#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_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_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	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_Description	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_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_AccessionNumbers	i_HGNC_CCDS IDs	i_HGNC_CCDSIDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_DateModified	i_HGNC_DateNameChanged	i_HGNC_DateSymbolChanged	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_EnsemblGeneID	i_HGNC_EnsemblIDsuppliedbyEnsembl	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_Genefamilydescription	i_HGNC_HGNC ID	i_HGNC_HGNCID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_LocusGroup	i_HGNC_LocusType	i_HGNC_Name Synonyms	i_HGNC_NameSynonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_OMIMIDsuppliedbyNCBI	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_PreviousNames	i_HGNC_PreviousSymbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_PubmedIDs	i_HGNC_Record Type	i_HGNC_RecordType	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_RefSeqsuppliedbyNCBI	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UCSCIDsuppliedbyUCSC	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_UniProtIDsuppliedbyUniProt	i_HGNC_VEGA IDs	i_HGNC_VEGAIDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	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_Region	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_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_folddegenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_hg18_pos1coor	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_init_n_lod	i_init_t_lod	i_n_alt_count	i_n_alt_count_full	i_n_ref_count	i_n_ref_count_full	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_lod_fstar	i_t_lod_fstar_full	i_t_ref_count_full	i_tumor_f_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	tumor_f
NFATC2	4773	broad.mit.edu	37	20	50090554	50090554	+	Silent	SNP	G	G	T			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr20:50090554G>T	ENST00000396009.3	-	5	1890	c.1671C>A	c.(1669-1671)atC>atA	p.I557I	NFATC2_ENST00000609943.1_Silent_p.I537I|NFATC2_ENST00000610033.1_Silent_p.I338I|NFATC2_ENST00000414705.1_Silent_p.I537I|NFATC2_ENST00000609507.1_Silent_p.I338I|NFATC2_ENST00000371564.3_Silent_p.I557I	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	557	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GTAAAGAGACGATTCTGCCAC	0.567																																						ENST00000371564.3											0			breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53						c.(1669-1671)atC>atA	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2						141.0	113.0	122.0					20																	50090554		2203	4300	6503	SO:0001819	synonymous_variant	4773			B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity	g.chr20:50090554G>T	U43342, U43341	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			2009-11-24			ENSG00000101096	ENSG00000101096	ENSG00000101096	ENSG00000101096		"""Nuclear factor of activated T-cells"""	"""Nuclear factor of activated T-cells"""	7776	7776	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			600490	600490						8202141	8202141	Standard	Standard	NM_012340	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	uc002xwd.4	Q13469	Q13469	OTTHUMG00000032747	OTTHUMG00000032747	ENST00000396009.3:c.1671C>A	20.37:g.50090554G>T			NFATC2_ENST00000609507.1_Silent_p.I338I|NFATC2_ENST00000414705.1_Silent_p.I537I|NFATC2_ENST00000396009.3_Silent_p.I557I|NFATC2_ENST00000610033.1_Silent_p.I338I|NFATC2_ENST00000609943.1_Silent_p.I537I	p.I557I	NM_001258296.1|NM_012340.4	NP_001245225.1|NP_036472.2	Q13469	NFAC2_HUMAN			5	1890	-	Hepatocellular(150;0.248)		557	RHD.	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Silent	SNP	ENST00000396009.3	37	c.1671C>A	CCDS13437.1																																																																																									0.567	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2		-0.607734	-9	-9	44	44	NM_012340		3	7.072249	7.072249	38	0.073171	1	0	1	1	1	3	38	0.073171
ATG9A	79065	hgsc.bcm.edu	37	2	220086024	220086024	+	Splice_Site	SNP	G	G	C			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr2:220086024G>C	ENST00000409618.1	-	14	2585	c.2146C>G	c.(2146-2148)Ctc>Gtc	p.L716V	ATG9A_ENST00000409422.1_Splice_Site_p.L655V|ABCB6_ENST00000439002.2_5'Flank|ABCB6_ENST00000265316.3_5'Flank|ATG9A_ENST00000396761.2_Splice_Site_p.L716V|AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000361242.4_Splice_Site_p.L716V			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	716					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGCTTGTGGAGCTGGAGAAAT	0.602																																																	0																	11.0	12.0	12.0					2																	220086024		1985	4155	6140	SO:0001630	splice_region_variant	79065							AK021732	AK021732	CCDS42820.1	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925	ENSG00000198925	ENSG00000198925				22408	22408	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			612204	612204	"""APG9 autophagy 9-like 1 (S. cerevisiae)"", ""ATG9 autophagy related 9 homolog A (S. cerevisiae)"""	APG9L1	"""APG9 autophagy 9-like 1 (S. cerevisiae)"", ""ATG9 autophagy related 9 homolog A (S. cerevisiae)"""	APG9L1				Standard	Standard	NM_024085	NM_024085		Approved	FLJ22169	uc002vkf.1	uc002vkf.1	Q7Z3C6	Q7Z3C6	OTTHUMG00000154557	OTTHUMG00000154557	ENST00000409618.1:c.2146-1C>G	2.37:g.220086024G>C																		Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	37		CCDS42820.1	.	.	.	.	.	.	.	.	.	.	G	12.21	1.870543	0.33069	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422	T;T;T;T	0.53857	1.0;1.0;1.0;0.6	5.3	4.35	0.52113	5.3	4.35	0.52113	.	0.142087	0.47093	D	0.000253	T	0.34745	0.0908	L	0.42686	1.345	0.43457	D	0.995656	P	0.37955	0.612	B	0.32533	0.147	T	0.11867	-1.0570	10	0.22109	T	0.4	-16.7292	4.3548	0.11172	0.2818:0.0:0.7182:0.0	.	716	Q7Z3C6	ATG9A_HUMAN	V	716;716;716;655	ENSP00000379983:L716V;ENSP00000386710:L716V;ENSP00000355173:L716V;ENSP00000386535:L655V	ENSP00000355173:L716V	L	-	1	0	0	ATG9A	219794268	219794268	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.397000	0.34543	2.757000	0.94681	0.591000	0.81541	CTC		0.602	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1			1	1	18	18	NM_024085	Missense_Mutation	5			12							5	12	
AIM1L	55057	broad.mit.edu	37	1	26655240	26655240	+	Missense_Mutation	SNP	C	C	T			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr1:26655240C>T	ENST00000308182.5	-	15	1733	c.1304G>A	c.(1303-1305)cGg>cAg	p.R435Q	AIM1L_ENST00000527815.1_Missense_Mutation_p.R606Q			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	435	Beta/gamma crystallin 'Greek key' 9. {ECO:0000255|PROSITE-ProRule:PRU00028}.						carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		CCCCTTGATCCGCACAGACAG	0.617																																						ENST00000527815.1											0			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12						c.(1816-1818)cGg>cAg	absent in melanoma 1-like						153.0	129.0	137.0					1																	26655240		2203	4300	6503	SO:0001583	missense	55057					sugar binding	g.chr1:26655240C>T					1p35	2010-07-14			2010-07-14			ENSG00000176092	ENSG00000176092	ENSG00000176092	ENSG00000176092				17295	17295	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""beta-gamma crystallin domain containing 2"""	"""beta-gamma crystallin domain containing 2"""										Standard	Standard	NM_001039775	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	uc001bmd.4	Q8N1P7	Q8N1P7	OTTHUMG00000003490	OTTHUMG00000003490	ENST00000308182.5:c.1304G>A	1.37:g.26655240C>T	ENSP00000310435:p.Arg435Gln		AIM1L_ENST00000308182.5_Missense_Mutation_p.R435Q	p.R606Q	NM_001039775.3	NP_001034864.2	Q8N1P7	AIM1L_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)	15	1866	-		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)	435	Ricin B-type lectin.	B2RNG3|Q5T137|Q5T150	Missense_Mutation	SNP	ENST00000308182.5	37	c.1817G>A		.	.	.	.	.	.	.	.	.	.	C	9.021	0.984904	0.18889	.	.	ENSG00000176092	ENST00000527815;ENST00000308182	T;T	0.77489	-1.1;-1.1	5.03	1.05	0.20165	5.03	1.05	0.20165	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.354241	0.30791	N	0.008866	T	0.63792	0.2541	L	0.46947	1.48	0.80722	D	1	B	0.13594	0.008	B	0.12837	0.008	T	0.52533	-0.8563	10	0.05833	T	0.94	.	9.9776	0.41793	0.0:0.7148:0.0:0.2852	.	435	Q8N1P7	AIM1L_HUMAN	Q	606;435	ENSP00000433931:R606Q;ENSP00000310435:R435Q	ENSP00000310435:R435Q	R	-	2	0	0	AIM1L	26527827	26527827	0.854000	0.29725	0.999000	0.59377	0.711000	0.40976	1.418000	0.34782	0.316000	0.23135	-0.258000	0.10820	CGG		0.617	AIM1L-201	KNOWN	basic	protein_coding	protein_coding			89.225668	-12	-12	97	97	NM_001039775.2		30	91.192938	91.192938	58	0.340909	0	0	0	1	0	30	58	0.340909
ZNF702P	79986	broad.mit.edu	37	19	53473365	53473365	+	RNA	SNP	G	G	C			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr19:53473365G>C	ENST00000600068.1	-	0	489				ZNF702P_ENST00000270443.4_RNA																							CATTACACTTGTGAGGTTTCT	0.383																																						ENST00000600068.1											0																	62.0	55.0	57.0					19																	53473365		692	1591	2283			0						g.chr19:53473365G>C																																																		19.37:g.53473365G>C			ZNF702P_ENST00000270443.4_RNA								0	489	-						RNA	SNP	ENST00000600068.1	37																																																																																											0.383	CTD-2620I22.1-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000463881.1		7.615242	-17	-17	46	46			3	9.078323	9.078323	13	0.187500	0	0	0	1	0	3	13	0.1875
GNAQ	2776	broad.mit.edu	37	9	80409488	80409488	+	Missense_Mutation	SNP	T	T	G	rs121913492		TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr9:80409488T>G	ENST00000286548.4	-	5	848	c.626A>C	c.(625-627)cAa>cCa	p.Q209P	GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7P	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	209			Q -> L (found in blue naevi and uveal melanoma samples; somatic mutation; constitutive activation).		action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.Q209L(87)|p.Q209P(64)|p.Q209Y(1)|p.Q209R(1)		NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						CTCTGACCTTTGGCCCCCTAC	0.348			Mis		uveal melanoma																																	ENST00000286548.4		Dom	yes		9	9q21	2776	"""guanine nucleotide binding protein (G protein), q polypeptide"""		E	153	Substitution - Missense(153)	eye(99)|skin(43)|meninges(10)|NS(1)	NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						c.(625-627)cAa>cCa	guanine nucleotide binding protein (G protein), q polypeptide						108.0	105.0	106.0					9																	80409488		2203	4300	6503	SO:0001583	missense	2776			activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity	g.chr9:80409488T>G			CCDS6658.1	CCDS6658.1	9q21	2010-03-17			2010-03-17			ENSG00000156052	ENSG00000156052	ENSG00000156052	ENSG00000156052				4390	4390	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			600998	600998						8825633	8825633	Standard	Standard	NM_002072	NM_002072		Approved	G-ALPHA-q, GAQ	uc004akw.3	uc004akw.3	P50148	P50148	OTTHUMG00000020059	OTTHUMG00000020059	ENST00000286548.4:c.626A>C	9.37:g.80409488T>G	ENSP00000286548:p.Gln209Pro		GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7P	p.Q209P	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN			5	848	-			209		O15108|Q13462|Q6NT27|Q92471|Q9BZB9	Missense_Mutation	SNP	ENST00000286548.4	37	c.626A>C	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614273	0.87359	.	.	ENSG00000156052	ENST00000286548;ENST00000397476	D;D	0.91237	-2.81;-2.81	5.69	5.69	0.88448	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.97164	0.9073	H	0.97291	3.975	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.98607	1.0661	10	0.87932	D	0	.	15.9502	0.79827	0.0:0.0:0.0:1.0	.	209	P50148	GNAQ_HUMAN	P	209;7	ENSP00000286548:Q209P;ENSP00000443197:Q7P	ENSP00000286548:Q209P	Q	-	2	0	0	GNAQ	79599308	79599308	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.040000	0.89188	2.167000	0.68274	0.460000	0.39030	CAA		0.348	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1		99.843706	-8	-8	104	104	NM_002072		30	100.048327	100.048327	38	0.441176	0	0	0	1	0	30	38	0.441176
OR56A3	390083	broad.mit.edu	37	11	5968660	5968660	+	Silent	SNP	G	G	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr11:5968660G>A	ENST00000329564.6	+	1	91	c.84G>A	c.(82-84)caG>caA	p.Q28Q	AC025016.1_ENST00000528915.1_lincRNA	NM_001003443.2	NP_001003443.2	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A, member 3	28						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(27)|stomach(1)|upper_aerodigestive_tract(1)	41		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCAGCTGGCAGCACTGGCTGT	0.537																																						ENST00000329564.6											0			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(27)|stomach(1)|upper_aerodigestive_tract(1)	41						c.(82-84)caG>caA	olfactory receptor, family 56, subfamily A, member 3						91.0	97.0	95.0					11																	5968660		2200	4296	6496	SO:0001819	synonymous_variant	390083			sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:5968660G>A			CCDS41614.1	CCDS41614.1	11p15.4	2012-08-09		2004-03-10	2012-08-09		2004-03-10	ENSG00000184478	ENSG00000184478	ENSG00000184478	ENSG00000184478		"""GPCR / Class A : Olfactory receptors"""	"""GPCR / Class A : Olfactory receptors"""	14786	14786	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product						OR56A6, OR56A3P		OR56A6, OR56A3P				Standard	Standard	NM_001003443	NM_001003443		Approved		uc010qzt.2	uc010qzt.2	Q8NH54	Q8NH54	OTTHUMG00000165373	OTTHUMG00000165373	ENST00000329564.6:c.84G>A	11.37:g.5968660G>A				p.Q28Q	NM_001003443.2	NP_001003443.2	Q8NH54	O56A3_HUMAN		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	1	91	+		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)	28		A6NN77|Q6IFF7	Silent	SNP	ENST00000329564.6	37	c.84G>A	CCDS41614.1																																																																																									0.537	OR56A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383753.1		-3.417803	22	22	77	77	NM_001003443		3	6.705186	6.705186	47	0.060000	0	0	0	1	0	3	47	0.06
SLC18B1	116843	broad.mit.edu	37	6	133105166	133105166	+	Silent	SNP	C	C	T			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr6:133105166C>T	ENST00000275227.4	-	6	660	c.564G>A	c.(562-564)ttG>ttA	p.L188L	SLC18B1_ENST00000367918.1_Intron|SLC18B1_ENST00000538764.1_Silent_p.L62L	NM_052831.2	NP_439896.1	Q6NT16	S18B1_HUMAN	solute carrier family 18, subfamily B, member 1	188					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)											AGGATTGATACAAAAAGCCAC	0.368																																						ENST00000275227.4											0										c.(562-564)ttG>ttA	solute carrier family 18, subfamily B, member 1						111.0	115.0	114.0					6																	133105166		2203	4300	6503	SO:0001819	synonymous_variant	116843			transmembrane transport	integral to membrane		g.chr6:133105166C>T	AK124442	AK124442	CCDS5163.1	CCDS5163.1	6q22.3-q23.3	2013-05-22	2012-03-09	2012-03-09	2013-05-22	2012-03-09	2012-03-09	ENSG00000146409	ENSG00000146409	ENSG00000146409	ENSG00000146409		"""Solute carriers"""	"""Solute carriers"""	21573	21573	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			613361	613361	"""chromosome 6 open reading frame 192"""	C6orf192	"""chromosome 6 open reading frame 192"""	C6orf192		19697161	19697161	Standard	Standard	XM_006715328	XM_006715328		Approved	dJ55C23.6	uc003qdw.1	uc003qdw.1	Q6NT16	Q6NT16	OTTHUMG00000015595	OTTHUMG00000015595	ENST00000275227.4:c.564G>A	6.37:g.133105166C>T			SLC18B1_ENST00000367918.1_Intron|SLC18B1_ENST00000538764.1_Silent_p.L62L	p.L188L	NM_052831.2	NP_439896.1	Q6NT16	CF192_HUMAN			6	660	-			188		A8K1K3|B3KW77|Q6ISF2	Silent	SNP	ENST00000275227.4	37	c.564G>A	CCDS5163.1																																																																																									0.368	SLC18B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042273.1		27.433068	-14	-14	94	94	NM_052831		13	33.495437	33.495437	55	0.191176	0	0	0	1	0	13	55	0.191176
KIAA1244	57221	broad.mit.edu	37	6	138608050	138608050	+	Missense_Mutation	SNP	C	C	G			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr6:138608050C>G	ENST00000251691.4	+	16	2948	c.2782C>G	c.(2782-2784)Cta>Gta	p.L928V		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		GAGCTGCGCTCTAGGTACCAG	0.622																																						ENST00000251691.4											0			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44						c.(2782-2784)Cta>Gta	KIAA1244						33.0	31.0	32.0					6																	138608050		2203	4300	6503	SO:0001583	missense	57221			regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity	g.chr6:138608050C>G	AB033070	AB033070	CCDS5189.2	CCDS5189.2	6q23.3	2012-04-17			2012-04-17			ENSG00000112379	ENSG00000112379	ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	21213	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""	"""protein phosphatase 1, regulatory subunit 33"""			"""chromosome 6 open reading frame 92"""	C6orf92	"""chromosome 6 open reading frame 92"""	C6orf92				Standard	Standard	NM_020340	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	uc003qhu.3	Q5TH69	Q5TH69	OTTHUMG00000015670	OTTHUMG00000015670	ENST00000251691.4:c.2782C>G	6.37:g.138608050C>G	ENSP00000251691:p.Leu928Val			p.L928V	NM_020340.4	NP_065073.3	Q5TH69	BIG3_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)	16	2948	+	Breast(32;0.135)		928			Missense_Mutation	SNP	ENST00000251691.4	37	c.2782C>G	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	C	17.60	3.429550	0.62844	.	.	ENSG00000112379	ENST00000251691	T	0.57273	0.41	5.25	4.31	0.51392	5.25	4.31	0.51392	.	0.068008	0.64402	D	0.000018	T	0.64216	0.2578	M	0.75777	2.31	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	T	0.66689	-0.5860	10	0.72032	D	0.01	-11.2175	11.8879	0.52613	0.0:0.8647:0.0:0.1353	.	928	Q5TH69	BIG3_HUMAN	V	928	ENSP00000251691:L928V	ENSP00000251691:L928V	L	+	1	2	2	KIAA1244	138649743	138649743	0.953000	0.32496	0.978000	0.43139	0.744000	0.42396	2.136000	0.42121	2.738000	0.93877	0.655000	0.94253	CTA		0.622	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4		12.497831	0	0	26	26	NM_020340		4	12.585346	12.585346	6	0.400000	0	0	0	1	0	4	6	0.4
PHF7	51533	broad.mit.edu	37	3	52443574	52443574	+	5'Flank	SNP	G	G	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr3:52443574G>A	ENST00000327906.3	+	0	0				BAP1_ENST00000296288.5_Nonsense_Mutation_p.Q40*|BAP1_ENST00000460680.1_Nonsense_Mutation_p.Q40*|PHF7_ENST00000347025.2_5'Flank	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.Q40*(2)		breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		ACTCACCCCTGACATTTGCTC	0.582																																						ENST00000460680.1											2	Substitution - Nonsense(2)	kidney(1)|pleura(1)	NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180						c.(118-120)Cag>Tag	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)						218.0	228.0	224.0					3																	52443574		2203	4300	6503	SO:0001631	upstream_gene_variant	8314			monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	g.chr3:52443574G>A	AY014283	AF045581	CCDS2854.1, CCDS2855.1	CCDS2853.1	3p21.31	2013-01-28			2014-09-17			ENSG00000010318	ENSG00000010318	ENSG00000163930	ENSG00000163930		"""Zinc fingers, PHD-type"""		18458	950	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product				603089						11042152, 11829468	9528852	Standard	Standard	NM_016483	NM_004656		Approved	NYD-SP6, HSPC226	uc003ddy.3	uc003ddx.4	Q9BWX1	Q92560	OTTHUMG00000158495	OTTHUMG00000158392		3.37:g.52443574G>A	Exception_encountered		BAP1_ENST00000296288.5_Nonsense_Mutation_p.Q40*	p.Q40*	NM_004656.2	NP_004647.1	Q92560	BAP1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	3	589	-			40		K4DI82	Nonsense_Mutation	SNP	ENST00000327906.3	37	c.118C>T	CCDS2854.1	.	.	.	.	.	.	.	.	.	.	G	34	5.352033	0.95830	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	.	.	.	4.97	4.97	0.65823	4.97	4.97	0.65823	.	0.114511	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	18.2399	0.89963	0.0:0.0:1.0:0.0	.	.	.	.	X	40	.	ENSP00000296288:Q40X	Q	-	1	0	0	BAP1	52418614	52418614	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.607000	0.82883	2.312000	0.78011	0.655000	0.94253	CAG		0.582	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1		277.919426	-46	-46	233	233	NM_016483		85	287.318056	287.318056	20	0.809524	0	0	0	1	0	85	20	0.809524
SSFA2	6744	broad.mit.edu	37	2	182786871	182786871	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr2:182786871G>A	ENST00000431877.2	+	16	3586	c.3407G>A	c.(3406-3408)gGc>gAc	p.G1136D	SSFA2_ENST00000409136.1_Missense_Mutation_p.G645D|SSFA2_ENST00000320370.7_Missense_Mutation_p.G1136D|SSFA2_ENST00000467172.2_3'UTR|SSFA2_ENST00000428267.2_Missense_Mutation_p.G961D|SSFA2_ENST00000409001.1_Missense_Mutation_p.G1114D	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	1136						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			GCCTCAGTGGGCAAATCCAAA	0.478																																						ENST00000431877.2											0			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38						c.(3406-3408)gGc>gAc	sperm specific antigen 2						118.0	122.0	121.0					2																	182786871		2203	4300	6503	SO:0001583	missense	6744				cytoplasm|plasma membrane	actin binding	g.chr2:182786871G>A	M61199	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			2012-02-01			ENSG00000138434	ENSG00000138434	ENSG00000138434	ENSG00000138434				11319	11319	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""cleavage signal-1 protein"", ""KRAS-induced actin-interacting protein"", ""sperm associated antigen 13"""	"""cleavage signal-1 protein"", ""KRAS-induced actin-interacting protein"", ""sperm associated antigen 13"""	118990	118990						1555770	1555770	Standard	Standard	XM_005246812	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	uc002uoh.3	P28290	P28290	OTTHUMG00000132584	OTTHUMG00000132584	ENST00000431877.2:c.3407G>A	2.37:g.182786871G>A	ENSP00000388731:p.Gly1136Asp		SSFA2_ENST00000409136.1_Missense_Mutation_p.G645D|SSFA2_ENST00000467172.2_3'UTR|SSFA2_ENST00000409001.1_Missense_Mutation_p.G1114D|SSFA2_ENST00000428267.2_Missense_Mutation_p.G961D|SSFA2_ENST00000320370.7_Missense_Mutation_p.G1136D	p.G1136D	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0856)		16	3586	+			1136		A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	c.3407G>A	CCDS46467.1	.	.	.	.	.	.	.	.	.	.	G	10.89	1.477171	0.26511	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136;ENST00000451836	T;T;T;T;T	0.15603	2.65;2.41;2.59;2.6;2.46	5.95	0.965	0.19661	5.95	0.965	0.19661	.	0.984794	0.08352	N	0.959120	T	0.17916	0.0430	L	0.55103	1.725	0.09310	N	1	P;P;P;P;P	0.49185	0.92;0.92;0.649;0.649;0.775	P;P;B;B;B	0.48030	0.564;0.564;0.344;0.344;0.344	T	0.14504	-1.0470	10	0.27082	T	0.32	0.6002	0.9245	0.01321	0.264:0.117:0.3785:0.2406	.	961;645;1114;1136;1136	E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.;.;.;SSFA2_HUMAN;.	D	1136;1136;1114;961;645;81	ENSP00000388731:G1136D;ENSP00000314669:G1136D;ENSP00000387319:G1114D;ENSP00000409867:G961D;ENSP00000386916:G645D	ENSP00000314669:G1136D	G	+	2	0	0	SSFA2	182495116	182495116	0.950000	0.32346	0.012000	0.15200	0.409000	0.31022	1.168000	0.31859	-0.095000	0.12351	-0.253000	0.11424	GGC		0.478	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2		-17.531433	-10	-10	82	82	NM_006751		4	7.771451	7.771451	105	0.036697	0	0	0	1	0	4	105	0.036697
RPTN	126638	broad.mit.edu	37	1	152128689	152128689	+	Missense_Mutation	SNP	C	C	T	rs201025925		TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr1:152128689C>T	ENST00000316073.3	-	3	950	c.886G>A	c.(886-888)Ggt>Agt	p.G296S		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	296	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						TCCGTCTGACCGTAGTGGGAA	0.498													C|||	1	0.000199681	0.0008	0.0	5008	,	,		22400	0.0		0.0	False		,,,				2504	0.0					ENST00000316073.3											0			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						c.(886-888)Ggt>Agt	repetin						597.0	514.0	540.0					1																	152128689		1568	3582	5150	SO:0001583	missense	126638				proteinaceous extracellular matrix	calcium ion binding	g.chr1:152128689C>T	AK096436	AK096436	CCDS41397.1	CCDS41397.1	1q21.3	2013-01-10			2013-01-10			ENSG00000215853	ENSG00000215853	ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	"""EF-hand domain containing"""	26809	26809	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			613259	613259						15854042	15854042	Standard	Standard	NM_001122965	NM_001122965		Approved	FLJ39117	uc001ezs.1	uc001ezs.1	Q6XPR3	Q6XPR3	OTTHUMG00000154095	OTTHUMG00000154095	ENST00000316073.3:c.886G>A	1.37:g.152128689C>T	ENSP00000317895:p.Gly296Ser			p.G296S	NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN			3	950	-			296	Gln-rich.	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	c.886G>A	CCDS41397.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	16.30	3.083172	0.55861	.	.	ENSG00000215853	ENST00000316073	T	0.12984	2.63	4.73	-0.515	0.11954	4.73	-0.515	0.11954	.	.	.	.	.	T	0.07098	0.0180	L	0.33792	1.035	0.09310	N	1	D	0.65815	0.995	P	0.54140	0.743	T	0.25398	-1.0133	9	0.49607	T	0.09	-8.2231	8.1514	0.31143	0.0:0.4582:0.0:0.5418	.	296	Q6XPR3	RPTN_HUMAN	S	296	ENSP00000317895:G296S	ENSP00000317895:G296S	G	-	1	0	0	RPTN	150395313	150395313	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.770000	0.04705	0.098000	0.17522	-0.409000	0.06214	GGT		0.498	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1		-83.795869	-97	-97	454	454	XM_371312		4	6.426938	6.426938	327	0.012085	0	0	0	1	0	4	327	0.012085
TNFRSF1A	7132	broad.mit.edu	37	12	6439098	6439098	+	Silent	SNP	G	G	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr12:6439098G>A	ENST00000162749.2	-	9	1202	c.903C>T	c.(901-903)ccC>ccT	p.P301P	TNFRSF1A_ENST00000437813.3_5'Flank|TNFRSF1A_ENST00000540022.1_Silent_p.P258P	NM_001065.3	NP_001056.1	P19438	TNR1A_HUMAN	tumor necrosis factor receptor superfamily, member 1A	301					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 production (GO:0032715)|positive regulation of angiogenesis (GO:0045766)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|prostaglandin metabolic process (GO:0006693)|protein heterooligomerization (GO:0051291)|response to alkaloid (GO:0043279)|response to amino acid (GO:0043200)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|tetrapyrrole metabolic process (GO:0033013)|viral process (GO:0016032)	axon (GO:0030424)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	tumor necrosis factor-activated receptor activity (GO:0005031)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	19						GACAGTCACCGGGGGTATAGG	0.652																																						ENST00000162749.2											0			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	19						c.(901-903)ccC>ccT	tumor necrosis factor receptor superfamily, member 1A						27.0	29.0	28.0					12																	6439098		2194	4268	6462	SO:0001819	synonymous_variant	7132			apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|inflammatory response|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of inflammatory response|positive regulation of transcription from RNA polymerase II promoter|prostaglandin metabolic process	extracellular region|integral to plasma membrane|membrane raft	tumor necrosis factor receptor activity	g.chr12:6439098G>A	M75866	M75866	CCDS8542.1	CCDS8542.1	12p13.2	2014-09-17			2014-09-17			ENSG00000067182	ENSG00000067182	ENSG00000067182	ENSG00000067182		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11916	11916	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			191190	191190		TNFR1		TNFR1		1655358, 2158863	1655358, 2158863	Standard	Standard	NM_001065	NM_001065		Approved	TNF-R, TNFAR, TNFR60, TNF-R-I, CD120a, TNF-R55	uc001qnu.3	uc001qnu.3	P19438	P19438	OTTHUMG00000168267	OTTHUMG00000168267	ENST00000162749.2:c.903C>T	12.37:g.6439098G>A			TNFRSF1A_ENST00000540022.1_Silent_p.P258P	p.P301P	NM_001065.3	NP_001056.1	P19438	TNR1A_HUMAN			9	1202	-			301		A8K4X3|B2RDE4|B3KPQ1|B4DQB7|B4E309|B5M0B5|D3DUR1|Q9UCA4	Silent	SNP	ENST00000162749.2	37	c.903C>T	CCDS8542.1																																																																																									0.652	TNFRSF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399038.1		16.576834	1	1	10	10	NM_001065		5	16.686552	16.686552	3	0.625000	0	0	0	1	0	5	3	0.625
PDE4DIP	9659	broad.mit.edu	37	1	144856945	144856945	+	Silent	SNP	G	G	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr1:144856945G>A	ENST00000369354.3	-	40	6729	c.6540C>T	c.(6538-6540)gtC>gtT	p.V2180V	PDE4DIP_ENST00000369356.4_Silent_p.V2180V|PDE4DIP_ENST00000313382.9_Silent_p.V2074V|PDE4DIP_ENST00000369359.4_Silent_p.V2316V|PDE4DIP_ENST00000524974.1_5'UTR|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000530740.1_Silent_p.V2265V			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2180					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGTGGCCAATGACATGGCGGC	0.512			T	PDGFRB	MPD																																	ENST00000369359.4		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176						c.(6946-6948)gtC>gtT	phosphodiesterase 4D interacting protein						47.0	46.0	46.0					1																	144856945		2202	4292	6494	SO:0001819	synonymous_variant	9659			cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding	g.chr1:144856945G>A	AB007923, AB007946	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	ENSG00000178104	ENSG00000178104				15580	15580	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""myomegalin"""	"""myomegalin"""	608117	608117	"""cardiomyopathy associated 2"""	CMYA2	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	9455484, 11134006	Standard	Standard	NM_022359	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	uc021ouh.1	Q5VU43	Q5VU43	OTTHUMG00000013846	OTTHUMG00000013846	ENST00000369354.3:c.6540C>T	1.37:g.144856945G>A			PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Silent_p.V2265V|PDE4DIP_ENST00000369354.3_Silent_p.V2180V|PDE4DIP_ENST00000369356.4_Silent_p.V2180V|PDE4DIP_ENST00000313382.9_Silent_p.V2074V	p.V2316V			Q5VU43	MYOME_HUMAN		Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)	43	6986	-			2180		A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	c.6948C>T	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	.	10.45	1.354175	0.24512	.	.	ENSG00000178104	ENST00000530130	.	.	.	4.48	-2.2	0.06994	4.48	-2.2	0.06994	.	.	.	.	.	T	0.32823	0.0842	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35076	-0.9803	4	.	.	.	.	5.6072	0.17387	0.0861:0.4289:0.3666:0.1185	.	.	.	.	L	257	.	.	S	-	2	0	0	PDE4DIP	143568302	143568302	0.976000	0.34144	0.985000	0.45067	0.975000	0.68041	-0.034000	0.12225	-0.122000	0.11766	0.449000	0.29647	TCA		0.512	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2		51.534355	-6	-6	74	74	NM_022359		21	55.619767	55.619767	59	0.262500	0	0	0	1	0	21	59	0.2625
SBDS	51119	broad.mit.edu	37	7	66456163	66456163	+	Missense_Mutation	SNP	C	C	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr7:66456163C>A	ENST00000246868.2	-	4	768	c.585G>T	c.(583-585)aaG>aaT	p.K195N		NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	195					bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						TTTCTATGACCTTGATCAGTG	0.363			Gene Conversion			"""AML, MDS"""			Shwachman-Diamond syndrome																													ENST00000246868.2	yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	0			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						c.(583-585)aaG>aaT	Shwachman-Bodian-Diamond syndrome						162.0	134.0	144.0					7																	66456163		2203	4300	6503	SO:0001583	missense	51119	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	bone marrow development|bone mineralization|leukocyte chemotaxis|mature ribosome assembly|mitotic spindle stabilization|positive regulation of translation|ribosomal large subunit biogenesis|rRNA processing	cytoplasm|nucleolus|nucleoplasm|spindle pole	microtubule binding|ribosome binding|rRNA binding	g.chr7:66456163C>A	AF151855	AF151855	CCDS5537.1	CCDS5537.1	7q11.22	2014-09-17			2014-09-17			ENSG00000126524	ENSG00000126524	ENSG00000126524	ENSG00000126524				19440	19440	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			607444	607444						12496757	12496757	Standard	Standard	NM_016038	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	uc003tvm.1	Q9Y3A5	Q9Y3A5	OTTHUMG00000023165	OTTHUMG00000023165	ENST00000246868.2:c.585G>T	7.37:g.66456163C>A	ENSP00000246868:p.Lys195Asn			p.K195N	NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN			4	768	-			195		A8K0P4|Q96FX0|Q9NV53	Missense_Mutation	SNP	ENST00000246868.2	37	c.585G>T	CCDS5537.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.232682	0.39498	.	.	ENSG00000126524	ENST00000246868	D	0.96073	-3.9	5.04	5.04	0.67666	5.04	5.04	0.67666	Ribosome maturation protein SBDS, C-terminal (1);	0.042740	0.85682	D	0.000000	D	0.92708	0.7682	L	0.47716	1.5	0.80722	D	1	B	0.11235	0.004	B	0.19946	0.027	D	0.88911	0.3359	10	0.17832	T	0.49	-17.7777	15.9306	0.79656	0.0:1.0:0.0:0.0	.	195	Q9Y3A5	SBDS_HUMAN	N	195	ENSP00000246868:K195N	ENSP00000246868:K195N	K	-	3	2	2	SBDS	66093598	66093598	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.258000	0.51507	2.641000	0.89580	0.555000	0.69702	AAG		0.363	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2		-7.129469	-10	-10	93	93	NM_016038		3	6.318062	6.318062	59	0.048387	1	0	1	1	1	3	59	0.048387
PTPN23	25930	broad.mit.edu	37	3	47454066	47454066	+	Silent	SNP	T	T	C			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr3:47454066T>C	ENST00000265562.4	+	24	4457	c.4380T>C	c.(4378-4380)caT>caC	p.H1460H	PTPN23_ENST00000431726.1_Silent_p.H1334H	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1460					cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGCAGCGCCATGGTGTGCCTC	0.612																																						ENST00000265562.4											0			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23						c.(4378-4380)caT>caC	protein tyrosine phosphatase, non-receptor type 23						99.0	90.0	93.0					3																	47454066		2203	4300	6503	SO:0001819	synonymous_variant	25930			cilium morphogenesis	cilium|cytoplasmic membrane-bounded vesicle|microtubule basal body	protein tyrosine phosphatase activity	g.chr3:47454066T>C	AB025194	AB025194	CCDS2754.1	CCDS2754.1	3p21.3	2011-06-09			2011-06-09			ENSG00000076201	ENSG00000076201	ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	14406	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			606584	606584						11095967	11095967	Standard	Standard	NM_015466	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	uc003crf.1	Q9H3S7	Q9H3S7	OTTHUMG00000133520	OTTHUMG00000133520	ENST00000265562.4:c.4380T>C	3.37:g.47454066T>C			PTPN23_ENST00000431726.1_Silent_p.H1334H	p.H1460H	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)	24	4457	+			1460		A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Silent	SNP	ENST00000265562.4	37	c.4380T>C	CCDS2754.1																																																																																									0.612	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2		33.155504	8	8	54	54	NM_015466		10	34.018621	34.018621	3	0.769231	0	0	0	1	0	10	3	0.769231
KIAA1551	55196	broad.mit.edu	37	12	32137648	32137648	+	Silent	SNP	C	C	T	rs150095870		TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr12:32137648C>T	ENST00000312561.4	+	4	4173	c.3759C>T	c.(3757-3759)gaC>gaT	p.D1253D	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1253																	AACTACAAGACGACAGTAGAA	0.353																																						ENST00000312561.4											0										c.(3757-3759)gaC>gaT	KIAA1551	C		0,4406		0,0,2203	56.0	54.0	55.0		3759	-2.5	0.0	12	dbSNP_134	55	1,8597	2.2+/-6.3	0,1,4298	no	coding-synonymous	C12orf35	NM_018169.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		1253/1748	32137648	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	55196						g.chr12:32137648C>T	AK001514	AK001514	CCDS8725.2	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718	ENSG00000174718	ENSG00000174718				25559	25559	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product					"""chromosome 12 open reading frame 35"""	C12orf35	"""chromosome 12 open reading frame 35"""	C12orf35		10997877	10997877	Standard	Standard	NM_018169	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	uc001rks.3	Q9HCM1	Q9HCM1	OTTHUMG00000128501	OTTHUMG00000128501	ENST00000312561.4:c.3759C>T	12.37:g.32137648C>T			KIAA1551_ENST00000535596.1_Intron	p.D1253D	NM_018169.3	NP_060639					4	4173	+					B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Silent	SNP	ENST00000312561.4	37	c.3759C>T	CCDS8725.2																																																																																									0.353	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2		75.591357	12	12	53	53	NM_018169		24	76.196237	76.196237	37	0.393443	0	0	0	1	0	24	37	0.393443
GLIS3	169792	broad.mit.edu	37	9	3856041	3856041	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr9:3856041G>A	ENST00000324333.10	-	8	2169	c.1976C>T	c.(1975-1977)tCt>tTt	p.S659F	GLIS3_ENST00000461870.1_5'UTR|GLIS3_ENST00000381971.3_Missense_Mutation_p.S814F	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	659					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		TTGAAAAGAAGAGTTTGTTTC	0.443																																						ENST00000324333.10											0			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26						c.(1975-1977)tCt>tTt	GLIS family zinc finger 3						151.0	146.0	147.0					9																	3856041		2203	4300	6503	SO:0001583	missense	169792			negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding	g.chr9:3856041G>A	BC033899	BC033899	CCDS6451.1, CCDS43784.1	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	"""Zinc fingers, C2H2-type"""	28510	28510	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			610192	610192	"""zinc finger protein 515"""	ZNF515	"""zinc finger protein 515"""	ZNF515		14500813	14500813	Standard	Standard	NM_152629	NM_152629		Approved	MGC33662	uc003zhx.1	uc003zhx.1	Q8NEA6	Q8NEA6	OTTHUMG00000019463	OTTHUMG00000019463	ENST00000324333.10:c.1976C>T	9.37:g.3856041G>A	ENSP00000325494:p.Ser659Phe		GLIS3_ENST00000461870.1_5'UTR|GLIS3_ENST00000381971.3_Missense_Mutation_p.S814F	p.S659F	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)	8	2169	-		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)	659		B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	c.1976C>T	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	g	19.98	3.926811	0.73327	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.11930	2.74;2.73	5.8	4.9	0.64082	5.8	4.9	0.64082	.	0.245141	0.27946	N	0.017218	T	0.20047	0.0482	L	0.27053	0.805	0.24718	N	0.993167	D;P;D;P	0.59767	0.974;0.894;0.986;0.956	P;B;P;P	0.54100	0.66;0.365;0.742;0.459	T	0.04855	-1.0922	10	0.72032	D	0.01	.	16.952	0.86248	0.0:0.1277:0.8723:0.0	.	254;327;814;659	Q59FQ6;Q1PHK3;Q8NEA6-2;Q8NEA6	.;.;.;GLIS3_HUMAN	F	659;814	ENSP00000325494:S659F;ENSP00000371398:S814F	ENSP00000325494:S659F	S	-	2	0	0	GLIS3	3846041	3846041	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	4.066000	0.57520	1.454000	0.47793	0.561000	0.74099	TCT		0.443	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1		145.945991	2	2	93	93	NM_152629		46	145.948368	145.948368	47	0.494624	0	0	0	1	0	46	47	0.494624
DMXL2	23312	broad.mit.edu	37	15	51791218	51791219	+	Frame_Shift_Ins	INS	-	-	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr15:51791218_51791219insA	ENST00000251076.5	-	18	4489_4490	c.4202_4203insT	c.(4201-4203)gtafs	p.V1401fs	DMXL2_ENST00000543779.2_Frame_Shift_Ins_p.V1401fs|DMXL2_ENST00000449909.3_Intron|RP11-707P17.1_ENST00000561007.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1401						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TACTGCCACTTACACTAATAGT	0.406																																						ENST00000251076.5											0			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101						c.(4201-4203)gtafs	Dmx-like 2																																			SO:0001589	frameshift_variant	23312				cell junction|synaptic vesicle membrane	Rab GTPase binding	g.chr15:51791218_51791219insA	AB020663	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			2013-01-10			ENSG00000104093	ENSG00000104093	ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	"""WD repeat domain containing"""	2938	2938	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""rabconnectin 3"""	"""rabconnectin 3"""	612186	612186								Standard	Standard	NM_001174116	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	uc010ufy.2	Q8TDJ6	Q8TDJ6	OTTHUMG00000131749	OTTHUMG00000131749	ENST00000251076.5:c.4203dupT	15.37:g.51791219_51791219dupA	ENSP00000251076:p.Val1401fs		DMXL2_ENST00000543779.2_Frame_Shift_Ins_p.V1401fs|DMXL2_ENST00000449909.3_Intron	p.V1401fs	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN		all cancers(107;0.00494)	18	4489_4490	-			1401		B2RTR3|B7ZMH3|F5GWF1|O94938	Frame_Shift_Ins	INS	ENST00000251076.5	37	c.4202_4203insT	CCDS10141.1																																																																																									0.406	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	.	.	-32	-32	178	178	NM_015263		79			114	0.41						79	114	0.41
