#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
C1orf162	128346	broad.mit.edu	37	1	112020367	112020367	+	Silent	SNP	C	C	G			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr1:112020367C>G	ENST00000343534.5	+	5	547	c.297C>G	c.(295-297)gcC>gcG	p.A99A	C1orf162_ENST00000369718.3_Silent_p.A74A|C1orf162_ENST00000464591.1_Intron	NM_174896.2	NP_777556.1	Q8NEQ5	CA162_HUMAN	chromosome 1 open reading frame 162	99						integral component of membrane (GO:0016021)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5		all_cancers(81;0.00116)|all_epithelial(167;0.000761)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0236)|Colorectal(144;0.0286)|all cancers(265;0.0572)|Epithelial(280;0.0862)|COAD - Colon adenocarcinoma(174;0.112)|LUSC - Lung squamous cell carcinoma(189;0.134)		AGCCCCAGGCCCCAGATCCTC	0.552																																						ENST00000343534.5																			0				NS(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5						c.(295-297)gcC>gcG		chromosome 1 open reading frame 162							107.0	109.0	108.0					1																	112020367		2203	4300	6503	SO:0001819	synonymous_variant	128346					integral to membrane		g.chr1:112020367C>G	BC017973	CCDS837.1, CCDS72837.1	1p13.2	2008-02-05			ENSG00000143110	ENSG00000143110			28344	protein-coding gene	gene with protein product						12477932	Standard	XM_005270475		Approved	MGC24133	uc001ebe.3	Q8NEQ5	OTTHUMG00000011750	ENST00000343534.5:c.297C>G	1.37:g.112020367C>G						C1orf162_ENST00000464591.1_Intron|C1orf162_ENST00000369718.3_Silent_p.A74A	p.A99A	NM_174896.2	NP_777556.1	Q8NEQ5	CA162_HUMAN		Lung(183;0.0236)|Colorectal(144;0.0286)|all cancers(265;0.0572)|Epithelial(280;0.0862)|COAD - Colon adenocarcinoma(174;0.112)|LUSC - Lung squamous cell carcinoma(189;0.134)	5	547	+		all_cancers(81;0.00116)|all_epithelial(167;0.000761)|all_lung(203;0.00277)|Lung NSC(277;0.0043)	99					Q5QNZ1	Silent	SNP	ENST00000343534.5	37	c.297C>G	CCDS837.1																																																																																				0.552	C1orf162-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032471.1	NM_174896		16	92	0	0	0	1	0	16	92				
TMEM67	91147	broad.mit.edu	37	8	94767325	94767325	+	Silent	SNP	G	G	A			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr8:94767325G>A	ENST00000453321.3	+	1	241	c.183G>A	c.(181-183)tcG>tcA	p.S61S	TMEM67_ENST00000409623.3_5'UTR	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	61					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			CCGCCCTCTCGTGTGTTCCTT	0.567																																						ENST00000453321.3																			0				breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41						c.(181-183)tcG>tcA		transmembrane protein 67							110.0	106.0	107.0					8																	94767325		2203	4300	6503	SO:0001819	synonymous_variant	91147				cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding	g.chr8:94767325G>A	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"""Meckelin"""	609884	"""Meckel syndrome, type 3"""	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.183G>A	8.37:g.94767325G>A						TMEM67_ENST00000409623.3_5'UTR	p.S61S	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	BRCA - Breast invasive adenocarcinoma(8;0.00896)		1	241	+	Breast(36;4.14e-07)		61					B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Silent	SNP	ENST00000453321.3	37	c.183G>A	CCDS6258.2	.	.	.	.	.	.	.	.	.	.	G	3.576	-0.086701	0.07097	.	.	ENSG00000164953	ENST00000521517	.	.	.	5.35	4.48	0.54585	.	.	.	.	.	T	0.69205	0.3085	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68625	-0.5359	4	.	.	.	-5.3862	13.4667	0.61258	0.0:0.8412:0.1588:0.0	.	.	.	.	M	59	.	.	V	+	1	0	TMEM67	94836501	0.994000	0.37717	0.999000	0.59377	0.124000	0.20399	0.382000	0.20635	1.501000	0.48654	-0.211000	0.12701	GTG		0.567	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		4	138	0	0	0	1	0	4	138				
FRG1B	284802	broad.mit.edu	37	20	29625934	29625934	+	Missense_Mutation	SNP	C	C	T			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr20:29625934C>T	ENST00000278882.3	+	5	558	c.178C>T	c.(178-180)Cat>Tat	p.H60Y	FRG1B_ENST00000439954.2_Missense_Mutation_p.H65Y|FRG1B_ENST00000358464.4_Missense_Mutation_p.H60Y			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	60										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						ACTTGTTGGGCATTCAGATGC	0.338																																						ENST00000278882.3																			0				endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(178-180)Cat>Tat																																						SO:0001583	missense	0							g.chr20:29625934C>T			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.178C>T	20.37:g.29625934C>T	ENSP00000278882:p.His60Tyr					FRG1B_ENST00000358464.4_Missense_Mutation_p.H60Y|FRG1B_ENST00000439954.2_Missense_Mutation_p.H65Y	p.H60Y							5	558	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.178C>T		.	.	.	.	.	.	.	.	.	.	c	3.585	-0.084798	0.07097	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.42131	0.98	1.68	1.68	0.24146	.	0.109676	0.64402	D	0.000005	T	0.32615	0.0835	.	.	.	0.23210	N	0.998115	B	0.26363	0.147	B	0.35859	0.212	T	0.27905	-1.0060	9	0.34782	T	0.22	.	9.3557	0.38164	0.0:1.0:0.0:0.0	.	65	F5H5R5	.	Y	60;65;60	ENSP00000408863:H65Y	ENSP00000278882:H60Y	H	+	1	0	FRG1B	28239595	1.000000	0.71417	0.997000	0.53966	0.021000	0.10359	6.442000	0.73443	1.250000	0.43966	0.184000	0.17185	CAT		0.338	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		5	70	0	0	0	1	0	5	70				
HNRNPD	3184	broad.mit.edu	37	4	83280727	83280727	+	Missense_Mutation	SNP	T	T	C			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr4:83280727T>C	ENST00000313899.7	-	3	633	c.356A>G	c.(355-357)aAa>aGa	p.K119R	HNRNPD_ENST00000352301.4_Missense_Mutation_p.K100R|HNRNPD_ENST00000543098.1_Missense_Mutation_p.K67R|HNRNPD_ENST00000353341.4_Missense_Mutation_p.K119R|HNRNPD_ENST00000541060.1_Intron|HNRNPD_ENST00000508119.1_5'Flank	NM_031370.2	NP_112738.1	Q14103	HNRPD_HUMAN	heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)	119	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				circadian regulation of translation (GO:0097167)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|regulation of circadian rhythm (GO:0042752)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	7						TTCACCAAATTTGGAAAAGTA	0.383																																						ENST00000313899.7																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	7						c.(355-357)aAa>aGa		heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)							121.0	119.0	120.0					4																	83280727		2203	4300	6503	SO:0001583	missense	3184				nuclear mRNA splicing, via spliceosome|positive regulation of transcription, DNA-dependent|RNA catabolic process|transcription, DNA-dependent	cytosol|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding|telomeric DNA binding	g.chr4:83280727T>C	AF026126	CCDS3590.1, CCDS3591.1, CCDS3592.1	4q21	2013-02-12	2002-08-29	2008-04-18	ENSG00000138668	ENSG00000138668		"""RNA binding motif (RRM) containing"""	5036	protein-coding gene	gene with protein product		601324	"""heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA-binding protein 1, 37kD)"""	AUF1, HNRPD		9615222	Standard	NM_001003810		Approved		uc003hmm.1	Q14103	OTTHUMG00000130290	ENST00000313899.7:c.356A>G	4.37:g.83280727T>C	ENSP00000313199:p.Lys119Arg					HNRNPD_ENST00000541060.1_Intron|HNRNPD_ENST00000353341.4_Missense_Mutation_p.K119R|HNRNPD_ENST00000543098.1_Missense_Mutation_p.K67R|HNRNPD_ENST00000352301.4_Missense_Mutation_p.K100R	p.K119R	NM_031370.2	NP_112738.1	Q14103	HNRPD_HUMAN			3	633	-			119			RRM 1.		A8K9J2|P07029|Q01858|Q14100|Q14101|Q14102|Q4W5A1|Q9UCE8|Q9UCE9	Missense_Mutation	SNP	ENST00000313899.7	37	c.356A>G	CCDS3592.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.185784	0.57909	.	.	ENSG00000138668	ENST00000313899;ENST00000353341;ENST00000352301;ENST00000543098;ENST00000307213;ENST00000509263;ENST00000507010;ENST00000515432;ENST00000503822;ENST00000509107	T;T;T;T;T;T;T;T;T	0.19105	2.17;2.17;2.17;2.17;2.17;2.17;2.17;2.17;2.17	5.86	5.86	0.93980	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.19327	0.0464	L	0.28608	0.87	0.80722	D	1	B;B;B;B	0.31077	0.307;0.16;0.078;0.236	B;B;B;B	0.33960	0.144;0.091;0.108;0.173	T	0.04103	-1.0977	10	0.30078	T	0.28	.	16.5602	0.84551	0.0:0.0:0.0:1.0	.	100;119;100;119	Q14103-4;Q14103-3;Q14103-2;Q14103	.;.;.;HNRPD_HUMAN	R	119;119;100;67;94;52;119;21;100;73	ENSP00000313199:K119R;ENSP00000313327:K119R;ENSP00000305860:K100R;ENSP00000439380:K67R;ENSP00000420926:K52R;ENSP00000421952:K119R;ENSP00000426666:K21R;ENSP00000422615:K100R;ENSP00000425439:K73R	ENSP00000307544:K94R	K	-	2	0	HNRNPD	83499751	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.606000	0.82863	2.367000	0.80283	0.528000	0.53228	AAA		0.383	HNRNPD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252630.2	NM_031370		15	69	0	0	0	1	0	15	69				
FRG1B	284802	broad.mit.edu	37	20	29625956	29625956	+	Missense_Mutation	SNP	G	G	A	rs147809085		TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr20:29625956G>A	ENST00000278882.3	+	5	580	c.200G>A	c.(199-201)aGa>aAa	p.R67K	FRG1B_ENST00000439954.2_Missense_Mutation_p.R72K|FRG1B_ENST00000358464.4_Missense_Mutation_p.R67K			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	67								p.R67K(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						ATTGGACCAAGAGAACAATGG	0.338																																						ENST00000278882.3																			2	Substitution - Missense(2)	p.R67K(2)	kidney(2)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(199-201)aGa>aAa																																						SO:0001583	missense	0							g.chr20:29625956G>A			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.200G>A	20.37:g.29625956G>A	ENSP00000278882:p.Arg67Lys					FRG1B_ENST00000358464.4_Missense_Mutation_p.R67K|FRG1B_ENST00000439954.2_Missense_Mutation_p.R72K	p.R67K							5	580	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.200G>A		.	.	.	.	.	.	.	.	.	.	g	9.648	1.140706	0.21205	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.46063	0.88	1.68	1.68	0.24146	.	0.000000	0.85682	D	0.000000	T	0.27241	0.0668	.	.	.	0.46901	D	0.99924	B	0.02656	0.0	B	0.15484	0.013	T	0.07986	-1.0744	9	0.28530	T	0.3	.	9.3557	0.38164	0.0:0.0:1.0:0.0	.	72	F5H5R5	.	K	67;72;67	ENSP00000408863:R72K	ENSP00000278882:R67K	R	+	2	0	FRG1B	28239617	1.000000	0.71417	1.000000	0.80357	0.134000	0.20937	6.360000	0.73064	1.250000	0.43966	0.184000	0.17185	AGA		0.338	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		4	83	0	0	0	1	0	4	83				
FHOD3	80206	broad.mit.edu	37	18	34261476	34261476	+	Missense_Mutation	SNP	G	G	A			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr18:34261476G>A	ENST00000359247.4	+	12	1388	c.1388G>A	c.(1387-1389)cGg>cAg	p.R463Q	FHOD3_ENST00000590592.1_Missense_Mutation_p.R638Q|FHOD3_ENST00000445677.1_Missense_Mutation_p.R425Q|FHOD3_ENST00000257209.4_Missense_Mutation_p.R463Q|FHOD3_ENST00000591635.1_Intron	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	463					actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				GAGAGGCGGCGGCAGGAGAGA	0.433																																						ENST00000257209.4																			0				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90						c.(1387-1389)cGg>cAg		formin homology 2 domain containing 3							81.0	91.0	87.0					18																	34261476		2203	4300	6503	SO:0001583	missense	80206				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding	g.chr18:34261476G>A	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.1388G>A	18.37:g.34261476G>A	ENSP00000352186:p.Arg463Gln					FHOD3_ENST00000445677.1_Missense_Mutation_p.R425Q|FHOD3_ENST00000359247.4_Missense_Mutation_p.R463Q|FHOD3_ENST00000590592.1_Missense_Mutation_p.R638Q|FHOD3_ENST00000591635.1_Intron	p.R463Q	NM_025135.2	NP_079411.2	Q2V2M9	FHOD3_HUMAN			12	1510	+		all_epithelial(2;0.0181)|Colorectal(2;0.0195)	463					A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37	c.1388G>A		.	.	.	.	.	.	.	.	.	.	G	29.8	5.039890	0.93630	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.43294	1.15;0.95;1.31	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.64972	0.2647	M	0.70275	2.135	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.83275	0.975;0.988;0.996;0.992	T	0.68401	-0.5418	10	0.72032	D	0.01	.	17.3308	0.87262	0.0:0.0:1.0:0.0	.	425;463;463;638	Q2V2M9-2;Q2V2M9;Q2V2M9-3;E5F5Q0	.;FHOD3_HUMAN;.;.	Q	463;463;425	ENSP00000257209:R463Q;ENSP00000352186:R463Q;ENSP00000411430:R425Q	ENSP00000257209:R463Q	R	+	2	0	FHOD3	32515474	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.014000	0.93635	2.501000	0.84356	0.655000	0.94253	CGG		0.433	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		11	47	0	0	0	1	0	11	47				
PTH2	113091	broad.mit.edu	37	19	49926533	49926533	+	Missense_Mutation	SNP	G	G	C	rs200733272|rs371950649	byFrequency	TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr19:49926533G>C	ENST00000270631.1	-	1	165	c.64C>G	c.(64-66)Ctg>Gtg	p.L22V	CTD-3148I10.1_ENST00000576655.1_5'Flank	NM_178449.3	NP_848544.1	Q96A98	TIP39_HUMAN	parathyroid hormone 2	22					neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)		p.L22V(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(262;0.0015)|GBM - Glioblastoma multiforme(486;0.044)|Lung(386;0.0785)|LUSC - Lung squamous cell carcinoma(496;0.0836)		GGCACCACcagcagcagcagc	0.692													g|||	17	0.00339457	0.003	0.0043	5008	,	,		11369	0.004		0.002	False		,,,				2504	0.0041					ENST00000270631.1																			2	Substitution - Missense(2)	p.L22V(2)	endometrium(2)	endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|skin(1)	6						c.(64-66)Ctg>Gtg		parathyroid hormone 2			VAL/LEU	12,4376		0,12,2182	12.0	16.0	14.0		64	3.3	0.0	19		14	11,8561		0,11,4275	no	missense	PTH2	NM_178449.3	32	0,23,6457	CC,CG,GG		0.1283,0.2735,0.1775	possibly-damaging	22/101	49926533	23,12937	2194	4286	6480	SO:0001583	missense	113091				neuropeptide signaling pathway	extracellular region		g.chr19:49926533G>C	AY037555	CCDS12763.1	19q13.33	2013-02-28				ENSG00000142538		"""Endogenous ligands"""	30828	protein-coding gene	gene with protein product	"""tuberoinfundibular 39 residues"""	608386				11861531	Standard	NM_178449		Approved	TIP39	uc002pnn.1	Q96A98		ENST00000270631.1:c.64C>G	19.37:g.49926533G>C	ENSP00000270631:p.Leu22Val						p.L22V	NM_178449.3	NP_848544.1	Q96A98	TIP39_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.0015)|GBM - Glioblastoma multiforme(486;0.044)|Lung(386;0.0785)|LUSC - Lung squamous cell carcinoma(496;0.0836)	1	165	-			22					Q96DJ4	Missense_Mutation	SNP	ENST00000270631.1	37	c.64C>G	CCDS12763.1	.	.	.	.	.	.	.	.	.	.	g	6.292	0.421904	0.11928	0.002735	0.001283	ENSG00000142538	ENST00000270631	.	.	.	4.3	3.26	0.37387	.	0.489236	0.15528	U	0.257640	T	0.26521	0.0648	L	0.27053	0.805	0.09310	N	1	P	0.46142	0.873	B	0.39419	0.299	T	0.08066	-1.0740	9	0.87932	D	0	-7.2733	12.3672	0.55234	0.0:0.1717:0.8283:0.0	.	22	Q96A98	TIP39_HUMAN	V	22	.	ENSP00000270631:L22V	L	-	1	2	PTH2	54618345	0.088000	0.21588	0.012000	0.15200	0.011000	0.07611	-0.504000	0.06375	0.947000	0.37659	-0.370000	0.07254	CTG		0.692	PTH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465366.1	NM_178449		3	27	0	0	0	1	0	3	27				
YBX2	51087	broad.mit.edu	37	17	7193617	7193617	+	Missense_Mutation	SNP	G	G	A			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr17:7193617G>A	ENST00000007699.5	-	5	760	c.697C>T	c.(697-699)Cgg>Tgg	p.R233W	YBX2_ENST00000570627.1_5'Flank	NM_015982.3	NP_057066.2	Q9Y2T7	YBOX2_HUMAN	Y box binding protein 2	233	Pro-rich.|Required for mRNA-binding.				mRNA stabilization (GO:0048255)|negative regulation of binding (GO:0051100)|negative regulation of translation (GO:0017148)|oocyte development (GO:0048599)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|translational attenuation (GO:0009386)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lipid binding (GO:0008289)|mRNA 3'-UTR binding (GO:0003730)|ribonucleoprotein complex binding (GO:0043021)|translation regulator activity (GO:0045182)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|skin(3)	12						CGCACAAACCGCCGTCGGTAG	0.652																																						ENST00000007699.5																			0				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|skin(3)	12						c.(697-699)Cgg>Tgg		Y box binding protein 2							89.0	109.0	102.0					17																	7193617		2199	4290	6489	SO:0001583	missense	51087				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter|translational attenuation	cytoplasm|nucleus	DNA binding	g.chr17:7193617G>A	AF096834	CCDS11098.1	17p13.1	2013-12-20			ENSG00000006047	ENSG00000006047			17948	protein-coding gene	gene with protein product		611447				10100484, 9780336	Standard	NM_015982		Approved	MSY2, CSDA3	uc002gfq.2	Q9Y2T7	OTTHUMG00000177992	ENST00000007699.5:c.697C>T	17.37:g.7193617G>A	ENSP00000007699:p.Arg233Trp						p.R233W	NM_015982.3	NP_057066.2	Q9Y2T7	YBOX2_HUMAN			5	760	-			233			Pro-rich.|Required for mRNA-binding.		D3DTP1|Q8N4P0	Missense_Mutation	SNP	ENST00000007699.5	37	c.697C>T	CCDS11098.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.587076	0.66105	.	.	ENSG00000006047	ENST00000007699	T	0.26518	1.73	4.73	4.73	0.59995	.	0.077721	0.48767	D	0.000178	T	0.47358	0.1441	L	0.61218	1.895	0.49687	D	0.999817	D	0.89917	1.0	D	0.79784	0.993	T	0.29701	-1.0003	10	0.39692	T	0.17	-13.6292	15.6129	0.76740	0.0:0.0:1.0:0.0	.	233	Q9Y2T7	YBOX2_HUMAN	W	233	ENSP00000007699:R233W	ENSP00000007699:R233W	R	-	1	2	YBX2	7134341	1.000000	0.71417	0.997000	0.53966	0.963000	0.63663	2.219000	0.42899	2.642000	0.89623	0.561000	0.74099	CGG		0.652	YBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440172.2	NM_015982		65	206	0	0	0	1	0	65	206				
GBA2	57704	broad.mit.edu	37	9	35748347	35748347	+	Missense_Mutation	SNP	A	A	C			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr9:35748347A>C	ENST00000378103.3	-	1	878	c.355T>G	c.(355-357)Ttg>Gtg	p.L119V	RGP1_ENST00000456972.2_5'Flank|GBA2_ENST00000545786.1_Missense_Mutation_p.L119V|GBA2_ENST00000378094.4_Missense_Mutation_p.L119V|RGP1_ENST00000378078.4_5'Flank	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2	119					bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			ACTCACCTCAAGCCCATGCCT	0.483																																						ENST00000378094.4																			0				NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21						c.(355-357)Ttg>Gtg		glucosidase, beta (bile acid) 2							77.0	62.0	67.0					9																	35748347		2203	4300	6503	SO:0001583	missense	57704				bile acid metabolic process|glucosylceramide catabolic process|O-glycoside catabolic process	integral to membrane|microsome|plasma membrane|smooth endoplasmic reticulum	beta-glucosidase activity|glucosylceramidase activity	g.chr9:35748347A>C	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"""bile acid beta-glucosidase"", ""non-lysosomal glucosylceramidase"""	609471	"""spastic paraplegia 46 (autosomal recessive)"""	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024	ENST00000378103.3:c.355T>G	9.37:g.35748347A>C	ENSP00000367343:p.Leu119Val					GBA2_ENST00000545786.1_Missense_Mutation_p.L119V|GBA2_ENST00000378103.3_Missense_Mutation_p.L119V	p.L119V			Q9HCG7	GBA2_HUMAN	Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		1	868	-	all_epithelial(49;0.167)		119					D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Missense_Mutation	SNP	ENST00000378103.3	37	c.355T>G	CCDS6589.1	.	.	.	.	.	.	.	.	.	.	A	12.14	1.848580	0.32699	.	.	ENSG00000070610	ENST00000378103;ENST00000378094;ENST00000545786	.	.	.	5.78	0.605	0.17553	.	0.476626	0.22135	N	0.064132	T	0.22322	0.0538	L	0.31664	0.95	0.20074	N	0.999935	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.003;0.001	T	0.08953	-1.0697	9	0.25751	T	0.34	.	1.9311	0.03327	0.3717:0.1418:0.0763:0.4102	.	119;119;119	F5H7P6;Q9HCG7-2;Q9HCG7	.;.;GBA2_HUMAN	V	119	.	ENSP00000367334:L119V	L	-	1	2	GBA2	35738347	0.870000	0.30015	0.890000	0.34922	0.996000	0.88848	0.015000	0.13355	0.138000	0.18790	0.482000	0.46254	TTG		0.483	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		13	39	0	0	0	1	0	13	39				
LOC101927209	101927209	broad.mit.edu	37	1	142713773	142713773	+	lincRNA	SNP	C	C	G	rs199933143		TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr1:142713773C>G	ENST00000610091.1	-	0	1885																											TCTTTTTCCACATTGTCATTT	0.284																																						ENST00000369381.2																			0																																																			0							g.chr1:142713773C>G																													1.37:g.142713773C>G														0	832	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.284	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			4	34	0	0	0	1	0	4	34				
S100PBP	64766	broad.mit.edu	37	1	33292091	33292091	+	Nonsense_Mutation	SNP	A	A	T	rs370904573		TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr1:33292091A>T	ENST00000373475.5	+	3	645	c.391A>T	c.(391-393)Aaa>Taa	p.K131*	S100PBP_ENST00000398243.3_Nonsense_Mutation_p.K131*|S100PBP_ENST00000356689.3_3'UTR|S100PBP_ENST00000373476.1_Nonsense_Mutation_p.K131*	NM_022753.3	NP_073590.2			S100P binding protein											endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|stomach(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				AGCTCATACTAAACCATTAAA	0.413																																						ENST00000373475.5																			0				endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|stomach(1)	16						c.(391-393)Aaa>Taa		S100P binding protein							57.0	57.0	57.0					1																	33292091		2203	4300	6503	SO:0001587	stop_gained	64766					nucleus	calcium-dependent protein binding	g.chr1:33292091A>T	BX647916	CCDS30666.1	1p35.1	2008-02-05			ENSG00000116497	ENSG00000116497			25768	protein-coding gene	gene with protein product	"""S100P binding protein 1"""	611889				12477932	Standard	NM_022753		Approved	FLJ12903, S100PBPR	uc001bwc.4	Q96BU1	OTTHUMG00000003955	ENST00000373475.5:c.391A>T	1.37:g.33292091A>T	ENSP00000362574:p.Lys131*					S100PBP_ENST00000373476.1_Nonsense_Mutation_p.K131*|S100PBP_ENST00000398243.3_Nonsense_Mutation_p.K131*|S100PBP_ENST00000356689.3_3'UTR	p.K131*	NM_022753.3	NP_073590.2	Q96BU1	S1PBP_HUMAN			3	645	+		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)	131						Nonsense_Mutation	SNP	ENST00000373475.5	37	c.391A>T	CCDS30666.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.992711	0.74703	.	.	ENSG00000116497	ENST00000373476;ENST00000373475;ENST00000531123;ENST00000398243;ENST00000356689;ENST00000531256;ENST00000482212	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.8383	12.9295	0.58278	1.0:0.0:0.0:0.0	.	.	.	.	X	131	.	.	K	+	1	0	S100PBP	33064678	0.992000	0.36948	0.987000	0.45799	0.844000	0.47949	3.998000	0.57024	2.371000	0.80710	0.533000	0.62120	AAA		0.413	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011266.1	NM_022753		10	38	0	0	0	1	0	10	38				
LOC101927209	101927209	broad.mit.edu	37	1	142713774	142713774	+	lincRNA	SNP	A	A	G	rs201023195		TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr1:142713774A>G	ENST00000610091.1	-	0	1884																											CTTTTTCCACATTGTCATTTT	0.284																																						ENST00000369381.2																			0																																																			0							g.chr1:142713774A>G																													1.37:g.142713774A>G														0	831	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.284	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			4	33	0	0	0	1	0	4	33				
RP11-423O2.5	0	broad.mit.edu	37	1	142803543	142803543	+	lincRNA	SNP	C	C	T			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr1:142803543C>T	ENST00000423385.1	-	0	1422																											TGTTGGAATTCCTGATGAATC	0.269																																						ENST00000423385.1																			0																																																			0							g.chr1:142803543C>T																													1.37:g.142803543C>T														0	1422	-									RNA	SNP	ENST00000423385.1	37																																																																																						0.269	RP11-423O2.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000193203.1			5	114	0	0	0	1	0	5	114				
ASB10	136371	broad.mit.edu	37	7	150878400	150878400	+	Missense_Mutation	SNP	G	G	A	rs199755542		TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr7:150878400G>A	ENST00000420175.2	-	3	754	c.730C>T	c.(730-732)Cgc>Tgc	p.R244C	ASB10_ENST00000434669.1_Missense_Mutation_p.R289C|ASB10_ENST00000422024.1_Missense_Mutation_p.R289C|ASB10_ENST00000377867.3_Missense_Mutation_p.R229C|ASB10_ENST00000275838.1_Missense_Mutation_p.R244C			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	244					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCGGCATTGCGGGCATCAGGA	0.657													G|||	1	0.000199681	0.0	0.0	5008	,	,		15729	0.001		0.0	False		,,,				2504	0.0					ENST00000422024.1																			0				NS(1)|endometrium(2)|lung(7)|skin(2)	12						c.(865-867)Cgc>Tgc		ankyrin repeat and SOCS box containing 10							35.0	35.0	35.0					7																	150878400		2203	4300	6503	SO:0001583	missense	136371				intracellular signal transduction			g.chr7:150878400G>A	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"""Ankyrin repeat domain containing"""	17185	protein-coding gene	gene with protein product		615054	"""ankyrin repeat and SOCS box-containing 10"", ""glaucoma 1, open angle, F (adult-onset)"""	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.730C>T	7.37:g.150878400G>A	ENSP00000391137:p.Arg244Cys					ASB10_ENST00000434669.1_Missense_Mutation_p.R289C|ASB10_ENST00000377867.3_Missense_Mutation_p.R229C|ASB10_ENST00000275838.1_Missense_Mutation_p.R244C|ASB10_ENST00000420175.2_Missense_Mutation_p.R244C	p.R289C	NM_001142459.1	NP_001135931.2	Q8WXI3	ASB10_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	3	990	-			244					A0AVH0|Q6ZUL6	Missense_Mutation	SNP	ENST00000420175.2	37	c.865C>T	CCDS47750.2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.52	3.145780	0.57044	.	.	ENSG00000146926	ENST00000275838;ENST00000377867;ENST00000422024;ENST00000434669;ENST00000420175	T;T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32;-0.32	5.24	5.24	0.73138	Ankyrin repeat-containing domain (3);	0.191712	0.46145	D	0.000311	T	0.75376	0.3841	L	0.52823	1.66	0.41596	D	0.988824	D;D;D	0.89917	0.999;1.0;1.0	P;D;D	0.65874	0.899;0.939;0.926	T	0.76526	-0.2927	10	0.56958	D	0.05	-7.3683	11.9617	0.53011	0.0:0.0:0.7268:0.2732	.	229;244;289	Q8WXI3-3;Q8WXI3;D5MNW9	.;ASB10_HUMAN;.	C	244;229;289;289;244	ENSP00000275838:R244C;ENSP00000367098:R229C;ENSP00000401369:R289C;ENSP00000398247:R289C;ENSP00000391137:R244C	ENSP00000275838:R244C	R	-	1	0	ASB10	150509333	0.031000	0.19500	0.559000	0.28332	0.551000	0.35334	2.131000	0.42074	2.606000	0.88127	0.655000	0.94253	CGC		0.657	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871		3	45	0	0	0	1	0	3	45				
PLEKHM1P	440456	broad.mit.edu	37	17	62818136	62818136	+	RNA	SNP	G	G	C	rs200037995		TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr17:62818136G>C	ENST00000582986.1	-	0	362					NR_024386.1		Q69YJ1	PKHMP_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1 pseudogene						intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)										CTGAAGAATGGGAAATGGAAT	0.572																																						ENST00000582986.1																			0																																																			0							g.chr17:62818136G>C			17q24.1	2012-10-03			ENSG00000214176	ENSG00000214176			35411	pseudogene	pseudogene							Standard	NR_024386		Approved	LOC440456	uc002jew.4	Q69YJ1	OTTHUMG00000179296		17.37:g.62818136G>C								NR_024386.1						0	362	-									RNA	SNP	ENST00000582986.1	37																																																																																						0.572	PLEKHM1P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445598.1	NR_024386		5	40	0	0	0	1	0	5	40				
FOXD2	2306	broad.mit.edu	37	1	47904295	47904295	+	Missense_Mutation	SNP	A	A	G			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr1:47904295A>G	ENST00000334793.5	+	1	2607	c.488A>G	c.(487-489)tAc>tGc	p.Y163C		NM_004474.3	NP_004465.3	O60548	FOXD2_HUMAN	forkhead box D2	163					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(4)	4				READ - Rectum adenocarcinoma(2;0.0908)		CGCTTCCCCTACTACCGGGAG	0.622																																						ENST00000334793.5																			0				lung(4)	4						c.(487-489)tAc>tGc		forkhead box D2							47.0	60.0	56.0					1																	47904295		2203	4300	6503	SO:0001583	missense	2306				axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|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	g.chr1:47904295A>G	AF042832	CCDS30708.1	1p34-p32	2008-02-05			ENSG00000186564	ENSG00000186564		"""Forkhead boxes"""	3803	protein-coding gene	gene with protein product		602211		FKHL17		9403061, 12621056	Standard	NM_004474		Approved	FREAC9	uc001crm.3	O60548	OTTHUMG00000007950	ENST00000334793.5:c.488A>G	1.37:g.47904295A>G	ENSP00000335493:p.Tyr163Cys						p.Y163C	NM_004474.3	NP_004465.3	O60548	FOXD2_HUMAN		READ - Rectum adenocarcinoma(2;0.0908)	1	2607	+			163					Q5SVZ3	Missense_Mutation	SNP	ENST00000334793.5	37	c.488A>G	CCDS30708.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.402406	0.62288	.	.	ENSG00000186564	ENST00000334793	D	0.97598	-4.45	4.19	4.19	0.49359	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.85682	U	0.000000	D	0.98723	0.9571	H	0.94925	3.6	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.99414	1.0931	10	0.87932	D	0	.	12.2367	0.54520	1.0:0.0:0.0:0.0	.	163	O60548	FOXD2_HUMAN	C	163	ENSP00000335493:Y163C	ENSP00000335493:Y163C	Y	+	2	0	FOXD2	47676882	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.194000	0.51005	1.517000	0.48917	0.352000	0.21897	TAC		0.622	FOXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021831.1	NM_004474		43	108	0	0	0	1	0	43	108				
LINC00842	643650	broad.mit.edu	37	10	47133709	47133709	+	lincRNA	SNP	G	G	C	rs527241646	byFrequency	TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr10:47133709G>C	ENST00000422732.2	-	0	435					NR_033957.2				long intergenic non-protein coding RNA 842																		GAACCACTTCGACCTCTTTGG	0.468																																						ENST00000422732.2																			0																																																			0							g.chr10:47133709G>C			10q11.22	2013-01-04			ENSG00000223477	ENSG00000274909		"""Long non-coding RNAs"""	44989	non-coding RNA	RNA, long non-coding							Standard	NR_033957		Approved		uc001jef.3		OTTHUMG00000018109		10.37:g.47133709G>C								NR_033957.1						0	435	-									RNA	SNP	ENST00000422732.2	37																																																																																						0.468	LINC00842-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000047838.2	NR_033957		4	89	0	0	0	1	0	4	89				
SOGA1	140710	broad.mit.edu	37	20	35444296	35444296	+	Nonsense_Mutation	SNP	G	G	A			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr20:35444296G>A	ENST00000357779.3	-	5	1161	c.835C>T	c.(835-837)Cag>Tag	p.Q279*	SOGA1_ENST00000279034.6_Nonsense_Mutation_p.Q279*|SOGA1_ENST00000237536.4_Nonsense_Mutation_p.Q517*|SOGA1_ENST00000456801.2_Nonsense_Mutation_p.Q120*			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	279					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						TCGACAAACTGCAGGTGTCGC	0.667																																						ENST00000237536.4																			0				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						c.(1549-1551)Cag>Tag		suppressor of glucose, autophagy associated 1							30.0	36.0	34.0					20																	35444296		2136	4244	6380	SO:0001587	stop_gained	140710							g.chr20:35444296G>A	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"""suppressor of glucose by autophagy"", ""suppressor of glucose from autophagy"""		"""chromosome 20 open reading frame 117"", ""KIAA0889"""	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.835C>T	20.37:g.35444296G>A	ENSP00000350424:p.Gln279*					SOGA1_ENST00000357779.3_Nonsense_Mutation_p.Q279*|SOGA1_ENST00000279034.5_Nonsense_Mutation_p.Q279*|SOGA1_ENST00000456801.2_Nonsense_Mutation_p.Q120*	p.Q517*	NM_080627.2	NP_542194.2	O94964	K0889_HUMAN			5	1890	-			279					A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Nonsense_Mutation	SNP	ENST00000357779.3	37	c.1549C>T		.	.	.	.	.	.	.	.	.	.	G	43	10.186865	0.99354	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	.	.	.	5.24	5.24	0.73138	.	0.114202	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-43.5489	17.7588	0.88457	0.0:0.0:1.0:0.0	.	.	.	.	X	517;279;120;279	.	ENSP00000237536:Q517X	Q	-	1	0	KIAA0889	34877710	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.615000	0.98356	2.723000	0.93209	0.655000	0.94253	CAG		0.667	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		5	11	0	0	0	1	0	5	11				
BTD	686	broad.mit.edu	37	3	15686446	15686446	+	Silent	SNP	T	T	C			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr3:15686446T>C	ENST00000303498.5	+	4	1192	c.1083T>C	c.(1081-1083)ttT>ttC	p.F361F	BTD_ENST00000449107.1_Silent_p.F363F|BTD_ENST00000437172.1_Silent_p.F363F|BTD_ENST00000383778.4_Silent_p.F341F	NM_000060.2|NM_001281723.1	NP_000051.1|NP_001268652.1	P43251	BTD_HUMAN	biotinidase	361	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				biotin metabolic process (GO:0006768)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	biotin carboxylase activity (GO:0004075)|biotinidase activity (GO:0047708)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	18						ATAGTAAGTTTTTAAAAATTT	0.473																																						ENST00000383778.4																			0				breast(2)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	18						c.(1021-1023)ttT>ttC		biotinidase							79.0	80.0	80.0					3																	15686446		2203	4300	6503	SO:0001819	synonymous_variant	686				central nervous system development|epidermis development|nitrogen compound metabolic process	extracellular space	biotin carboxylase activity|biotinidase activity	g.chr3:15686446T>C	AF018631	CCDS2628.1, CCDS63563.1, CCDS63564.1, CCDS63565.1	3p25	2007-03-26			ENSG00000169814	ENSG00000169814	3.5.1.12		1122	protein-coding gene	gene with protein product		609019				8001986	Standard	NM_001281723		Approved		uc003cah.3	P43251	OTTHUMG00000129861	ENST00000303498.5:c.1083T>C	3.37:g.15686446T>C						BTD_ENST00000303498.5_Silent_p.F361F|BTD_ENST00000437172.1_Silent_p.F363F|BTD_ENST00000449107.1_Silent_p.F363F	p.F341F			P43251	BTD_HUMAN			4	1381	+			361			CN hydrolase.		A6NHF2|B2R865|B4DFX1|B4DLJ9|B7Z7C9|F8W1Q3|Q96EM9	Silent	SNP	ENST00000303498.5	37	c.1023T>C	CCDS2628.1																																																																																				0.473	BTD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252103.2	NM_000060		30	93	0	0	0	1	0	30	93				
WAPAL	23063	broad.mit.edu	37	10	88260115	88260115	+	Silent	SNP	C	C	T			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr10:88260115C>T	ENST00000298767.5	-	3	1357	c.885G>A	c.(883-885)acG>acA	p.T295T		NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	295	Mediates interaction with the cohesin complex.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						CCCTACAGTACGTCCTACAGT	0.413																																						ENST00000298767.5																			0				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						c.(883-885)acG>acA		wings apart-like homolog (Drosophila)							135.0	124.0	127.0					10																	88260115		2203	4300	6503	SO:0001819	synonymous_variant	23063				cell division|interspecies interaction between organisms|mitosis|negative regulation of chromatin binding|negative regulation of DNA replication|negative regulation of sister chromatid cohesion|protein localization to chromatin|regulation of cohesin localization to chromatin	chromatin|cohesin complex|cytoplasm	protein binding	g.chr10:88260115C>T	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"""friend of EBNA2"""	610754	"""KIAA0261"""	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.885G>A	10.37:g.88260115C>T							p.T295T	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN			3	1357	-			295			Mediates interaction with the cohesin complex.		A7E2B5|Q5VSK5|Q8IX10|Q92549	Silent	SNP	ENST00000298767.5	37	c.885G>A	CCDS7375.1																																																																																				0.413	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		19	119	0	0	0	1	0	19	119				
PPP1R9B	84687	broad.mit.edu	37	17	48221042	48221042	+	Missense_Mutation	SNP	C	C	T			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr17:48221042C>T	ENST00000316878.6	-	5	1542	c.1540G>A	c.(1540-1542)Ggg>Agg	p.G514R	PPP1R9B_ENST00000501501.2_5'UTR|AC002401.1_ENST00000451776.1_RNA	NM_032595.3	NP_115984.3	Q96SB3	NEB2_HUMAN	protein phosphatase 1, regulatory subunit 9B	514	Interacts with RGS2. {ECO:0000250}.|PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to morphine (GO:0071315)|dendrite development (GO:0016358)|filopodium assembly (GO:0046847)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of cell proliferation (GO:0042127)|regulation of exit from mitosis (GO:0007096)|regulation of opioid receptor signaling pathway (GO:2000474)|regulation of protein phosphorylation (GO:0001932)|RNA splicing (GO:0008380)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|protein phosphatase type 1 complex (GO:0000164)|ruffle membrane (GO:0032587)|synapse (GO:0045202)	protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8						ATGTCTGCCCCGGCGCCCATG	0.627																																						ENST00000316878.6																			0				endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8						c.(1540-1542)Ggg>Agg		protein phosphatase 1, regulatory subunit 9B							77.0	87.0	84.0					17																	48221042		2096	4212	6308	SO:0001583	missense	84687				cell cycle arrest|cell differentiation|cell migration|filopodium assembly|negative regulation of cell growth|nervous system development|regulation of cell growth by extracellular stimulus|regulation of cell proliferation|regulation of exit from mitosis|RNA splicing	adherens junction|cytoskeleton|dendritic spine|filopodium|lamellipodium|nucleoplasm|protein phosphatase type 1 complex|ruffle membrane|synapse	actin binding|protein phosphatase 1 binding|protein phosphatase inhibitor activity	g.chr17:48221042C>T	AJ401189	CCDS74102.1	17q21.33	2013-01-31	2011-10-04	2001-07-02	ENSG00000108819	ENSG00000108819		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9298	protein-coding gene	gene with protein product	"""spinophilin"", ""Neurabin-2"""	603325	"""protein phosphatase 1, regulatory subunit 9B, spinophilin"", ""protein phosphatase 1, regulatory (inhibitor) subunit 9B"""	PPP1R6, PPP1R9		9275233	Standard	NM_032595		Approved	Spn, SPINO	uc002iqh.4	Q96SB3	OTTHUMG00000162008	ENST00000316878.6:c.1540G>A	17.37:g.48221042C>T	ENSP00000475417:p.Gly514Arg					PPP1R9B_ENST00000501501.2_5'UTR|AC002401.1_ENST00000451776.1_RNA	p.G514R	NM_032595.3	NP_115984.3	Q96SB3	NEB2_HUMAN			5	1542	-			514			Interacts with RGS2 (By similarity).|PDZ.		Q8TCR9	Missense_Mutation	SNP	ENST00000316878.6	37	c.1540G>A																																																																																					0.627	PPP1R9B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032595		21	84	0	0	0	1	0	21	84				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		13	53	0	0	0	1	0	13	53				
LINC00969	440993	broad.mit.edu	37	3	195400728	195400728	+	lincRNA	SNP	A	A	G	rs12107841	byFrequency	TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr3:195400728A>G	ENST00000445430.1	+	0	1324									long intergenic non-protein coding RNA 969																		GATTGTGCCCAGCCTGTACGC	0.587																																						ENST00000445430.1																			0																																																			0							g.chr3:195400728A>G	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195400728A>G														0	1324	+									RNA	SNP	ENST00000445430.1	37																																																																																						0.587	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			4	15	0	0	0	1	0	4	15				
LINC00842	643650	broad.mit.edu	37	10	47133727	47133727	+	lincRNA	SNP	A	A	G			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr10:47133727A>G	ENST00000422732.2	-	0	435					NR_033957.2				long intergenic non-protein coding RNA 842																		TGGCTGGATGAAGCACTAGCC	0.458																																						ENST00000422732.2																			0																																																			0							g.chr10:47133727A>G			10q11.22	2013-01-04			ENSG00000223477	ENSG00000274909		"""Long non-coding RNAs"""	44989	non-coding RNA	RNA, long non-coding							Standard	NR_033957		Approved		uc001jef.3		OTTHUMG00000018109		10.37:g.47133727A>G								NR_033957.1						0	435	-									RNA	SNP	ENST00000422732.2	37																																																																																						0.458	LINC00842-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000047838.2	NR_033957		4	97	0	0	0	1	0	4	97				
SDHAP1	255812	broad.mit.edu	37	3	195713385	195713386	+	RNA	INS	-	-	T	rs199843390		TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr3:195713385_195713386insT	ENST00000427841.1	-	0	176					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		AAAGCATGAACTTACGGAATCT	0.401																																					Ovarian(67;1158 1227 12109 20189 43170)	ENST00000427841.1																			0																																																			0							g.chr3:195713385_195713386insT	BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195713387_195713387dupT								NR_003264.2						0	176	-									RNA	INS	ENST00000427841.1	37																																																																																						0.401	SDHAP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341367.1			3	6						3	6	---	---	---	---
PHKG1	5260	broad.mit.edu	37	7	62693664	62693664	+	RNA	DEL	T	T	-			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr7:62693664delT	ENST00000451381.1	-	0	181																											AGCGATCACCTGAAGGCCACG	0.647																																						ENST00000451381.1																			0																																																			0							g.chr7:62693664delT																													7.37:g.62693664delT														0	181	-									RNA	DEL	ENST00000451381.1	37																																																																																						0.647	RP5-905H7.3-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000343675.1			2	4						2	4	---	---	---	---
MIR3687-2	103504728	broad.mit.edu	37	21	9825852	9825853	+	RNA	INS	-	-	A			TCGA-J8-A3O2-01A-11D-A23M-08	TCGA-J8-A3O2-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ade6333-73db-4993-83a1-00da914ab0c5	899b05a1-7e18-4e92-8cb0-94a6c8efcd64	g.chr21:9825852_9825853insA	ENST00000577708.1	+	0	0				MIR3648_ENST00000581792.1_RNA	NR_037458.1																						gcggcggtggtggggggagccg	0.837																																						ENST00000581792.1																			0																																																			0							g.chr21:9825852_9825853insA																													21.37:g.9825852_9825853insA								NR_037421.1						0	21_22	+									RNA	INS	ENST00000577708.1	37																																																																																						0.837	MIR3687-201	KNOWN	basic	miRNA	miRNA				2	4						2	4	---	---	---	---
