#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
ACBD5	91452	broad.mit.edu	37	10	27499972	27499972	+	Silent	SNP	C	C	T			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr10:27499972C>T	ENST00000375888.1	-	9	1066	c.1002G>A	c.(1000-1002)caG>caA	p.Q334Q	ACBD5_ENST00000476758.1_5'UTR|ACBD5_ENST00000375905.4_Silent_p.Q290Q|ACBD5_ENST00000396271.3_Silent_p.Q325Q|ACBD5_ENST00000375897.3_Silent_p.Q148Q|ACBD5_ENST00000375901.1_Silent_p.Q216Q			Q5T8D3	ACBD5_HUMAN	acyl-CoA binding domain containing 5	334					peroxisome degradation (GO:0030242)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisome (GO:0005777)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)			breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						CCAAGTAATACTGAAATGGTC	0.373																																						ENST00000396271.3																			0				breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						c.(973-975)caG>caA		acyl-CoA binding domain containing 5							97.0	93.0	94.0					10																	27499972		2203	4300	6503	SO:0001819	synonymous_variant	91452				transport	integral to membrane|peroxisomal membrane	fatty-acyl-CoA binding	g.chr10:27499972C>T	AF505653	CCDS7154.1, CCDS44368.1, CCDS73079.1	10p12.1	2010-04-30	2010-04-30		ENSG00000107897	ENSG00000107897			23338	protein-coding gene	gene with protein product			"""acyl-Coenzyme A binding domain containing 5"""			12056414	Standard	NR_024150		Approved	DKFZp434A2417, KIAA1996	uc010qdp.2	Q5T8D3	OTTHUMG00000017854	ENST00000375888.1:c.1002G>A	10.37:g.27499972C>T						ACBD5_ENST00000375897.3_Silent_p.Q148Q|ACBD5_ENST00000375901.1_Silent_p.Q216Q|ACBD5_ENST00000476758.1_5'UTR|ACBD5_ENST00000375905.4_Silent_p.Q290Q|ACBD5_ENST00000375888.1_Silent_p.Q334Q	p.Q325Q	NM_145698.3	NP_663736.2	Q5T8D3	ACBD5_HUMAN			9	1101	-			334					B3KQ56|D3DRW0|Q5T8D4|Q5T8E1|Q5T8E2|Q86UV1|Q8N6E3|Q9UFB5	Silent	SNP	ENST00000375888.1	37	c.975G>A																																																																																					0.373	ACBD5-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000047314.1	NM_145698		8	68	0	0	0	1	0	8	68				
FAM65A	79567	broad.mit.edu	37	16	67575406	67575406	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr16:67575406C>T	ENST00000379312.3	+	11	1008	c.887C>T	c.(886-888)gCc>gTc	p.A296V	CTD-2012K14.2_ENST00000567122.1_RNA|FAM65A_ENST00000428437.2_Missense_Mutation_p.A306V|FAM65A_ENST00000042381.4_Missense_Mutation_p.A292V|FAM65A_ENST00000540839.3_Missense_Mutation_p.A312V|FAM65A_ENST00000422602.2_Missense_Mutation_p.A312V|CTD-2012K14.3_ENST00000563083.1_RNA|CTD-2012K14.4_ENST00000564717.1_RNA	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	296						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		GACCTGTTTGCCGCCCTGCCC	0.572																																						ENST00000540839.3																			0				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39						c.(934-936)gCc>gTc		family with sequence similarity 65, member A							181.0	160.0	167.0					16																	67575406		2198	4300	6498	SO:0001583	missense	79567					cytoplasm	binding	g.chr16:67575406C>T	AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.887C>T	16.37:g.67575406C>T	ENSP00000368614:p.Ala296Val					FAM65A_ENST00000422602.2_Missense_Mutation_p.A312V|FAM65A_ENST00000428437.2_Missense_Mutation_p.A306V|FAM65A_ENST00000379312.3_Missense_Mutation_p.A296V|FAM65A_ENST00000042381.4_Missense_Mutation_p.A292V	p.A312V			Q6ZS17	FA65A_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)	12	1155	+		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)	296					B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	37	c.935C>T	CCDS54028.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.746006	0.89663	.	.	ENSG00000039523	ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839	T;T;T	0.02085	4.46;4.46;4.46	4.86	3.91	0.45181	.	0.160136	0.56097	N	0.000038	T	0.04003	0.0112	L	0.58810	1.83	0.80722	D	1	P;P;P;P	0.43287	0.686;0.686;0.686;0.802	B;B;B;B	0.40940	0.173;0.173;0.173;0.344	T	0.46428	-0.9192	10	0.56958	D	0.05	-6.5751	12.9985	0.58662	0.0:0.9213:0.0:0.0787	.	306;312;296;312	B4DIM2;E9PBS3;Q6ZS17;B4DEQ9	.;.;FA65A_HUMAN;.	V	296;292;312;306	ENSP00000368614:A296V;ENSP00000042381:A292V;ENSP00000400099:A312V	ENSP00000042381:A292V	A	+	2	0	FAM65A	66132907	1.000000	0.71417	0.494000	0.27515	0.956000	0.61745	7.474000	0.81024	1.051000	0.40369	0.561000	0.74099	GCC		0.572	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519		4	163	0	0	0	1	0	4	163				
RASGRP3	25780	broad.mit.edu	37	2	33747057	33747057	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr2:33747057G>A	ENST00000403687.3	+	7	1144	c.404G>A	c.(403-405)aGg>aAg	p.R135K	RASGRP3_ENST00000407811.1_Missense_Mutation_p.R135K|RASGRP3_ENST00000402538.3_Missense_Mutation_p.R135K	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	135					MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)			large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					GTCACACAGAGGAAAAAAGTA	0.418																																						ENST00000403687.3																			0				large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11						c.(403-405)aGg>aAg		RAS guanyl releasing protein 3 (calcium and DAG-regulated)							130.0	127.0	128.0					2																	33747057		1877	4106	5983	SO:0001583	missense	25780				MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity|protein binding|Rap GTPase activator activity|signal transducer activity	g.chr2:33747057G>A	AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"""EF-hand domain containing"""	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.404G>A	2.37:g.33747057G>A	ENSP00000384192:p.Arg135Lys					RASGRP3_ENST00000402538.3_Missense_Mutation_p.R135K|RASGRP3_ENST00000407811.1_Missense_Mutation_p.R135K	p.R135K	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN			7	1144	+	all_hematologic(175;0.115)		135					D6W583|O94931|Q53SD7	Missense_Mutation	SNP	ENST00000403687.3	37	c.404G>A	CCDS46256.1	.	.	.	.	.	.	.	.	.	.	G	33	5.216376	0.95104	.	.	ENSG00000152689	ENST00000402538;ENST00000437184;ENST00000403687;ENST00000407811	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	6.03	6.03	0.97812	Ras guanine nucleotide exchange factor, domain (1);	0.049420	0.85682	N	0.000000	T	0.47563	0.1452	L	0.50333	1.59	0.48696	D	0.999695	D;D	0.59767	0.986;0.986	P;P	0.59288	0.855;0.855	T	0.05068	-1.0908	10	0.24483	T	0.36	-13.7361	20.5752	0.99366	0.0:0.0:1.0:0.0	.	135;135	D6W583;Q8IV61	.;GRP3_HUMAN	K	135	ENSP00000385886:R135K;ENSP00000393866:R135K;ENSP00000384192:R135K;ENSP00000383917:R135K	ENSP00000385886:R135K	R	+	2	0	RASGRP3	33600561	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.609000	0.61148	2.868000	0.98415	0.557000	0.71058	AGG		0.418	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376		8	86	0	0	0	1	0	8	86				
CIC	23152	broad.mit.edu	37	19	42791715	42791715	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr19:42791715C>T	ENST00000575354.2	+	5	641	c.601C>T	c.(601-603)Cgg>Tgg	p.R201W	CIC_ENST00000572681.2_Missense_Mutation_p.R1110W|CIC_ENST00000160740.3_Missense_Mutation_p.R201W	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	201					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R201W(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				GGACCACATCCGGCGGCCCAT	0.622			"""Mis, F, S"""		oligodendroglioma																																	ENST00000572681.2				Rec	yes		19	19q13.2	23152	"""Mis, F, S"""	capicua homolog			O			oligodendroglioma		1	Substitution - Missense(1)	p.R201W(1)	central_nervous_system(1)	autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82						c.(3328-3330)Cgg>Tgg		capicua transcriptional repressor							65.0	70.0	68.0					19																	42791715		2203	4300	6503	SO:0001583	missense	23152				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding	g.chr19:42791715C>T	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.601C>T	19.37:g.42791715C>T	ENSP00000458663:p.Arg201Trp					CIC_ENST00000575354.2_Missense_Mutation_p.R201W|CIC_ENST00000160740.3_Missense_Mutation_p.R201W	p.R1110W			Q96RK0	CIC_HUMAN			6	3396	+		Prostate(69;0.00682)	201			Pro-rich.		Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	c.3328C>T	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.960036	0.53400	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.39	4.39	0.52855	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	.	.	.	.	D	0.85133	0.5627	M	0.92555	3.32	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.88918	0.3364	8	0.87932	D	0	-12.0024	14.5138	0.67807	0.0:1.0:0.0:0.0	.	201	Q96RK0	CIC_HUMAN	W	201	.	ENSP00000160740:R201W	R	+	1	2	CIC	47483555	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	3.466000	0.53071	2.284000	0.76573	0.555000	0.69702	CGG		0.622	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			4	37	0	0	0	1	0	4	37				
AMMECR1	9949	broad.mit.edu	37	X	109459810	109459810	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chrX:109459810C>T	ENST00000262844.5	-	3	802	c.635G>A	c.(634-636)cGg>cAg	p.R212Q	AMMECR1_ENST00000372059.2_Missense_Mutation_p.R175Q|AMMECR1_ENST00000372057.1_Missense_Mutation_p.R89Q	NM_015365.2	NP_056180.1	Q9Y4X0	AMMR1_HUMAN	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	212	AMMECR1. {ECO:0000255|PROSITE- ProRule:PRU00467}.									large_intestine(1)|lung(4)|ovary(1)|stomach(1)	7						GCAGAAAAGCCGTGGCAGCTC	0.378																																						ENST00000262844.5																			0				large_intestine(1)|lung(4)|ovary(1)|stomach(1)	7						c.(634-636)cGg>cAg		Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1							92.0	88.0	89.0					X																	109459810		2203	4300	6503	SO:0001583	missense	9949							g.chrX:109459810C>T	AJ007014	CCDS14551.1, CCDS35368.1, CCDS55476.1	Xq22.3	2014-06-17	2008-09-12		ENSG00000101935	ENSG00000101935			467	protein-coding gene	gene with protein product		300195				10049589, 9480748	Standard	NM_001171689		Approved		uc004eoo.3	Q9Y4X0	OTTHUMG00000022197	ENST00000262844.5:c.635G>A	X.37:g.109459810C>T	ENSP00000262844:p.Arg212Gln					AMMECR1_ENST00000372057.1_Missense_Mutation_p.R89Q|AMMECR1_ENST00000372059.2_Missense_Mutation_p.R175Q	p.R212Q	NM_015365.2	NP_056180.1	Q9Y4X0	AMER1_HUMAN			3	802	-			212			AMMECR1.		Q5JYV9|Q6P9D8|Q8WX22|Q9UIQ8	Missense_Mutation	SNP	ENST00000262844.5	37	c.635G>A	CCDS14551.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.772517	0.90108	.	.	ENSG00000101935	ENST00000262844;ENST00000372059;ENST00000372057	.	.	.	5.75	5.75	0.90469	AMMECR1 domain (2);	0.000000	0.85682	D	0.000000	T	0.52041	0.1710	L	0.43598	1.365	0.80722	D	1	P;P	0.45986	0.87;0.68	B;B	0.38842	0.186;0.283	T	0.54282	-0.8317	9	0.41790	T	0.15	-25.1748	18.91	0.92479	0.0:1.0:0.0:0.0	.	175;212	Q9Y4X0-3;Q9Y4X0	.;AMER1_HUMAN	Q	212;175;89	.	ENSP00000262844:R212Q	R	-	2	0	AMMECR1	109346466	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.484000	0.81180	2.413000	0.81919	0.600000	0.82982	CGG		0.378	AMMECR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057907.1			3	58	0	0	0	1	0	3	58				
TAOK2	9344	broad.mit.edu	37	16	29994404	29994404	+	Silent	SNP	C	C	G			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr16:29994404C>G	ENST00000308893.4	+	12	2054	c.1011C>G	c.(1009-1011)ccC>ccG	p.P337P	TAOK2_ENST00000279394.3_Silent_p.P337P|TAOK2_ENST00000416441.2_Silent_p.P164P|TAOK2_ENST00000543033.1_Silent_p.P337P	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	337					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						AGGCCGAGCCCTACATGCACC	0.632																																						ENST00000308893.4																			0				breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						c.(1009-1011)ccC>ccG		TAO kinase 2							117.0	135.0	129.0					16																	29994404		2197	4300	6497	SO:0001819	synonymous_variant	9344				actin cytoskeleton organization|activation of MAPKK activity|apoptosis|cell migration|focal adhesion assembly|positive regulation of JNK cascade|protein targeting to membrane|regulation of cell growth|regulation of cell shape|response to stress	cytoplasmic vesicle membrane|cytoskeleton|dendrite|integral to membrane|nucleolus	ATP binding|protein serine/threonine kinase activity	g.chr16:29994404C>G	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.1011C>G	16.37:g.29994404C>G						TAOK2_ENST00000543033.1_Silent_p.P337P|TAOK2_ENST00000416441.2_Silent_p.P164P|TAOK2_ENST00000279394.3_Silent_p.P337P	p.P337P	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN			12	2054	+			337					A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Silent	SNP	ENST00000308893.4	37	c.1011C>G	CCDS10663.1																																																																																				0.632	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151		8	143	0	0	0	1	0	8	143				
TKTL2	84076	broad.mit.edu	37	4	164393861	164393861	+	Silent	SNP	C	C	A			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr4:164393861C>A	ENST00000280605.3	-	1	1186	c.1026G>T	c.(1024-1026)ctG>ctT	p.L342L		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	342						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TGTCACCACTCAGaacaataa	0.428																																						ENST00000280605.3																			0				breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70						c.(1024-1026)ctG>ctT		transketolase-like 2							117.0	114.0	115.0					4																	164393861		2203	4300	6503	SO:0001819	synonymous_variant	84076					cytoplasm	metal ion binding|transketolase activity	g.chr4:164393861C>A	BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"""similar to transketolase"""					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.1026G>T	4.37:g.164393861C>A							p.L342L	NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN			1	1186	-	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)	342					A4FVB4|Q8NCT0|Q96M82	Silent	SNP	ENST00000280605.3	37	c.1026G>T	CCDS3805.1																																																																																				0.428	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136		5	100	1	0	0.0215528	1	0.0227501	5	100				
KRCC1	51315	broad.mit.edu	37	2	88327833	88327833	+	Missense_Mutation	SNP	G	G	A	rs148657110	byFrequency	TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr2:88327833G>A	ENST00000347055.3	-	4	643	c.250C>T	c.(250-252)Cgg>Tgg	p.R84W		NM_016618.1	NP_057702.1	Q9NPI7	KRCC1_HUMAN	lysine-rich coiled-coil 1	84										cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	7						TGAGGCAACCGATTTTCCACT	0.463													G|||	3	0.000599042	0.0	0.0014	5008	,	,		18801	0.001		0.0	False		,,,				2504	0.001					ENST00000347055.3																			0				cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	7						c.(250-252)Cgg>Tgg		lysine-rich coiled-coil 1		G	TRP/ARG	0,4406		0,0,2203	120.0	108.0	112.0		250	1.4	0.0	2	dbSNP_134	112	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KRCC1	NM_016618.1	101	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	84/260	88327833	3,13003	2203	4300	6503	SO:0001583	missense	51315							g.chr2:88327833G>A	AF208845	CCDS2000.1	2p11.2	2008-02-05			ENSG00000172086	ENSG00000172086			28039	protein-coding gene	gene with protein product						12477932	Standard	XM_005264360		Approved	FLJ22333	uc002sso.1	Q9NPI7	OTTHUMG00000130315	ENST00000347055.3:c.250C>T	2.37:g.88327833G>A	ENSP00000340083:p.Arg84Trp						p.R84W	NM_016618.1	NP_057702.1	Q9NPI7	KRCC1_HUMAN			4	643	-			84					Q3B7J7	Missense_Mutation	SNP	ENST00000347055.3	37	c.250C>T	CCDS2000.1	.	.	.	.	.	.	.	.	.	.	G	9.454	1.091269	0.20471	0.0	3.49E-4	ENSG00000172086	ENST00000347055	T	0.33865	1.39	5.8	1.41	0.22369	.	1.259100	0.05740	N	0.601190	T	0.34308	0.0893	L	0.48642	1.525	0.09310	N	1	B	0.18741	0.03	B	0.12156	0.007	T	0.38520	-0.9657	10	0.72032	D	0.01	-9.2838	9.4918	0.38965	0.0725:0.0:0.5619:0.3657	.	84	Q9NPI7	KRCC1_HUMAN	W	84	ENSP00000340083:R84W	ENSP00000340083:R84W	R	-	1	2	KRCC1	88108948	0.584000	0.26766	0.009000	0.14445	0.076000	0.17211	0.455000	0.21843	0.355000	0.24131	-0.836000	0.03065	CGG		0.463	KRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252664.1	NM_016618		3	69	0	0	0	1	0	3	69				
UNC79	57578	broad.mit.edu	37	14	94160680	94160680	+	Splice_Site	SNP	G	G	T			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr14:94160680G>T	ENST00000393151.2	+	48	7587		c.e48-1		UNC79_ENST00000256339.4_Splice_Site|UNC79_ENST00000555664.1_Splice_Site|UNC79_ENST00000553484.1_Splice_Site			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)						behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TGTTGTTTCAGATGGTAGAAA	0.398																																						ENST00000553484.1																			0				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						c.e49-1		unc-79 homolog (C. elegans)							164.0	154.0	158.0					14																	94160680		2203	4300	6503	SO:0001630	splice_region_variant	57578					integral to membrane		g.chr14:94160680G>T	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.7588-1G>T	14.37:g.94160680G>T						UNC79_ENST00000393151.2_Splice_Site|UNC79_ENST00000256339.4_Splice_Site|UNC79_ENST00000555664.1_Splice_Site				Q9P2D8	UNC79_HUMAN			49	7807	+								B5MDL6|Q6ZUT7	Splice_Site	SNP	ENST00000393151.2	37			.	.	.	.	.	.	.	.	.	.	G	26.5	4.741114	0.89573	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8179	0.96578	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIAA1409	93230433	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.775000	0.98995	2.789000	0.95967	0.655000	0.94253	.		0.398	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	Intron	10	47	1	0	0.000442599	1	0.00049467	10	47				
CHRNA1	1134	broad.mit.edu	37	2	175618969	175618969	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr2:175618969C>T	ENST00000261007.5	-	6	659	c.593G>A	c.(592-594)gGc>gAc	p.G198D	CHRNA1_ENST00000409542.1_Missense_Mutation_p.G91D|CHRNA1_ENST00000409219.1_Missense_Mutation_p.G173D|CHRNA1_ENST00000409323.1_Missense_Mutation_p.G173D|CHRNA1_ENST00000348749.5_Missense_Mutation_p.G173D|AC018890.6_ENST00000442996.1_RNA	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	198			G -> S (in SCCMS). {ECO:0000269|PubMed:7619526, ECO:0000269|PubMed:9158151}.		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	CACGACAGAGCCGTCGTAGGT	0.502																																						ENST00000348749.5																			0				breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37						c.(517-519)gGc>gAc		cholinergic receptor, nicotinic, alpha 1 (muscle)							107.0	102.0	104.0					2																	175618969		2203	4300	6503	SO:0001583	missense	1134				muscle cell homeostasis|neuromuscular junction development|neuromuscular process|neuromuscular synaptic transmission|neuron homeostasis|regulation of action potential in neuron|skeletal muscle contraction|skeletal muscle tissue growth	cell junction|cell surface|neuromuscular junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity	g.chr2:175618969C>T	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1955	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 1 (muscle)"""	100690	"""cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"""	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.593G>A	2.37:g.175618969C>T	ENSP00000261007:p.Gly198Asp					CHRNA1_ENST00000409323.1_Missense_Mutation_p.G173D|CHRNA1_ENST00000409219.1_Missense_Mutation_p.G173D|AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000409542.1_Missense_Mutation_p.G91D|CHRNA1_ENST00000261007.5_Missense_Mutation_p.G198D	p.G173D	NM_000079.3	NP_000070.1	P02708	ACHA_HUMAN			5	595	-			198					B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	37	c.518G>A	CCDS33331.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.421450	0.83559	.	.	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219;ENST00000409323	T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27	5.78	5.78	0.91487	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.90123	0.6914	M	0.89785	3.06	0.80722	D	1	D;D;P	0.69078	0.997;0.987;0.933	P;D;P	0.63033	0.837;0.91;0.882	D	0.91159	0.4959	10	0.87932	D	0	.	20.3668	0.98882	0.0:1.0:0.0:0.0	.	173;173;198	G5E9G9;Q53SH4;P02708	.;.;ACHA_HUMAN	D	173;198;91;173;173	ENSP00000261008:G173D;ENSP00000261007:G198D;ENSP00000387026:G91D;ENSP00000386611:G173D;ENSP00000386684:G173D	ENSP00000261007:G198D	G	-	2	0	CHRNA1	175327215	1.000000	0.71417	0.998000	0.56505	0.569000	0.35902	6.027000	0.70881	2.894000	0.99253	0.655000	0.94253	GGC		0.502	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			3	49	0	0	0	1	0	3	49				
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)	ENST00000415913.1				Dom	yes		2	2q33.3	3417	Mis	"""isocitrate dehydrogenase 1 (NADP+), soluble"""			O			gliobastoma		2835	Substitution - Missense(2834)|Complex - compound substitution(1)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)	NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887						c.(394-396)cGt>cAt		isocitrate dehydrogenase 1 (NADP+), soluble							79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	g.chr2:209113112C>T		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His					IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	p.R132H			O75874	IDHC_HUMAN		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	4	776	-			132		R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).			Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	c.395G>A	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			10	64	0	0	0	1	0	10	64				
KRTAP4-11	653240	broad.mit.edu	37	17	39274415	39274415	+	Silent	SNP	C	C	T	rs425487		TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr17:39274415C>T	ENST00000391413.2	-	1	191	c.153G>A	c.(151-153)agG>agA	p.R51R		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	51	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)		p.R51R(6)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGCACTGGGGCCTGCAGCAGC	0.667																																						ENST00000391413.2																			6	Substitution - coding silent(6)	p.R51R(6)	endometrium(3)|kidney(2)|lung(1)	endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33						c.(151-153)agG>agA		keratin associated protein 4-11							9.0	15.0	13.0					17																	39274415		682	1579	2261	SO:0001819	synonymous_variant	653240					keratin filament		g.chr17:39274415C>T	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.153G>A	17.37:g.39274415C>T							p.R51R	NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	STAD - Stomach adenocarcinoma(17;0.000371)		1	191	-		Breast(137;0.000496)	51		Missing (in allele KAP4.14).	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		A0AUY2	Silent	SNP	ENST00000391413.2	37	c.153G>A	CCDS45675.1																																																																																				0.667	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			4	44	0	0	0	1	0	4	44				
REG3G	130120	broad.mit.edu	37	2	79255361	79255361	+	Missense_Mutation	SNP	T	T	A			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr2:79255361T>A	ENST00000272324.5	+	6	671	c.487T>A	c.(487-489)Tgt>Agt	p.C163S	REG3G_ENST00000393897.2_Missense_Mutation_p.C163S|REG3G_ENST00000409471.1_Missense_Mutation_p.C117S	NM_001008387.2	NP_001008388.1	Q6UW15	REG3G_HUMAN	regenerating islet-derived 3 gamma	163	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|defense response to Gram-positive bacterium (GO:0050830)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(27)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						AGATTATAACTGTGATGCAAA	0.488																																						ENST00000272324.5																			0				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(27)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						c.(487-489)Tgt>Agt		regenerating islet-derived 3 gamma							92.0	86.0	88.0					2																	79255361		2203	4300	6503	SO:0001583	missense	130120				acute-phase response	extracellular region	sugar binding	g.chr2:79255361T>A	AY359047	CCDS1962.1, CCDS58714.1	2p12	2005-02-11			ENSG00000143954	ENSG00000143954			29595	protein-coding gene	gene with protein product		609933				12975309	Standard	NM_001008387		Approved	UNQ429, LPPM429, PAP1B	uc002snx.4	Q6UW15	OTTHUMG00000130018	ENST00000272324.5:c.487T>A	2.37:g.79255361T>A	ENSP00000272324:p.Cys163Ser					REG3G_ENST00000409471.1_Missense_Mutation_p.C117S|REG3G_ENST00000393897.2_Missense_Mutation_p.C163S	p.C163S	NM_001008387.2	NP_001008388.1	Q6UW15	REG3G_HUMAN			6	671	+			163			C-type lectin.		A8K980|D6W5J6|Q3SYE4|Q3SYE6|Q6FH18	Missense_Mutation	SNP	ENST00000272324.5	37	c.487T>A	CCDS1962.1	.	.	.	.	.	.	.	.	.	.	T	16.54	3.151164	0.57151	.	.	ENSG00000143954	ENST00000393897;ENST00000272324;ENST00000409471	T;T;T	0.59906	0.23;0.23;0.23	4.66	4.66	0.58398	C-type lectin fold (1);C-type lectin, conserved site (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.56097	D	0.000022	T	0.80121	0.4565	M	0.93638	3.44	0.19575	N	0.999966	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.74077	-0.3781	10	0.87932	D	0	.	10.6919	0.45875	0.0:0.0:0.0:1.0	.	117;163	Q3SYE6;Q6UW15	.;REG3G_HUMAN	S	163;163;117	ENSP00000377475:C163S;ENSP00000272324:C163S;ENSP00000387105:C117S	ENSP00000272324:C163S	C	+	1	0	REG3G	79108869	0.874000	0.30092	0.055000	0.19348	0.003000	0.03518	3.233000	0.51311	2.090000	0.63153	0.528000	0.53228	TGT		0.488	REG3G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328247.1	NM_198448		3	52	0	0	0	1	0	3	52				
PLCG2	5336	broad.mit.edu	37	16	81953130	81953130	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr16:81953130G>A	ENST00000359376.3	+	20	2310	c.2096G>A	c.(2095-2097)gGc>gAc	p.G699D		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	699	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						AACCGGGACGGCCGGCACTTT	0.532																																						ENST00000359376.3																			0				NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						c.(2095-2097)gGc>gAc		phospholipase C, gamma 2 (phosphatidylinositol-specific)							75.0	80.0	79.0					16																	81953130		1960	4129	6089	SO:0001583	missense	5336				intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity	g.chr16:81953130G>A		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.2096G>A	16.37:g.81953130G>A	ENSP00000352336:p.Gly699Asp						p.G699D	NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN			20	2310	+			699			SH2 2.		D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	c.2096G>A	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.091017	0.76756	.	.	ENSG00000197943	ENST00000359376	D	0.91843	-2.92	4.99	4.04	0.47022	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);SH2 motif (5);	0.098369	0.64402	D	0.000001	D	0.95156	0.8430	M	0.71296	2.17	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.95207	0.8322	10	0.87932	D	0	.	12.9854	0.58588	0.078:0.0:0.922:0.0	.	566;699	B4E3H3;P16885	.;PLCG2_HUMAN	D	699	ENSP00000352336:G699D	ENSP00000352336:G699D	G	+	2	0	PLCG2	80510631	1.000000	0.71417	0.978000	0.43139	0.570000	0.35934	7.832000	0.86757	1.095000	0.41419	0.655000	0.94253	GGC		0.532	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			7	76	0	0	0	1	0	7	76				
HOXD1	3231	broad.mit.edu	37	2	177054653	177054653	+	Missense_Mutation	SNP	C	C	T	rs560389650		TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr2:177054653C>T	ENST00000331462.4	+	2	993	c.770C>T	c.(769-771)gCc>gTc	p.A257V	HOXD-AS1_ENST00000436126.1_RNA|HOXD-AS1_ENST00000452365.1_RNA|HOXD-AS1_ENST00000417086.1_RNA|HOXD-AS1_ENST00000425005.1_RNA|HOXD-AS1_ENST00000413969.1_RNA	NM_024501.2	NP_078777.1	Q9GZZ0	HXD1_HUMAN	homeobox D1	257					embryonic skeletal system development (GO:0048706)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.0226)		TTAACTCGAGCCCGGCGCATC	0.502																																						ENST00000331462.4																			0				kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	10						c.(769-771)gCc>gTc		homeobox D1							136.0	152.0	146.0					2																	177054653		2203	4300	6503	SO:0001583	missense	3231					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr2:177054653C>T		CCDS2271.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128645	ENSG00000128645		"""Homeoboxes / ANTP class : HOXL subclass"""	5132	protein-coding gene	gene with protein product		142987	"""homeo box D1"""	HOX4, HOX4G		1973146, 1358459	Standard	NM_024501		Approved		uc002ukv.5	Q9GZZ0	OTTHUMG00000132512	ENST00000331462.4:c.770C>T	2.37:g.177054653C>T	ENSP00000328598:p.Ala257Val						p.A257V	NM_024501.1	NP_078777.1	Q9GZZ0	HXD1_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.0226)	2	993	+			257					B2RAB4	Missense_Mutation	SNP	ENST00000331462.4	37	c.770C>T	CCDS2271.1	.	.	.	.	.	.	.	.	.	.	C	35	5.537549	0.96460	.	.	ENSG00000128645	ENST00000331462	D	0.96365	-3.99	5.45	5.45	0.79879	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.47852	D	0.000214	D	0.97188	0.9081	L	0.42008	1.315	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.99;0.996	D	0.97312	0.9938	10	0.48119	T	0.1	.	18.903	0.92451	0.0:1.0:0.0:0.0	.	257;257	Q96CA4;Q9GZZ0	.;HXD1_HUMAN	V	257	ENSP00000328598:A257V	ENSP00000328598:A257V	A	+	2	0	HOXD1	176762899	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.796000	0.85898	2.550000	0.86006	0.655000	0.94253	GCC		0.502	HOXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255693.2			8	134	0	0	0	1	0	8	134				
MAGI1	9223	broad.mit.edu	37	3	65372850	65372851	+	Frame_Shift_Del	DEL	TC	TC	-	rs139764373		TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr3:65372850_65372851delTC	ENST00000330909.8	-	15	2466_2467	c.2467_2468delGA	c.(2467-2469)gaafs	p.E823fs	MAGI1_ENST00000497477.2_Intron|MAGI1_ENST00000483466.1_Frame_Shift_Del_p.E823fs|MAGI1_ENST00000402939.2_Intron	NM_015520.1	NP_056335.1	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	823	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		GGAATTGATTTCTCTCTCTCTC	0.401																																						ENST00000330909.8																			0				breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51						c.(2467-2469)afs		membrane associated guanylate kinase, WW and PDZ domain containing 1																																				SO:0001589	frameshift_variant	9223				cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding	g.chr3:65372850_65372851delTC	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000330909.8:c.2467_2468delGA	3.37:g.65372860_65372861delTC	ENSP00000331157:p.Glu823fs					MAGI1_ENST00000402939.2_Intron|MAGI1_ENST00000497477.2_Intron|MAGI1_ENST00000483466.1_Frame_Shift_Del_p.E823fs	p.E823fs	NM_015520.1	NP_056335.1	Q96QZ7	MAGI1_HUMAN		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)	15	2466_2467	-		Lung NSC(201;0.0016)	823			PDZ 4.		A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Frame_Shift_Del	DEL	ENST00000330909.8	37	c.2467_2468delGA	CCDS33781.1																																																																																				0.401	MAGI1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000349127.2	NM_004742		8	42						8	42	---	---	---	---
SLC12A7	10723	broad.mit.edu	37	5	1078124	1078125	+	Splice_Site	INS	-	-	GCAG	rs369273236|rs369196468|rs200032397	byFrequency	TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr5:1078124_1078125insGCAG	ENST00000264930.5	-	12	1498		c.e12-2			NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7						cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	TCCCCGAACCTgcaggcaggcg	0.673														58	0.0115815	0.0159	0.0144	5008	,	,		15824	0.0		0.0209	False		,,,				2504	0.0061					ENST00000264930.5																			0				breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32						c.e12-2		solute carrier family 12 (potassium/chloride transporter), member 7	Potassium Chloride(DB00761)			94,3970		14,66,1952						3.5	1.0			11	265,7685		24,217,3734	no	splice-3	SLC12A7	NM_006598.2		38,283,5686	A1A1,A1R,RR		3.3333,2.313,2.9882				359,11655				SO:0001630	splice_region_variant	10723				potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity	g.chr5:1078124_1078125insGCAG	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.1455-2->CTGC	5.37:g.1078129_1078132dupGCAG								NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		12	1498	-	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)							A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Splice_Site	INS	ENST00000264930.5	37		CCDS34129.1																																																																																				0.673	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	Intron	3	3						3	3	---	---	---	---
DNM1P47	100216544	broad.mit.edu	37	15	102299886	102299887	+	RNA	INS	-	-	G	rs199996275	byFrequency	TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr15:102299886_102299887insG	ENST00000561463.1	+	0	7932_7933									DNM1 pseudogene 47																		AACCTGTACTCGCGTCGGAACC	0.589													|||unknown(NO_COVERAGE)	758	0.151358	0.2511	0.1167	5008	,	,		74102	0.0595		0.163	False		,,,				2504	0.1237					ENST00000561463.1																			0																																																			0							g.chr15:102299886_102299887insG	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102299887_102299887dupG														0	7932_7933	+									RNA	INS	ENST00000561463.1	37																																																																																						0.589	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149		4	5						4	5	---	---	---	---
PRR12	57479	broad.mit.edu	37	19	50100465	50100465	+	Frame_Shift_Del	DEL	C	C	-			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chr19:50100465delC	ENST00000418929.2	+	4	2885	c.2873delC	c.(2872-2874)gccfs	p.A959fs		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		GGTGGAGGGGCCGCGGACGAC	0.672																																						ENST00000418929.2																			0				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11						c.(2872-2874)gcfs		proline rich 12							7.0	8.0	8.0					19																	50100465		2014	4126	6140	SO:0001589	frameshift_variant	57479						DNA binding	g.chr19:50100465delC	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.2873delC	19.37:g.50100465delC	ENSP00000394510:p.Ala959fs						p.A959fs	NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)	4	2885	+		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)	138					E9PB06|Q8N4J6	Frame_Shift_Del	DEL	ENST00000418929.2	37	c.2873delC	CCDS46143.1																																																																																				0.672	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		2	4						2	4	---	---	---	---
WDR44	54521	broad.mit.edu	37	X	117582883	117582885	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-E1-A7YY-01A-11D-A34J-08	TCGA-E1-A7YY-10A-01D-A34M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2415587-d4b6-4b6b-983f-8c3017ba2f09	ac126c0b-e17f-481c-8331-dc355f8ae993	g.chrX:117582883_117582885delTTC	ENST00000254029.3	+	20	3070_3072	c.2675_2677delTTC	c.(2674-2679)gttctt>gtt	p.L894del	WDR44_ENST00000371822.5_In_Frame_Del_p.L805del|WDR44_ENST00000371825.3_In_Frame_Del_p.L886del	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	894						endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						AACACAGAAGTTCTTCTCTCTGC	0.286																																						ENST00000254029.3																			0				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						c.(2674-2679)gtt>g		WD repeat domain 44																																				SO:0001651	inframe_deletion	54521					cytosol|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm		g.chrX:117582883_117582885delTTC	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"""WD repeat domain containing"""	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.2675_2677delTTC	X.37:g.117582886_117582888delTTC	ENSP00000254029:p.Leu894del					WDR44_ENST00000371822.5_In_Frame_Del_p.VL803del|WDR44_ENST00000371825.3_In_Frame_Del_p.VL884del	p.VL892del	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN			20	3070_3072	+			892					B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	In_Frame_Del	DEL	ENST00000254029.3	37	c.2675_2677delTTC	CCDS14572.1																																																																																				0.286	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045		7	61						7	61	---	---	---	---
