#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
POFUT2	23275	broad.mit.edu	37	21	46689817	46689817	+	Missense_Mutation	SNP	G	G	A			TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr21:46689817G>A	ENST00000349485.5	-	7	975	c.949C>T	c.(949-951)Cgc>Tgc	p.R317C	POFUT2_ENST00000471540.1_5'UTR|POFUT2_ENST00000331343.7_Missense_Mutation_p.R317C	NM_133635.4	NP_598368.2	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2	317					fucose metabolic process (GO:0006004)|mesoderm formation (GO:0001707)|protein O-linked fucosylation (GO:0036066)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of gene expression (GO:0010468)|regulation of secretion (GO:0051046)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	20				Colorectal(79;0.243)		ATGAGGCTGCGGATCTTCCTC	0.542																																						ENST00000331343.7																			0				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	20						c.(949-951)Cgc>Tgc		protein O-fucosyltransferase 2							92.0	86.0	88.0					21																	46689817		2203	4300	6503	SO:0001583	missense	23275				fucose metabolic process	endoplasmic reticulum	peptide-O-fucosyltransferase activity	g.chr21:46689817G>A	AJ203079	CCDS13719.1, CCDS13721.1	21q22.3	2013-03-06	2004-06-07	2004-06-09	ENSG00000186866	ENSG00000186866	2.4.1.221	"""Fucosyltransferases"""	14683	protein-coding gene	gene with protein product	"""peptide-O-fucosyltransferase"", ""GDP-fucose protein O-fucosyltransferase 2"""	610249	"""chromosome 21 open reading frame 80"""	C21orf80			Standard	NM_133635		Approved	KIAA0958, FUT13	uc002zhc.3	Q9Y2G5	OTTHUMG00000084874	ENST00000349485.5:c.949C>T	21.37:g.46689817G>A	ENSP00000339613:p.Arg317Cys					POFUT2_ENST00000471540.1_5'UTR|POFUT2_ENST00000349485.5_Missense_Mutation_p.R317C	p.R317C	NM_015227.4	NP_056042.1	Q9Y2G5	OFUT2_HUMAN		Colorectal(79;0.243)	7	975	-			317					Q6PJV1|Q7Z4N0|Q8WWU6|Q9BQS4|Q9BQS5|Q9UFY3	Missense_Mutation	SNP	ENST00000349485.5	37	c.949C>T	CCDS13719.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.45|18.45	3.627516|3.627516	0.66901|0.66901	.|.	.|.	ENSG00000186866|ENSG00000186866	ENST00000451615|ENST00000331343;ENST00000349485	.|T;T	.|0.31510	.|1.49;1.49	4.35|4.35	4.35|4.35	0.52113|0.52113	.|.	.|0.160446	.|0.53938	.|D	.|0.000042	T|T	0.50394|0.50394	0.1613|0.1613	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.999	.|P;P	.|0.60682	.|0.854;0.878	T|T	0.54583|0.54583	-0.8272|-0.8272	5|10	.|0.54805	.|T	.|0.06	-16.253|-16.253	14.743|14.743	0.69469|0.69469	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|317;317	.|Q9Y2G5-1;Q9Y2G5	.|.;OFUT2_HUMAN	L|C	239|317	.|ENSP00000329682:R317C;ENSP00000339613:R317C	.|ENSP00000329682:R317C	P|R	-|-	2|1	0|0	POFUT2|POFUT2	45514245|45514245	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.516000|0.516000	0.34256|0.34256	4.108000|4.108000	0.57817|0.57817	2.144000|2.144000	0.66660|0.66660	0.655000|0.655000	0.94253|0.94253	CCG|CGC		0.542	POFUT2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192573.2	NM_015227		9	55	0	0	0	1	0	9	55				
PCDH12	51294	broad.mit.edu	37	5	141329142	141329142	+	Silent	SNP	T	T	C			TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr5:141329142T>C	ENST00000231484.3	-	3	4195	c.2985A>G	c.(2983-2985)gcA>gcG	p.A995A	AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	995					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTCTGGGATTGCACTCCTGC	0.493																																						ENST00000231484.3																			0				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38						c.(2983-2985)gcA>gcG		protocadherin 12							119.0	113.0	115.0					5																	141329142		2203	4300	6503	SO:0001819	synonymous_variant	51294				neuron recognition	integral to plasma membrane	calcium ion binding	g.chr5:141329142T>C	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2985A>G	5.37:g.141329142T>C							p.A995A	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		3	4195	-		all_hematologic(541;0.0999)	995					Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	37	c.2985A>G	CCDS4269.1																																																																																				0.493	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		16	77	0	0	0	1	0	16	77				
SH2D3A	10045	broad.mit.edu	37	19	6754188	6754188	+	Intron	SNP	T	T	C	rs2305807	byFrequency	TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr19:6754188T>C	ENST00000245908.6	-	8	1542				SH2D3A_ENST00000437152.3_Missense_Mutation_p.D327G|SH2D3A_ENST00000599563.1_5'Flank|CTD-3128G10.6_ENST00000594056.1_RNA	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A						JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						GGAGAAGAGATCTGAGCACGC	0.657													C|||	1724	0.344249	0.5325	0.3184	5008	,	,		13391	0.3671		0.2664	False		,,,				2504	0.1646					ENST00000437152.3																			0				breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						c.(979-981)gAt>gGt		SH2 domain containing 3A		C		2125,2281	568.5+/-382.4	522,1081,600	24.0	28.0	27.0			-5.4	0.0	19	dbSNP_100	27	2399,6201	667.8+/-402.5	353,1693,2254	no	intron	SH2D3A	NM_005490.2		875,2774,2854	CC,CT,TT		27.8953,48.2297,34.7839			6754188	4524,8482	2203	4300	6503	SO:0001627	intron_variant	10045				JNK cascade|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity	g.chr19:6754188T>C	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"""SH2 domain containing"""	16885	protein-coding gene	gene with protein product		604721	"""SH2 domain-containing 3A"""			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.1273-14A>G	19.37:g.6754188T>C						SH2D3A_ENST00000245908.6_Intron	p.D327G			Q9BRG2	SH23A_HUMAN			6	1112	-			425					A8K9R6|B4DRS7|Q9Y2X4	Missense_Mutation	SNP	ENST00000245908.6	37	c.980A>G	CCDS12173.1	761	0.3484432234432234	244	0.4959349593495935	110	0.30386740331491713	209	0.36538461538461536	198	0.2612137203166227	C	2.401	-0.337537	0.05278	0.482297	0.278953	ENSG00000125731	ENST00000437152	T	0.31510	1.49	4.15	-5.42	0.02640	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.50101	-0.8867	6	.	.	.	.	0.2532	0.00208	0.2481:0.164:0.2486:0.3394	rs2305807	327	B4DRS7	.	G	327	ENSP00000393303:D327G	.	D	-	2	0	SH2D3A	6705188	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.549000	0.06041	-0.816000	0.04340	-0.642000	0.03964	GAT		0.657	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490		3	18	0	0	0	1	0	3	18				
TERT	7015	broad.mit.edu	37	5	1280291	1280291	+	Silent	SNP	C	C	T	rs148582238	byFrequency	TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr5:1280291C>T	ENST00000310581.5	-	4	1989	c.1932G>A	c.(1930-1932)acG>acA	p.T644T	TERT_ENST00000334602.6_Silent_p.T644T|TERT_ENST00000508104.2_Silent_p.T644T|TERT_ENST00000296820.5_Silent_p.T644T	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	644	Reverse transcriptase. {ECO:0000255|PROSITE-ProRule:PRU00405}.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	CTCTGCGGAACGTTCTGGCTC	0.552									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis				C|||	3	0.000599042	0.0023	0.0	5008	,	,		18097	0.0		0.0	False		,,,				2504	0.0					ENST00000310581.5																			0				NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41						c.(1930-1932)acG>acA		telomerase reverse transcriptase		C	,	1,4405	2.1+/-5.4	0,1,2202	121.0	117.0	119.0		1932,1932	-9.0	0.0	5	dbSNP_134	119	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TERT	NM_001193376.1,NM_198253.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	644/1070,644/1133	1280291	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	0	TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	anti-apoptosis|DNA strand elongation|replicative senescence|telomere formation via telomerase|telomere maintenance via telomerase	cytoplasm|nucleolus|PML body|telomerase holoenzyme complex	protein homodimerization activity|telomeric DNA binding|telomeric RNA binding|telomeric template RNA reverse transcriptase activity	g.chr5:1280291C>T	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.1932G>A	5.37:g.1280291C>T						TERT_ENST00000296820.5_Silent_p.T644T|TERT_ENST00000508104.2_Silent_p.T644T|TERT_ENST00000334602.6_Silent_p.T644T	p.T644T	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		4	1989	-	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		644			Reverse transcriptase.		O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Silent	SNP	ENST00000310581.5	37	c.1932G>A	CCDS3861.2																																																																																				0.552	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			6	99	0	0	0	1	0	6	99				
ADAM21	8747	broad.mit.edu	37	14	70924812	70924812	+	Missense_Mutation	SNP	C	C	T	rs370238293		TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr14:70924812C>T	ENST00000603540.1	+	2	854	c.596C>T	c.(595-597)tCt>tTt	p.S199F	ADAM21_ENST00000267499.3_Missense_Mutation_p.S199F|RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	199					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GAACCAAAATCTGCTGGTGAC	0.448																																						ENST00000603540.1																			0				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31						c.(595-597)tCt>tTt		ADAM metallopeptidase domain 21							74.0	76.0	75.0					14																	70924812		2203	4300	6503	SO:0001583	missense	8747				proteolysis|single fertilization	integral to membrane	metalloendopeptidase activity|zinc ion binding	g.chr14:70924812C>T	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.596C>T	14.37:g.70924812C>T	ENSP00000474385:p.Ser199Phe					ADAM21_ENST00000267499.3_Missense_Mutation_p.S199F|RP11-486O13.4_ENST00000556646.1_lincRNA	p.S199F	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN		all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)	2	854	+			199					O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	c.596C>T	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	C	9.262	1.043355	0.19748	.	.	ENSG00000139985	ENST00000267499	T	0.01215	5.16	3.49	3.49	0.39957	.	0.378699	0.19013	U	0.125029	T	0.02230	0.0069	M	0.68593	2.085	0.26948	N	0.966098	B	0.32876	0.388	B	0.37422	0.249	T	0.24764	-1.0151	10	0.40728	T	0.16	.	10.6601	0.45698	0.0:1.0:0.0:0.0	.	199	Q9UKJ8	ADA21_HUMAN	F	199	ENSP00000267499:S199F	ENSP00000267499:S199F	S	+	2	0	ADAM21	69994565	0.001000	0.12720	0.813000	0.32504	0.022000	0.10575	0.380000	0.20602	1.947000	0.56498	0.557000	0.71058	TCT		0.448	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3			5	88	0	0	0	1	0	5	88				
KDR	3791	broad.mit.edu	37	4	55946325	55946325	+	Missense_Mutation	SNP	A	A	G			TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr4:55946325A>G	ENST00000263923.4	-	30	4149	c.3854T>C	c.(3853-3855)aTg>aCg	p.M1285T	RP11-530I17.1_ENST00000511222.1_RNA	NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	1285					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GCTGGGCACCATTCCACTGCA	0.507			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)																												ENST00000263923.4				Dom	yes		4	4q11-q12	3791	Mis	vascular endothelial growth factor receptor 2			E			"""NSCLC, angiosarcoma"""		0				NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135						c.(3853-3855)aTg>aCg		kinase insert domain receptor (a type III receptor tyrosine kinase)	Sorafenib(DB00398)|Sunitinib(DB01268)						89.0	87.0	88.0					4																	55946325		2203	4300	6503	SO:0001583	missense	3791				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity	g.chr4:55946325A>G	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.3854T>C	4.37:g.55946325A>G	ENSP00000263923:p.Met1285Thr	TSP Lung(20;0.16)				RP11-530I17.1_ENST00000511222.1_RNA	p.M1285T	NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	Epithelial(7;0.189)		30	4149	-	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		1285					A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	c.3854T>C	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	A	8.744	0.919759	0.17982	.	.	ENSG00000128052	ENST00000263923	T	0.74947	-0.89	5.63	5.63	0.86233	.	0.130613	0.53938	D	0.000058	T	0.58032	0.2094	N	0.08118	0	0.41401	D	0.987674	B	0.18741	0.03	B	0.19148	0.024	T	0.56323	-0.7998	10	0.45353	T	0.12	.	15.8397	0.78835	1.0:0.0:0.0:0.0	.	1285	P35968	VGFR2_HUMAN	T	1285	ENSP00000263923:M1285T	ENSP00000263923:M1285T	M	-	2	0	KDR	55641082	1.000000	0.71417	0.990000	0.47175	0.057000	0.15508	8.730000	0.91510	2.153000	0.67306	0.533000	0.62120	ATG		0.507	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			8	37	0	0	0	1	0	8	37				
TIAM2	26230	broad.mit.edu	37	6	155504495	155504495	+	Silent	SNP	G	G	C	rs145603552	byFrequency	TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr6:155504495G>C	ENST00000461783.3	+	16	4198	c.2925G>C	c.(2923-2925)ccG>ccC	p.P975P	TIAM2_ENST00000367174.2_Silent_p.P351P|TIAM2_ENST00000318981.5_Silent_p.P975P|TIAM2_ENST00000456877.2_Silent_p.P287P|TIAM2_ENST00000529824.2_Silent_p.P975P|TIAM2_ENST00000456144.1_Silent_p.P975P|TIAM2_ENST00000528391.2_Silent_p.P311P|TIAM2_ENST00000360366.4_Silent_p.P999P			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	975	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		CCCGGCCTCCGGACACAAAAG	0.547													G|||	11	0.00219649	0.0008	0.0	5008	,	,		17045	0.0		0.007	False		,,,				2504	0.0031					ENST00000461783.3																			0				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65						c.(2923-2925)ccG>ccC		T-cell lymphoma invasion and metastasis 2		G		6,4400	11.4+/-27.6	0,6,2197	81.0	80.0	80.0		2925	-3.6	0.0	6	dbSNP_134	80	40,8560	26.8+/-75.7	0,40,4260	no	coding-synonymous	TIAM2	NM_012454.3		0,46,6457	CC,CG,GG		0.4651,0.1362,0.3537		975/1702	155504495	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	26230				apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity	g.chr6:155504495G>C		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.2925G>C	6.37:g.155504495G>C						TIAM2_ENST00000456877.2_Silent_p.P287P|TIAM2_ENST00000318981.5_Silent_p.P975P|TIAM2_ENST00000456144.1_Silent_p.P975P|TIAM2_ENST00000529824.2_Silent_p.P975P|TIAM2_ENST00000528391.2_Silent_p.P311P|TIAM2_ENST00000367174.2_Silent_p.P351P|TIAM2_ENST00000360366.4_Silent_p.P999P	p.P975P			Q8IVF5	TIAM2_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)	16	4198	+		Ovarian(120;0.196)	975			PDZ.		B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	37	c.2925G>C	CCDS34558.1																																																																																				0.547	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		4	53	0	0	0	1	0	4	53				
KGFLP2	654466	broad.mit.edu	37	9	41962602	41962602	+	lincRNA	SNP	G	G	T	rs201713470	byFrequency	TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr9:41962602G>T	ENST00000454645.1	-	0	902					NR_003670.1																						TTCTTTCTTTGTTTTTTTTCC	0.373																																						ENST00000454645.1																			0																																																			0							g.chr9:41962602G>T																													9.37:g.41962602G>T								NR_003670.1						0	902	-									RNA	SNP	ENST00000454645.1	37																																																																																						0.373	RP11-204M4.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000143738.1			4	37	1	0	1	1	1	4	37				
LOC101927079	101927079	broad.mit.edu	37	15	22332432	22332432	+	RNA	SNP	C	C	T	rs376977769		TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr15:22332432C>T	ENST00000558896.1	+	0	239																											AAGATTCTAACGTGACAGAAC	0.343																																						ENST00000558896.1																			0																																																			0							g.chr15:22332432C>T																													15.37:g.22332432C>T														0	239	+									RNA	SNP	ENST00000558896.1	37																																																																																						0.343	RP11-69H14.6-001	KNOWN	basic	sense_overlapping	sense_overlapping	OTTHUMT00000417625.1			10	43	0	0	0	1	0	10	43				
LOC101927209	101927209	broad.mit.edu	37	1	142713773	142713773	+	lincRNA	SNP	C	C	G	rs199933143		TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	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			7	50	0	0	0	1	0	7	50				
SYN2	6854	broad.mit.edu	37	3	12183431	12183431	+	RNA	SNP	G	G	A			TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr3:12183431G>A	ENST00000432424.2	+	0	634							Q92777	SYN2_HUMAN	synapsin II						neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)			breast(5)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	18						TCAACCTGGTGGCCCATGCAG	0.478																																						ENST00000432424.2																			0				breast(5)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	18								synapsin II							144.0	135.0	138.0					3																	12183431		1926	4136	6062			6854				neurotransmitter secretion	synaptic vesicle	ATP binding|ligase activity	g.chr3:12183431G>A		CCDS74900.1, CCDS74901.1	3p25.2	2013-09-20			ENSG00000157152	ENSG00000157152			11495	protein-coding gene	gene with protein product		600755				8530057	Standard	XM_006713311		Approved	SYNII, SYNIIa, SYNIIb	uc003bwm.3	Q92777	OTTHUMG00000155335		3.37:g.12183431G>A										Q86VA8	Q86VA8_HUMAN			0	634	+								A8MY98	RNA	SNP	ENST00000432424.2	37																																																																																						0.478	SYN2-002	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000339528.3	NM_133625		7	38	0	0	0	1	0	7	38				
LOC101927209	101927209	broad.mit.edu	37	1	142713774	142713774	+	lincRNA	SNP	A	A	G	rs201023195		TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	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			7	49	0	0	0	1	0	7	49				
LOC101927209	101927209	broad.mit.edu	37	1	142713944	142713944	+	lincRNA	SNP	C	C	T	rs199960649		TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr1:142713944C>T	ENST00000610091.1	-	0	1714																											TGATTACCTCCGAAGTTAAAG	0.308																																						ENST00000369381.2																			0																																																			0							g.chr1:142713944C>T																													1.37:g.142713944C>T														0	661	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.308	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			3	22	0	0	0	1	0	3	22				
OR8K5	219453	broad.mit.edu	37	11	55927697	55927697	+	Missense_Mutation	SNP	C	C	T	rs200015077		TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr11:55927697C>T	ENST00000313447.1	-	1	96	c.97G>A	c.(97-99)Gtc>Atc	p.V33I		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	33						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				AGGTAGATGACGAGGAAGACT	0.433																																						ENST00000313447.1																			0				large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34						c.(97-99)Gtc>Atc		olfactory receptor, family 8, subfamily K, member 5		C	ILE/VAL	0,4402		0,0,2201	135.0	132.0	133.0		97	-7.1	0.5	11		133	2,8590	2.2+/-6.3	0,2,4294	yes	missense	OR8K5	NM_001004058.2	29	0,2,6495	TT,TC,CC		0.0233,0.0,0.0154	benign	33/308	55927697	2,12992	2201	4296	6497	SO:0001583	missense	219453				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55927697C>T	BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"""GPCR / Class A : Olfactory receptors"""	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.97G>A	11.37:g.55927697C>T	ENSP00000323853:p.Val33Ile						p.V33I	NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN			1	96	-	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)	33					Q6IFB5	Missense_Mutation	SNP	ENST00000313447.1	37	c.97G>A	CCDS31521.1	.	.	.	.	.	.	.	.	.	.	C	0.013	-1.636717	0.00806	0.0	2.33E-4	ENSG00000181752	ENST00000313447	T	0.00438	7.42	3.74	-7.1	0.01547	.	.	.	.	.	T	0.00109	0.0003	N	0.02865	-0.47	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.31251	-0.9950	9	0.12766	T	0.61	.	0.5541	0.00668	0.2806:0.167:0.3185:0.234	.	33	Q8NH50	OR8K5_HUMAN	I	33	ENSP00000323853:V33I	ENSP00000323853:V33I	V	-	1	0	OR8K5	55684273	0.000000	0.05858	0.482000	0.27366	0.497000	0.33675	-4.408000	0.00238	-1.009000	0.03400	-0.673000	0.03796	GTC		0.433	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058		19	72	0	0	0	1	0	19	72				
CDH8	1006	broad.mit.edu	37	16	61761114	61761114	+	Missense_Mutation	SNP	G	G	T			TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr16:61761114G>T	ENST00000577390.1	-	9	2374	c.1420C>A	c.(1420-1422)Cac>Aac	p.H474N	CDH8_ENST00000577730.1_Missense_Mutation_p.H474N|CDH8_ENST00000584337.1_Missense_Mutation_p.H474N|CDH8_ENST00000299345.6_Missense_Mutation_p.H474N	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	474	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		ATCTGACTGTGGTTCCCTATG	0.398																																						ENST00000577390.1																			0				biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112						c.(1420-1422)Cac>Aac		cadherin 8, type 2							172.0	155.0	161.0					16																	61761114		2203	4299	6502	SO:0001583	missense	1006				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr16:61761114G>T	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"""Cadherins / Major cadherins"""	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1420C>A	16.37:g.61761114G>T	ENSP00000462701:p.His474Asn					CDH8_ENST00000299345.6_Missense_Mutation_p.H474N|CDH8_ENST00000584337.1_Missense_Mutation_p.H474N|CDH8_ENST00000577730.1_Missense_Mutation_p.H474N	p.H474N	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)	9	2374	-		Ovarian(137;0.0799)|Melanoma(118;0.16)	474			Cadherin 4.		B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	c.1420C>A	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.813638	0.70912	.	.	ENSG00000150394	ENST00000299345	T	0.01705	4.68	5.75	5.75	0.90469	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.03827	0.0108	L	0.31157	0.91	0.80722	D	1	P;P	0.37688	0.605;0.486	B;P	0.45538	0.369;0.484	T	0.57877	-0.7735	10	0.54805	T	0.06	.	19.9498	0.97195	0.0:0.0:1.0:0.0	.	290;474	Q3LID3;P55286	.;CADH8_HUMAN	N	474	ENSP00000299345:H474N	ENSP00000299345:H474N	H	-	1	0	CDH8	60318615	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.130000	0.77235	2.715000	0.92844	0.650000	0.86243	CAC		0.398	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		14	117	1	0	6.31663e-08	1	6.52718e-08	14	117				
FBXO3	26273	broad.mit.edu	37	11	33777500	33777500	+	Silent	SNP	C	C	T			TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr11:33777500C>T	ENST00000265651.3	-	5	513	c.495G>A	c.(493-495)ctG>ctA	p.L165L	FBXO3_ENST00000531080.1_5'Flank|FBXO3_ENST00000533103.1_5'Flank|FBXO3_ENST00000534136.1_Silent_p.L165L|FBXO3_ENST00000532057.1_5'Flank|FBXO3_ENST00000530401.1_Silent_p.L160L|FBXO3_ENST00000448981.2_Silent_p.L165L|FBXO3_ENST00000526785.1_Silent_p.L52L	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	165					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		AGTGATTAGACAGTGCCATGC	0.428																																						ENST00000530401.1																			0				NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13						c.(478-480)ctG>ctA		F-box protein 3							71.0	64.0	66.0					11																	33777500		2202	4298	6500	SO:0001819	synonymous_variant	26273				proteolysis	nucleus	ubiquitin-protein ligase activity	g.chr11:33777500C>T	AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"""F-boxes /  ""other"""""	13582	protein-coding gene	gene with protein product		609089	"""F-box only protein 3"""			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.495G>A	11.37:g.33777500C>T						FBXO3_ENST00000534136.1_Silent_p.L165L|FBXO3_ENST00000526785.1_Silent_p.L52L|FBXO3_ENST00000448981.2_Silent_p.L165L|FBXO3_ENST00000265651.3_Silent_p.L165L	p.L160L			Q9UK99	FBX3_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)	5	500	-		Lung NSC(402;0.0804)	165					B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Silent	SNP	ENST00000265651.3	37	c.480G>A	CCDS7887.1	.	.	.	.	.	.	.	.	.	.	C	9.808	1.182491	0.21870	.	.	ENSG00000110429	ENST00000321458	.	.	.	5.63	1.33	0.21861	.	.	.	.	.	T	0.54532	0.1864	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54886	-0.8226	5	0.59425	D	0.04	-9.4257	2.7057	0.05161	0.1142:0.4322:0.2465:0.2072	.	.	.	.	Y	163	.	ENSP00000315066:C163Y	C	-	2	0	FBXO3	33734076	1.000000	0.71417	0.998000	0.56505	0.946000	0.59487	0.815000	0.27253	0.709000	0.31976	-0.300000	0.09419	TGT		0.428	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1	NM_012175		3	24	0	0	0	1	0	3	24				
BMS1P20	96610	broad.mit.edu	37	22	22664141	22664141	+	RNA	SNP	G	G	A	rs369590722		TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr22:22664141G>A	ENST00000426066.1	+	0	664					NR_027293.1				BMS1 pseudogene 20																		AAATTTGAAGGTGCTGTGATT	0.448																																						ENST00000426066.1																			0																																																			0							g.chr22:22664141G>A			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22664141G>A								NR_027293.1						0	664	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.448	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			4	54	0	0	0	1	0	4	54				
DYSF	8291	broad.mit.edu	37	2	71909724	71909724	+	Missense_Mutation	SNP	C	C	T	rs200990851		TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr2:71909724C>T	ENST00000258104.3	+	54	6398	c.6121C>T	c.(6121-6123)Cgg>Tgg	p.R2041W	DYSF_ENST00000410020.3_Missense_Mutation_p.R2080W|DYSF_ENST00000413539.2_Missense_Mutation_p.R2072W|DYSF_ENST00000409366.1_Missense_Mutation_p.R2063W|DYSF_ENST00000394120.2_Missense_Mutation_p.R2042W|DYSF_ENST00000410041.1_Missense_Mutation_p.R2059W|DYSF_ENST00000409651.1_Missense_Mutation_p.R2073W|DYSF_ENST00000409762.1_Missense_Mutation_p.R2058W|DYSF_ENST00000429174.2_Missense_Mutation_p.R2062W|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409744.1_Missense_Mutation_p.R2049W|DYSF_ENST00000409582.3_Missense_Mutation_p.R2079W	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	2041					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CATCCTGTGGCGGCGTTTCCG	0.582																																						ENST00000258104.3																			0				autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						c.(6121-6123)Cgg>Tgg		dysferlin							173.0	125.0	141.0					2																	71909724		2203	4300	6503	SO:0001583	missense	8291					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding	g.chr2:71909724C>T	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.6121C>T	2.37:g.71909724C>T	ENSP00000258104:p.Arg2041Trp					DYSF_ENST00000413539.2_Missense_Mutation_p.R2072W|DYSF_ENST00000409651.1_Missense_Mutation_p.R2073W|DYSF_ENST00000409582.3_Missense_Mutation_p.R2079W|DYSF_ENST00000429174.2_Missense_Mutation_p.R2062W|DYSF_ENST00000410041.1_Missense_Mutation_p.R2059W|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409366.1_Missense_Mutation_p.R2063W|DYSF_ENST00000410020.3_Missense_Mutation_p.R2080W|DYSF_ENST00000394120.2_Missense_Mutation_p.R2042W|DYSF_ENST00000409762.1_Missense_Mutation_p.R2058W|DYSF_ENST00000409744.1_Missense_Mutation_p.R2049W	p.R2041W	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN			54	6398	+			2041					A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	c.6121C>T	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.059284	0.76074	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.84660	-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88	5.1	3.13	0.36017	.	0.050411	0.85682	D	0.000000	D	0.91908	0.7438	M	0.84773	2.715	0.53005	D	0.999969	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.985;1.0;1.0;1.0;1.0;0.999;0.999;0.999;0.995;1.0;0.975;0.982;1.0;1.0;0.999	D	0.92459	0.5976	10	0.87932	D	0	-25.7551	11.4408	0.50096	0.4266:0.5734:0.0:0.0	.	805;2073;2080;2063;2028;2059;2049;2058;2048;2072;2079;2062;2027;2042;2041	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	W	2072;2058;2079;2062;2041;2073;2042;2049;2063;2080;2059	ENSP00000407046:R2072W;ENSP00000387137:R2058W;ENSP00000386547:R2079W;ENSP00000398305:R2062W;ENSP00000258104:R2041W;ENSP00000386683:R2073W;ENSP00000377678:R2042W;ENSP00000386285:R2049W;ENSP00000386512:R2063W;ENSP00000386881:R2080W;ENSP00000386617:R2059W	ENSP00000258104:R2041W	R	+	1	2	DYSF	71763232	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.570000	0.36439	1.220000	0.43490	0.655000	0.94253	CGG		0.582	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		12	68	0	0	0	1	0	12	68				
VWA2	340706	broad.mit.edu	37	10	116045953	116045953	+	Missense_Mutation	SNP	G	G	C	rs147199528		TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr10:116045953G>C	ENST00000392982.3	+	11	1503	c.1253G>C	c.(1252-1254)gGc>gCc	p.G418A	VWA2_ENST00000603594.1_Missense_Mutation_p.G418A			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	418	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		TTCCGTGGTGGCCCCACCCTG	0.672																																						ENST00000603594.1																			0				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26						c.(1252-1254)gGc>gCc		von Willebrand factor A domain containing 2							68.0	62.0	64.0					10																	116045953		2203	4300	6503	SO:0001583	missense	340706					extracellular region		g.chr10:116045953G>C	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.1253G>C	10.37:g.116045953G>C	ENSP00000376708:p.Gly418Ala					VWA2_ENST00000392982.3_Missense_Mutation_p.G418A	p.G418A	NM_001272046.1	NP_001258975.1	Q5GFL6	VWA2_HUMAN		Epithelial(162;0.036)|all cancers(201;0.0793)	11	1574	+			418			VWFA 2.		A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37	c.1253G>C		.	.	.	.	.	.	.	.	.	.	G	26.5	4.744265	0.89663	.	.	ENSG00000165816	ENST00000392982;ENST00000298715	D	0.84660	-1.88	5.6	5.6	0.85130	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.94696	0.8289	M	0.93720	3.45	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.995;1.0;1.0	D	0.95515	0.8589	10	0.72032	D	0.01	.	19.2056	0.93729	0.0:0.0:1.0:0.0	.	114;418;418	Q5GFL6-3;Q5GFL6;Q5GFL6-2	.;VWA2_HUMAN;.	A	418	ENSP00000376708:G418A	ENSP00000298715:G418A	G	+	2	0	VWA2	116035943	1.000000	0.71417	0.991000	0.47740	0.926000	0.56050	9.275000	0.95738	2.625000	0.88918	0.563000	0.77884	GGC		0.672	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496		14	49	0	0	0	1	0	14	49				
TMSB15A	11013	broad.mit.edu	37	X	101770045	101770045	+	Missense_Mutation	SNP	G	G	A			TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chrX:101770045G>A	ENST00000289373.4	-	2	182	c.47C>T	c.(46-48)tCa>tTa	p.S16L		NM_021992.2	NP_068832.1	P0CG34	TB15A_HUMAN	thymosin beta 15a	16					actin cytoskeleton organization (GO:0030036)|sequestering of actin monomers (GO:0042989)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				large_intestine(1)|lung(1)	2						CTTCAGTTTTGACCTGTCAAA	0.368																																						ENST00000289373.4																			0				large_intestine(1)|lung(1)	2						c.(46-48)tCa>tTa		thymosin beta 15a							124.0	117.0	120.0					X																	101770045		2203	4300	6503	SO:0001583	missense	11013				actin cytoskeleton organization|sequestering of actin monomers	cytoplasm|cytoskeleton	actin binding	g.chrX:101770045G>A	D82345	CCDS14498.1	Xq21.33-q22.3	2009-01-12	2009-01-12	2009-01-12	ENSG00000158164	ENSG00000158164			30744	protein-coding gene	gene with protein product		601587	"""thymosin-like 8"""	TMSL8		9039501, 17567946	Standard	NM_021992		Approved	TMSNB	uc004eje.3	P0CG34	OTTHUMG00000022054	ENST00000289373.4:c.47C>T	X.37:g.101770045G>A	ENSP00000289373:p.Ser16Leu						p.S16L	NM_021992.2	NP_068832.1	P0CG34	TB15A_HUMAN			2	182	-			16					A8K614|Q99406	Missense_Mutation	SNP	ENST00000289373.4	37	c.47C>T	CCDS14498.1	.	.	.	.	.	.	.	.	.	.	G	9.202	1.028615	0.19512	.	.	ENSG00000158164	ENST00000289373	T	0.47869	0.83	3.65	1.55	0.23275	.	0.502464	0.13113	N	0.412858	T	0.35335	0.0928	.	.	.	0.22796	N	0.998725	B	0.31949	0.348	B	0.34652	0.187	T	0.30179	-0.9987	9	0.59425	D	0.04	-18.8619	5.0532	0.14520	0.0:0.1854:0.3758:0.4388	.	16	P0CG34	TB15A_HUMAN	L	16	ENSP00000289373:S16L	ENSP00000289373:S16L	S	-	2	0	TMSB15A	101656701	0.993000	0.37304	0.993000	0.49108	0.968000	0.65278	0.398000	0.20899	0.567000	0.29293	0.529000	0.55759	TCA		0.368	TMSB15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057621.1	NM_021992		9	79	0	0	0	1	0	9	79				
IGKV2D-24	28885	broad.mit.edu	37	2	90044429	90044429	+	RNA	SNP	C	C	T			TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr2:90044429C>T	ENST00000462693.1	+	0	380									immunoglobulin kappa variable 2D-24 (non-functional)																		ACGCAAGCTACACAATTTCCT	0.522																																						ENST00000462693.1																			0																				141.0	136.0	137.0					2																	90044429		1919	4124	6043			0							g.chr2:90044429C>T	X63401		2p11.2	2012-02-08	2008-09-10		ENSG00000241566	ENSG00000241566		"""Immunoglobulins / IGK locus"""	5797	other	immunoglobulin gene			"""immunoglobulin kappa variable 2D-24"""				Standard	NG_000833		Approved				OTTHUMG00000151618		2.37:g.90044429C>T														0	380	+									RNA	SNP	ENST00000462693.1	37																																																																																						0.522	IGKV2D-24-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000323290.1	NG_000833		17	90	0	0	0	1	0	17	90				
CSPG4P5	114817	broad.mit.edu	37	15	84957480	84957499	+	RNA	DEL	GGCCCCACATCCATTGAGAA	GGCCCCACATCCATTGAGAA	-	rs554759799|rs529134831|rs548880213	byFrequency	TCGA-DE-A4M8-01A-21D-A257-08	TCGA-DE-A4M8-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21090199-d43b-4ef6-a376-cb3ca837a2e1	f49ebc02-7d89-4558-809e-5ae294a0559b	g.chr15:84957480_84957499delGGCCCCACATCCATTGAGAA	ENST00000558801.1	-	0	7230_7249									DNM1 pseudogene 51																		TGTGTGCACTGGCCCCACATCCATTGAGAAGGCCCCACAT	0.586														762	0.152157	0.146	0.3256	5008	,	,		24353	0.1339		0.1481	False		,,,				2504	0.0603					ENST00000558801.1																			0																																																			0							g.chr15:84957480_84957499delGGCCCCACATCCATTGAGAA			15q25.2	2013-05-16			ENSG00000259297	ENSG00000235370			48500	pseudogene	pseudogene							Standard			Approved				OTTHUMG00000172438		15.37:g.84957480_84957499delGGCCCCACATCCATTGAGAA														0	7230_7249	-									RNA	DEL	ENST00000558801.1	37																																																																																						0.586	DNM1P51-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000471721.1			2	4						2	4	---	---	---	---
