	0.41498	.	.	ENSG00000176299	ENST00000315957	T	0.00414	7.52	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000188	T	0.00356	0.0011	L	0.47716	1.5	0.25030	N	0.991275	B	0.30439	0.279	B	0.27608	0.081	T	0.47315	-0.9127	10	0.49607	T	0.09	-15.447	11.5315	0.50614	0.0:0.0:0.0:1.0	.	106	Q8NGD0	OR4M1_HUMAN	I	106	ENSP00000319654:F106I	ENSP00000319654:F106I	F	+	1	0	OR4M1	19318637	0.002000	0.14202	1.000000	0.80357	0.823000	0.46562	0.873000	0.28052	1.894000	0.54839	0.330000	0.21533	TTT		0.473	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1			9	261	0	0	0	1	0	9	261				
RNASE1	6035	broad.mit.edu	37	14	21270003	21270003	+	Silent	SNP	C	C	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr14:21270003C>T	ENST00000397967.4	-	2	731	c.225G>A	c.(223-225)gtG>gtA	p.V75V	RNASE1_ENST00000340900.3_Silent_p.V75V|RNASE1_ENST00000555698.1_Silent_p.V35V|RNASE1_ENST00000397970.4_Silent_p.V75V|RNASE1_ENST00000412779.2_Silent_p.V75V	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	75					RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	Guanidine(DB00536)|L-Aspartic Acid(DB00128)	GGGGCTCGTGCACAAAGGTGT	0.542																																						ENST00000397967.4																			0				central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5						c.(223-225)gtG>gtA		ribonuclease, RNase A family, 1 (pancreatic)							143.0	127.0	132.0					14																	21270003		2203	4300	6503	SO:0001819	synonymous_variant	6035					extracellular region	nucleic acid binding|pancreatic ribonuclease activity|protein binding	g.chr14:21270003C>T	BC005324	CCDS9559.1	14q11.2	2014-03-13			ENSG00000129538	ENSG00000129538	3.1.27.5	"""Ribonucleases, RNase A"""	10044	protein-coding gene	gene with protein product		180440		RNS1		8588814	Standard	NM_002933		Approved		uc001vyi.3	P07998	OTTHUMG00000029603	ENST00000397967.4:c.225G>A	14.37:g.21270003C>T						RNASE1_ENST00000397970.4_Silent_p.V75V|RNASE1_ENST00000340900.3_Silent_p.V75V|RNASE1_ENST00000555698.1_Silent_p.V35V|RNASE1_ENST00000412779.2_Silent_p.V75V	p.V75V	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	2	731	-	all_cancers(95;0.00671)	all_lung(585;0.235)	75					B2R589|D3DS06|Q16830|Q16869|Q1KHR2|Q6ICS5|Q9UCB4|Q9UCB5	Silent	SNP	ENST00000397967.4	37	c.225G>A	CCDS9559.1																																																																																				0.542	RNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073791.3			5	73	0	0	0	1	0	5	73				
SIRPA	140885	broad.mit.edu	37	20	1902292	1902292	+	Missense_Mutation	SNP	G	G	A	rs200513155		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr20:1902292G>A	ENST00000358771.4	+	3	840	c.688G>A	c.(688-690)Gtg>Atg	p.V230M	SIRPA_ENST00000400068.3_Missense_Mutation_p.V230M|SIRPA_ENST00000356025.3_Missense_Mutation_p.V230M	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	230	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.V230M(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CATCTGCGAGGTGGCCCACGT	0.612																																					GBM(155;1668 1920 5945 42733 48121)	ENST00000358771.4																			1	Substitution - Missense(1)	p.V230M(1)	lung(1)	cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21						c.(688-690)Gtg>Atg		signal-regulatory protein alpha							66.0	57.0	60.0					20																	1902292		2203	4296	6499	SO:0001583	missense	140885				blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding	g.chr20:1902292G>A	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.688G>A	20.37:g.1902292G>A	ENSP00000351621:p.Val230Met					SIRPA_ENST00000356025.3_Missense_Mutation_p.V230M|SIRPA_ENST00000400068.3_Missense_Mutation_p.V230M	p.V230M	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN		Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)	3	840	+			230			Ig-like C1-type 1.		A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	c.688G>A	CCDS13022.1	23	0.010531135531135532	4	0.008130081300813009	2	0.0055248618784530384	6	0.01048951048951049	11	0.014511873350923483	G	19.90	3.912586	0.72983	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.13538	2.58;2.58;2.58	4.86	4.86	0.63082	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.115071	0.38720	N	0.001599	T	0.38081	0.1027	H	0.95294	3.65	0.45634	D	0.99856	D;D;D	0.69078	0.993;0.984;0.997	D;P;P	0.62955	0.909;0.562;0.878	T	0.57556	-0.7791	10	0.66056	D	0.02	.	13.7542	0.62926	0.0:0.0:1.0:0.0	.	210;230;230	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	M	230	ENSP00000382941:V230M;ENSP00000348307:V230M;ENSP00000351621:V230M	ENSP00000348307:V230M	V	+	1	0	SIRPA	1850292	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	1.834000	0.39171	2.718000	0.92993	0.650000	0.86243	GTG		0.612	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792		3	39	0	0	0	1	0	3	39				
MMAA	166785	broad.mit.edu	37	4	146560393	146560393	+	Silent	SNP	C	C	T	rs146372922	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr4:146560393C>T	ENST00000281317.5	+	2	1312	c.102C>T	c.(100-102)ctC>ctT	p.L34L	MMAA_ENST00000541599.1_5'UTR	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	34					cellular lipid metabolic process (GO:0044255)|cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTACTCATCTCGGATCAGGAA	0.443													c|||	9	0.00179712	0.0068	0.0	5008	,	,		19886	0.0		0.0	False		,,,				2504	0.0					ENST00000281317.5																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17						c.(100-102)ctC>ctT		methylmalonic aciduria (cobalamin deficiency) cblA type	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	C		16,4390	24.3+/-50.5	0,16,2187	149.0	143.0	145.0		102	-0.3	0.0	4	dbSNP_134	145	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MMAA	NM_172250.2		0,18,6485	TT,TC,CC		0.0233,0.3631,0.1384		34/419	146560393	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	166785					mitochondrion	GTP binding|nucleoside-triphosphatase activity	g.chr4:146560393C>T	AF524841	CCDS3766.1	4q31.1	2011-05-12	2005-07-11			ENSG00000151611			18871	protein-coding gene	gene with protein product		607481	"""methylmalonic aciduria (cobalamin deficiency) type A"""			12438653	Standard	NM_172250		Approved	cblA	uc003ikh.4	Q8IVH4		ENST00000281317.5:c.102C>T	4.37:g.146560393C>T						MMAA_ENST00000541599.1_5'UTR	p.L34L	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN			2	1312	+	all_hematologic(180;0.151)		34					B3KX40|Q495G7	Silent	SNP	ENST00000281317.5	37	c.102C>T	CCDS3766.1																																																																																				0.443	MMAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364668.2			46	78	0	0	0	1	0	46	78				
KRTAP10-12	386685	broad.mit.edu	37	21	46117516	46117516	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr21:46117516C>T	ENST00000400365.3	+	1	430	c.400C>T	c.(400-402)Cag>Tag	p.Q134*	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	134	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						ATGCTGCCAGCAGTCTAGCTG	0.617																																						ENST00000400365.3																			0				large_intestine(1)|lung(8)	9						c.(400-402)Cag>Tag		keratin associated protein 10-12							140.0	142.0	141.0					21																	46117516		2203	4300	6503	SO:0001587	stop_gained	386685					keratin filament		g.chr21:46117516C>T	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"""Keratin associated proteins"""	20533	protein-coding gene	gene with protein product			"""keratin associated protein 18-12"""	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.400C>T	21.37:g.46117516C>T	ENSP00000383216:p.Gln134*					TSPEAR_ENST00000323084.4_Intron	p.Q134*	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN			1	430	+			134			19 X 5 AA repeats of C-C-X(3).		B2RPA3	Nonsense_Mutation	SNP	ENST00000400365.3	37	c.400C>T	CCDS42967.1	.	.	.	.	.	.	.	.	.	.	c	10.77	1.443271	0.25987	.	.	ENSG00000189169	ENST00000400365	.	.	.	2.75	1.81	0.25067	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	6.9112	0.24336	0.0:0.8464:0.0:0.1536	.	.	.	.	X	134	.	ENSP00000383216:Q134X	Q	+	1	0	KRTAP10-12	44941944	0.000000	0.05858	0.814000	0.32528	0.061000	0.15899	-0.511000	0.06321	1.248000	0.43934	0.298000	0.19748	CAG		0.617	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699		6	122	0	0	0	1	0	6	122				
IGFBP7	3490	broad.mit.edu	37	4	57898634	57898634	+	Missense_Mutation	SNP	T	T	C			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr4:57898634T>C	ENST00000295666.4	-	4	820	c.787A>G	c.(787-789)Att>Gtt	p.I263V	IGFBP7_ENST00000537922.1_Missense_Mutation_p.I263V|IGFBP7_ENST00000512512.1_5'UTR	NM_001553.2	NP_001544.1	Q16270	IBP7_HUMAN	insulin-like growth factor binding protein 7	263	Ig-like C2-type.				cell adhesion (GO:0007155)|cellular response to hormone stimulus (GO:0032870)|embryo implantation (GO:0007566)|inner ear development (GO:0048839)|negative regulation of cell proliferation (GO:0008285)|regulation of cell growth (GO:0001558)|regulation of steroid biosynthetic process (GO:0050810)|response to cortisol (GO:0051414)|response to heat (GO:0009408)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|lung(3)	5	Glioma(25;0.08)|all_neural(26;0.181)				"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	ACCACTGTAATTTTTGCTGAT	0.368																																						ENST00000295666.4																			0				central_nervous_system(1)|endometrium(1)|lung(3)	5						c.(787-789)Att>Gtt		insulin-like growth factor binding protein 7	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)						141.0	131.0	134.0					4																	57898634		2203	4300	6503	SO:0001583	missense	3490				cell adhesion|negative regulation of cell proliferation|regulation of cell growth	extracellular space	insulin-like growth factor binding	g.chr4:57898634T>C	S75725	CCDS3512.1	4q12	2013-01-11			ENSG00000163453	ENSG00000163453		"""Immunoglobulin superfamily / I-set domain containing"""	5476	protein-coding gene	gene with protein product		602867				7694637, 7980422	Standard	NM_001553		Approved	MAC25, IGFBP-7, PSF, FSTL2	uc003hcn.3	Q16270	OTTHUMG00000128772	ENST00000295666.4:c.787A>G	4.37:g.57898634T>C	ENSP00000295666:p.Ile263Val					IGFBP7_ENST00000512512.1_5'UTR|IGFBP7_ENST00000537922.1_Missense_Mutation_p.I263V	p.I263V	NM_001553.2	NP_001544.1	Q16270	IBP7_HUMAN			4	820	-	Glioma(25;0.08)|all_neural(26;0.181)		263			Ig-like C2-type.		B4E1N2|B7Z9W7|Q07822|Q53YE6|Q9UCA8	Missense_Mutation	SNP	ENST00000295666.4	37	c.787A>G	CCDS3512.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.947232	0.53186	.	.	ENSG00000163453	ENST00000295666;ENST00000537922	T;T	0.38240	1.15;1.15	5.71	5.71	0.89125	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.34658	0.0905	N	0.03115	-0.41	0.47009	D	0.999289	D;D	0.63880	0.958;0.993	D;D	0.76071	0.97;0.987	T	0.40194	-0.9576	10	0.18710	T	0.47	-5.5568	14.5594	0.68126	0.0:0.0:0.0:1.0	.	263;263	B4E1N2;Q16270	.;IBP7_HUMAN	V	263	ENSP00000295666:I263V;ENSP00000444146:I263V	ENSP00000295666:I263V	I	-	1	0	IGFBP7	57593391	1.000000	0.71417	0.926000	0.36857	0.916000	0.54674	6.820000	0.75267	2.172000	0.68678	0.533000	0.62120	ATT		0.368	IGFBP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250693.1			6	35	0	0	0	1	0	6	35				
TRMT1	55621	broad.mit.edu	37	19	13220604	13220604	+	Silent	SNP	T	T	C			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr19:13220604T>C	ENST00000592062.1	-	11	1725	c.1155A>G	c.(1153-1155)gaA>gaG	p.E385E	TRMT1_ENST00000437766.1_Silent_p.E385E|TRMT1_ENST00000357720.4_Silent_p.E385E|TRMT1_ENST00000221504.8_Silent_p.E356E			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	385	Trm1 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00958}.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)		GCCCACAGTGTTCACACTCGG	0.627																																						ENST00000592062.1																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14						c.(1153-1155)gaA>gaG		tRNA methyltransferase 1 homolog (S. cerevisiae)							76.0	78.0	77.0					19																	13220604		2203	4300	6503	SO:0001819	synonymous_variant	55621						RNA binding|tRNA (guanine-N2-)-methyltransferase activity|zinc ion binding	g.chr19:13220604T>C	AF196479	CCDS12293.1, CCDS45997.1	19p13.13	2012-06-12	2012-06-12						25980	protein-coding gene	gene with protein product		611669				10982862	Standard	NM_001142554		Approved	FLJ20244, TRM1	uc002mwl.3	Q9NXH9		ENST00000592062.1:c.1155A>G	19.37:g.13220604T>C						TRMT1_ENST00000357720.4_Silent_p.E385E|TRMT1_ENST00000437766.1_Silent_p.E385E|TRMT1_ENST00000221504.8_Silent_p.E356E	p.E385E			Q9NXH9	TRM1_HUMAN	OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)	11	1725	-			385					O76103|Q548Y5|Q8WVA6	Silent	SNP	ENST00000592062.1	37	c.1155A>G	CCDS12293.1																																																																																				0.627	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722		10	26	0	0	0	1	0	10	26				
B3GNT3	10331	broad.mit.edu	37	19	17922809	17922809	+	Missense_Mutation	SNP	G	G	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr19:17922809G>T	ENST00000318683.6	+	3	1144	c.997G>T	c.(997-999)Gac>Tac	p.D333Y	B3GNT3_ENST00000595387.1_Missense_Mutation_p.D333Y	NM_014256.3	NP_055071.2	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	333					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)|galactosyltransferase activity (GO:0008378)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	21						GTCCTCCTTTGACCCCTGCTT	0.622																																						ENST00000318683.6																			0				breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	21						c.(997-999)Gac>Tac		UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3							130.0	119.0	123.0					19																	17922809		2203	4300	6503	SO:0001583	missense	10331				protein glycosylation	Golgi membrane|integral to plasma membrane	galactosyltransferase activity	g.chr19:17922809G>T	AB015630	CCDS12364.1	19p13.1	2013-02-19				ENSG00000179913		"""Beta 3-glycosyltransferases"""	13528	protein-coding gene	gene with protein product	"""putative type II membrane protein"", ""beta-1,3-N-acetylglucosaminyltransferase bGnT-3"", ""transmembrane protein 3"""	605863		TMEM3		10072769, 11042166	Standard	NM_014256		Approved	B3GN-T3, beta3Gn-T3, HP10328, B3GNT-3	uc002nhl.1	Q9Y2A9		ENST00000318683.6:c.997G>T	19.37:g.17922809G>T	ENSP00000321874:p.Asp333Tyr					B3GNT3_ENST00000595387.1_Missense_Mutation_p.D333Y	p.D333Y	NM_014256.3	NP_055071.2	Q9Y2A9	B3GN3_HUMAN			3	1144	+			333					B2RAS4|Q6NWU9|Q6NXU9|Q8WWR6|Q9C0J2	Missense_Mutation	SNP	ENST00000318683.6	37	c.997G>T	CCDS12364.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.577846	0.65878	.	.	ENSG00000179913	ENST00000318683	T	0.57107	0.42	5.23	5.23	0.72850	.	0.055773	0.64402	D	0.000002	T	0.78317	0.4264	M	0.91818	3.245	0.58432	D	0.99999	D	0.89917	1.0	D	0.78314	0.991	D	0.83673	0.0167	10	0.87932	D	0	.	16.2661	0.82579	0.0:0.0:1.0:0.0	.	333	Q9Y2A9	B3GN3_HUMAN	Y	333	ENSP00000321874:D333Y	ENSP00000321874:D333Y	D	+	1	0	B3GNT3	17783809	1.000000	0.71417	0.999000	0.59377	0.560000	0.35617	4.537000	0.60643	2.452000	0.82932	0.561000	0.74099	GAC		0.622	B3GNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466877.1	NM_014256		13	114	1	0	2.32078e-09	1	2.40674e-09	13	114				
NPR1	4881	broad.mit.edu	37	1	153660685	153660685	+	Missense_Mutation	SNP	G	G	A	rs148747309		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr1:153660685G>A	ENST00000368680.3	+	15	2877	c.2405G>A	c.(2404-2406)cGc>cAc	p.R802H		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	802	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CTGACGTTGCGCAAATTTAAC	0.582																																					Pancreas(141;1349 1870 15144 15830 40702)	ENST00000368680.3																			0				NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42						c.(2404-2406)cGc>cAc		natriuretic peptide receptor A/guanylate cyclase A (atrionatriuretic peptide receptor A)	Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)		HIS/ARG	0,4406		0,0,2203	107.0	96.0	100.0		2405	3.4	1.0	1	dbSNP_134	100	1,8599	1.2+/-3.3	0,1,4299	no	missense	NPR1	NM_000906.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	802/1062	153660685	1,13005	2203	4300	6503	SO:0001583	missense	4881				body fluid secretion|intracellular signal transduction|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation		ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity	g.chr1:153660685G>A	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.2405G>A	1.37:g.153660685G>A	ENSP00000357669:p.Arg802His						p.R802H	NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.151)		15	2877	+	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		802			Protein kinase.		B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	37	c.2405G>A	CCDS1051.1	.	.	.	.	.	.	.	.	.	.	g	19.14	3.769733	0.69992	0.0	1.16E-4	ENSG00000169418	ENST00000368680;ENST00000428723	T	0.62498	0.02	4.45	3.44	0.39384	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000005	T	0.63141	0.2486	M	0.82716	2.605	0.80722	D	1	P;D	0.56521	0.801;0.976	B;P	0.50082	0.199;0.63	T	0.70539	-0.4844	10	0.72032	D	0.01	.	11.267	0.49116	0.0:0.0:0.8168:0.1832	.	281;802	B7Z4Y7;P16066	.;ANPRA_HUMAN	H	802;281	ENSP00000357669:R802H	ENSP00000357669:R802H	R	+	2	0	NPR1	151927309	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	2.788000	0.47806	2.438000	0.82558	0.457000	0.33378	CGC		0.582	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906		5	36	0	0	0	1	0	5	36				
EP400	57634	broad.mit.edu	37	12	132547087	132547087	+	Silent	SNP	G	G	A	rs12366766	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr12:132547087G>A	ENST00000333577.4	+	48	8392	c.8283G>A	c.(8281-8283)caG>caA	p.Q2761Q	EP400_ENST00000332482.4_Silent_p.Q2688Q|EP400_ENST00000330386.6_Silent_p.Q2644Q|EP400_ENST00000389562.2_Silent_p.Q2724Q|EP400_ENST00000389561.2_Silent_p.Q2725Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2761	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.Q2724Q(16)|p.Q2725Q(1)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcagcaacaacagc	0.562													G|||	37	0.00738818	0.0038	0.0072	5008	,	,		15585	0.002		0.0149	False		,,,				2504	0.0102					ENST00000333577.4																			17	Substitution - coding silent(17)	p.Q2724Q(16)|p.Q2725Q(1)	prostate(4)|kidney(4)|central_nervous_system(3)|lung(3)|endometrium(2)|urinary_tract(1)	NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161						c.(8281-8283)caG>caA		E1A binding protein p400							28.0	31.0	30.0					12																	132547087		2199	4282	6481	SO:0001819	synonymous_variant	57634				histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity	g.chr12:132547087G>A	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8283G>A	12.37:g.132547087G>A						EP400_ENST00000389562.2_Silent_p.Q2724Q|EP400_ENST00000332482.4_Silent_p.Q2688Q|EP400_ENST00000389561.2_Silent_p.Q2725Q|EP400_ENST00000330386.6_Silent_p.Q2644Q	p.Q2761Q			Q96L91	EP400_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)	48	8392	+	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)	2761			Interaction with ZNF42 (By similarity).|Poly-Gln.		O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37	c.8283G>A																																																																																					0.562	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		3	29	0	0	0	1	0	3	29				
FOXP4	116113	broad.mit.edu	37	6	41555115	41555115	+	Missense_Mutation	SNP	A	A	T	rs200305782	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr6:41555115A>T	ENST00000307972.4	+	6	749	c.737A>T	c.(736-738)aAg>aTg	p.K246M	FOXP4_ENST00000409208.1_Missense_Mutation_p.K246M|FOXP4_ENST00000373057.3_Missense_Mutation_p.K244M|FOXP4_ENST00000373060.1_Missense_Mutation_p.K246M|FOXP4_ENST00000373063.3_Missense_Mutation_p.K245M			Q8IVH2	FOXP4_HUMAN	forkhead box P4	246					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GACAGCGTCAAGCAGGAGGGG	0.692											OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	A|||	5	0.000998403	0.0	0.0	5008	,	,		14662	0.005		0.0	False		,,,				2504	0.0					ENST00000373060.1																			0				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16						c.(736-738)aAg>aTg		forkhead box P4							63.0	66.0	65.0					6																	41555115		2203	4299	6502	SO:0001583	missense	116113				embryonic foregut morphogenesis|heart development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr6:41555115A>T	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.737A>T	6.37:g.41555115A>T	ENSP00000309823:p.Lys246Met		OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	902	FOXP4_ENST00000373063.3_Missense_Mutation_p.K245M|FOXP4_ENST00000373057.3_Missense_Mutation_p.K244M|FOXP4_ENST00000409208.1_Missense_Mutation_p.K246M|FOXP4_ENST00000307972.4_Missense_Mutation_p.K246M	p.K246M	NM_001012426.1|NM_001012427.1	NP_001012426.1|NP_001012427.1	Q8IVH2	FOXP4_HUMAN			7	1195	+	Ovarian(28;0.0327)|Colorectal(47;0.196)		246					Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	37	c.737A>T	CCDS34447.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	A	15.07	2.725393	0.48833	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95	4.92	3.52	0.40303	.	0.119501	0.56097	D	0.000027	T	0.33089	0.0851	M	0.69823	2.125	0.46317	D	0.998982	P;P;B	0.46621	0.881;0.881;0.06	P;P;B	0.46718	0.525;0.525;0.09	T	0.21109	-1.0255	10	0.66056	D	0.02	.	8.6657	0.34118	0.8811:0.0:0.1189:0.0	.	245;244;246	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	M	246;245;246;244;246	ENSP00000362151:K246M;ENSP00000362154:K245M;ENSP00000386958:K246M;ENSP00000362148:K244M;ENSP00000309823:K246M	ENSP00000309823:K246M	K	+	2	0	FOXP4	41663093	1.000000	0.71417	1.000000	0.80357	0.140000	0.21249	5.542000	0.67218	0.695000	0.31675	0.533000	0.62120	AAG		0.692	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		4	71	0	0	0	1	0	4	71				
FAM111A	63901	broad.mit.edu	37	11	58920619	58920619	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr11:58920619G>A	ENST00000528737.1	+	5	4296	c.1478G>A	c.(1477-1479)cGa>cAa	p.R493Q	FAM111A_ENST00000531147.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000533703.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000420244.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000361723.3_Missense_Mutation_p.R493Q			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	493	Interaction with SV40 large T antigen.				defense response to virus (GO:0051607)|DNA replication (GO:0006260)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_epithelial(135;0.139)				CAGGGTCAGCGAGCAAAGAAA	0.403																																						ENST00000528737.1																			0				breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22						c.(1477-1479)cGa>cAa		family with sequence similarity 111, member A							96.0	98.0	97.0					11																	58920619		2201	4295	6496	SO:0001583	missense	63901				proteolysis		serine-type endopeptidase activity	g.chr11:58920619G>A	AK092953	CCDS7973.1	11q12.1	2014-03-13				ENSG00000166801			24725	protein-coding gene	gene with protein product		615292				11572484, 23996431, 23684011	Standard	NM_022074		Approved	FLJ22794, KIAA1895	uc001nnq.3	Q96PZ2		ENST00000528737.1:c.1478G>A	11.37:g.58920619G>A	ENSP00000434435:p.Arg493Gln					FAM111A_ENST00000361723.3_Missense_Mutation_p.R493Q|FAM111A_ENST00000533703.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000420244.1_Missense_Mutation_p.R493Q|FAM111A_ENST00000531147.1_Missense_Mutation_p.R493Q	p.R493Q			Q96PZ2	F111A_HUMAN			5	4296	+		all_epithelial(135;0.139)	493					A8K5Y8|Q5RKS9|Q5XKM2|Q68DK9|Q6IPR7|Q9H5Y1	Missense_Mutation	SNP	ENST00000528737.1	37	c.1478G>A	CCDS7973.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.211715	0.58452	.	.	ENSG00000166801	ENST00000528737;ENST00000420244;ENST00000361723;ENST00000533703;ENST00000531147	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	4.67	2.66	0.31614	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.413349	0.21534	N	0.073015	T	0.58278	0.2111	M	0.83953	2.67	0.09310	N	1	D	0.69078	0.997	P	0.54629	0.757	T	0.49808	-0.8900	10	0.42905	T	0.14	-0.2031	7.2558	0.26175	0.0929:0.0:0.739:0.1681	.	493	Q96PZ2	F111A_HUMAN	Q	493	ENSP00000434435:R493Q;ENSP00000406683:R493Q;ENSP00000355264:R493Q;ENSP00000433154:R493Q;ENSP00000431631:R493Q	ENSP00000355264:R493Q	R	+	2	0	FAM111A	58677195	0.002000	0.14202	0.091000	0.20842	0.014000	0.08584	0.942000	0.29017	1.340000	0.45581	-0.136000	0.14681	CGA		0.403	FAM111A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393975.1	NM_022074		7	89	0	0	0	1	0	7	89				
ANO8	57719	broad.mit.edu	37	19	17435806	17435806	+	Silent	SNP	G	G	A	rs540938848		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr19:17435806G>A	ENST00000159087.4	-	17	3209	c.3051C>T	c.(3049-3051)agC>agT	p.S1017S		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	1017					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						GGCGGGTGTCGCTGCCTGTGG	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		12103	0.001		0.0	False		,,,				2504	0.0					ENST00000159087.4																			0				autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						c.(3049-3051)agC>agT		anoctamin 8							62.0	79.0	73.0					19																	17435806		2202	4299	6501	SO:0001819	synonymous_variant	57719					chloride channel complex	chloride channel activity	g.chr19:17435806G>A	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	29329	protein-coding gene	gene with protein product		610216	"""KIAA1623"", ""transmembrane protein 16H"""	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.3051C>T	19.37:g.17435806G>A							p.S1017S	NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN			17	3209	-			1017					A6NIJ0	Silent	SNP	ENST00000159087.4	37	c.3051C>T	CCDS32949.1																																																																																				0.667	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644		6	104	0	0	0	1	0	6	104				
NRAS	4893	broad.mit.edu	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	rs11554290	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACTCTTCTTGTCCAGCTGT	0.458	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												ENST00000369535.4	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50		Dom	yes		1	1p13.2	4893	Mis	neuroblastoma RAS viral (v-ras) oncogene homolog			"""L, E"""			"""melanoma, MM, AML, thyroid"""		1016	Substitution - Missense(1016)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)	skin(466)|thyroid(279)|haematopoietic_and_lymphoid_tissue(124)|NS(50)|large_intestine(27)|lung(17)|urinary_tract(11)|adrenal_gland(7)|liver(7)|breast(7)|soft_tissue(4)|testis(3)|endometrium(3)|ovary(3)|central_nervous_system(2)|pancreas(2)|eye(1)|prostate(1)|meninges(1)|autonomic_ganglia(1)	NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085						c.(181-183)cAa>cGa		neuroblastoma RAS viral (v-ras) oncogene homolog							180.0	156.0	164.0					1																	115256529		2203	4300	6503	SO:0001583	missense	4893	Noonan syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity	g.chr1:115256529T>C	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.182A>G	1.37:g.115256529T>C	ENSP00000358548:p.Gln61Arg	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)					p.Q61R	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	3	435	-	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)	61		Q -> K (in neuroblastoma cell).|Q -> R (in lung carcinoma cell and melanoma; dbSNP:rs11554290).			Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	c.182A>G	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.004139	0.74932	.	.	ENSG00000213281	ENST00000369535	D	0.83673	-1.75	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.86489	0.5945	M	0.92604	3.325	0.80722	D	1	B	0.28512	0.214	B	0.39590	0.304	D	0.88255	0.2919	10	0.66056	D	0.02	.	15.0132	0.71565	0.0:0.0:0.0:1.0	rs11554290;rs11554290	61	P01111	RASN_HUMAN	R	61	ENSP00000358548:Q61R	ENSP00000358548:Q61R	Q	-	2	0	NRAS	115058052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	CAA		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		52	62	0	0	0	1	0	52	62				
NODAL	4838	broad.mit.edu	37	10	72195326	72195326	+	Missense_Mutation	SNP	C	C	T	rs10999334	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr10:72195326C>T	ENST00000287139.3	-	2	606	c.607G>A	c.(607-609)Gag>Aag	p.E203K	AC022532.1_ENST00000420338.2_Silent_p.L91L	NM_018055.4	NP_060525.3	Q96S42	NODAL_HUMAN	nodal growth differentiation factor	203			E -> K (in HTX5; decrease in signal transduction; dbSNP:rs10999334). {ECO:0000269|PubMed:19064609}.		axial mesodermal cell fate specification (GO:0048327)|brain development (GO:0007420)|cell migration involved in gastrulation (GO:0042074)|digestive tract morphogenesis (GO:0048546)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic pattern specification (GO:0009880)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endodermal cell differentiation (GO:0035987)|epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification (GO:0060802)|floor plate morphogenesis (GO:0033505)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|heart looping (GO:0001947)|inhibition of neuroepithelial cell differentiation (GO:0002085)|left lung morphogenesis (GO:0060460)|liver development (GO:0001889)|maternal placenta development (GO:0001893)|maternal process involved in parturition (GO:0060137)|mesendoderm development (GO:0048382)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of chorionic trophoblast cell proliferation (GO:1901383)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of trophoblast cell migration (GO:1901164)|neural fold formation (GO:0001842)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|placenta development (GO:0001890)|polarity specification of proximal/distal axis (GO:0010085)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gastrulation (GO:0010470)|regulation of stem cell maintenance (GO:2000036)|SMAD protein signal transduction (GO:0060395)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway involved in primitive streak formation (GO:0090010)|trophectodermal cellular morphogenesis (GO:0001831)|vasculature development (GO:0001944)	extracellular space (GO:0005615)	morphogen activity (GO:0016015)|type I activin receptor binding (GO:0070698)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	15						TGCCTCTGCTCCTGCGAGAGG	0.662													C|||	13	0.00259585	0.0	0.0	5008	,	,		18479	0.0119		0.0	False		,,,				2504	0.001					ENST00000287139.3																			0				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	15						c.(607-609)Gag>Aag		nodal growth differentiation factor							32.0	34.0	33.0					10																	72195326		2203	4300	6503	SO:0001583	missense	4838				growth	extracellular space	cytokine activity|growth factor activity	g.chr10:72195326C>T	BC033585	CCDS7304.1	10q22.1	2012-12-07	2012-12-07		ENSG00000156574	ENSG00000156574			7865	protein-coding gene	gene with protein product		601265	"""nodal, mouse, homolog"", ""nodal homolog (mouse)"""			9354794	Standard	NM_018055		Approved		uc001jrc.2	Q96S42	OTTHUMG00000018408	ENST00000287139.3:c.607G>A	10.37:g.72195326C>T	ENSP00000287139:p.Glu203Lys					AC022532.1_ENST00000420338.2_Silent_p.L91L	p.E203K	NM_018055.4	NP_060525.3	Q96S42	NODAL_HUMAN			2	606	-			203		E -> K (in HTX5; decrease in signal transduction; dbSNP:rs10999334).			Q2M3A5|Q8N4V3	Missense_Mutation	SNP	ENST00000287139.3	37	c.607G>A	CCDS7304.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	C	6.904	0.536390	0.13188	.	.	ENSG00000156574	ENST00000287139;ENST00000414871	D;D	0.84944	-1.92;-1.9	5.88	4.99	0.66335	.	0.414253	0.29172	N	0.012930	T	0.69602	0.3129	L	0.32530	0.975	0.32354	N	0.558023	B	0.06786	0.001	B	0.04013	0.001	T	0.70439	-0.4871	10	0.19590	T	0.45	.	10.3912	0.44168	0.0:0.8488:0.0:0.1512	rs10999334;rs52824892;rs10999334	203	Q96S42	NODAL_HUMAN	K	203;148	ENSP00000287139:E203K;ENSP00000394468:E148K	ENSP00000287139:E203K	E	-	1	0	NODAL	71865332	0.963000	0.33076	0.882000	0.34594	0.014000	0.08584	2.126000	0.42026	1.497000	0.48584	-0.137000	0.14449	GAG		0.662	NODAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048511.1	NM_018055		3	32	0	0	0	1	0	3	32				
NPAS4	266743	broad.mit.edu	37	11	66189993	66189993	+	Silent	SNP	G	G	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr11:66189993G>A	ENST00000311034.2	+	3	575	c.399G>A	c.(397-399)caG>caA	p.Q133Q		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	133	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						CTGTGCGCCAGCAACTCACCC	0.582																																						ENST00000311034.2																			0				breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						c.(397-399)caG>caA		neuronal PAS domain protein 4							147.0	125.0	133.0					11																	66189993		2200	4295	6495	SO:0001819	synonymous_variant	266743				transcription, DNA-dependent		DNA binding|signal transducer activity	g.chr11:66189993G>A	AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"""Basic helix-loop-helix proteins"""	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.399G>A	11.37:g.66189993G>A							p.Q133Q	NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN			3	575	+			133			PAS 1.		B7ZL81|Q8N8S5|Q8N9Q9	Silent	SNP	ENST00000311034.2	37	c.399G>A	CCDS8138.1																																																																																				0.582	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		3	45	0	0	0	1	0	3	45				
ACAN	176	broad.mit.edu	37	15	89391161	89391161	+	Missense_Mutation	SNP	C	C	T	rs143697605		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr15:89391161C>T	ENST00000561243.1	+	8	1624	c.1624C>T	c.(1624-1626)Cgg>Tgg	p.R542W	ACAN_ENST00000559004.1_Missense_Mutation_p.R542W|ACAN_ENST00000352105.7_Missense_Mutation_p.R542W|ACAN_ENST00000439576.2_Missense_Mutation_p.R542W|ACAN_ENST00000558207.1_Missense_Mutation_p.R542W			P16112	PGCA_HUMAN	aggrecan	542	G2-B.|Link 3. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)	p.R542W(1)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TGTGAGCCCCCGGACCCCATG	0.607													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11533	0.0		0.0	False		,,,				2504	0.0					ENST00000439576.2																			1	Substitution - Missense(1)	p.R542W(1)	large_intestine(1)	NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93						c.(1624-1626)Cgg>Tgg		aggrecan							72.0	75.0	74.0					15																	89391161		1949	4147	6096	SO:0001583	missense	176				cell adhesion		hyaluronic acid binding|sugar binding	g.chr15:89391161C>T	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.1624C>T	15.37:g.89391161C>T	ENSP00000453342:p.Arg542Trp					ACAN_ENST00000559004.1_Missense_Mutation_p.R542W|ACAN_ENST00000352105.7_Missense_Mutation_p.R542W|ACAN_ENST00000558207.1_Missense_Mutation_p.R542W|ACAN_ENST00000561243.1_Missense_Mutation_p.R542W	p.R542W	NM_013227.3	NP_037359.3	E7EX88	E7EX88_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.146)		9	1998	+	Lung NSC(78;0.0392)|all_lung(78;0.077)		542					Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	c.1624C>T	CCDS53970.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	15.01	2.707015	0.48412	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.13901	2.55;2.55	5.35	3.4	0.38934	.	.	.	.	.	T	0.49541	0.1563	H	0.97103	3.94	0.40088	D	0.976221	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.63817	-0.6551	9	0.87932	D	0	-18.098	11.6973	0.51551	0.3215:0.6785:0.0:0.0	.	542;542;542	E7ENV9;E7EX88;Q6PID9	.;.;.	W	542	ENSP00000387356:R542W;ENSP00000341615:R542W	ENSP00000268134:R542W	R	+	1	2	ACAN	87192165	0.202000	0.23423	0.676000	0.29932	0.976000	0.68499	0.725000	0.25970	0.581000	0.29539	0.563000	0.77884	CGG		0.607	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		4	56	0	0	0	1	0	4	56				
MT1A	4489	broad.mit.edu	37	16	56670827	56670827	+	5'Flank	SNP	C	C	T	rs11076159	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr16:56670827C>T	ENST00000290705.8	+	0	0				MT1JP_ENST00000564564.1_RNA	NM_005946.2	NP_005937.2	P04731	MT1A_HUMAN	metallothionein 1A						cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(1)	3					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGCAAAGGGACGTCGGAGAAG	0.537													.|||	439	0.0876597	0.1982	0.0432	5008	,	,		18660	0.1052		0.0229	False		,,,				2504	0.0184					ENST00000564564.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr16:56670827C>T	BC029475	CCDS32454.1	16q13	2012-10-02	2007-03-02			ENSG00000205362		"""Metallothioneins"""	7393	protein-coding gene	gene with protein product		156350	"""metallothionein 1S"""	MT1, MT1S		6089206, 6327055	Standard	NM_005946		Approved		uc002ejq.3	P04731			16.37:g.56670827C>T	Exception_encountered													0	806	+								Q86YX5	RNA	SNP	ENST00000290705.8	37		CCDS32454.1																																																																																				0.537	MT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434324.1	NM_005946		3	47	0	0	0	1	0	3	47				
OR4M1	441670	broad.mit.edu	37	14	20248797	20248797	+	Missense_Mutation	SNP	T	T	A			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr14:20248797T>A	ENST00000315957.4	+	1	397	c.316T>A	c.(316-318)Ttt>Att	p.F106I		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	106						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CTTCTTACACTTTGTTGGGGC	0.473																																						ENST00000315957.4																			0				NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42						c.(316-318)Ttt>Att		olfactory receptor, family 4, subfamily M, member 1							234.0	253.0	246.0					14																	20248797		2203	4300	6503	SO:0001583	missense	441670				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr14:20248797T>A		CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"""GPCR / Class A : Olfactory receptors"""	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.316T>A	14.37:g.20248797T>A	ENSP00000319654:p.Phe106Ile						p.F106I	NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)	1	397	+	all_cancers(95;0.00108)		106					B9EH18|Q6IFA3	Missense_Mutation	SNP	ENST00000315957.4	37	c.316T>A	CCDS32021.1	.	.	.	.	.	.	.	.	.	.	.	13.79	2.343637	0.41498	.	.	ENSG00000176299	ENST00000315957	T	0.00414	7.52	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000188	T	0.00356	0.0011	L	0.47716	1.5	0.25030	N	0.991275	B	0.30439	0.279	B	0.27608	0.081	T	0.47315	-0.9127	10	0.49607	T	0.09	-15.447	11.5315	0.50614	0.0:0.0:0.0:1.0	.	106	Q8NGD0	OR4M1_HUMAN	I	106	ENSP00000319654:F106I	ENSP00000319654:F106I	F	+	1	0	OR4M1	19318637	0.002000	0.14202	1.000000	0.80357	0.823000	0.46562	0.873000	0.28052	1.894000	0.54839	0.330000	0.21533	TTT		0.473	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1			9	261	0	0	0	1	0	9	261				
RNASE1	6035	broad.mit.edu	37	14	21270003	21270003	+	Silent	SNP	C	C	T			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr14:21270003C>T	ENST00000397967.4	-	2	731	c.225G>A	c.(223-225)gtG>gtA	p.V75V	RNASE1_ENST00000340900.3_Silent_p.V75V|RNASE1_ENST00000555698.1_Silent_p.V35V|RNASE1_ENST00000397970.4_Silent_p.V75V|RNASE1_ENST00000412779.2_Silent_p.V75V	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	75					RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	Guanidine(DB00536)|L-Aspartic Acid(DB00128)	GGGGCTCGTGCACAAAGGTGT	0.542																																						ENST00000397967.4																			0				central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5						c.(223-225)gtG>gtA		ribonuclease, RNase A family, 1 (pancreatic)							143.0	127.0	132.0					14																	21270003		2203	4300	6503	SO:0001819	synonymous_variant	6035					extracellular region	nucleic acid binding|pancreatic ribonuclease activity|protein binding	g.chr14:21270003C>T	BC005324	CCDS9559.1	14q11.2	2014-03-13			ENSG00000129538	ENSG00000129538	3.1.27.5	"""Ribonucleases, RNase A"""	10044	protein-coding gene	gene with protein product		180440		RNS1		8588814	Standard	NM_002933		Approved		uc001vyi.3	P07998	OTTHUMG00000029603	ENST00000397967.4:c.225G>A	14.37:g.21270003C>T						RNASE1_ENST00000412779.2_Silent_p.V75V|RNASE1_ENST00000340900.3_Silent_p.V75V|RNASE1_ENST00000397970.4_Silent_p.V75V|RNASE1_ENST00000555698.1_Silent_p.V35V	p.V75V	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	2	731	-	all_cancers(95;0.00671)	all_lung(585;0.235)	75					B2R589|D3DS06|Q16830|Q16869|Q1KHR2|Q6ICS5|Q9UCB4|Q9UCB5	Silent	SNP	ENST00000397967.4	37	c.225G>A	CCDS9559.1																																																																																				0.542	RNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073791.3			5	73	0	0	0	1	0	5	73				
COG7	91949	broad.mit.edu	37	16	23428325	23428325	+	Missense_Mutation	SNP	A	A	G			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr16:23428325A>G	ENST00000307149.5	-	9	1440	c.1255T>C	c.(1255-1257)Tgc>Cgc	p.C419R		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	419					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		AACAGGCCGCAGGTCCCCAGG	0.567																																						ENST00000307149.5																			0				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27						c.(1255-1257)Tgc>Cgc		component of oligomeric golgi complex 7							85.0	67.0	73.0					16																	23428325		2197	4300	6497	SO:0001583	missense	91949				intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding	g.chr16:23428325A>G	AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"""Components of oligomeric golgi complex"""	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.1255T>C	16.37:g.23428325A>G	ENSP00000305442:p.Cys419Arg						p.C419R	NM_153603.3	NP_705831.1	P83436	COG7_HUMAN		GBM - Glioblastoma multiforme(48;0.0401)	9	1440	-			419					Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	37	c.1255T>C	CCDS10610.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.246237	0.80024	.	.	ENSG00000168434	ENST00000307149	T	0.44482	0.92	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.59783	0.2219	M	0.66939	2.045	0.80722	D	1	D	0.71674	0.998	D	0.68353	0.957	T	0.56159	-0.8025	10	0.21540	T	0.41	-8.1377	14.9498	0.71064	1.0:0.0:0.0:0.0	.	419	P83436	COG7_HUMAN	R	419	ENSP00000305442:C419R	ENSP00000305442:C419R	C	-	1	0	COG7	23335826	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	4.920000	0.63390	2.135000	0.66039	0.533000	0.62120	TGC		0.567	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1			3	37	0	0	0	1	0	3	37				
SIRPA	140885	broad.mit.edu	37	20	1902292	1902292	+	Missense_Mutation	SNP	G	G	A	rs200513155		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr20:1902292G>A	ENST00000358771.4	+	3	840	c.688G>A	c.(688-690)Gtg>Atg	p.V230M	SIRPA_ENST00000400068.3_Missense_Mutation_p.V230M|SIRPA_ENST00000356025.3_Missense_Mutation_p.V230M	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	230	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.V230M(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CATCTGCGAGGTGGCCCACGT	0.612																																					GBM(155;1668 1920 5945 42733 48121)	ENST00000358771.4																			1	Substitution - Missense(1)	p.V230M(1)	lung(1)	cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21						c.(688-690)Gtg>Atg		signal-regulatory protein alpha							66.0	57.0	60.0					20																	1902292		2203	4296	6499	SO:0001583	missense	140885				blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding	g.chr20:1902292G>A	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.688G>A	20.37:g.1902292G>A	ENSP00000351621:p.Val230Met					SIRPA_ENST00000356025.3_Missense_Mutation_p.V230M|SIRPA_ENST00000400068.3_Missense_Mutation_p.V230M	p.V230M	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN		Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)	3	840	+			230			Ig-like C1-type 1.		A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	c.688G>A	CCDS13022.1	23	0.010531135531135532	4	0.008130081300813009	2	0.0055248618784530384	6	0.01048951048951049	11	0.014511873350923483	G	19.90	3.912586	0.72983	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.13538	2.58;2.58;2.58	4.86	4.86	0.63082	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.115071	0.38720	N	0.001599	T	0.38081	0.1027	H	0.95294	3.65	0.45634	D	0.99856	D;D;D	0.69078	0.993;0.984;0.997	D;P;P	0.62955	0.909;0.562;0.878	T	0.57556	-0.7791	10	0.66056	D	0.02	.	13.7542	0.62926	0.0:0.0:1.0:0.0	.	210;230;230	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	M	230	ENSP00000382941:V230M;ENSP00000348307:V230M;ENSP00000351621:V230M	ENSP00000348307:V230M	V	+	1	0	SIRPA	1850292	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	1.834000	0.39171	2.718000	0.92993	0.650000	0.86243	GTG		0.612	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792		3	39	0	0	0	1	0	3	39				
MMAA	166785	broad.mit.edu	37	4	146560393	146560393	+	Silent	SNP	C	C	T	rs146372922	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr4:146560393C>T	ENST00000281317.5	+	2	1312	c.102C>T	c.(100-102)ctC>ctT	p.L34L	MMAA_ENST00000541599.1_5'UTR	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	34					cellular lipid metabolic process (GO:0044255)|cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTACTCATCTCGGATCAGGAA	0.443													c|||	9	0.00179712	0.0068	0.0	5008	,	,		19886	0.0		0.0	False		,,,				2504	0.0					ENST00000281317.5																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17						c.(100-102)ctC>ctT		methylmalonic aciduria (cobalamin deficiency) cblA type	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	C		16,4390	24.3+/-50.5	0,16,2187	149.0	143.0	145.0		102	-0.3	0.0	4	dbSNP_134	145	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MMAA	NM_172250.2		0,18,6485	TT,TC,CC		0.0233,0.3631,0.1384		34/419	146560393	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	166785					mitochondrion	GTP binding|nucleoside-triphosphatase activity	g.chr4:146560393C>T	AF524841	CCDS3766.1	4q31.1	2011-05-12	2005-07-11			ENSG00000151611			18871	protein-coding gene	gene with protein product		607481	"""methylmalonic aciduria (cobalamin deficiency) type A"""			12438653	Standard	NM_172250		Approved	cblA	uc003ikh.4	Q8IVH4		ENST00000281317.5:c.102C>T	4.37:g.146560393C>T						MMAA_ENST00000541599.1_5'UTR	p.L34L	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN			2	1312	+	all_hematologic(180;0.151)		34					B3KX40|Q495G7	Silent	SNP	ENST00000281317.5	37	c.102C>T	CCDS3766.1																																																																																				0.443	MMAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364668.2			46	78	0	0	0	1	0	46	78				
SIRPA	140885	broad.mit.edu	37	20	1902301	1902301	+	Missense_Mutation	SNP	G	G	A	rs199733185		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr20:1902301G>A	ENST00000358771.4	+	3	849	c.697G>A	c.(697-699)Gtc>Atc	p.V233I	SIRPA_ENST00000400068.3_Missense_Mutation_p.V233I|SIRPA_ENST00000356025.3_Missense_Mutation_p.V233I	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	233	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.V233I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		GGTGGCCCACGTCACCTTGCA	0.617																																					GBM(155;1668 1920 5945 42733 48121)	ENST00000358771.4																			1	Substitution - Missense(1)	p.V233I(1)	lung(1)	cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21						c.(697-699)Gtc>Atc		signal-regulatory protein alpha							67.0	60.0	62.0					20																	1902301		2203	4296	6499	SO:0001583	missense	140885				blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding	g.chr20:1902301G>A	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.697G>A	20.37:g.1902301G>A	ENSP00000351621:p.Val233Ile					SIRPA_ENST00000356025.3_Missense_Mutation_p.V233I|SIRPA_ENST00000400068.3_Missense_Mutation_p.V233I	p.V233I	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN		Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)	3	849	+			233			Ig-like C1-type 1.		A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	c.697G>A	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.382458	0.24944	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02863	4.13;4.13;4.13	4.86	-7.7	0.01259	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	2.216010	0.01765	N	0.030825	T	0.02727	0.0082	L	0.27053	0.805	0.09310	N	1	B;B;B	0.14805	0.002;0.011;0.008	B;B;B	0.12156	0.002;0.007;0.006	T	0.30765	-0.9967	10	0.20519	T	0.43	.	13.8982	0.63785	0.7446:0.0:0.2554:0.0	.	213;233;233	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	I	233	ENSP00000382941:V233I;ENSP00000348307:V233I;ENSP00000351621:V233I	ENSP00000348307:V233I	V	+	1	0	SIRPA	1850301	0.000000	0.05858	0.000000	0.03702	0.766000	0.43426	-2.041000	0.01415	-1.573000	0.01659	-0.355000	0.07637	GTC		0.617	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792		3	37	0	0	0	1	0	3	37				
FAM46A	55603	broad.mit.edu	37	6	82461727	82461727	+	Silent	SNP	A	A	G	rs373591596		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr6:82461727A>G	ENST00000320172.6	-	2	446	c.132T>C	c.(130-132)ggT>ggC	p.G44G	FAM46A_ENST00000369754.3_Silent_p.G63G|FAM46A_ENST00000369756.3_Silent_p.G125G	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	44					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		Agctgccgccaccgccgaagt	0.682																																						ENST00000369754.3																			0				endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12						c.(187-189)ggT>ggC		family with sequence similarity 46, member A							11.0	12.0	12.0					6																	82461727		1974	3964	5938	SO:0001819	synonymous_variant	55603							g.chr6:82461727A>G	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"""chromosome 6 open reading frame 37"""	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.132T>C	6.37:g.82461727A>G						FAM46A_ENST00000369756.3_Silent_p.G125G|FAM46A_ENST00000320172.6_Silent_p.G44G	p.G63G			Q96IP4	FA46A_HUMAN		BRCA - Breast invasive adenocarcinoma(397;0.0428)	2	501	-		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)	44					A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Silent	SNP	ENST00000320172.6	37	c.189T>C	CCDS34489.1																																																																																				0.682	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			3	16	0	0	0	1	0	3	16				
RHOA	387	broad.mit.edu	37	3	49395674	49395676	+	IGR	DEL	GCC	GCC	-	rs71077799|rs56041243|rs139760138|rs17838762	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr3:49395674_49395676delGCC	ENST00000418115.1	-	0	2031				GPX1_ENST00000496791.1_5'UTR|GPX1_ENST00000419783.1_In_Frame_Del_p.12_13AA>A|GPX1_ENST00000419349.1_In_Frame_Del_p.12_13AA>A	NM_001664.2	NP_001655.1	P61586	RHOA_HUMAN	ras homolog family member A						actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|apical junction assembly (GO:0043297)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cerebral cortex cell migration (GO:0021795)|cleavage furrow formation (GO:0036089)|forebrain radial glial cell differentiation (GO:0021861)|negative chemotaxis (GO:0050919)|negative regulation of axonogenesis (GO:0050771)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification involved in bone maturation (GO:0043931)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of podosome assembly (GO:0071803)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of translation (GO:0045727)|positive regulation of vasoconstriction (GO:0045907)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion transport (GO:0051924)|regulation of cell migration (GO:0030334)|regulation of dendrite development (GO:0050773)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of osteoblast proliferation (GO:0033688)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|Rho protein signal transduction (GO:0007266)|skeletal muscle tissue development (GO:0007519)|small GTPase mediated signal transduction (GO:0007264)|spindle assembly involved in mitosis (GO:0090307)|stress fiber assembly (GO:0043149)|stress-activated protein kinase signaling cascade (GO:0031098)|substantia nigra development (GO:0021762)|trabecula morphogenesis (GO:0061383)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	apical junction complex (GO:0043296)|axon (GO:0030424)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin binding (GO:0017022)	p.A12_A13delAA(1)		cervix(1)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CACCGACTGGgccgccgccgccg	0.69														3825	0.763778	0.5257	0.7406	5008	,	,		9124	0.9742		0.7386	False		,,,				2504	0.911					ENST00000419783.1																			1	Deletion - In frame(1)	p.A12_A13delAA(1)	breast(1)	breast(1)|large_intestine(2)|lung(1)	4						c.(34-39)gcc>gc		glutathione peroxidase 1	Glutathione(DB00143)																																			SO:0001628	intergenic_variant	2876				anti-apoptosis|cell redox homeostasis|glutathione metabolic process|heart contraction|hydrogen peroxide catabolic process|negative regulation of caspase activity|purine base metabolic process|purine nucleotide catabolic process|regulation of gene expression, epigenetic|regulation of mammary gland epithelial cell proliferation|regulation of proteasomal protein catabolic process|release of cytochrome c from mitochondria|response to selenium ion|UV protection	cytosol|mitochondrion	endopeptidase inhibitor activity|glutathione peroxidase activity|SH3 domain binding	g.chr3:49395674_49395676delGCC	BC001360	CCDS2795.1	3p21.3	2012-02-27	2012-02-27	2004-03-23	ENSG00000067560	ENSG00000067560			667	protein-coding gene	gene with protein product		165390	"""ras homolog gene family, member A"""	ARH12, ARHA		9605859	Standard	NM_001664		Approved	RhoA, Rho12, RHOH12	uc003cwu.3	P61586	OTTHUMG00000156838		3.37:g.49395683_49395685delGCC						GPX1_ENST00000496791.1_5'UTR|GPX1_ENST00000419349.1_In_Frame_Del_p.AA12del	p.AA12del	NM_000581.2	NP_000572.2	P07203	GPX1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	1	357_359	-			12					P06749|Q53HM4|Q5U024|Q9UDJ0|Q9UEJ4	In_Frame_Del	DEL	ENST00000418115.1	37	c.36_38delGGC	CCDS2795.1																																																																																				0.690	RHOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346157.3	NM_001664		2	4						2	4	---	---	---	---
NKD2	85409	broad.mit.edu	37	5	1038447	1038449	+	In_Frame_Del	DEL	CAC	CAC	-	rs3840989		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr5:1038447_1038449delCAC	ENST00000296849.5	+	10	1544_1546	c.1315_1317delCAC	c.(1315-1317)cacdel	p.H447del	NKD2_ENST00000382730.2_In_Frame_Del_p.P86del|NKD2_ENST00000274150.4_3'UTR	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	447	His-rich.				exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			ccaccacgagcaccaccaccacc	0.69																																						ENST00000296849.5																			0				breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14						c.(1315-1317)del		naked cuticle homolog 2 (Drosophila)																																				SO:0001651	inframe_deletion	85409				exocytosis|Wnt receptor signaling pathway	cytoplasmic membrane-bounded vesicle|plasma membrane	calcium ion binding|ubiquitin protein ligase binding	g.chr5:1038447_1038449delCAC	AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"""EF-hand domain containing"""	17046	protein-coding gene	gene with protein product	"""naked cuticle-2"", ""Dvl-binding protein NKD2"""	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.1315_1317delCAC	5.37:g.1038456_1038458delCAC	ENSP00000296849:p.His447del					NKD2_ENST00000382730.2_In_Frame_Del_p.AP78del|NKD2_ENST00000274150.4_3'UTR	p.H447del	NM_033120.2	NP_149111.1	Q969F2	NKD2_HUMAN	Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)		10	1544_1546	+	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		447			His-rich.		Q96EK8|Q9BSN0	In_Frame_Del	DEL	ENST00000296849.5	37	c.1315_1317delCAC	CCDS3859.1																																																																																				0.690	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120		2	4						2	4	---	---	---	---
MED13	9969	broad.mit.edu	37	17	60142516	60142516	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	c65e4fef-29d8-47ae-aa97-f65bf352c24d	g.chr17:60142516delA	ENST00000397786.2	-	1	127	c.51delT	c.(49-51)tgtfs	p.C17fs		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	17					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AGAAGAGGTTACAGTGACAAT	0.716																																						ENST00000397786.2																			0				breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						c.(49-51)tgfs		mediator complex subunit 13							7.0	10.0	9.0					17																	60142516		1933	4134	6067	SO:0001589	frameshift_variant	9969				androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding	g.chr17:60142516delA	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.51delT	17.37:g.60142516delA	ENSP00000380888:p.Cys17fs						p.C17fs	NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN			1	127	-			17					B2RU05|O60334	Frame_Shift_Del	DEL	ENST00000397786.2	37	c.51delT	CCDS42366.1																																																																																				0.716	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		2	4						2	4	---	---	---	---
AC016995.3	0	broad.mit.edu	37	2	38710019	38710019	+	lincRNA	DEL	T	T	-	rs2005502|rs57303101|rs538061888|rs200292719	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr2:38710019delT	ENST00000417039.1	-	0	696																											CTTtaaaaaataaataaataa	0.244																																						ENST00000417039.1																			0																																																			0							g.chr2:38710019delT																													2.37:g.38710019delT														0	696	-									RNA	DEL	ENST00000417039.1	37																																																																																						0.244	AC016995.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000331173.1			5	4						5	4	---	---	---	---
NKD2	85409	broad.mit.edu	37	5	1038447	1038449	+	In_Frame_Del	DEL	CAC	CAC	-	rs3840989		TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr5:1038447_1038449delCAC	ENST00000296849.5	+	10	1544_1546	c.1315_1317delCAC	c.(1315-1317)cacdel	p.H447del	NKD2_ENST00000382730.2_In_Frame_Del_p.P86del|NKD2_ENST00000274150.4_3'UTR	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	447	His-rich.				exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			ccaccacgagcaccaccaccacc	0.69																																						ENST00000296849.5																			0				breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14						c.(1315-1317)del		naked cuticle homolog 2 (Drosophila)																																				SO:0001651	inframe_deletion	85409				exocytosis|Wnt receptor signaling pathway	cytoplasmic membrane-bounded vesicle|plasma membrane	calcium ion binding|ubiquitin protein ligase binding	g.chr5:1038447_1038449delCAC	AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"""EF-hand domain containing"""	17046	protein-coding gene	gene with protein product	"""naked cuticle-2"", ""Dvl-binding protein NKD2"""	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.1315_1317delCAC	5.37:g.1038456_1038458delCAC	ENSP00000296849:p.His447del					NKD2_ENST00000274150.4_3'UTR|NKD2_ENST00000382730.2_In_Frame_Del_p.AP78del	p.H447del	NM_033120.2	NP_149111.1	Q969F2	NKD2_HUMAN	Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)		10	1544_1546	+	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		447			His-rich.		Q96EK8|Q9BSN0	In_Frame_Del	DEL	ENST00000296849.5	37	c.1315_1317delCAC	CCDS3859.1																																																																																				0.690	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120		2	4						2	4	---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11871470	11871481	+	In_Frame_Del	DEL	GCAGCGGCAGCG	GCAGCGGCAGCG	-	rs536177295	byFrequency	TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr7:11871470_11871481delGCAGCGGCAGCG	ENST00000423059.4	-	1	343_354	c.92_103delCGCTGCCGCTGC	c.(91-105)ccgctgccgctgctc>ctc	p.PLPL31del		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	31					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		agcagcaggagcagcggcagcggcagcggcag	0.774										HNSCC(18;0.044)				192	0.0383387	0.0068	0.0086	5008	,	,		7998	0.0615		0.0249	False		,,,				2504	0.092					ENST00000423059.3																			0				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113						c.(91-105)ctc>c		thrombospondin, type I, domain containing 7A				3,26,1613		1,0,1,10,6,803						1.7	0.2			6	40,97,3805		11,0,18,22,53,1867	no	codingComplex	THSD7A	NM_015204.2		12,0,19,32,59,2670	A1A1,A1A2,A1R,A2A2,A2R,RR		3.4754,1.7661,2.9728				43,123,5418				SO:0001651	inframe_deletion	221981					integral to membrane		g.chr7:11871470_11871481delGCAGCGGCAGCG		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.92_103delCGCTGCCGCTGC	7.37:g.11871470_11871481delGCAGCGGCAGCG	ENSP00000406482:p.Pro31_Leu34del	HNSCC(18;0.044)					p.PLPLL31del	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.163)	1	343_354	-			31						In_Frame_Del	DEL	ENST00000423059.4	37	c.92_103delCGCTGCCGCTGC	CCDS47543.1																																																																																				0.774	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		4	6						4	6	---	---	---	---
MED13	9969	broad.mit.edu	37	17	60142516	60142516	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chr17:60142516delA	ENST00000397786.2	-	1	127	c.51delT	c.(49-51)tgtfs	p.C17fs		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	17					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AGAAGAGGTTACAGTGACAAT	0.716																																						ENST00000397786.2																			0				breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						c.(49-51)tgfs		mediator complex subunit 13							7.0	10.0	9.0					17																	60142516		1933	4134	6067	SO:0001589	frameshift_variant	9969				androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding	g.chr17:60142516delA	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.51delT	17.37:g.60142516delA	ENSP00000380888:p.Cys17fs						p.C17fs	NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN			1	127	-			17					B2RU05|O60334	Frame_Shift_Del	DEL	ENST00000397786.2	37	c.51delT	CCDS42366.1																																																																																				0.716	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		2	4						2	4	---	---	---	---
LRCH2	57631	broad.mit.edu	37	X	114414309	114414309	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BJ-A45G-01A-11D-A23U-08	TCGA-BJ-A45G-11A-11D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c664ae81-8962-418c-8335-db2aa5ad98d3	d962e1b5-46ff-4ce3-8372-69616984a546	g.chrX:114414309delA	ENST00000317135.8	-	4	657	c.627delT	c.(625-627)attfs	p.I209fs	LRCH2_ENST00000538422.1_Frame_Shift_Del_p.I209fs	NM_020871.3	NP_065922.3	Q5VUJ6	LRCH2_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 2	209										breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	19						CATTGCAGCTAATATCCTAAG	0.279																																						ENST00000317135.8																			0				breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	19						c.(625-627)atfs		leucine-rich repeats and calponin homology (CH) domain containing 2							43.0	36.0	38.0					X																	114414309		1790	4047	5837	SO:0001589	frameshift_variant	57631							g.chrX:114414309delA	AB040928	CCDS48155.1, CCDS59175.1	Xq24	2008-02-05			ENSG00000130224	ENSG00000130224			29292	protein-coding gene	gene with protein product						10819331	Standard	NM_020871		Approved	KIAA1495	uc010nqe.3	Q5VUJ6	OTTHUMG00000022233	ENST00000317135.8:c.627delT	X.37:g.114414309delA	ENSP00000325091:p.Ile209fs					LRCH2_ENST00000538422.1_Frame_Shift_Del_p.I209fs	p.I209fs	NM_020871.3	NP_065922.3	Q5VUJ6	LRCH2_HUMAN			4	657	-			209					F5H2T1|Q08AD5|Q9HA88|Q9P233	Frame_Shift_Del	DEL	ENST00000317135.8	37	c.627delT	CCDS48155.1																																																																																				0.279	LRCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057971.2	NM_020871		2	4						2	4	---	---	---	---
