#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
BANP	54971	broad.mit.edu	37	16	88061088	88061088	+	Splice_Site	SNP	G	G	C			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr16:88061088G>C	ENST00000393207.1	+	8	1092		c.e8-1		BANP_ENST00000286122.7_Splice_Site|BANP_ENST00000538234.1_Splice_Site|BANP_ENST00000393208.2_Splice_Site|BANP_ENST00000355022.4_Splice_Site|BANP_ENST00000355163.5_Splice_Site|BANP_ENST00000479780.2_Splice_Site	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein						cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.?(2)		NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		TGTCCTTCCAGGTCACCTTTT	0.612																																						ENST00000393207.1																			2	Unknown(2)	p.?(2)	prostate(2)	NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12						c.e8-1		BTG3 associated nuclear protein							59.0	62.0	61.0					16																	88061088		2198	4300	6498	SO:0001630	splice_region_variant	54971				cell cycle|chromatin modification|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding	g.chr16:88061088G>C	AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"""BEN domain containing"""	13450	protein-coding gene	gene with protein product	"""BEN domain containing 1"""	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.872-1G>C	16.37:g.88061088G>C						BANP_ENST00000538234.1_Splice_Site|BANP_ENST00000479780.2_Splice_Site|BANP_ENST00000393208.2_Splice_Site|BANP_ENST00000286122.7_Splice_Site|BANP_ENST00000355022.4_Splice_Site|BANP_ENST00000355163.5_Splice_Site		NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN		BRCA - Breast invasive adenocarcinoma(80;0.00551)	8	1092	+								A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Splice_Site	SNP	ENST00000393207.1	37		CCDS54054.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.440267	0.43326	.	.	ENSG00000172530	ENST00000286122;ENST00000355163;ENST00000289484;ENST00000479780;ENST00000393208;ENST00000540932;ENST00000355022;ENST00000538234;ENST00000393207	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.3871	0.90470	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BANP	86618589	1.000000	0.71417	1.000000	0.80357	0.187000	0.23431	8.976000	0.93442	2.585000	0.87301	0.462000	0.41574	.		0.612	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869	Intron	10	111	0	0	0	0.361761	0	10	111				
PTCD3	55037	broad.mit.edu	37	2	86360495	86360495	+	Missense_Mutation	SNP	G	G	A	rs369504418		TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr2:86360495G>A	ENST00000254630.7	+	19	1545	c.1479G>A	c.(1477-1479)atG>atA	p.M493I	SNORD94_ENST00000386037.1_RNA	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	493					mitochondrial translation (GO:0032543)|regulation of translation (GO:0006417)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)	p.M493I(1)		NS(1)|breast(2)|endometrium(3)|kidney(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	22						CCCAAACAATGATACATCTTC	0.373																																						ENST00000254630.7																			1	Substitution - Missense(1)	p.M493I(1)	prostate(1)	NS(1)|breast(2)|endometrium(3)|kidney(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	22						c.(1477-1479)atG>atA		pentatricopeptide repeat domain 3							198.0	192.0	194.0					2																	86360495		2203	4300	6503	SO:0001583	missense	55037					mitochondrion	protein binding	g.chr2:86360495G>A		CCDS33235.1	2p11.2	2014-02-12	2012-02-24		ENSG00000132300	ENSG00000132300			24717	protein-coding gene	gene with protein product		614918				8889548	Standard	NM_017952		Approved	FLJ20758, DKFZp666K071	uc002sqw.2	Q96EY7	OTTHUMG00000153168	ENST00000254630.7:c.1479G>A	2.37:g.86360495G>A	ENSP00000254630:p.Met493Ile						p.M493I	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN			19	1545	+			493					A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Missense_Mutation	SNP	ENST00000254630.7	37	c.1479G>A	CCDS33235.1	.	.	.	.	.	.	.	.	.	.	G	11.04	1.521508	0.27211	.	.	ENSG00000132300	ENST00000254630	T	0.31769	1.48	5.88	0.37	0.16160	.	0.428043	0.27105	N	0.020905	T	0.13756	0.0333	N	0.12746	0.255	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.05989	-1.0852	10	0.46703	T	0.11	-2.0956	5.0829	0.14666	0.1307:0.2934:0.4755:0.1004	.	84;493	Q96EY7-2;Q96EY7	.;PTCD3_HUMAN	I	493	ENSP00000254630:M493I	ENSP00000254630:M493I	M	+	3	0	PTCD3	86214006	0.998000	0.40836	0.983000	0.44433	0.971000	0.66376	0.853000	0.27777	0.386000	0.24997	-0.140000	0.14226	ATG		0.373	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952		16	309	0	0	0	0.520397	0	16	309				
COMP	1311	broad.mit.edu	37	19	18898325	18898325	+	Silent	SNP	C	C	G			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr19:18898325C>G	ENST00000222271.2	-	10	1154	c.1110G>C	c.(1108-1110)gcG>gcC	p.A370A	COMP_ENST00000542601.2_Silent_p.A337A|COMP_ENST00000425807.1_Silent_p.A317A	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	370			Missing (in PSACH). {ECO:0000269|PubMed:21922596}.		apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)	p.A370A(1)		breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CGTCGTCGCACGCATCGCCCC	0.697																																						ENST00000542601.2																			1	Substitution - coding silent(1)	p.A370A(1)	prostate(1)	breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						c.(1009-1011)gcG>gcC		cartilage oligomeric matrix protein							149.0	129.0	136.0					19																	18898325		2203	4300	6503	SO:0001819	synonymous_variant	1311				anti-apoptosis|apoptosis|cell adhesion|limb development	extracellular space|proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent|heparan sulfate proteoglycan binding|heparin binding	g.chr19:18898325C>G	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"""thrombospondin-5"""	600310	"""cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"""	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.1110G>C	19.37:g.18898325C>G						COMP_ENST00000425807.1_Silent_p.A317A|COMP_ENST00000222271.2_Silent_p.A370A	p.A337A			P49747	COMP_HUMAN			9	1400	-			370					B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Silent	SNP	ENST00000222271.2	37	c.1011G>C	CCDS12385.1																																																																																				0.697	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095		39	149	0	0	0	0.853193	0	39	149				
USH2A	7399	broad.mit.edu	37	1	215848631	215848631	+	Missense_Mutation	SNP	C	C	T	rs529589990		TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr1:215848631C>T	ENST00000307340.3	-	63	13008	c.12622G>A	c.(12622-12624)Gac>Aac	p.D4208N	USH2A_ENST00000366943.2_Missense_Mutation_p.D4208N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4208	Fibronectin type-III 27. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.D4208N(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ATTTTCTCGTCGGCCTGGATT	0.393										HNSCC(13;0.011)			C|||	1	0.000199681	0.0	0.0	5008	,	,		21149	0.0		0.0	False		,,,				2504	0.001					ENST00000366943.2																			1	Substitution - Missense(1)	p.D4208N(1)	prostate(1)	NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527						c.(12622-12624)Gac>Aac		Usher syndrome 2A (autosomal recessive, mild)							118.0	118.0	118.0					1																	215848631		2203	4300	6503	SO:0001583	missense	7399				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding	g.chr1:215848631C>T	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.12622G>A	1.37:g.215848631C>T	ENSP00000305941:p.Asp4208Asn	HNSCC(13;0.011)				USH2A_ENST00000307340.3_Missense_Mutation_p.D4208N	p.D4208N			O75445	USH2A_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)	63	13008	-			4208			Fibronectin type-III 27.		Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	c.12622G>A	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	3.358	-0.131034	0.06753	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	D;T	0.84589	-1.87;2.49	5.25	1.37	0.22104	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.293134	0.23770	N	0.044724	T	0.76877	0.4049	L	0.43923	1.385	0.09310	N	0.999998	B	0.22211	0.066	B	0.20184	0.028	T	0.63065	-0.6720	10	0.37606	T	0.19	.	8.6272	0.33897	0.0:0.6412:0.0:0.3588	.	4208	O75445	USH2A_HUMAN	N	4208	ENSP00000305941:D4208N;ENSP00000355910:D4208N	ENSP00000305941:D4208N	D	-	1	0	USH2A	213915254	0.000000	0.05858	0.000000	0.03702	0.156000	0.22039	0.053000	0.14184	0.007000	0.14760	-0.133000	0.14855	GAC		0.393	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		44	126	0	0	0	0.870114	0	44	126				
PPP4R1	9989	broad.mit.edu	37	18	9547949	9547949	+	Splice_Site	SNP	G	G	C			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr18:9547949G>C	ENST00000400556.3	-	20	2764	c.2691C>G	c.(2689-2691)gaC>gaG	p.D897E	PPP4R1_ENST00000400555.3_Splice_Site_p.D880E	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	897					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)	p.D897E(1)		large_intestine(1)|skin(2)	3						CCAAGAAATAGTCTGGAAATG	0.478																																					Melanoma(188;1232 2082 5061 11948 35994)	ENST00000400556.3																			1	Substitution - Missense(1)	p.D897E(1)	prostate(1)	large_intestine(1)|skin(2)	3						c.e20-1		protein phosphatase 4, regulatory subunit 1							49.0	51.0	50.0					18																	9547949		2024	4186	6210	SO:0001630	splice_region_variant	9989				protein phosphorylation|signal transduction	protein phosphatase 4 complex	protein binding|protein phosphatase type 4 regulator activity	g.chr18:9547949G>C	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.2690-1C>G	18.37:g.9547949G>C						PPP4R1_ENST00000400555.3_Splice_Site_p.D880_splice	p.D897_splice	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN			20	2764	-			897					Q99774|Q9UNQ7	Splice_Site	SNP	ENST00000400556.3	37	c.2689_splice	CCDS42412.1	.	.	.	.	.	.	.	.	.	.	G	0.215	-1.033565	0.02029	.	.	ENSG00000154845	ENST00000400556;ENST00000400555	T;T	0.32753	1.44;1.44	5.65	-11.3	0.00108	Armadillo-like helical (1);Armadillo-type fold (1);	0.439500	0.25732	N	0.028675	T	0.04588	0.0125	N	0.00742	-1.23	0.09310	N	0.999996	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.24548	-1.0157	9	.	.	.	.	5.0814	0.14659	0.1354:0.4209:0.3:0.1437	.	880;897;880	A8K923;Q8TF05;Q8TF05-2	.;PP4R1_HUMAN;.	E	897;880	ENSP00000383402:D897E;ENSP00000383401:D880E	.	D	-	3	2	PPP4R1	9537949	0.000000	0.05858	0.012000	0.15200	0.961000	0.63080	-3.481000	0.00456	-3.620000	0.00131	-0.467000	0.05162	GAC		0.478	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134	Missense_Mutation	24	41	0	0	0	0.667858	0	24	41				
RORB	6096	broad.mit.edu	37	9	77280437	77280437	+	Missense_Mutation	SNP	G	G	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr9:77280437G>A	ENST00000396204.2	+	7	959	c.959G>A	c.(958-960)cGt>cAt	p.R320H	RORB_ENST00000376896.3_Missense_Mutation_p.R309H			Q92753	RORB_HUMAN	RAR-related orphan receptor B	320	Ligand-binding. {ECO:0000255}.				amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R309H(1)		breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	AGAATGTGCCGTGCCTTCAAC	0.313																																						ENST00000376896.2																			1	Substitution - Missense(1)	p.R309H(1)	prostate(1)	breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12						c.(925-927)cGt>cAt		RAR-related orphan receptor B							171.0	147.0	155.0					9																	77280437		2203	4300	6503	SO:0001583	missense	6096				eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding	g.chr9:77280437G>A	Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"""Nuclear hormone receptors"""	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.959G>A	9.37:g.77280437G>A	ENSP00000379507:p.Arg320His					RORB_ENST00000396204.2_Missense_Mutation_p.R320H	p.R309H	NM_006914.3	NP_008845.2	Q92753	RORB_HUMAN			7	1538	+			320			Ligand-binding (Potential).		Q8WX73	Missense_Mutation	SNP	ENST00000396204.2	37	c.926G>A		.	.	.	.	.	.	.	.	.	.	G	35	5.435942	0.96168	.	.	ENSG00000198963	ENST00000376896;ENST00000396204	D;D	0.96619	-4.07;-4.07	5.92	5.92	0.95590	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.100525	0.64402	D	0.000002	D	0.98469	0.9490	M	0.88181	2.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.992	D	0.98113	1.0421	10	0.45353	T	0.12	.	20.3343	0.98733	0.0:0.0:1.0:0.0	.	320;309	Q92753;Q58EY0	RORB_HUMAN;.	H	309;320	ENSP00000366093:R309H;ENSP00000379507:R320H	ENSP00000366093:R309H	R	+	2	0	RORB	76470257	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.822000	0.97130	0.650000	0.86243	CGT		0.313	RORB-201	KNOWN	basic	protein_coding	protein_coding				54	130	0	0	0	0.870114	0	54	130				
MT-ND5	4540	broad.mit.edu	37	M	13711	13711	+	Missense_Mutation	SNP	G	G	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chrM:13711G>A	ENST00000361567.2	+	1	1375	c.1375G>A	c.(1375-1377)Gcc>Acc	p.A459T	MT-TH_ENST00000387441.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TT_ENST00000387460.2_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	459					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						AACGCCTGGCAGCCGGAAGCC	0.483																																						ENST00000361567.2																			0				breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						c.(1375-1377)Gcc>Acc		mitochondrially encoded NADH dehydrogenase 5	NADH(DB00157)																																			SO:0001583	missense	4540				mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity	g.chrM:13711G>A			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1375G>A	M.37:g.13711G>A	ENSP00000354813:p.Ala459Thr						p.A459T			P03915	NU5M_HUMAN			1	1375	+			459					Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37	c.1375G>A																																																																																					0.483	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036		3	3	0	0	0	0.115264	0	3	3				
MYO18B	84700	broad.mit.edu	37	22	26299697	26299697	+	Missense_Mutation	SNP	G	G	A	rs200295571		TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr22:26299697G>A	ENST00000407587.2	+	31	5219	c.5050G>A	c.(5050-5052)Gtt>Att	p.V1684I	MYO18B_ENST00000536204.1_3'UTR|CTA-125H2.2_ENST00000453457.3_RNA|CTA-125H2.2_ENST00000609157.1_RNA|MYO18B_ENST00000536101.1_Missense_Mutation_p.V1683I|CTA-125H2.2_ENST00000608257.1_RNA|CTA-125H2.2_ENST00000599080.1_RNA|CTA-125H2.2_ENST00000600211.1_RNA|CTA-125H2.2_ENST00000608115.1_RNA|CTA-125H2.2_ENST00000609275.1_RNA|MYO18B_ENST00000335473.7_Missense_Mutation_p.V1683I|CTA-125H2.2_ENST00000597284.1_RNA|CTA-125H2.2_ENST00000609889.1_RNA|CTA-125H2.2_ENST00000609570.1_RNA			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1683	Gln-rich.|Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.V1684I(1)|p.V1683I(1)		NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GGAAAATTGCGTTGCTGGCTT	0.552																																						ENST00000335473.7																			2	Substitution - Missense(2)	p.V1684I(1)|p.V1683I(1)	prostate(2)	NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						c.(5047-5049)Gtt>Att		myosin XVIIIB		G	ILE/VAL	0,3842		0,0,1921	44.0	50.0	48.0		5047	-2.3	0.0	22		48	2,8266		0,2,4132	yes	missense	MYO18B	NM_032608.5	29	0,2,6053	AA,AG,GG		0.0242,0.0,0.0165	benign	1683/2568	26299697	2,12108	1921	4134	6055	SO:0001583	missense	84700					nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity	g.chr22:26299697G>A	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.5050G>A	22.37:g.26299697G>A	ENSP00000386096:p.Val1684Ile					MYO18B_ENST00000536101.1_Missense_Mutation_p.V1683I|MYO18B_ENST00000407587.2_Missense_Mutation_p.V1684I|MYO18B_ENST00000536204.1_3'UTR	p.V1683I	NM_032608.5	NP_115997.5	Q8IUG5	MY18B_HUMAN			31	5297	+			1683			Gln-rich.|Tail.		B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37	c.5047G>A		.	.	.	.	.	.	.	.	.	.	G	5.137	0.210948	0.09757	0.0	2.42E-4	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86694	-2.14;-2.14;-2.16	4.74	-2.29	0.06805	.	0.398450	0.23448	N	0.048073	T	0.73102	0.3544	L	0.38175	1.15	0.09310	N	1	B;B;B;B	0.33826	0.161;0.166;0.427;0.255	B;B;B;B	0.23419	0.04;0.018;0.046;0.04	T	0.61955	-0.6956	10	0.16896	T	0.51	.	9.5074	0.39056	0.4698:0.0:0.5302:0.0	.	1196;1683;1684;1683	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	I	1683;1683;1684	ENSP00000441229:V1683I;ENSP00000334563:V1683I;ENSP00000386096:V1684I	ENSP00000334563:V1683I	V	+	1	0	MYO18B	24629697	0.020000	0.18652	0.000000	0.03702	0.018000	0.09664	0.204000	0.17335	-0.497000	0.06641	-0.150000	0.13652	GTT		0.552	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		11	13	0	0	0	0.387290	0	11	13				
CCDC3	83643	broad.mit.edu	37	10	12940424	12940424	+	Missense_Mutation	SNP	G	G	A	rs571990387		TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr10:12940424G>A	ENST00000378825.3	-	3	931	c.805C>T	c.(805-807)Cgg>Tgg	p.R269W	CCDC3_ENST00000378839.1_Missense_Mutation_p.R144W	NM_031455.3	NP_113643.1	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3	269						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)		p.R269W(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)	11		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			CGTTACCCCCGCAGGTAGGGG	0.637													G|||	1	0.000199681	0.0	0.0014	5008	,	,		13491	0.0		0.0	False		,,,				2504	0.0					ENST00000378839.1																			1	Substitution - Missense(1)	p.R269W(1)	prostate(1)	central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)	11						c.(430-432)Cgg>Tgg		coiled-coil domain containing 3							12.0	15.0	14.0					10																	12940424		1927	3912	5839	SO:0001583	missense	83643					endoplasmic reticulum|extracellular region		g.chr10:12940424G>A	BC051334	CCDS7093.1, CCDS60484.1	10p14	2004-02-13			ENSG00000151468	ENSG00000151468			23813	protein-coding gene	gene with protein product							Standard	NM_031455		Approved	DKFZp761F241	uc001ilq.1	Q9BQI4	OTTHUMG00000017689	ENST00000378825.3:c.805C>T	10.37:g.12940424G>A	ENSP00000368102:p.Arg269Trp					CCDC3_ENST00000378825.3_Missense_Mutation_p.R269W	p.R144W			Q9BQI4	CCDC3_HUMAN	BRCA - Breast invasive adenocarcinoma(52;0.163)		7	1382	-		Ovarian(717;0.0822)	269					Q5VYV8|Q5VYV9	Missense_Mutation	SNP	ENST00000378825.3	37	c.430C>T	CCDS7093.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.570044	0.28003	.	.	ENSG00000151468	ENST00000378839;ENST00000378825	.	.	.	4.78	2.68	0.31781	.	2.023030	0.03384	N	0.200799	T	0.28499	0.0705	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.24728	-1.0152	9	0.87932	D	0	-4.1584	4.8814	0.13681	0.1173:0.0:0.6046:0.2781	.	269	Q9BQI4	CCDC3_HUMAN	W	144;269	.	ENSP00000368102:R269W	R	-	1	2	CCDC3	12980430	0.528000	0.26314	0.285000	0.24819	0.318000	0.28184	0.954000	0.29175	1.177000	0.42855	0.561000	0.74099	CGG		0.637	CCDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046829.1	NM_031455		10	54	0	0	0	0.387290	0	10	54				
C1QTNF7	114905	broad.mit.edu	37	4	15444073	15444073	+	Missense_Mutation	SNP	G	G	A	rs563271263		TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr4:15444073G>A	ENST00000444304.2	+	3	846	c.520G>A	c.(520-522)Gag>Aag	p.E174K	C1QTNF7_ENST00000429690.1_Missense_Mutation_p.E174K|C1QTNF7_ENST00000295297.4_Missense_Mutation_p.E181K			Q9BXJ2	C1QT7_HUMAN	C1q and tumor necrosis factor related protein 7	174	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				protein homooligomerization (GO:0051260)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)		p.E174Q(1)|p.E174K(1)		endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	16						CCTCTTCAACGAGGGAGAGCA	0.443													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20062	0.0		0.0	False		,,,				2504	0.0					ENST00000295297.4																			2	Substitution - Missense(2)	p.E174Q(1)|p.E174K(1)	prostate(1)|lung(1)	endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	16						c.(541-543)Gag>Aag		C1q and tumor necrosis factor related protein 7							160.0	176.0	170.0					4																	15444073		2203	4300	6503	SO:0001583	missense	114905					collagen		g.chr4:15444073G>A	AF329839	CCDS3414.1, CCDS47025.1	4p15.3	2008-08-29			ENSG00000163145	ENSG00000163145			14342	protein-coding gene	gene with protein product							Standard	NM_001135170		Approved	CTRP7	uc003gnp.3	Q9BXJ2	OTTHUMG00000097095	ENST00000444304.2:c.520G>A	4.37:g.15444073G>A	ENSP00000388914:p.Glu174Lys					C1QTNF7_ENST00000429690.1_Missense_Mutation_p.E174K|C1QTNF7_ENST00000444304.2_Missense_Mutation_p.E174K	p.E181K	NM_001135170.1	NP_001128642.1	Q9BXJ2	C1QT7_HUMAN			3	800	+			174			C1q.		B2RBT3|J3KPW3	Missense_Mutation	SNP	ENST00000444304.2	37	c.541G>A	CCDS3414.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.048379	0.93740	.	.	ENSG00000163145	ENST00000295297;ENST00000429690;ENST00000444304	D;D;D	0.85861	-2.04;-2.04;-2.04	5.8	5.8	0.92144	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.054356	0.64402	D	0.000001	D	0.88633	0.6489	M	0.62209	1.925	0.80722	D	1	D	0.61080	0.989	P	0.51833	0.681	D	0.87327	0.2322	9	.	.	.	.	20.0545	0.97645	0.0:0.0:1.0:0.0	.	174	Q9BXJ2	C1QT7_HUMAN	K	181;174;174	ENSP00000295297:E181K;ENSP00000410722:E174K;ENSP00000388914:E174K	.	E	+	1	0	C1QTNF7	15053171	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	9.830000	0.99415	2.748000	0.94277	0.655000	0.94253	GAG		0.443	C1QTNF7-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250891.2			15	486	0	0	0	0.457914	0	15	486				
BSN	8927	broad.mit.edu	37	3	49698154	49698154	+	Missense_Mutation	SNP	G	G	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr3:49698154G>A	ENST00000296452.4	+	6	8990	c.8876G>A	c.(8875-8877)cGc>cAc	p.R2959H		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	2959					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)	p.R2959H(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		ACCAAACTGCGCAAGAAGCAG	0.602																																						ENST00000296452.4																			1	Substitution - Missense(1)	p.R2959H(1)	prostate(1)	breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106						c.(8875-8877)cGc>cAc		bassoon presynaptic cytomatrix protein							29.0	29.0	29.0					3																	49698154		2203	4300	6503	SO:0001583	missense	8927				synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding	g.chr3:49698154G>A	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.8876G>A	3.37:g.49698154G>A	ENSP00000296452:p.Arg2959His						p.R2959H	NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN		BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)	6	8990	+			2959					O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	c.8876G>A	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.813606	0.50527	.	.	ENSG00000164061	ENST00000296452	T	0.50548	0.74	4.4	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.68339	0.2990	M	0.71206	2.165	0.58432	D	0.999997	D	0.89917	1.0	D	0.85130	0.997	T	0.74016	-0.3800	10	0.87932	D	0	-12.2497	16.995	0.86365	0.0:0.0:1.0:0.0	.	2959	Q9UPA5	BSN_HUMAN	H	2959	ENSP00000296452:R2959H	ENSP00000296452:R2959H	R	+	2	0	BSN	49673158	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.818000	0.99354	1.985000	0.57927	0.561000	0.74099	CGC		0.602	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		4	31	0	0	0	0.150653	0	4	31				
PIEZO2	63895	broad.mit.edu	37	18	10671739	10671739	+	Missense_Mutation	SNP	C	C	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr18:10671739C>T	ENST00000503781.3	-	52	8043	c.8044G>A	c.(8044-8046)Ggg>Agg	p.G2682R	PIEZO2_ENST00000538948.1_Missense_Mutation_p.G639R|PIEZO2_ENST00000302079.6_Missense_Mutation_p.G2619R|PIEZO2_ENST00000581680.1_5'UTR|PIEZO2_ENST00000285141.4_Missense_Mutation_p.G474R|PIEZO2_ENST00000580640.1_Missense_Mutation_p.G2707R	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2682					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)	p.G2682R(1)|p.G474R(1)									ACAAATTTCCCAATCACAAGG	0.333																																						ENST00000302079.6																			2	Substitution - Missense(2)	p.G2682R(1)|p.G474R(1)	prostate(2)								c.(7855-7857)Ggg>Agg		piezo-type mechanosensitive ion channel component 2							69.0	71.0	70.0					18																	10671739		2203	4300	6503	SO:0001583	missense	63895					integral to membrane	ion channel activity	g.chr18:10671739C>T	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"""chromosome 18 open reading frame 30"", ""chromosome 18 open reading frame 58"", ""family with sequence similarity 38, member B"""	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.8044G>A	18.37:g.10671739C>T	ENSP00000421377:p.Gly2682Arg					PIEZO2_ENST00000580640.1_Missense_Mutation_p.G2707R|PIEZO2_ENST00000503781.3_Missense_Mutation_p.G2682R|PIEZO2_ENST00000285141.4_Missense_Mutation_p.G474R|PIEZO2_ENST00000538948.1_Missense_Mutation_p.G639R|PIEZO2_ENST00000581680.1_5'UTR	p.G2619R			Q9H5I5	PIEZ2_HUMAN			51	7854	-			2682					B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Missense_Mutation	SNP	ENST00000503781.3	37	c.7855G>A		.	.	.	.	.	.	.	.	.	.	C	23.8	4.460632	0.84317	.	.	ENSG00000154864	ENST00000503781;ENST00000302079;ENST00000538948;ENST00000285141	D;D	0.84146	-1.81;-1.81	4.62	4.62	0.57501	.	0.000000	0.64402	D	0.000001	D	0.93044	0.7786	M	0.85630	2.765	0.46336	D	0.998998	D	0.89917	1.0	D	0.91635	0.999	D	0.94232	0.7477	10	0.87932	D	0	.	17.6336	0.88116	0.0:1.0:0.0:0.0	.	576	D6RFZ0	.	R	576;2682;639;474	ENSP00000443129:G639R;ENSP00000285141:G474R	ENSP00000285141:G474R	G	-	1	0	FAM38B	10661739	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.617000	0.83032	2.409000	0.81822	0.563000	0.77884	GGG		0.333	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068		42	132	0	0	0	0.827153	0	42	132				
RP11-156P1.3	0	broad.mit.edu	37	17	45128792	45128792	+	RNA	SNP	G	G	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr17:45128792G>T	ENST00000575173.1	-	0	418				LRRC37A17P_ENST00000570478.1_RNA																							AATTCAGGTTGTCAGAATGCA	0.373																																						ENST00000575173.1																			0																																																			0							g.chr17:45128792G>T																													17.37:g.45128792G>T														0	418	-									RNA	SNP	ENST00000575173.1	37																																																																																						0.373	RP11-156P1.3-009	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000440924.1			4	79	1	0	0.00909568	0.150653	0.0100843	4	79				
URGCP	55665	broad.mit.edu	37	7	43918497	43918497	+	Missense_Mutation	SNP	C	C	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr7:43918497C>A	ENST00000453200.1	-	6	1058	c.565G>T	c.(565-567)Gcc>Tcc	p.A189S	URGCP_ENST00000447717.3_Missense_Mutation_p.A146S|URGCP_ENST00000497914.1_5'UTR|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000336086.6_Missense_Mutation_p.A146S|URGCP_ENST00000223341.7_Missense_Mutation_p.A146S|URGCP_ENST00000443736.1_Missense_Mutation_p.A146S|URGCP_ENST00000402306.3_Missense_Mutation_p.A180S			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	189					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)	p.A146S(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						AGCAGCAGGGCACAGAGAAGG	0.532																																						ENST00000336086.6																			1	Substitution - Missense(1)	p.A146S(1)	prostate(1)	breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						c.(436-438)Gcc>Tcc		upregulator of cell proliferation							63.0	67.0	66.0					7																	43918497		2036	4195	6231	SO:0001583	missense	55665				cell cycle	centrosome|nucleus	GTP binding	g.chr7:43918497C>A		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"""up-regulated gene 4"""	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.565G>T	7.37:g.43918497C>A	ENSP00000396918:p.Ala189Ser					URGCP_ENST00000447717.3_Missense_Mutation_p.A146S|URGCP_ENST00000497914.1_5'UTR|RP5-1165K10.1_ENST00000603700.1_Intron|URGCP_ENST00000223341.7_Missense_Mutation_p.A146S|URGCP_ENST00000402306.3_Missense_Mutation_p.A180S|URGCP_ENST00000453200.1_Missense_Mutation_p.A189S|URGCP_ENST00000443736.1_Missense_Mutation_p.A146S	p.A146S			Q8TCY9	URGCP_HUMAN			4	2672	-			189					E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Missense_Mutation	SNP	ENST00000453200.1	37	c.436G>T	CCDS47578.1	.	.	.	.	.	.	.	.	.	.	C	19.53	3.844624	0.71488	.	.	ENSG00000106608	ENST00000223341;ENST00000336086;ENST00000402306;ENST00000443736;ENST00000453200;ENST00000447717;ENST00000426198	T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.66	4.78	0.61160	.	0.174257	0.49305	D	0.000142	T	0.53302	0.1788	M	0.80982	2.52	0.33487	D	0.588266	P;P	0.41673	0.759;0.759	B;B	0.41860	0.368;0.368	T	0.71337	-0.4623	10	0.62326	D	0.03	-29.2336	12.3081	0.54914	0.0:0.9178:0.0:0.0822	.	180;189	Q8TCY9-2;Q8TCY9	.;URGCP_HUMAN	S	146;146;180;146;189;146;146	ENSP00000223341:A146S;ENSP00000336872:A146S;ENSP00000384955:A180S;ENSP00000392136:A146S;ENSP00000396918:A189S;ENSP00000402803:A146S;ENSP00000389990:A146S	ENSP00000223341:A146S	A	-	1	0	URGCP	43885022	0.998000	0.40836	0.997000	0.53966	0.971000	0.66376	3.731000	0.55013	1.403000	0.46800	0.591000	0.81541	GCC		0.532	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		21	54	1	0	3.73194e-20	0.592651	4.42625e-20	21	54				
PIK3CA	5290	broad.mit.edu	37	3	178927980	178927980	+	Missense_Mutation	SNP	T	T	C	rs121913272		TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr3:178927980T>C	ENST00000263967.3	+	8	1415	c.1258T>C	c.(1258-1260)Tgt>Cgt	p.C420R		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	420	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.		C -> R (in CLOVE and CRC; shows an increase in lipid kinase activity; may increase the affinity for lipid membranes). {ECO:0000269|PubMed:22658544}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.C420R(40)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TAAGGAACACTGTCCATTGGC	0.328	C420R(CCK81_LARGE_INTESTINE)|C420R(EFM192A_BREAST)|C420R(HEC151_ENDOMETRIUM)|C420R(OVISE_OVARY)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	ENST00000263967.3	C420R(CCK81_LARGE_INTESTINE)|C420R(EFM192A_BREAST)|C420R(HEC151_ENDOMETRIUM)|C420R(OVISE_OVARY)	57		Dom	yes		3	3q26.3	5290	Mis	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			"""E, O"""			"""colorectal, gastric, gliobastoma, breast"""		40	Substitution - Missense(40)	p.C420R(40)	breast(15)|large_intestine(10)|endometrium(7)|central_nervous_system(2)|lung(2)|prostate(2)|stomach(1)|NS(1)	NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269						c.(1258-1260)Tgt>Cgt		phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha							85.0	80.0	82.0					3																	178927980		1822	4078	5900	SO:0001583	missense	5290				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	g.chr3:178927980T>C		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1258T>C	3.37:g.178927980T>C	ENSP00000263967:p.Cys420Arg	HNSCC(19;0.045)|TSP Lung(28;0.18)					p.C420R	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		8	1415	+	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		420		C -> R (in cancer; shows an increase in lipid kinase activity; may increase the affinity for lipid membranes).	C2 PI3K-type.		Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	c.1258T>C	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	T	19.97	3.925687	0.73213	.	.	ENSG00000121879	ENST00000263967	T	0.68903	-0.36	5.51	5.51	0.81932	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.000000	0.85682	D	0.000000	T	0.76856	0.4046	M	0.61703	1.905	0.80722	D	1	D	0.69078	0.997	P	0.62885	0.908	T	0.74284	-0.3715	10	0.25751	T	0.34	-11.2314	15.6207	0.76805	0.0:0.0:0.0:1.0	.	420	P42336	PK3CA_HUMAN	R	420	ENSP00000263967:C420R	ENSP00000263967:C420R	C	+	1	0	PIK3CA	180410674	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	7.698000	0.84413	2.105000	0.64084	0.460000	0.39030	TGT		0.328	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			5	205	0	0	0	0.217242	0	5	205				
LRRTM4	80059	broad.mit.edu	37	2	76975914	76975914	+	Silent	SNP	G	G	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr2:76975914G>A	ENST00000409093.1	-	4	2016	c.1680C>T	c.(1678-1680)agC>agT	p.S560S	LRRTM4_ENST00000409884.1_Silent_p.S560S|LRRTM4_ENST00000409911.1_Silent_p.S561S			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	560					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|regulation of presynaptic membrane organization (GO:1901629)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)		p.S560S(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64				Colorectal(11;0.059)		CCAGGCCGGGGCTTTCGTCCT	0.587																																						ENST00000409911.1																			1	Substitution - coding silent(1)	p.S560S(1)	prostate(1)	autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64						c.(1681-1683)agC>agT		leucine rich repeat transmembrane neuronal 4							115.0	108.0	110.0					2																	76975914		1568	3582	5150	SO:0001819	synonymous_variant	80059					integral to membrane		g.chr2:76975914G>A	AK122612	CCDS46346.1, CCDS46347.1, CCDS74530.1	2p12	2008-02-05			ENSG00000176204	ENSG00000176204			19411	protein-coding gene	gene with protein product		610870				12676565	Standard	NM_024993		Approved	FLJ12568	uc002snr.3	Q86VH4	OTTHUMG00000152842	ENST00000409093.1:c.1680C>T	2.37:g.76975914G>A						LRRTM4_ENST00000409093.1_Silent_p.S560S|LRRTM4_ENST00000409884.1_Silent_p.S560S	p.S561S	NM_001134745.1	NP_001128217.1	Q86VH4	LRRT4_HUMAN		Colorectal(11;0.059)	3	1906	-			560					Q4FZ98|Q6UXJ7	Silent	SNP	ENST00000409093.1	37	c.1683C>T	CCDS46346.1																																																																																				0.587	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		54	165	0	0	0	0.870114	0	54	165				
RREB1	6239	broad.mit.edu	37	6	7230059	7230059	+	Missense_Mutation	SNP	G	G	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr6:7230059G>A	ENST00000349384.6	+	10	2041	c.1727G>A	c.(1726-1728)cGg>cAg	p.R576Q	RREB1_ENST00000379938.2_Missense_Mutation_p.R576Q|RREB1_ENST00000334984.6_Missense_Mutation_p.R576Q|RREB1_ENST00000379933.3_Missense_Mutation_p.R576Q	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	576					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R576Q(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GCGGCCACGCGGCTCTCCCTG	0.711																																						ENST00000379938.2																			1	Substitution - Missense(1)	p.R576Q(1)	prostate(1)	breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						c.(1726-1728)cGg>cAg		ras responsive element binding protein 1							8.0	9.0	9.0					6																	7230059		2046	4073	6119	SO:0001583	missense	6239				multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding	g.chr6:7230059G>A	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.1727G>A	6.37:g.7230059G>A	ENSP00000305560:p.Arg576Gln					RREB1_ENST00000334984.6_Missense_Mutation_p.R576Q|RREB1_ENST00000379933.3_Missense_Mutation_p.R576Q|RREB1_ENST00000349384.6_Missense_Mutation_p.R576Q	p.R576Q	NM_001003699.3|NM_001003700.1	NP_001003699.1|NP_001003700.1	Q92766	RREB1_HUMAN			10	2264	+	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)	576					A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	c.1727G>A	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.629014	0.00813	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984;ENST00000483150	T;T;T;T;T	0.10099	3.05;3.01;3.05;2.91;3.0	5.27	0.0902	0.14462	.	.	.	.	.	T	0.00695	0.0023	N	0.00926	-1.1	0.25388	N	0.98855	B;B;B	0.10296	0.001;0.001;0.003	B;B;B	0.04013	0.0;0.0;0.001	T	0.46652	-0.9176	9	0.09590	T	0.72	-17.5151	5.7871	0.18338	0.5923:0.2652:0.1425:0.0	.	576;576;576	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	Q	576	ENSP00000369265:R576Q;ENSP00000369270:R576Q;ENSP00000305560:R576Q;ENSP00000335574:R576Q;ENSP00000419511:R576Q	ENSP00000335574:R576Q	R	+	2	0	RREB1	7175058	1.000000	0.71417	0.527000	0.27925	0.225000	0.24961	2.810000	0.47979	-0.113000	0.11958	-1.058000	0.02302	CGG		0.711	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			4	13	0	0	0	0.335167	0	4	13				
SSR3	6747	broad.mit.edu	37	3	156266713	156266713	+	Missense_Mutation	SNP	G	G	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr3:156266713G>A	ENST00000265044.2	-	3	434	c.340C>T	c.(340-342)Cgg>Tgg	p.R114W	SSR3_ENST00000478842.1_5'UTR|SSR3_ENST00000463503.1_Missense_Mutation_p.R62W|SSR3_ENST00000496050.1_Missense_Mutation_p.R62W|SSR3_ENST00000467789.1_Missense_Mutation_p.R114W|SSR3_ENST00000476217.1_Missense_Mutation_p.R114W	NM_007107.3	NP_009038.1	Q9UNL2	SSRG_HUMAN	signal sequence receptor, gamma (translocon-associated protein gamma)	114					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	integral component of endoplasmic reticulum membrane (GO:0030176)|Sec61 translocon complex (GO:0005784)		p.R114W(1)		endometrium(1)|prostate(2)	3			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TTCTCCTTCCGAGACATCTTT	0.363																																						ENST00000265044.2																			1	Substitution - Missense(1)	p.R114W(1)	prostate(1)	endometrium(1)|prostate(2)	3						c.(340-342)Cgg>Tgg		signal sequence receptor, gamma (translocon-associated protein gamma)							90.0	88.0	89.0					3																	156266713		2203	4300	6503	SO:0001583	missense	6747				cotranslational protein targeting to membrane	integral to endoplasmic reticulum membrane|microsome|Sec61 translocon complex	protein binding|signal sequence binding	g.chr3:156266713G>A	BC017203	CCDS3176.1	3q25.31	2004-02-27			ENSG00000114850	ENSG00000114850			11325	protein-coding gene	gene with protein product		606213					Standard	NM_007107		Approved	TRAPG	uc003fau.3	Q9UNL2	OTTHUMG00000158632	ENST00000265044.2:c.340C>T	3.37:g.156266713G>A	ENSP00000265044:p.Arg114Trp					SSR3_ENST00000496050.1_Missense_Mutation_p.R62W|SSR3_ENST00000478842.1_5'UTR|SSR3_ENST00000467789.1_Missense_Mutation_p.R114W|SSR3_ENST00000463503.1_Missense_Mutation_p.R62W|SSR3_ENST00000476217.1_Missense_Mutation_p.R114W	p.R114W	NM_007107.3	NP_009038.1	Q9UNL2	SSRG_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)		3	434	-			114					B2R7D0|B4E2P2|D3DNK5|Q549M4	Missense_Mutation	SNP	ENST00000265044.2	37	c.340C>T	CCDS3176.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.980214	0.74474	.	.	ENSG00000114850	ENST00000265044;ENST00000467789;ENST00000476217;ENST00000463503;ENST00000496050	.	.	.	5.41	4.53	0.55603	.	0.116472	0.64402	D	0.000018	T	0.72407	0.3456	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.983	T	0.74847	-0.3525	9	0.87932	D	0	-11.8151	9.1524	0.36971	0.0736:0.0:0.7808:0.1456	.	114;114	B4E2P2;Q9UNL2	.;SSRG_HUMAN	W	114;114;114;62;62	.	ENSP00000265044:R114W	R	-	1	2	SSR3	157749407	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.299000	0.72770	1.407000	0.46875	0.650000	0.86243	CGG		0.363	SSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351521.1	NM_007107		24	82	0	0	0	0.654019	0	24	82				
SAMSN1	64092	broad.mit.edu	37	21	15884893	15884893	+	Splice_Site	SNP	T	T	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr21:15884893T>A	ENST00000400566.1	-	4	362	c.281A>T	c.(280-282)gAt>gTt	p.D94V	SAMSN1_ENST00000285670.2_Splice_Site_p.D162V|SAMSN1_ENST00000400564.1_Intron	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	94					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)	p.D162V(1)|p.D94V(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		ATCTTCCTCATCCTTCAGAAA	0.413																																						ENST00000285670.2																			2	Substitution - Missense(2)	p.D162V(1)|p.D94V(1)	prostate(2)	breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24						c.e5-1		SAM domain, SH3 domain and nuclear localization signals 1							143.0	137.0	139.0					21																	15884893		1891	4114	6005	SO:0001630	splice_region_variant	64092				negative regulation of adaptive immune response|negative regulation of B cell activation|negative regulation of peptidyl-tyrosine phosphorylation	cytoplasm|nucleus|ruffle	phosphotyrosine binding	g.chr21:15884893T>A	AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	10528	protein-coding gene	gene with protein product	"""nuclear localization signals, SAM and SH3 domain containing 1"", ""SAM and SH3 domain containing 2"", ""hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1"", ""Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"""	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.280-1A>T	21.37:g.15884893T>A						SAMSN1_ENST00000400564.1_Intron|SAMSN1_ENST00000400566.1_Splice_Site_p.D94_splice	p.D162_splice	NM_001256370.1	NP_001243299.1	Q9NSI8	SAMN1_HUMAN		Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)	5	659	-			94					B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Splice_Site	SNP	ENST00000400566.1	37	c.483_splice	CCDS42906.1	.	.	.	.	.	.	.	.	.	.	T	14.17	2.456559	0.43634	.	.	ENSG00000155307	ENST00000285670;ENST00000400566	T;T	0.42131	0.98;0.98	5.72	3.37	0.38596	.	0.740767	0.12951	N	0.425791	T	0.35008	0.0917	L	0.44542	1.39	0.42829	D	0.994018	P;P	0.41848	0.763;0.629	B;B	0.39771	0.293;0.309	T	0.02553	-1.1142	10	0.32370	T	0.25	-8.4809	9.8056	0.40791	0.0:0.1406:0.0:0.8594	.	162;94	F8WAA1;Q9NSI8	.;SAMN1_HUMAN	V	162;94	ENSP00000285670:D162V;ENSP00000383411:D94V	ENSP00000285670:D162V	D	-	2	0	SAMSN1	14806764	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.182000	0.50910	0.447000	0.26695	0.528000	0.53228	GAT		0.413	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1		Missense_Mutation	55	146	0	0	0	0.870114	0	55	146				
ACER3	55331	broad.mit.edu	37	11	76730798	76730798	+	Missense_Mutation	SNP	T	T	G			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr11:76730798T>G	ENST00000532485.1	+	10	832	c.728T>G	c.(727-729)cTg>cGg	p.L243R	ACER3_ENST00000526597.1_Missense_Mutation_p.L148R|ACER3_ENST00000538157.1_Missense_Mutation_p.L201R|ACER3_ENST00000533873.1_Missense_Mutation_p.L206R|ACER3_ENST00000544113.1_Missense_Mutation_p.L110R	NM_018367.5	NP_060837.3	Q9NUN7	ACER3_HUMAN	alkaline ceramidase 3	243					ceramide metabolic process (GO:0006672)|phytosphingosine biosynthetic process (GO:0071602)|positive regulation of cell proliferation (GO:0008284)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of Golgi membrane (GO:0030173)	phytoceramidase activity (GO:0070774)	p.L243R(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	9						ACACTTTACCTGAGATATAGG	0.428																																						ENST00000532485.1																			1	Substitution - Missense(1)	p.L243R(1)	prostate(1)	endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	9						c.(727-729)cTg>cGg		alkaline ceramidase 3							195.0	172.0	180.0					11																	76730798		2200	4292	6492	SO:0001583	missense	55331				ceramide metabolic process|phytosphingosine biosynthetic process|positive regulation of cell proliferation|sphingosine biosynthetic process	integral to endoplasmic reticulum membrane|integral to Golgi membrane	phytoceramidase activity	g.chr11:76730798T>G	AF214454	CCDS8247.1, CCDS73352.1	11q13.5	2013-01-25	2008-12-19	2008-12-19	ENSG00000078124	ENSG00000078124	3.5.1.23	"""Alkaline ceramidase"""	16066	protein-coding gene	gene with protein product	"""alkaline phytoceramidase"""		"""phytoceramidase, alkaline"""	PHCA		11356846, 18619555	Standard	XM_005274090		Approved	FLJ11238, APHC	uc009yum.1	Q9NUN7	OTTHUMG00000165225	ENST00000532485.1:c.728T>G	11.37:g.76730798T>G	ENSP00000434480:p.Leu243Arg					ACER3_ENST00000538157.1_Missense_Mutation_p.L201R|ACER3_ENST00000526597.1_Missense_Mutation_p.L148R|ACER3_ENST00000533873.1_Missense_Mutation_p.L206R|ACER3_ENST00000544113.1_Missense_Mutation_p.L110R	p.L243R	NM_018367.5	NP_060837.3	Q9NUN7	ACER3_HUMAN			10	832	+			243					B2RC99	Missense_Mutation	SNP	ENST00000532485.1	37	c.728T>G	CCDS8247.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.176065	0.78564	.	.	ENSG00000078124	ENST00000534206;ENST00000532485;ENST00000526597;ENST00000533873;ENST00000538157;ENST00000544113	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	6.06	6.06	0.98353	.	0.165032	0.41500	D	0.000879	T	0.57902	0.2085	L	0.60845	1.875	0.50632	D	0.999888	D;D	0.89917	0.999;1.0	D;D	0.81914	0.986;0.995	T	0.52290	-0.8595	10	0.15066	T	0.55	-6.5932	14.578	0.68265	0.0:0.0:0.0:1.0	.	206;243	B7Z2Q2;Q9NUN7	.;ACER3_HUMAN	R	201;243;148;206;201;110	ENSP00000434480:L243R;ENSP00000431149:L148R;ENSP00000436252:L206R;ENSP00000440916:L201R;ENSP00000440663:L110R	ENSP00000431149:L148R	L	+	2	0	ACER3	76408446	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.620000	0.67736	2.327000	0.79052	0.533000	0.62120	CTG		0.428	ACER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382770.2	NM_018367		35	193	0	0	0	0.804634	0	35	193				
RBPMS2	348093	broad.mit.edu	37	15	65041630	65041630	+	Splice_Site	SNP	G	G	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr15:65041630G>A	ENST00000300069.4	-	4	534	c.267C>T	c.(265-267)aaC>aaT	p.N89N	RBPMS2_ENST00000560606.1_De_novo_Start_OutOfFrame	NM_194272.1	NP_919248.1	Q6ZRY4	RBPS2_HUMAN	RNA binding protein with multiple splicing 2	89	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)	p.N89N(1)		breast(1)|large_intestine(3)|lung(3)|prostate(1)	8						ACCTACTCACGTTCAGCGCAT	0.512																																						ENST00000560606.1																			1	Substitution - coding silent(1)	p.N89N(1)	prostate(1)	breast(1)|large_intestine(3)|lung(3)|prostate(1)	8								RNA binding protein with multiple splicing 2							178.0	157.0	164.0					15																	65041630		2202	4299	6501	SO:0001630	splice_region_variant	348093						nucleic acid binding|nucleotide binding	g.chr15:65041630G>A	AY369207	CCDS32271.1	15q22.31	2014-05-15			ENSG00000166831	ENSG00000166831		"""RNA binding motif (RRM) containing"""	19098	protein-coding gene	gene with protein product							Standard	NM_194272		Approved		uc002anq.3	Q6ZRY4	OTTHUMG00000172423	ENST00000300069.4:c.267+1C>T	15.37:g.65041630G>A						RBPMS2_ENST00000300069.4_Splice_Site_p.N89_splice				Q6ZRY4	RBPS2_HUMAN			0	266	-								A2RRG0	Translation_Start_Site	SNP	ENST00000300069.4	37		CCDS32271.1																																																																																				0.512	RBPMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418466.1		Silent	30	113	0	0	0	0.740014	0	30	113				
MTHFR	4524	broad.mit.edu	37	1	11855381	11855381	+	Missense_Mutation	SNP	C	C	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr1:11855381C>T	ENST00000376592.1	-	5	933	c.805G>A	c.(805-807)Gtg>Atg	p.V269M	MTHFR_ENST00000376585.1_Missense_Mutation_p.V310M|MTHFR_ENST00000376583.3_Missense_Mutation_p.V310M|MTHFR_ENST00000376590.3_Missense_Mutation_p.V269M			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	269					blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)	p.V269M(1)		NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	GACAGCTTCACAAGCTGCCGA	0.582																																						ENST00000376592.1																			1	Substitution - Missense(1)	p.V269M(1)	prostate(1)	NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33						c.(805-807)Gtg>Atg		methylenetetrahydrofolate reductase (NAD(P)H)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)						57.0	55.0	56.0					1																	11855381		2203	4300	6503	SO:0001583	missense	4524				blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding	g.chr1:11855381C>T	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.805G>A	1.37:g.11855381C>T	ENSP00000365777:p.Val269Met					MTHFR_ENST00000376583.3_Missense_Mutation_p.V310M|MTHFR_ENST00000376585.1_Missense_Mutation_p.V310M|MTHFR_ENST00000376590.3_Missense_Mutation_p.V269M	p.V269M			P42898	MTHR_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	5	933	-	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	269					B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	37	c.805G>A	CCDS137.1	.	.	.	.	.	.	.	.	.	.	C	32	5.135827	0.94517	.	.	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	D;D;D;D	0.91577	-2.87;-2.87;-2.87;-2.87	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	D	0.92714	0.7684	L	0.55017	1.72	0.80722	D	1	P;P	0.50710	0.851;0.938	P;P	0.55824	0.646;0.785	D	0.93552	0.6887	10	0.72032	D	0.01	.	17.2839	0.87136	0.0:1.0:0.0:0.0	.	269;310	P42898;Q5SNW6	MTHR_HUMAN;.	M	269;310;269;310	ENSP00000365777:V269M;ENSP00000365767:V310M;ENSP00000365775:V269M;ENSP00000365770:V310M	ENSP00000365767:V310M	V	-	1	0	MTHFR	11777968	1.000000	0.71417	0.971000	0.41717	0.995000	0.86356	5.405000	0.66351	2.385000	0.81259	0.561000	0.74099	GTG		0.582	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957		19	44	0	0	0	0.624587	0	19	44				
KIF16B	55614	broad.mit.edu	37	20	16347999	16347999	+	Intron	SNP	A	A	C			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr20:16347999A>C	ENST00000354981.2	-	22	3656				KIF16B_ENST00000378003.2_Intron|KIF16B_ENST00000355755.3_Intron|KIF16B_ENST00000408042.1_Missense_Mutation_p.V1324G	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B						ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)	p.V1324G(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						GACTAGTTCTACTGTTGACAC	0.433																																						ENST00000408042.1																			1	Substitution - Missense(1)	p.V1324G(1)	prostate(1)	NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						c.(3970-3972)gTa>gGa		kinesin family member 16B							253.0	239.0	243.0					20																	16347999		876	1991	2867	SO:0001627	intron_variant	55614				cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity	g.chr20:16347999A>C	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.3498+3231T>G	20.37:g.16347999A>C						KIF16B_ENST00000378003.2_Intron|KIF16B_ENST00000355755.3_Intron|KIF16B_ENST00000354981.2_Intron	p.V1324G	NM_001199866.1	NP_001186795.1	Q96L93	KI16B_HUMAN			23	4128	-			0					A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	37	c.3971T>G	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.259946	0.59321	.	.	ENSG00000089177	ENST00000408042	T	0.76316	-1.01	5.5	5.5	0.81552	.	0.685736	0.12358	N	0.475933	D	0.83087	0.5178	.	.	.	0.80722	D	1	D	0.53885	0.963	P	0.50754	0.649	D	0.83490	0.0069	9	0.87932	D	0	.	15.598	0.76602	1.0:0.0:0.0:0.0	.	1324	Q96L93-2	.	G	1324	ENSP00000384164:V1324G	ENSP00000384164:V1324G	V	-	2	0	KIF16B	16295999	0.218000	0.23608	0.005000	0.12908	0.412000	0.31113	4.635000	0.61332	2.084000	0.62774	0.445000	0.29226	GTA		0.433	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		47	295	0	0	0	0.870114	0	47	295				
RP11-156P1.3	0	broad.mit.edu	37	17	45128812	45128812	+	RNA	SNP	C	C	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr17:45128812C>T	ENST00000575173.1	-	0	418				LRRC37A17P_ENST00000570478.1_RNA																							AGTCCTGTTTCTGTGTGGATT	0.373																																						ENST00000575173.1																			0																																																			0							g.chr17:45128812C>T																													17.37:g.45128812C>T														0	418	-									RNA	SNP	ENST00000575173.1	37																																																																																						0.373	RP11-156P1.3-009	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000440924.1			3	65	0	0	0	0.115264	0	3	65				
JPH2	57158	broad.mit.edu	37	20	42788455	42788455	+	Silent	SNP	G	G	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr20:42788455G>A	ENST00000372980.3	-	2	1844	c.972C>T	c.(970-972)caC>caT	p.H324H		NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	324					calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)	p.H324H(2)		NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			AGCCATAGCCGTGGCGCAGGT	0.662																																						ENST00000372980.3																			2	Substitution - coding silent(2)	p.H324H(2)	prostate(1)|endometrium(1)	NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32						c.(970-972)caC>caT		junctophilin 2							50.0	43.0	46.0					20																	42788455		2203	4299	6502	SO:0001819	synonymous_variant	57158				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane		g.chr20:42788455G>A	AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.972C>T	20.37:g.42788455G>A							p.H324H	NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	COAD - Colon adenocarcinoma(18;0.00189)		2	1844	-		Myeloproliferative disorder(115;0.0122)	324					E1P5X1|O95913|Q5JY74|Q9UJN4	Silent	SNP	ENST00000372980.3	37	c.972C>T	CCDS13325.1																																																																																				0.662	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1			4	13	0	0	0	0.387290	0	4	13				
OSGIN1	29948	broad.mit.edu	37	16	83999180	83999180	+	Silent	SNP	C	C	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr16:83999180C>T	ENST00000343939.2	+	7	1634	c.1251C>T	c.(1249-1251)taC>taT	p.Y417Y	OSGIN1_ENST00000393306.1_Silent_p.Y334Y|OSGIN1_ENST00000361711.3_Silent_p.Y334Y			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	417					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)	p.Y417Y(1)		autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						AGATGCTGTACCCCGAGTACC	0.637																																						ENST00000343939.2																			1	Substitution - coding silent(1)	p.Y417Y(1)	prostate(1)	autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						c.(1249-1251)taC>taT		oxidative stress induced growth inhibitor 1							63.0	58.0	60.0					16																	83999180		2200	4300	6500	SO:0001819	synonymous_variant	29948				cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity	g.chr16:83999180C>T	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"""bone marrow stromal cell-derived growth inhibitor"", ""pregnancy induced growth inhibitor"""	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.1251C>T	16.37:g.83999180C>T						OSGIN1_ENST00000361711.3_Silent_p.Y334Y|OSGIN1_ENST00000393306.1_Silent_p.Y334Y	p.Y417Y			Q9UJX0	OSGI1_HUMAN			7	1634	+			417					Q52M33|Q86UQ1|Q96S88|Q9BZ70	Silent	SNP	ENST00000343939.2	37	c.1251C>T																																																																																					0.637	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		22	62	0	0	0	0.608945	0	22	62				
CBFA2T3	863	broad.mit.edu	37	16	88967911	88967911	+	Splice_Site	SNP	C	C	A			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr16:88967911C>A	ENST00000268679.4	-	2	701		c.e2+1		CBFA2T3_ENST00000448839.1_Intron|CBFA2T3_ENST00000436887.2_Splice_Site|CBFA2T3_ENST00000360302.2_Splice_Site|CBFA2T3_ENST00000327483.5_Splice_Site	NM_005187.5	NP_005178.4	O75081	MTG16_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 3						cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0275)		GGGCTACTTACGTGTGTGTGG	0.677			T	RUNX1	AML																																	ENST00000268679.4				Dom	yes		16	16q24	863	T	"""core-binding factor, runt domain, alpha subunit 2; translocated to, 3 (MTG-16)"""			L	RUNX1		AML		1	Unknown(1)	p.?(1)	prostate(1)	endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17						c.e2+1		core-binding factor, runt domain, alpha subunit 2; translocated to, 3							16.0	21.0	19.0					16																	88967911		2178	4279	6457	SO:0001630	splice_region_variant	863				cell proliferation|granulocyte differentiation	Golgi membrane|nucleolus|nucleoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr16:88967911C>A	AF052213	CCDS10972.1, CCDS10973.1	16q24	2013-10-16			ENSG00000129993	ENSG00000129993		"""Zinc fingers, MYND-type"", ""A-kinase anchor proteins"""	1537	protein-coding gene	gene with protein product	"""myeloid translocation gene 8 and 16b"""	603870				9790752, 20150326	Standard	NM_005187		Approved	MTGR2, ZMYND4, MTG16	uc002fmm.2	O75081	OTTHUMG00000137864	ENST00000268679.4:c.304+1G>T	16.37:g.88967911C>A						CBFA2T3_ENST00000448839.1_Intron|CBFA2T3_ENST00000436887.2_Splice_Site|CBFA2T3_ENST00000360302.2_Splice_Site|CBFA2T3_ENST00000327483.5_Splice_Site		NM_005187.5	NP_005178.4	O75081	MTG16_HUMAN		BRCA - Breast invasive adenocarcinoma(80;0.0275)	2	701	-								D3DX78|O60615|O60616|O60617|O75082|O75107|O75108|Q0P5Z6|Q6P5W6	Splice_Site	SNP	ENST00000268679.4	37		CCDS10972.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.376209	0.61735	.	.	ENSG00000129993	ENST00000327483;ENST00000268679;ENST00000436887;ENST00000360302	.	.	.	3.95	3.95	0.45737	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9453	0.79789	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CBFA2T3	87495412	1.000000	0.71417	0.998000	0.56505	0.742000	0.42306	7.500000	0.81588	1.918000	0.55548	0.491000	0.48974	.		0.677	CBFA2T3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269545.2	NM_005187	Intron	10	40	1	0	9.31168e-06	0.435327	1.05532e-05	10	40				
XK	7504	broad.mit.edu	37	X	37553558	37553558	+	Missense_Mutation	SNP	A	A	G			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chrX:37553558A>G	ENST00000378616.3	+	2	468	c.265A>G	c.(265-267)Atc>Gtc	p.I89V	TM4SF2_ENST00000465127.1_Intron	NM_021083.2	NP_066569.1	P51811	XK_HUMAN	X-linked Kx blood group	89					amino acid transport (GO:0006865)|transport (GO:0006810)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.I89V(1)		breast(1)|endometrium(4)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15		all_lung(315;0.175)				AGTCTTCTGCATCTACTTTCA	0.408																																						ENST00000378616.3																			1	Substitution - Missense(1)	p.I89V(1)	prostate(1)	breast(1)|endometrium(4)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15						c.(265-267)Atc>Gtc		X-linked Kx blood group (McLeod syndrome)							76.0	62.0	67.0					X																	37553558		2202	4300	6502	SO:0001583	missense	7504				amino acid transport	integral to membrane	protein binding|transporter activity	g.chrX:37553558A>G	Z32684	CCDS14241.1	Xp21.1	2014-07-19	2014-06-18		ENSG00000047597	ENSG00000047597		"""Blood group antigens"""	12811	protein-coding gene	gene with protein product	"""Kx antigen"", ""McLeod syndrome"""	314850	"""Kell blood group precursor (McLeod phenotype)"", ""XK, Kell blood group complex subunit (McLeod syndrome)"", ""neuroacanthocytosis"", ""neurocanthocytosis"""	NA, NAC		8004674, 11761473	Standard	NM_021083		Approved	XKR1, Kx, X1k	uc004ddq.3	P51811	OTTHUMG00000033171	ENST00000378616.3:c.265A>G	X.37:g.37553558A>G	ENSP00000367879:p.Ile89Val					TM4SF2_ENST00000465127.1_Intron	p.I89V	NM_021083.2	NP_066569.1	P51811	XK_HUMAN			2	468	+		all_lung(315;0.175)	89					Q4TTN6|Q8IUK6|Q9UC77	Missense_Mutation	SNP	ENST00000378616.3	37	c.265A>G	CCDS14241.1	.	.	.	.	.	.	.	.	.	.	A	8.709	0.911691	0.17833	.	.	ENSG00000047597	ENST00000378616	T	0.62364	0.03	6.04	2.12	0.27331	.	0.046090	0.85682	D	0.000000	T	0.53658	0.1810	L	0.43152	1.355	0.53005	D	0.999967	B	0.25169	0.119	B	0.33392	0.163	T	0.34950	-0.9808	10	0.14656	T	0.56	-23.8592	13.2983	0.60311	0.5624:0.4376:0.0:0.0	.	89	P51811	XK_HUMAN	V	89	ENSP00000367879:I89V	ENSP00000367879:I89V	I	+	1	0	XK	37438497	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	3.388000	0.52509	-0.012000	0.14223	0.417000	0.27973	ATC		0.408	XK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080875.1	NM_021083		19	26	0	0	0	0.575678	0	19	26				
PROX1	5629	broad.mit.edu	37	1	214171237	214171237	+	Silent	SNP	C	C	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr1:214171237C>T	ENST00000366958.4	+	2	1967	c.1359C>T	c.(1357-1359)tcC>tcT	p.S453S	PROX1_ENST00000498508.2_Silent_p.S453S|PROX1_ENST00000261454.4_Silent_p.S453S|PROX1_ENST00000435016.1_Silent_p.S453S	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	453					aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.S453S(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		AGTCTGCCTCCGGCCCTGCCG	0.647																																						ENST00000366958.4																			1	Substitution - coding silent(1)	p.S453S(1)	prostate(1)	autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47						c.(1357-1359)tcC>tcT		prospero homeobox 1							60.0	72.0	68.0					1																	214171237		2203	4300	6503	SO:0001819	synonymous_variant	5629				aorta smooth muscle tissue morphogenesis|atrial cardiac muscle tissue morphogenesis|brain development|dorsal spinal cord development|embryonic retina morphogenesis in camera-type eye|endocardium formation|hepatocyte differentiation|kidney development|lens fiber cell morphogenesis|lung development|lymphangiogenesis|negative regulation of bile acid biosynthetic process|negative regulation of cell proliferation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of viral genome replication|neural tube development|olfactory placode formation|optic placode formation involved in camera-type eye formation|otic placode formation|pancreas development|positive regulation of cyclin-dependent protein kinase activity|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of heart growth|positive regulation of S phase of mitotic cell cycle|positive regulation of sarcomere organization|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment|skeletal muscle thin filament assembly|venous blood vessel morphogenesis|ventricular cardiac muscle tissue morphogenesis|ventricular cardiac myofibril development|ventricular septum morphogenesis	cytoplasm|nucleus	DBD domain binding|LBD domain binding|ligand-dependent nuclear receptor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding	g.chr1:214171237C>T	U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"""Homeoboxes / PROS class"""	9459	protein-coding gene	gene with protein product		601546	"""prospero-related homeobox 1"""			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.1359C>T	1.37:g.214171237C>T						PROX1_ENST00000261454.4_Silent_p.S453S|PROX1_ENST00000498508.2_Silent_p.S453S|PROX1_ENST00000435016.1_Silent_p.S453S	p.S453S	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)	2	1967	+			453					A6NK29|A8K2B1|Q5SW76|Q8TB91	Silent	SNP	ENST00000366958.4	37	c.1359C>T	CCDS31021.1																																																																																				0.647	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763		27	85	0	0	0	0.788014	0	27	85				
LCN2	3934	broad.mit.edu	37	9	130914560	130914560	+	Missense_Mutation	SNP	A	A	G			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr9:130914560A>G	ENST00000373017.1	+	6	811	c.574A>G	c.(574-576)Atc>Gtc	p.I192V	LCN2_ENST00000372998.1_Missense_Mutation_p.I194V|LCN2_ENST00000470902.1_3'UTR|LCN2_ENST00000540948.1_Missense_Mutation_p.I192V|LCN2_ENST00000277480.2_Missense_Mutation_p.I192V|LCN2_ENST00000373013.2_Missense_Mutation_p.I194V			P80188	NGAL_HUMAN	lipocalin 2	192					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|small molecule binding (GO:0036094)|transporter activity (GO:0005215)	p.I192V(1)		central_nervous_system(1)|lung(3)|prostate(2)|skin(1)|urinary_tract(1)	8						CCCTGTCCCAATCGGTAATGG	0.562																																						ENST00000540948.1																			1	Substitution - Missense(1)	p.I192V(1)	prostate(1)	central_nervous_system(1)|lung(3)|prostate(2)|skin(1)|urinary_tract(1)	8						c.(574-576)Atc>Gtc		lipocalin 2							85.0	72.0	77.0					9																	130914560		2203	4300	6503	SO:0001583	missense	3934				apoptosis|innate immune response|regulation of apoptosis|siderophore transport		iron ion binding|transporter activity	g.chr9:130914560A>G		CCDS6892.1	9q34	2011-10-24	2007-12-18		ENSG00000148346	ENSG00000148346		"""Lipocalins"""	6526	protein-coding gene	gene with protein product	"""oncogene 24p3"", ""neutrophil gelatinase-associated lipocalin"", ""siderocalin"""	600181	"""lipocalin 2 (oncogene 24p3)"""			7683678	Standard	NM_005564		Approved	NGAL, 24p3	uc004bto.1	P80188	OTTHUMG00000020734	ENST00000373017.1:c.574A>G	9.37:g.130914560A>G	ENSP00000362108:p.Ile192Val					LCN2_ENST00000470902.1_3'UTR|LCN2_ENST00000372998.1_Missense_Mutation_p.I194V|LCN2_ENST00000373017.1_Missense_Mutation_p.I192V|LCN2_ENST00000277480.2_Missense_Mutation_p.I192V|LCN2_ENST00000373013.2_Missense_Mutation_p.I194V	p.I192V			P80188	NGAL_HUMAN			5	647	+			192					A6NII8|B4DWV4|B7ZAA2|P30150|Q5SYV9|Q5SYW0|Q6FGL5|Q92683	Missense_Mutation	SNP	ENST00000373017.1	37	c.574A>G	CCDS6892.1	.	.	.	.	.	.	.	.	.	.	A	9.825	1.186882	0.21870	.	.	ENSG00000148346	ENST00000373017;ENST00000277480;ENST00000373013;ENST00000540948;ENST00000372998	T;T;T;T;T	0.22336	1.97;1.97;1.97;1.96;1.98	4.05	2.93	0.34026	Calycin-like (1);Calycin (1);	0.300893	0.23680	N	0.045631	T	0.15305	0.0369	L	0.42245	1.32	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.15052	0.003;0.012	T	0.09465	-1.0673	10	0.35671	T	0.21	-20.9696	5.641	0.17565	0.8783:0.0:0.1217:0.0	.	192;192	P80188-2;P80188	.;NGAL_HUMAN	V	192;192;194;192;194	ENSP00000362108:I192V;ENSP00000277480:I192V;ENSP00000362104:I194V;ENSP00000441666:I192V;ENSP00000362089:I194V	ENSP00000277480:I192V	I	+	1	0	LCN2	129954381	0.008000	0.16893	0.087000	0.20705	0.351000	0.29236	1.288000	0.33296	1.848000	0.53677	0.374000	0.22700	ATC		0.562	LCN2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054375.1	NM_005564		23	48	0	0	0	0.654019	0	23	48				
OR52A1	23538	broad.mit.edu	37	11	5172911	5172911	+	Missense_Mutation	SNP	C	C	T	rs149615083	byFrequency	TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr11:5172911C>T	ENST00000380367.1	-	2	1106	c.689G>A	c.(688-690)cGt>cAt	p.R230H	OR52A1_ENST00000328942.1_Missense_Mutation_p.R230H			Q9UKL2	O52A1_HUMAN	olfactory receptor, family 52, subfamily A, member 1	230					sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|transmembrane signaling receptor activity (GO:0004888)	p.R230H(1)		breast(2)|endometrium(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	19		Medulloblastoma(188;0.00106)|Breast(177;0.0155)|all_neural(188;0.0189)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGGGGCAAACGAAAAACTGT	0.428													C|||	2	0.000399361	0.0015	0.0	5008	,	,		22186	0.0		0.0	False		,,,				2504	0.0					ENST00000380367.1																			1	Substitution - Missense(1)	p.R230H(1)	prostate(1)	breast(2)|endometrium(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	19						c.(688-690)cGt>cAt		olfactory receptor, family 52, subfamily A, member 1		C	HIS/ARG	2,4400	4.2+/-10.8	0,2,2199	172.0	158.0	162.0		689	-5.8	0.0	11	dbSNP_134	162	0,8596		0,0,4298	no	missense	OR52A1	NM_012375.2	29	0,2,6497	TT,TC,CC		0.0,0.0454,0.0154	benign	230/313	5172911	2,12996	2201	4298	6499	SO:0001583	missense	23538				sensory perception of smell	integral to plasma membrane	olfactory receptor activity	g.chr11:5172911C>T	AF154673	CCDS31374.1	11p15.4	2012-08-09			ENSG00000182070	ENSG00000182070		"""GPCR / Class A : Olfactory receptors"""	8318	protein-coding gene	gene with protein product						10512676	Standard	NM_012375		Approved	HPFH1OR	uc010qyy.2	Q9UKL2	OTTHUMG00000066603	ENST00000380367.1:c.689G>A	11.37:g.5172911C>T	ENSP00000369725:p.Arg230His					OR52A1_ENST00000328942.1_Missense_Mutation_p.R230H	p.R230H			Q9UKL2	O52A1_HUMAN		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	2	1106	-		Medulloblastoma(188;0.00106)|Breast(177;0.0155)|all_neural(188;0.0189)	230					Q6IF31	Missense_Mutation	SNP	ENST00000380367.1	37	c.689G>A	CCDS31374.1	.	.	.	.	.	.	.	.	.	.	C	2.029	-0.422821	0.04734	4.54E-4	0.0	ENSG00000182070	ENST00000380367;ENST00000328942	T;T	0.00262	8.4;8.4	5.33	-5.81	0.02340	GPCR, rhodopsin-like superfamily (1);	1.100120	0.06929	N	0.810707	T	0.00144	0.0004	N	0.17800	0.525	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	T	0.16778	-1.0391	10	0.20046	T	0.44	.	14.8761	0.70496	0.0:0.3382:0.0:0.6618	.	230	Q9UKL2	O52A1_HUMAN	H	230	ENSP00000369725:R230H;ENSP00000333684:R230H	ENSP00000333684:R230H	R	-	2	0	OR52A1	5129487	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.297000	0.01141	-1.489000	0.01844	-1.575000	0.00869	CGT		0.428	OR52A1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142810.2	NM_012375		30	121	0	0	0	0.717897	0	30	121				
MED11	400569	broad.mit.edu	37	17	4638741	4638741	+	IGR	SNP	G	G	T			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr17:4638741G>T	ENST00000293777.5	+	0	833				CXCL16_ENST00000293778.6_Missense_Mutation_p.P141T|CXCL16_ENST00000574412.1_Missense_Mutation_p.P141T|CXCL16_ENST00000576153.1_5'UTR	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN	mediator complex subunit 11							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			lung(2)|ovary(2)	4						TGAGAAATTGGGGGGCTGGTA	0.547																																						ENST00000293778.6																			0				large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5						c.(421-423)Cca>Aca		chemokine (C-X-C motif) ligand 16							39.0	45.0	43.0					17																	4638741		2203	4300	6503	SO:0001628	intergenic_variant	58191				lymphocyte chemotaxis|positive regulation of cell growth|positive regulation of cell migration|receptor-mediated endocytosis|response to interferon-gamma|response to tumor necrosis factor	extracellular space|integral to membrane|plasma membrane	chemokine activity|low-density lipoprotein receptor activity|scavenger receptor activity	g.chr17:4638741G>T	AF161414	CCDS32533.1	17p13.2	2007-07-30	2007-07-30			ENSG00000161920			32687	protein-coding gene	gene with protein product		612383	"""mediator of RNA polymerase II transcription, subunit 11 homolog (S. cerevisiae)"""			15175163, 12584197	Standard	NM_001001683		Approved	HSPC296, MGC88387	uc002fyp.3	Q9P086			17.37:g.4638741G>T						CXCL16_ENST00000574412.1_Missense_Mutation_p.P141T|CXCL16_ENST00000576153.1_5'UTR	p.P141T	NM_022059.2	NP_071342.2	Q9H2A7	CXL16_HUMAN			4	843	-			122					Q6NS89	Missense_Mutation	SNP	ENST00000293777.5	37	c.421C>A	CCDS32533.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.623138	0.28889	.	.	ENSG00000161921	ENST00000293778	T	0.30182	1.54	5.54	4.57	0.56435	.	0.899165	0.09431	N	0.803071	T	0.24661	0.0598	L	0.36672	1.1	0.09310	N	1	P	0.41910	0.764	B	0.36418	0.224	T	0.08680	-1.0710	10	0.39692	T	0.17	-1.7081	10.1981	0.43067	0.0916:0.0:0.9084:0.0	.	122	Q9H2A7	CXL16_HUMAN	T	141	ENSP00000293778:P141T	ENSP00000293778:P141T	P	-	1	0	CXCL16	4585490	0.004000	0.15560	0.002000	0.10522	0.004000	0.04260	1.415000	0.34748	1.350000	0.45770	0.462000	0.41574	CCA		0.547	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683		3	48	1	0	0.115264	0.115264	0.125074	3	48				
EFHB	151651	broad.mit.edu	37	3	19924217	19924217	+	Missense_Mutation	SNP	G	G	C			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr3:19924217G>C	ENST00000295824.9	-	12	2314	c.2153C>G	c.(2152-2154)cCc>cGc	p.P718R	EFHB_ENST00000344838.4_Missense_Mutation_p.P588R	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	718							calcium ion binding (GO:0005509)	p.P718R(2)|p.P716R(1)		breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						ACCACAAATGGGGTAACCTAG	0.428																																						ENST00000295824.9																			3	Substitution - Missense(3)	p.P718R(2)|p.P716R(1)	prostate(3)	breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						c.(2152-2154)cCc>cGc		EF-hand domain family, member B							91.0	76.0	81.0					3																	19924217		2203	4300	6503	SO:0001583	missense	151651				signal transduction	proteinaceous extracellular matrix	calcium ion binding	g.chr3:19924217G>C	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"""EF-hand domain containing"""	26330	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 21"""					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.2153C>G	3.37:g.19924217G>C	ENSP00000295824:p.Pro718Arg					EFHB_ENST00000344838.4_Missense_Mutation_p.P588R	p.P718R	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN			12	2314	-			718					A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Missense_Mutation	SNP	ENST00000295824.9	37	c.2153C>G	CCDS33715.2	.	.	.	.	.	.	.	.	.	.	G	2.183	-0.387122	0.04932	.	.	ENSG00000163576	ENST00000295824;ENST00000344838	T;T	0.22134	1.97;2.03	5.54	5.54	0.83059	.	0.264206	0.38548	N	0.001644	T	0.25568	0.0622	N	0.25992	0.78	0.35804	D	0.823339	P;B	0.50528	0.936;0.07	P;B	0.53401	0.725;0.019	T	0.07102	-1.0790	9	.	.	.	-10.6457	15.3446	0.74327	0.0:0.1391:0.8609:0.0	.	588;718	Q8N7U6-3;Q8N7U6	.;EFHB_HUMAN	R	718;588	ENSP00000295824:P718R;ENSP00000342263:P588R	.	P	-	2	0	EFHB	19899221	0.998000	0.40836	0.911000	0.35937	0.085000	0.17905	2.809000	0.47971	2.768000	0.95171	0.650000	0.86243	CCC		0.428	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715		11	31	0	0	0	0.361761	0	11	31				
FAM47B	170062	broad.mit.edu	37	X	34961794	34961794	+	Silent	SNP	T	T	C			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chrX:34961794T>C	ENST00000329357.5	+	1	882	c.846T>C	c.(844-846)caT>caC	p.H282H		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	282	Pro-rich.							p.H282H(2)		breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						GAGCGTCCCATCTCTGCCCGG	0.622																																						ENST00000329357.5																			2	Substitution - coding silent(2)	p.H282H(2)	prostate(2)	breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						c.(844-846)caT>caC		family with sequence similarity 47, member B							57.0	55.0	56.0					X																	34961794		2202	4300	6502	SO:0001819	synonymous_variant	170062							g.chrX:34961794T>C	BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.846T>C	X.37:g.34961794T>C							p.H282H	NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN			1	882	+			282			Pro-rich.		Q5JQN5|Q6PIG3	Silent	SNP	ENST00000329357.5	37	c.846T>C	CCDS14236.1																																																																																				0.622	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		32	25	0	0	0	0.760397	0	32	25				
LINC00971	440970	broad.mit.edu	37	3	84741480	84741480	+	lincRNA	DEL	A	A	-	rs71104976		TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr3:84741480delA	ENST00000484892.1	-	0	2354					NR_033860.1				long intergenic non-protein coding RNA 971																		CCTGTCCCAGAAAAAAAAAAA	0.388																																						ENST00000484892.1																			0																																																			0							g.chr3:84741480delA			3p12.1	2013-06-07			ENSG00000242641	ENSG00000242641		"""Long non-coding RNAs"""	48737	non-coding RNA	RNA, long non-coding							Standard	NR_033860		Approved				OTTHUMG00000158981		3.37:g.84741480delA								NR_033860.1						0	2354	-									RNA	DEL	ENST00000484892.1	37																																																																																						0.388	LINC00971-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000352776.2			5	5						5	5	---	---	---	---
IL6ST	3572	broad.mit.edu	37	5	55250760	55250772	+	Frame_Shift_Del	DEL	CATTCCACCCAAA	CATTCCACCCAAA	-			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr5:55250760_55250772delCATTCCACCCAAA	ENST00000381298.2	-	11	1628_1640	c.1316_1328delTTTGGGTGGAATG	c.(1315-1329)ctttgggtggaatggfs	p.LWVEW439fs	IL6ST_ENST00000536319.1_Intron|IL6ST_ENST00000522633.2_3'UTR|IL6ST_ENST00000336909.5_Frame_Shift_Del_p.LWVEW439fs|IL6ST_ENST00000502326.3_Frame_Shift_Del_p.LWVEW439fs|IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000381294.3_Intron|IL6ST_ENST00000381286.3_Intron	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	439	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				TGGAGTAGTCCATTCCACCCAAAGCATGTTATC	0.347			O		hepatocellular ca																																	ENST00000381298.2				Dom	yes		5	5q11	3572	O	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""			E			hepatocellular ca		0				breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26						c.(1315-1329)cgfs		interleukin 6 signal transducer (gp130, oncostatin M receptor)																																				SO:0001589	frameshift_variant	3572				interleukin-6-mediated signaling pathway|leukemia inhibitory factor signaling pathway|negative regulation of interleukin-6-mediated signaling pathway|positive regulation of anti-apoptosis|positive regulation of cardiac muscle hypertrophy|positive regulation of osteoblast differentiation|positive regulation of T cell proliferation|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation vascular endothelial growth factor production	ciliary neurotrophic factor receptor complex|extracellular region|extracellular space|interleukin-6 receptor complex|oncostatin-M receptor complex	ciliary neurotrophic factor receptor activity|ciliary neurotrophic factor receptor binding|growth factor binding|protein homodimerization activity	g.chr5:55250760_55250772delCATTCCACCCAAA	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6021	protein-coding gene	gene with protein product	"""gp130, oncostatin M receptor"""	600694	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.1316_1328delTTTGGGTGGAATG	5.37:g.55250760_55250772delCATTCCACCCAAA	ENSP00000370698:p.Leu439fs					IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000381294.3_Intron|IL6ST_ENST00000536319.1_Intron|IL6ST_ENST00000336909.5_Frame_Shift_Del_p.LWVEW439fs|IL6ST_ENST00000502326.3_Frame_Shift_Del_p.LWVEW439fs|IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000522633.2_3'UTR	p.LWVEW439fs	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN			11	1628_1640	-		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)	439			Fibronectin type-III 4.		A0N0L4|Q5FC04|Q9UQ41	Frame_Shift_Del	DEL	ENST00000381298.2	37	c.1316_1328delTTTGGGTGGAATG	CCDS3971.1																																																																																				0.347	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		45	290						45	290	---	---	---	---
PRRC2A	7916	broad.mit.edu	37	6	31590596	31590598	+	In_Frame_Del	DEL	GGG	GGG	-			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr6:31590596_31590598delGGG	ENST00000376033.2	+	2	264_266	c.30_32delGGG	c.(28-33)aaggga>aaa	p.G11del	PRRC2A_ENST00000469577.1_Intron|PRRC2A_ENST00000376007.4_In_Frame_Del_p.G11del|SNORA38_ENST00000363946.1_RNA	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	11						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CGACTGCCAAGGGAAAGGATGGA	0.547																																						ENST00000376033.2																			0				breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						c.(28-33)aaa>aa		proline-rich coiled-coil 2A																																				SO:0001651	inframe_deletion	7916					cytoplasm|nucleus	protein binding	g.chr6:31590596_31590598delGGG	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.30_32delGGG	6.37:g.31590596_31590598delGGG	ENSP00000365201:p.Gly11del					PRRC2A_ENST00000469577.1_Intron|PRRC2A_ENST00000376007.4_In_Frame_Del_p.KG10del	p.KG10del	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN			2	264_266	+			10					B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	In_Frame_Del	DEL	ENST00000376033.2	37	c.30_32delGGG	CCDS4708.1																																																																																				0.547	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		46	298						46	298	---	---	---	---
PLEKHA2	59339	broad.mit.edu	37	8	38793568	38793569	+	Splice_Site	DEL	GG	GG	-			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr8:38793568_38793569delGG	ENST00000521746.1	+	3	432	c.198delGG	c.(196-198)aag>aa	p.K66fs	PLEKHA2_ENST00000420274.1_Splice_Site_p.K66fs|PLEKHA2_ENST00000388745.4_3'UTR			Q9HB19	PKHA2_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 2	66	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of cell-matrix adhesion (GO:0001954)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	13		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)			ACATCTCGAAGGTAATGTTGAC	0.46																																						ENST00000420274.1																			0				breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	13						c.e3+1		pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 2																																				SO:0001630	splice_region_variant	59339				positive regulation of cell-matrix adhesion	cytoplasm|nucleus|plasma membrane|protein complex	fibronectin binding|laminin binding	g.chr8:38793568_38793569delGG	AF286164	CCDS75732.1	8p11.21	2013-01-10	2002-01-14			ENSG00000169499		"""Pleckstrin homology (PH) domain containing"""	14336	protein-coding gene	gene with protein product	"""tandem PH Domain containing protein-2"""	607773	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2"""			11001876	Standard	NM_021623		Approved	TAPP2	uc003xmi.4	Q9HB19		ENST00000521746.1:c.198+1GG>-	8.37:g.38793568_38793569delGG						PLEKHA2_ENST00000521746.1_Splice_Site_p.66_splice|PLEKHA2_ENST00000388745.4_3'UTR	p.66_splice	NM_021623.1	NP_067636.1	Q9HB19	PKHA2_HUMAN	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)		3	432	+		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	66			PH 1.			Splice_Site	DEL	ENST00000521746.1	37	c.198_splice																																																																																					0.460	PLEKHA2-002	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000377068.1	NM_021623	Frame_Shift_Del	24	203						24	203	---	---	---	---
PNLIPRP2	5408	broad.mit.edu	37	10	118383815	118383816	+	RNA	INS	-	-	CA	rs67295503|rs3217086|rs113988880	byFrequency	TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr10:118383815_118383816insCA	ENST00000298771.7	+	0	229				PNLIPRP2_ENST00000433618.4_RNA|PNLIPRP2_ENST00000537242.1_RNA	NR_103727.1		P54317	LIPR2_HUMAN	pancreatic lipase-related protein 2						galactolipid catabolic process (GO:0019376)|lipid digestion (GO:0044241)|phospholipid catabolic process (GO:0009395)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	acylglycerol lipase activity (GO:0047372)|calcium ion binding (GO:0005509)|galactolipase activity (GO:0047714)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			endometrium(1)|large_intestine(1)|lung(11)|prostate(3)	16				all cancers(201;0.015)		acttacacattcacacacactg	0.485														1806	0.360623	0.2315	0.4179	5008	,	,		16449	0.5784		0.338	False		,,,				2504	0.2935					ENST00000537242.1																			0				endometrium(1)|large_intestine(1)|lung(11)|prostate(3)	16								pancreatic lipase-related protein 2																																						5408				galactolipid catabolic process|lipid digestion|phospholipid catabolic process|triglyceride metabolic process	extracellular space	acylglycerol lipase activity|calcium ion binding|galactolipase activity|phospholipase activity|triglyceride lipase activity	g.chr10:118383815_118383816insCA	M93284		10q26.12	2014-03-14				ENSG00000266200	3.1.1.3		9157	protein-coding gene	gene with protein product		604423				1379598	Standard	NM_005396		Approved	PLRP2	uc001lcq.3	P54317			10.37:g.118383822_118383823dupCA						PNLIPRP2_ENST00000298771.7_RNA|PNLIPRP2_ENST00000433618.4_RNA		NM_005396.4	NP_005387.2	P54317	LIPR2_HUMAN		all cancers(201;0.015)	0	230	+								A8K627|Q6IB55	RNA	INS	ENST00000298771.7	37																																																																																						0.485	PNLIPRP2-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000050546.6	NM_005396		3	4						3	4	---	---	---	---
OVOS2	144203	broad.mit.edu	37	12	31269189	31269190	+	RNA	INS	-	-	ATCAT	rs25559|rs10665556	byFrequency	TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr12:31269189_31269190insATCAT	ENST00000542490.1	-	0	165																				central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(25)|prostate(3)|stomach(3)|urinary_tract(1)	41						CATGAGAACTCATTACCATGAT	0.351														3178	0.634585	0.7088	0.611	5008	,	,		12379	0.8274		0.4284	False		,,,				2504	0.5644					ENST00000542490.1																			0				central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(25)|prostate(3)|stomach(3)|urinary_tract(1)	41																																														0							g.chr12:31269189_31269190insATCAT																													12.37:g.31269189_31269190insATCAT														0	165	-									RNA	INS	ENST00000542490.1	37																																																																																						0.351	RP11-551L14.1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400342.1			12	18						12	18	---	---	---	---
LOC100507377	100507377	broad.mit.edu	37	12	74669120	74669120	+	lincRNA	DEL	T	T	-	rs35644413|rs397820200|rs73182763		TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr12:74669120delT	ENST00000515416.2	-	0	464				RP11-274M17.3_ENST00000552046.1_lincRNA																							TTTTTTGGGGTTTTTTTTTTT	0.308																																						ENST00000515416.2																			0																																																			0							g.chr12:74669120delT																													12.37:g.74669120delT						RP11-274M17.3_ENST00000552046.1_RNA								0	464	-									RNA	DEL	ENST00000515416.2	37																																																																																						0.308	RP11-81H3.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000405900.1			2	4						2	4	---	---	---	---
PLIN3	10226	broad.mit.edu	37	19	4847750	4847750	+	Frame_Shift_Del	DEL	G	G	-			TCGA-EJ-5526-01A-01D-1576-08	TCGA-EJ-5526-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28436e84-7985-4676-a36c-4b18f064db9a	764d600c-bbe7-4996-8f5d-4ec9a3adc6af	g.chr19:4847750delG	ENST00000221957.4	-	6	963	c.787delC	c.(787-789)cagfs	p.Q263fs	PLIN3_ENST00000585479.1_Frame_Shift_Del_p.Q263fs|PLIN3_ENST00000592528.1_Frame_Shift_Del_p.Q251fs	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	263					vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	TGTGCCCTCTGCTTGGTGGCT	0.662																																						ENST00000221957.4																			0				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9						c.(787-789)agfs		perilipin 3	Galsulfase(DB01279)|Idursulfase(DB01271)						31.0	25.0	27.0					19																	4847750		2203	4300	6503	SO:0001589	frameshift_variant	10226				vesicle-mediated transport	endosome membrane|Golgi apparatus|lipid particle	protein binding	g.chr19:4847750delG	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"""Perilipins"""	16893	protein-coding gene	gene with protein product	"""cargo selection protein (mannose 6 phosphate receptor binding protein)"", ""placental protein 17"", ""MPR-BINDING PROTEIN, 47-KD"""	602702	"""mannose-6-phosphate receptor binding protein 1"""	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.787delC	19.37:g.4847750delG	ENSP00000221957:p.Gln263fs					PLIN3_ENST00000592528.1_Frame_Shift_Del_p.Q251fs|PLIN3_ENST00000585479.1_Frame_Shift_Del_p.Q263fs	p.Q263fs	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN			6	963	-			263					A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Frame_Shift_Del	DEL	ENST00000221957.4	37	c.787delC	CCDS12137.1																																																																																				0.662	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817		9	16						9	16	---	---	---	---
