#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
FHL1	2273	broad.mit.edu	37	X	135290740	135290740	+	Missense_Mutation	SNP	G	G	A			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chrX:135290740G>A	ENST00000345434.3	+	5	709	c.628G>A	c.(628-630)Gtg>Atg	p.V210M	FHL1_ENST00000394155.2_Missense_Mutation_p.V210M|FHL1_ENST00000543669.1_Missense_Mutation_p.V210M|FHL1_ENST00000370683.1_Missense_Mutation_p.V226M|FHL1_ENST00000370690.3_Missense_Mutation_p.V210M|FHL1_ENST00000535737.1_Missense_Mutation_p.V210M|FHL1_ENST00000370676.3_Intron|FHL1_ENST00000539015.1_Missense_Mutation_p.V239M|FHL1_ENST00000394153.2_Missense_Mutation_p.V210M			Q13642	FHL1_HUMAN	four and a half LIM domains 1	210	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|organ morphogenesis (GO:0009887)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane depolarization (GO:0003254)|regulation of potassium ion transmembrane transporter activity (GO:1901016)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel binding (GO:0044325)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(192;0.000127)					GTATTACTGCGTGGATTGCTA	0.527																																						ENST00000543669.1																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19						c.(628-630)Gtg>Atg		four and a half LIM domains 1							239.0	205.0	217.0					X																	135290740		2203	4300	6503	SO:0001583	missense	2273				cell differentiation|cell growth|muscle organ development|organ morphogenesis	cytosol|nucleus|plasma membrane	protein binding|zinc ion binding	g.chrX:135290740G>A	U60115	CCDS14655.1, CCDS55505.1, CCDS55506.1, CCDS55507.1, CCDS76036.1	Xq26.3	2014-09-17			ENSG00000022267	ENSG00000022267			3702	protein-coding gene	gene with protein product	"""Four-and-a-half LIM domains 1"", ""LIM protein SLIMMER"""	300163				8753811, 9714789	Standard	NM_001449		Approved	SLIM1, KYO-T, bA535K18.1, FHL1B, XMPMA, FLH1A, MGC111107	uc004ezo.3	Q13642	OTTHUMG00000022504	ENST00000345434.3:c.628G>A	X.37:g.135290740G>A	ENSP00000071281:p.Val210Met					FHL1_ENST00000370676.3_Intron|FHL1_ENST00000370683.1_Missense_Mutation_p.V226M|FHL1_ENST00000394153.2_Missense_Mutation_p.V210M|FHL1_ENST00000394155.2_Missense_Mutation_p.V210M|FHL1_ENST00000370690.3_Missense_Mutation_p.V210M|FHL1_ENST00000345434.3_Missense_Mutation_p.V210M|FHL1_ENST00000535737.1_Missense_Mutation_p.V210M|FHL1_ENST00000539015.1_Missense_Mutation_p.V239M	p.V210M	NM_001159704.1	NP_001153176.1	Q13642	FHL1_HUMAN			5	1339	+	Acute lymphoblastic leukemia(192;0.000127)		210			LIM zinc-binding 3.		B7Z5T4|B7Z793|O95212|Q13230|Q13645|Q5JXI7|Q5M7Y6|Q6IB30|Q9NZ40|Q9UKZ8|Q9Y630	Missense_Mutation	SNP	ENST00000345434.3	37	c.628G>A	CCDS55507.1	.	.	.	.	.	.	.	.	.	.	g	19.14	3.770456	0.69992	.	.	ENSG00000022267	ENST00000394155;ENST00000370690;ENST00000536581;ENST00000535737;ENST00000543669;ENST00000394153;ENST00000456218;ENST00000345434;ENST00000539015;ENST00000370683;ENST00000542704;ENST00000370674	D;D;D;D;D;D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24	4.55	4.55	0.56014	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.93452	0.7911	M	0.80746	2.51	0.80722	D	1	D;D;D	0.89917	0.991;1.0;1.0	P;D;D	0.97110	0.782;0.998;1.0	D	0.94171	0.7423	10	0.56958	D	0.05	.	16.7068	0.85374	0.0:0.0:1.0:0.0	.	239;226;210	B7Z793;B7Z5T4;Q13642	.;.;FHL1_HUMAN	M	210;210;190;210;210;210;250;210;239;226;205;210	ENSP00000377710:V210M;ENSP00000359724:V210M;ENSP00000444815:V210M;ENSP00000443333:V210M;ENSP00000377709:V210M;ENSP00000071281:V210M;ENSP00000437673:V239M;ENSP00000359717:V226M;ENSP00000359708:V210M	ENSP00000071281:V210M	V	+	1	0	FHL1	135118406	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.939000	0.87685	1.857000	0.53885	0.431000	0.28591	GTG		0.527	FHL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058461.1	NM_001449		115	42	0	0	0	1	0	115	42				
UGDH	7358	broad.mit.edu	37	4	39522980	39522980	+	Silent	SNP	A	A	G			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr4:39522980A>G	ENST00000316423.6	-	2	495	c.153T>C	c.(151-153)ccT>ccC	p.P51P	UGDH_ENST00000507089.1_Intron|UGDH_ENST00000506179.1_Silent_p.P51P|UGDH_ENST00000501493.2_Silent_p.P51P|UGDH_ENST00000515398.1_Intron	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	51					cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)			breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						CCTCATAAATAGGAAGTGTAG	0.303																																						ENST00000316423.6																			0				breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						c.(151-153)ccT>ccC		UDP-glucose 6-dehydrogenase	NADH(DB00157)						121.0	112.0	115.0					4																	39522980		2203	4300	6503	SO:0001819	synonymous_variant	7358				glycosaminoglycan biosynthetic process|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	electron carrier activity|NAD binding|UDP-glucose 6-dehydrogenase activity	g.chr4:39522980A>G	AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"""UDP-glucose dehydrogenase"""			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.153T>C	4.37:g.39522980A>G						UGDH_ENST00000506179.1_Silent_p.P51P|UGDH_ENST00000515398.1_Intron|UGDH_ENST00000507089.1_Intron|UGDH_ENST00000501493.2_Silent_p.P51P	p.P51P	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN			2	495	-			51					B3KUU2|B4DN25|O60589	Silent	SNP	ENST00000316423.6	37	c.153T>C	CCDS3455.1																																																																																				0.303	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359		13	84	0	0	0	1	0	13	84				
PALM	5064	broad.mit.edu	37	19	726159	726159	+	Silent	SNP	G	G	A	rs377213814		TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr19:726159G>A	ENST00000338448.5	+	2	73	c.27G>A	c.(25-27)acG>acA	p.T9T	PALM_ENST00000264560.7_Silent_p.T9T	NM_002579.2	NP_002570.2	O75781	PALM_HUMAN	paralemmin	9					cellular component movement (GO:0006928)|cellular response to electrical stimulus (GO:0071257)|cytoskeleton organization (GO:0007010)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of filopodium assembly (GO:0051491)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)|synapse maturation (GO:0060074)	apicolateral plasma membrane (GO:0016327)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasmic membrane-bounded vesicle (GO:0016023)|dendrite membrane (GO:0032590)|dendritic spine membrane (GO:0032591)|filopodium membrane (GO:0031527)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)		CAGAGACCACGTCCCAGCAGG	0.672																																						ENST00000264560.7																			0				endometrium(2)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						c.(25-27)acG>acA		paralemmin		G	,	0,4406		0,0,2203	70.0	66.0	67.0		27,27	-7.3	0.0	19		67	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PALM	NM_001040134.1,NM_002579.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	9/344,9/388	726159	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5064				cellular component movement|negative regulation of adenylate cyclase activity|negative regulation of dopamine receptor signaling pathway|positive regulation of filopodium assembly|regulation of cell shape	cytoplasmic membrane-bounded vesicle|filopodium membrane|integral to plasma membrane		g.chr19:726159G>A	Y16270	CCDS32857.1, CCDS32858.1	19p13.3	2008-07-17				ENSG00000099864			8594	protein-coding gene	gene with protein product		608134				9615234, 9813098	Standard	XM_005259565		Approved	KIAA0270	uc002lpm.1	O75781		ENST00000338448.5:c.27G>A	19.37:g.726159G>A						PALM_ENST00000338448.5_Silent_p.T9T|PALM_ENST00000606643.1_3'UTR	p.T9T	NM_001040134.1	NP_001035224.1	O75781	PALM_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)	2	221	+		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)	9					O43359|O95673|Q92559|Q9UPJ4|Q9UQS2|Q9UQS3	Silent	SNP	ENST00000338448.5	37	c.27G>A	CCDS32857.1																																																																																				0.672	PALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457592.1	NM_002579		33	79	0	0	0	1	0	33	79				
KGFLP2	654466	broad.mit.edu	37	9	41962602	41962602	+	lincRNA	SNP	G	G	T	rs201713470	byFrequency	TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr9:41962602G>T	ENST00000454645.1	-	0	902					NR_003670.1																						TTCTTTCTTTGTTTTTTTTCC	0.373																																						ENST00000454645.1																			0																																																			0							g.chr9:41962602G>T																													9.37:g.41962602G>T								NR_003670.1						0	902	-									RNA	SNP	ENST00000454645.1	37																																																																																						0.373	RP11-204M4.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000143738.1			5	49	1	0	0.184627	1	0.188178	5	49				
NCAPH	23397	broad.mit.edu	37	2	97019969	97019969	+	Missense_Mutation	SNP	G	G	T			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr2:97019969G>T	ENST00000240423.4	+	9	1094	c.1051G>T	c.(1051-1053)Gac>Tac	p.D351Y	NCAPH_ENST00000427946.1_Missense_Mutation_p.D215Y|NCAPH_ENST00000455200.1_Missense_Mutation_p.D340Y	NM_001281710.1|NM_001281711.1|NM_015341.3	NP_001268639.1|NP_001268640.1|NP_056156.2	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H	351					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(717;0.0221)				CCAGGTATTTGACATCAATGC	0.493																																						ENST00000455200.1																			0				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						c.(1018-1020)Gac>Tac		non-SMC condensin I complex, subunit H							175.0	173.0	174.0					2																	97019969		2203	4300	6503	SO:0001583	missense	23397				cell division|mitotic chromosome condensation	condensin complex|cytoplasm|microtubule cytoskeleton|nucleus		g.chr2:97019969G>T	BC024211	CCDS2021.1, CCDS62960.1	2q11.2	2008-02-05	2006-09-04	2006-09-04	ENSG00000121152	ENSG00000121152			1112	protein-coding gene	gene with protein product		602332	"""barren (Drosophila) homolog"", ""barren homolog (Drosophila)"", ""barren homolog 1 (Drosophila)"""	BRRN1		9417923	Standard	NM_015341		Approved	CAP-H, hCAP-H	uc002svz.1	Q15003	OTTHUMG00000130451	ENST00000240423.4:c.1051G>T	2.37:g.97019969G>T	ENSP00000240423:p.Asp351Tyr					NCAPH_ENST00000240423.4_Missense_Mutation_p.D351Y|NCAPH_ENST00000427946.1_Missense_Mutation_p.D215Y	p.D340Y			Q15003	CND2_HUMAN			9	1313	+		Ovarian(717;0.0221)	351					B4E189|Q8TB87	Missense_Mutation	SNP	ENST00000240423.4	37	c.1018G>T	CCDS2021.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.990758	0.74589	.	.	ENSG00000121152	ENST00000240423;ENST00000427946;ENST00000435975;ENST00000455200	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.80481	0.4631	M	0.80847	2.515	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.83086	-0.0135	10	0.87932	D	0	-26.7825	16.6203	0.84928	0.0:0.0:1.0:0.0	.	327;340;340;351	B4DRG7;E9PHA2;C9J470;Q15003	.;.;.;CND2_HUMAN	Y	351;215;340;340	ENSP00000240423:D351Y;ENSP00000400774:D215Y;ENSP00000405237:D340Y;ENSP00000407308:D340Y	ENSP00000240423:D351Y	D	+	1	0	NCAPH	96383696	1.000000	0.71417	0.547000	0.28179	0.815000	0.46073	5.641000	0.67881	2.534000	0.85438	0.561000	0.74099	GAC		0.493	NCAPH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252842.2	NM_015341		56	147	1	0	1.72845e-40	1	1.99147e-40	56	147				
MAML3	55534	broad.mit.edu	37	4	140811099	140811099	+	Splice_Site	SNP	C	C	T			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr4:140811099C>T	ENST00000398940.1	-	1	107	c.108G>A	c.(106-108)caG>caA	p.Q36Q	MAML3_ENST00000327122.5_Silent_p.Q341Q|MAML3_ENST00000509479.2_Silent_p.Q497Q					mastermind-like 3 (Drosophila)									p.Q497Q(2)		breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.542																																						ENST00000398940.1																			2	Substitution - coding silent(2)	p.Q497Q(2)	prostate(2)	breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25						c.e1+1		mastermind-like 3 (Drosophila)							13.0	19.0	17.0					4																	140811099		2117	4226	6343	SO:0001630	splice_region_variant	55534				Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity	g.chr4:140811099C>T	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000398940.1:c.108+1G>A	4.37:g.140811099C>T						MAML3_ENST00000327122.5_Silent_p.Q341Q|MAML3_ENST00000509479.2_Silent_p.Q497Q	p.Q36_splice			Q96JK9	MAML3_HUMAN			1	107	-	all_hematologic(180;0.162)		497						Splice_Site	SNP	ENST00000398940.1	37	c.108_splice																																																																																					0.542	MAML3-202	KNOWN	basic	protein_coding	protein_coding			Silent	4	71	0	0	0	1	0	4	71				
CCT8L2	150160	broad.mit.edu	37	22	17073401	17073401	+	Missense_Mutation	SNP	G	G	A	rs553618420		TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr22:17073401G>A	ENST00000359963.3	-	1	299	c.40C>T	c.(40-42)Cgg>Tgg	p.R14W		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	14					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				AGTGCCAGCCGCTGGGGCAGC	0.637													g|||	1	0.000199681	0.0	0.0	5008	,	,		16237	0.001		0.0	False		,,,				2504	0.0					ENST00000359963.3																			0				breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67						c.(40-42)Cgg>Tgg		chaperonin containing TCP1, subunit 8 (theta)-like 2							32.0	38.0	36.0					22																	17073401		2203	4297	6500	SO:0001583	missense	150160				cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity	g.chr22:17073401G>A	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.40C>T	22.37:g.17073401G>A	ENSP00000353048:p.Arg14Trp						p.R14W	NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN			1	299	-	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)	14					A4QPH3|Q9UJS3	Missense_Mutation	SNP	ENST00000359963.3	37	c.40C>T	CCDS13738.1	.	.	.	.	.	.	.	.	.	.	g	8.460	0.855168	0.17106	.	.	ENSG00000198445	ENST00000359963	T	0.58506	0.33	2.0	-2.6	0.06190	.	0.248450	0.21118	U	0.079861	T	0.22322	0.0538	N	0.08118	0	0.09310	N	1	D	0.62365	0.991	B	0.31812	0.136	T	0.43925	-0.9361	10	0.72032	D	0.01	-4.57	5.2189	0.15358	0.0:0.2087:0.5615:0.2297	.	14	Q96SF2	TCPQM_HUMAN	W	14	ENSP00000353048:R14W	ENSP00000353048:R14W	R	-	1	2	CCT8L2	15453401	0.000000	0.05858	0.031000	0.17742	0.042000	0.13812	0.007000	0.13174	-0.193000	0.10415	-2.528000	0.00182	CGG		0.637	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			25	37	0	0	0	1	0	25	37				
SLC11A1	6556	broad.mit.edu	37	2	219259418	219259418	+	Silent	SNP	G	G	T			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr2:219259418G>T	ENST00000233202.6	+	14	1792	c.1452G>T	c.(1450-1452)gtG>gtT	p.V484V	SLC11A1_ENST00000539932.1_Silent_p.V366V	NM_000578.3	NP_000569.3	P49279	NRAM1_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1	484					activation of protein kinase activity (GO:0032147)|antigen processing and presentation of peptide antigen (GO:0048002)|cadmium ion transmembrane transport (GO:0070574)|cellular cadmium ion homeostasis (GO:0006876)|cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|divalent metal ion export (GO:0070839)|inflammatory response (GO:0006954)|interaction with host (GO:0051701)|interleukin-2 production (GO:0032623)|interleukin-3 production (GO:0032632)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|L-arginine import (GO:0043091)|macrophage activation (GO:0042116)|manganese ion transport (GO:0006828)|MHC class II biosynthetic process (GO:0045342)|mRNA stabilization (GO:0048255)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cytokine production (GO:0001818)|nitrite transport (GO:0015707)|phagocytosis (GO:0006909)|phagosome maturation (GO:0090382)|positive regulation of cytokine production (GO:0001819)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of gene expression (GO:0010628)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus, translocation (GO:0000060)|respiratory burst (GO:0045730)|response to bacterium (GO:0009617)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|T cell cytokine production (GO:0002369)|T cell proliferation involved in immune response (GO:0002309)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|wound healing (GO:0042060)	cell outer membrane (GO:0009279)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|tertiary granule membrane (GO:0070821)	manganese ion transmembrane transporter activity (GO:0005384)|metal ion:proton antiporter activity (GO:0051139)|protein homodimerization activity (GO:0042803)|transition metal ion transmembrane transporter activity (GO:0046915)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCTACTTCGTGGTCAGCTATC	0.612																																						ENST00000233202.6																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19						c.(1450-1452)gtG>gtT		solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1							137.0	127.0	130.0					2																	219259418		2203	4300	6503	SO:0001819	synonymous_variant	6556				activation of protein kinase activity|antigen processing and presentation of peptide antigen|cadmium ion transmembrane transport|cellular cadmium ion homeostasis|cellular iron ion homeostasis|defense response to Gram-negative bacterium|defense response to protozoan|divalent metal ion export|inflammatory response|interleukin-2 production|interleukin-3 production|iron ion transport|L-arginine import|macrophage activation|MHC class II biosynthetic process|mRNA stabilization|multicellular organismal iron ion homeostasis|negative regulation of cytokine production|nitrite transport|phagocytosis|positive regulation of dendritic cell antigen processing and presentation|positive regulation of interferon-gamma production|positive regulation of phagocytosis|positive regulation of T-helper 1 type immune response|positive regulation of transcription from RNA polymerase II promoter|respiratory burst|response to interferon-gamma|response to lipopolysaccharide|T cell cytokine production|T cell proliferation involved in immune response|vacuolar acidification|wound healing	integral to plasma membrane|late endosome membrane|lysosome|phagocytic vesicle membrane|tertiary granule membrane	manganese ion transmembrane transporter activity|metal ion:hydrogen antiporter activity|protein homodimerization activity	g.chr2:219259418G>T	D38171	CCDS2415.1	2q35	2013-07-18	2013-07-18		ENSG00000018280	ENSG00000018280		"""Solute carriers"""	10907	protein-coding gene	gene with protein product	"""natural resistance-associated macrophage protein 1"""	600266		LSH, NRAMP, NRAMP1		7964458, 7980580	Standard	NM_000578		Approved		uc002vhv.3	P49279	OTTHUMG00000086747	ENST00000233202.6:c.1452G>T	2.37:g.219259418G>T						SLC11A1_ENST00000539932.1_Silent_p.V366V	p.V484V	NM_000578.3	NP_000569.3	P49279	NRAM1_HUMAN		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	14	1792	+		Renal(207;0.0474)	484					C0H5Y3	Silent	SNP	ENST00000233202.6	37	c.1452G>T	CCDS2415.1																																																																																				0.612	SLC11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195076.2	NM_000578		12	121	1	0	9.31168e-06	1	1.02816e-05	12	121				
FOXP2	93986	broad.mit.edu	37	7	114270015	114270015	+	Silent	SNP	A	A	G	rs146945410	byFrequency	TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr7:114270015A>G	ENST00000393494.2	+	5	831	c.552A>G	c.(550-552)caA>caG	p.Q184Q	FOXP2_ENST00000393491.3_Silent_p.Q92Q|FOXP2_ENST00000393489.3_Silent_p.Q92Q|FOXP2_ENST00000378237.3_Silent_p.Q184Q|FOXP2_ENST00000390668.3_Silent_p.Q208Q|FOXP2_ENST00000403559.4_Silent_p.Q201Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393498.2_Silent_p.Q164Q|FOXP2_ENST00000350908.4_Silent_p.Q184Q|FOXP2_ENST00000393500.3_Silent_p.Q109Q|FOXP2_ENST00000408937.3_Silent_p.Q209Q|FOXP2_ENST00000360232.4_Silent_p.Q184Q			O15409	FOXP2_HUMAN	forkhead box P2	184	Gln-rich.				camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|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)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						agcagcagcaacagcagcagc	0.502													A|||	2	0.000399361	0.0	0.0	5008	,	,		15840	0.001		0.001	False		,,,				2504	0.0					ENST00000393500.3																			0				breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						c.(325-327)caA>caG		forkhead box P2		A	,,,,,	5,4383		0,5,2189	47.0	43.0	45.0		552,627,552,627,552,603	-2.6	0.9	7	dbSNP_134	45	13,8553		0,13,4270	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FOXP2	NM_001172766.2,NM_001172767.2,NM_014491.3,NM_148898.3,NM_148899.3,NM_148900.3	,,,,,	0,18,6459	GG,GA,AA		0.1518,0.1139,0.139	,,,,,	184/715,209/458,184/716,209/741,184/433,201/733	114270015	18,12936	2194	4283	6477	SO:0001819	synonymous_variant	93986				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr7:114270015A>G	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.552A>G	7.37:g.114270015A>G						FOXP2_ENST00000378237.3_Silent_p.Q184Q|FOXP2_ENST00000350908.4_Silent_p.Q184Q|FOXP2_ENST00000390668.3_Silent_p.Q208Q|FOXP2_ENST00000393498.2_Silent_p.Q164Q|FOXP2_ENST00000360232.4_Silent_p.Q184Q|FOXP2_ENST00000408937.3_Silent_p.Q209Q|FOXP2_ENST00000403559.4_Silent_p.Q201Q|FOXP2_ENST00000393491.3_Silent_p.Q92Q|FOXP2_ENST00000393489.3_Silent_p.Q92Q|FOXP2_ENST00000393494.2_Silent_p.Q184Q	p.Q109Q			O15409	FOXP2_HUMAN			11	1147	+			184			Gln-rich.		A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Silent	SNP	ENST00000393494.2	37	c.327A>G	CCDS5760.1																																																																																				0.502	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		4	76	0	0	0	1	0	4	76				
AIM1	202	broad.mit.edu	37	6	106968542	106968542	+	Missense_Mutation	SNP	T	T	G			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr6:106968542T>G	ENST00000369066.3	+	2	2722	c.2235T>G	c.(2233-2235)gaT>gaG	p.D745E		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		AGGTGTTTGATCCCAAAGTGT	0.443																																						ENST00000369066.3																			0				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69						c.(2233-2235)gaT>gaG		absent in melanoma 1							63.0	66.0	65.0					6																	106968542		2203	4300	6503	SO:0001583	missense	202						sugar binding	g.chr6:106968542T>G	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.2235T>G	6.37:g.106968542T>G	ENSP00000358062:p.Asp745Glu						p.D745E	NM_001624.2	NP_001615.1	Q9Y4K1	AIM1_HUMAN	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)	2	2722	+	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	745					Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	c.2235T>G	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.357333	0.82243	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	D	0.85171	-1.95	6.16	-2.91	0.05631	.	0.281183	0.34200	N	0.004180	D	0.88104	0.6347	M	0.78637	2.42	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.89189	0.3549	10	0.72032	D	0.01	.	14.1385	0.65303	0.0:0.5038:0.0:0.4962	.	745	Q9Y4K1	AIM1_HUMAN	E	1153;745	ENSP00000358062:D745E	ENSP00000285105:D1153E	D	+	3	2	AIM1	107075235	0.997000	0.39634	0.986000	0.45419	0.947000	0.59692	0.248000	0.18198	-0.248000	0.09583	0.528000	0.53228	GAT		0.443	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			4	104	0	0	0	1	0	4	104				
SCNN1B	6338	broad.mit.edu	37	16	23391983	23391983	+	Missense_Mutation	SNP	C	C	T			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr16:23391983C>T	ENST00000343070.2	+	13	1960	c.1784C>T	c.(1783-1785)gCc>gTc	p.A595V	SCNN1B_ENST00000568923.1_Missense_Mutation_p.A568V|SCNN1B_ENST00000307331.5_Missense_Mutation_p.A640V|SCNN1B_ENST00000568085.1_Missense_Mutation_p.A559V	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	595					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	CCTGACACGGCCCCCCGCAGC	0.711																																						ENST00000343070.2																			0				breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32						c.(1783-1785)gCc>gTc		sodium channel, non-voltage-gated 1, beta subunit	Amiloride(DB00594)|Triamterene(DB00384)						26.0	31.0	29.0					16																	23391983		2194	4297	6491	SO:0001583	missense	0				excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding	g.chr16:23391983C>T	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10600	protein-coding gene	gene with protein product	"""Liddle syndrome"""	600760	"""sodium channel, nonvoltage-gated 1, beta"", ""sodium channel, non-voltage-gated 1, beta"""				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.1784C>T	16.37:g.23391983C>T	ENSP00000345751:p.Ala595Val					SCNN1B_ENST00000568085.1_Missense_Mutation_p.A559V|SCNN1B_ENST00000307331.5_Missense_Mutation_p.A640V|SCNN1B_ENST00000568923.1_Missense_Mutation_p.A568V	p.A595V	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN		GBM - Glioblastoma multiforme(48;0.0465)	13	1960	+			595					C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Missense_Mutation	SNP	ENST00000343070.2	37	c.1784C>T	CCDS10609.1	.	.	.	.	.	.	.	.	.	.	C	3.189	-0.166204	0.06461	.	.	ENSG00000168447	ENST00000343070;ENST00000307331	T;T	0.80214	-1.35;-1.35	4.61	1.47	0.22746	.	1.414580	0.04442	N	0.371026	T	0.60894	0.2304	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.47005	-0.9150	10	0.12430	T	0.62	-15.8937	5.3525	0.16043	0.3563:0.5464:0.0:0.0973	.	595	P51168	SCNNB_HUMAN	V	595;640	ENSP00000345751:A595V;ENSP00000302874:A640V	ENSP00000302874:A640V	A	+	2	0	SCNN1B	23299484	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.122000	0.15687	0.034000	0.15491	-0.165000	0.13383	GCC		0.711	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2			26	59	0	0	0	1	0	26	59				
OR5AK2	390181	broad.mit.edu	37	11	56756464	56756464	+	Missense_Mutation	SNP	A	A	G			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr11:56756464A>G	ENST00000326855.2	+	1	118	c.76A>G	c.(76-78)Atc>Gtc	p.I26V		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	26						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						GTTTTGGTGTATCCTCTTCAT	0.398																																						ENST00000326855.2																			0				breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						c.(76-78)Atc>Gtc		olfactory receptor, family 5, subfamily AK, member 2							154.0	144.0	147.0					11																	56756464		2201	4296	6497	SO:0001583	missense	390181				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:56756464A>G	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"""GPCR / Class A : Olfactory receptors"""	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.76A>G	11.37:g.56756464A>G	ENSP00000322784:p.Ile26Val						p.I26V	NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN			1	118	+			26					B2RNZ9	Missense_Mutation	SNP	ENST00000326855.2	37	c.76A>G	CCDS31538.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.835709	0.00069	.	.	ENSG00000181273	ENST00000326855	T	0.00438	7.42	3.66	-7.32	0.01436	.	1.388660	0.05333	N	0.528642	T	0.00144	0.0004	N	0.02985	-0.445	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.38222	-0.9671	10	0.09084	T	0.74	-6.414	5.5393	0.17030	0.158:0.1524:0.5966:0.093	.	26	Q8NH90	O5AK2_HUMAN	V	26	ENSP00000322784:I26V	ENSP00000322784:I26V	I	+	1	0	OR5AK2	56513040	0.000000	0.05858	0.001000	0.08648	0.069000	0.16628	-4.211000	0.00273	-2.295000	0.00662	0.163000	0.16589	ATC		0.398	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323		4	135	0	0	0	1	0	4	135				
GJA4	2701	broad.mit.edu	37	1	35260022	35260022	+	Missense_Mutation	SNP	T	T	G			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr1:35260022T>G	ENST00000342280.4	+	2	296	c.208T>G	c.(208-210)Ttc>Gtc	p.F70V		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	70					blood vessel development (GO:0001568)|calcium ion transport (GO:0006816)|cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|endothelium development (GO:0003158)|response to pain (GO:0048265)|transport (GO:0006810)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(4)|stomach(1)	14		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TGACCAGGCCTTCCCCATCTC	0.607																																						ENST00000342280.4																			0				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(4)|stomach(1)	14						c.(208-210)Ttc>Gtc		gap junction protein, alpha 4, 37kDa							134.0	114.0	121.0					1																	35260022		2203	4300	6503	SO:0001583	missense	2701				cell-cell junction assembly	integral to plasma membrane		g.chr1:35260022T>G	M96789	CCDS30669.1	1p35.1	2008-02-05	2007-01-16		ENSG00000187513	ENSG00000187513		"""Ion channels / Gap junction proteins (connexins)"""	4278	protein-coding gene	gene with protein product	"""connexin 37"""	121012	"""gap junction protein, alpha 4, 37kD (connexin 37)"", ""gap junction protein, alpha 4, 37kDa (connexin 37)"""			9843209, 7680674	Standard	XM_005270750		Approved	CX37	uc001bya.3	P35212	OTTHUMG00000004050	ENST00000342280.4:c.208T>G	1.37:g.35260022T>G	ENSP00000343676:p.Phe70Val						p.F70V	NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN			2	296	+		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)	70					A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Missense_Mutation	SNP	ENST00000342280.4	37	c.208T>G	CCDS30669.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.542379	0.85917	.	.	ENSG00000187513	ENST00000342280;ENST00000450137;ENST00000543143	D;D	0.99186	-5.53;-5.53	5.48	5.48	0.80851	Connexin, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.99527	0.9831	H	0.95884	3.735	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.995;0.997	D	0.98019	1.0370	10	0.87932	D	0	.	15.5702	0.76330	0.0:0.0:0.0:1.0	.	70;70	Q5JW71;P35212	.;CXA4_HUMAN	V	70	ENSP00000343676:F70V;ENSP00000409186:F70V	ENSP00000343676:F70V	F	+	1	0	GJA4	35032609	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.991000	0.88244	2.060000	0.61445	0.533000	0.62120	TTC		0.607	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060		5	112	0	0	0	1	0	5	112				
CCDC144A	9720	broad.mit.edu	37	17	16593944	16593944	+	Missense_Mutation	SNP	G	G	T			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr17:16593944G>T	ENST00000360524.8	+	1	306	c.230G>T	c.(229-231)cGc>cTc	p.R77L	CCDC144A_ENST00000436374.1_3'UTR|CCDC144A_ENST00000340621.5_Missense_Mutation_p.R77L|RP11-219A15.1_ENST00000448331.3_Missense_Mutation_p.R77L|RNU6-405P_ENST00000516637.1_RNA|CCDC144A_ENST00000456009.1_Missense_Mutation_p.R77L|CCDC144A_ENST00000443444.2_Missense_Mutation_p.R77L|CCDC144A_ENST00000399273.1_Missense_Mutation_p.R77L	NM_014695.1	NP_055510.1	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	77																	CACGACGTCCGCCTGGAAGAT	0.647																																						ENST00000443444.2																			0											c.(229-231)cGc>cTc		coiled-coil domain containing 144A							78.0	87.0	84.0					17																	16593944		2203	4296	6499	SO:0001583	missense	9720							g.chr17:16593944G>T	BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	ENST00000360524.8:c.230G>T	17.37:g.16593944G>T	ENSP00000353717:p.Arg77Leu					CCDC144A_ENST00000436374.1_3'UTR|CCDC144A_ENST00000360524.8_Missense_Mutation_p.R77L|RP11-219A15.1_ENST00000448331.3_Missense_Mutation_p.R77L|CCDC144A_ENST00000399273.1_Missense_Mutation_p.R77L|CCDC144A_ENST00000456009.1_Missense_Mutation_p.R77L|CCDC144A_ENST00000340621.5_Missense_Mutation_p.R77L	p.R77L			A2RUR9	C144A_HUMAN			1	370	+			77					O60311|Q6ZU57	Missense_Mutation	SNP	ENST00000360524.8	37	c.230G>T	CCDS45621.1	.	.	.	.	.	.	.	.	.	.	.	2.965	-0.213791	0.06140	.	.	ENSG00000170160	ENST00000420937;ENST00000340621;ENST00000399273;ENST00000436374;ENST00000399264;ENST00000443444;ENST00000448331;ENST00000360524;ENST00000456009;ENST00000360495	T;T;T;T;T;T;T	0.19105	2.17;2.17;2.17;2.17;2.17;2.17;2.17	0.311	-0.622	0.11560	.	.	.	.	.	T	0.09113	0.0225	N	0.08118	0	0.09310	N	1	B	0.15473	0.013	B	0.08055	0.003	T	0.28004	-1.0057	8	0.66056	D	0.02	.	.	.	.	.	77	A2RUR9	C144A_HUMAN	L	77	ENSP00000344740:R77L;ENSP00000382215:R77L;ENSP00000439262:R77L;ENSP00000440655:R77L;ENSP00000353717:R77L;ENSP00000394201:R77L;ENSP00000353685:R77L	ENSP00000344740:R77L	R	+	2	0	CCDC144A	16534669	0.019000	0.18553	0.000000	0.03702	0.000000	0.00434	-0.728000	0.04925	-0.522000	0.06417	-0.523000	0.04350	CGC		0.647	CCDC144A-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444093.1			7	167	1	0	0.248553	1	0.248553	7	167				
NOS2	4843	broad.mit.edu	37	17	26099431	26099431	+	Missense_Mutation	SNP	C	C	T			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr17:26099431C>T	ENST00000313735.6	-	14	1840	c.1607G>A	c.(1606-1608)cGa>cAa	p.R536Q		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	536					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	GACTCTGACTCGGGACGCCAT	0.572																																						ENST00000313735.6																			0				autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56						c.(1606-1608)cGa>cAa		nitric oxide synthase 2, inducible	Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)						83.0	70.0	74.0					17																	26099431		2203	4300	6503	SO:0001583	missense	4843				arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding	g.chr17:26099431C>T	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.1607G>A	17.37:g.26099431C>T	ENSP00000327251:p.Arg536Gln						p.R536Q	NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN			14	1840	-			536					A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	37	c.1607G>A	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	C	36	5.838450	0.97009	.	.	ENSG00000007171	ENST00000313735;ENST00000379105;ENST00000302153	T	0.60040	0.22	5.97	5.97	0.96955	.	0.000000	0.64402	D	0.000001	T	0.80529	0.4640	M	0.87617	2.895	0.58432	D	0.999997	D;D	0.89917	0.999;1.0	D;D	0.91635	0.974;0.999	T	0.80839	-0.1203	10	0.49607	T	0.09	.	19.4269	0.94746	0.0:1.0:0.0:0.0	.	536;536	F8WEM3;P35228	.;NOS2_HUMAN	Q	536;497;536	ENSP00000327251:R536Q	ENSP00000305638:R536Q	R	-	2	0	NOS2	23123558	1.000000	0.71417	0.990000	0.47175	0.889000	0.51656	7.818000	0.86416	2.836000	0.97738	0.655000	0.94253	CGA		0.572	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		17	43	0	0	0	1	0	17	43				
PCDH11X	27328	broad.mit.edu	37	X	91133813	91133813	+	Silent	SNP	C	C	T			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chrX:91133813C>T	ENST00000373094.1	+	2	3419	c.2574C>T	c.(2572-2574)aaC>aaT	p.N858N	PCDH11X_ENST00000406881.1_Silent_p.N858N|PCDH11X_ENST00000373088.1_Silent_p.N858N|PCDH11X_ENST00000373097.1_Silent_p.N858N|PCDH11X_ENST00000361724.1_Silent_p.N858N|PCDH11X_ENST00000298274.8_Silent_p.N858N|PCDH11X_ENST00000395337.2_Silent_p.N858N|PCDH11X_ENST00000504220.2_Silent_p.N858N|PCDH11X_ENST00000361655.2_Silent_p.N858N	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	858					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						CTACCCCAAACCCAGAAAACA	0.393																																					NSCLC(38;925 1092 2571 38200 45895)	ENST00000373094.1																			0				NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						c.(2572-2574)aaC>aaT		protocadherin 11 X-linked							58.0	55.0	56.0					X																	91133813		2203	4300	6503	SO:0001819	synonymous_variant	27328				homophilic cell adhesion	integral to plasma membrane	calcium ion binding	g.chrX:91133813C>T	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"""Cadherins / Protocadherins : Non-clustered"""	8656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 119"""	300246	"""protocadherin 11"""	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.2574C>T	X.37:g.91133813C>T						PCDH11X_ENST00000395337.2_Silent_p.N858N|PCDH11X_ENST00000361724.1_Silent_p.N858N|PCDH11X_ENST00000406881.1_Silent_p.N858N|PCDH11X_ENST00000298274.8_Silent_p.N858N|PCDH11X_ENST00000373097.1_Silent_p.N858N|PCDH11X_ENST00000373088.1_Silent_p.N858N|PCDH11X_ENST00000361655.2_Silent_p.N858N|PCDH11X_ENST00000504220.1_Silent_p.N858N	p.N858N	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN			2	3419	+			858					A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Silent	SNP	ENST00000373094.1	37	c.2574C>T	CCDS14461.1																																																																																				0.393	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		31	13	0	0	0	1	0	31	13				
GNGT1	2792	broad.mit.edu	37	7	93536062	93536062	+	Missense_Mutation	SNP	C	C	A			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr7:93536062C>A	ENST00000248572.5	+	2	152	c.4C>A	c.(4-6)Cca>Aca	p.P2T	GNGT1_ENST00000429473.1_Missense_Mutation_p.P2T|GNGT1_ENST00000455502.1_Missense_Mutation_p.P2T|GNGT1_ENST00000430875.1_Missense_Mutation_p.P2T|GNGT1_ENST00000428834.1_Missense_Mutation_p.P2T	NM_021955.3	NP_068774.1	P63211	GBG1_HUMAN	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	2					cardiac muscle cell apoptotic process (GO:0010659)|cellular response to hypoxia (GO:0071456)|eye photoreceptor cell development (GO:0042462)|GTP catabolic process (GO:0006184)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	heterotrimeric G-protein complex (GO:0005834)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	6	all_cancers(62;2.39e-10)|all_epithelial(64;1.54e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			CAAAAAGATGCCAGTAATCAA	0.403																																						ENST00000455502.1																			0				endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	6						c.(4-6)Cca>Aca		guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1							115.0	112.0	113.0					7																	93536062		2203	4300	6503	SO:0001583	missense	2792				G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|signal transducer activity	g.chr7:93536062C>A		CCDS5633.1	7q21.3	2008-07-18			ENSG00000127928	ENSG00000127928			4411	protein-coding gene	gene with protein product		189970				8661128	Standard	NM_021955		Approved	GNG1	uc003unc.1	P63211	OTTHUMG00000022908	ENST00000248572.5:c.4C>A	7.37:g.93536062C>A	ENSP00000248572:p.Pro2Thr					GNGT1_ENST00000428834.1_Missense_Mutation_p.P2T|GNGT1_ENST00000429473.1_Missense_Mutation_p.P2T|GNGT1_ENST00000430875.1_Missense_Mutation_p.P2T|GNGT1_ENST00000248572.5_Missense_Mutation_p.P2T	p.P2T			P63211	GBG1_HUMAN	STAD - Stomach adenocarcinoma(171;0.000967)		3	258	+	all_cancers(62;2.39e-10)|all_epithelial(64;1.54e-09)|Lung NSC(181;0.218)		2					A4D1H2|O43835|Q08447|Q16026|Q6LCP6	Missense_Mutation	SNP	ENST00000248572.5	37	c.4C>A	CCDS5633.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.518307	0.44763	.	.	ENSG00000127928	ENST00000455502;ENST00000248572;ENST00000429473;ENST00000430875;ENST00000428834	T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63	5.75	5.75	0.90469	G-protein gamma domain (2);	0.000000	0.85682	D	0.000000	T	0.41259	0.1151	.	.	.	0.54753	D	0.999989	D	0.58268	0.982	P	0.47118	0.538	T	0.29671	-1.0004	9	0.72032	D	0.01	-8.3311	19.0975	0.93258	0.0:1.0:0.0:0.0	.	2	P63211	GBG1_HUMAN	T	2	ENSP00000395857:P2T;ENSP00000248572:P2T;ENSP00000388777:P2T;ENSP00000395756:P2T;ENSP00000401781:P2T	ENSP00000248572:P2T	P	+	1	0	GNGT1	93373998	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	6.631000	0.74277	2.885000	0.99019	0.655000	0.94253	CCA		0.403	GNGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254718.2	NM_021955		20	66	1	0	8.00594e-06	1	9.02797e-06	20	66				
EIF4G3	8672	broad.mit.edu	37	1	21329207	21329207	+	Splice_Site	SNP	G	G	A			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr1:21329207G>A	ENST00000264211.8	-	2	223	c.29C>T	c.(28-30)cCg>cTg	p.P10L	EIF4G3_ENST00000374935.3_Splice_Site_p.P10L|EIF4G3_ENST00000374927.4_Splice_Site_p.P10L|EIF4G3_ENST00000356916.3_Splice_Site_p.P10L|EIF4G3_ENST00000602326.1_Splice_Site_p.P10L|EIF4G3_ENST00000400422.1_Splice_Site_p.P10L|EIF4G3_ENST00000374937.3_Splice_Site_p.P10L	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	10					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		CTTACTTACCGGAGAACGGGT	0.448																																						ENST00000602326.1																			0				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70						c.e5+1		eukaryotic translation initiation factor 4 gamma, 3							306.0	298.0	300.0					1																	21329207		2203	4300	6503	SO:0001630	splice_region_variant	8672				interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity	g.chr1:21329207G>A	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.30+1C>T	1.37:g.21329207G>A						EIF4G3_ENST00000356916.3_Splice_Site_p.P10_splice|EIF4G3_ENST00000400422.1_Splice_Site_p.P10_splice|EIF4G3_ENST00000264211.8_Splice_Site_p.P10_splice|EIF4G3_ENST00000374927.4_Splice_Site_p.P10_splice|EIF4G3_ENST00000374935.3_Splice_Site_p.P10_splice|EIF4G3_ENST00000374937.3_Splice_Site_p.P10_splice	p.P10_splice	NM_001198802.1	NP_001185731.1	O43432	IF4G3_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)	5	612	-		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)	10					B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Splice_Site	SNP	ENST00000264211.8	37	c.30_splice	CCDS214.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.647342	0.67358	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000374937;ENST00000356916;ENST00000374927;ENST00000438975;ENST00000411888	T;T;T;T;T;T;T;T	0.38887	2.12;2.12;2.12;2.1;2.0;2.12;2.12;1.11	5.6	5.6	0.85130	.	0.380726	0.30051	N	0.010534	T	0.49712	0.1573	N	0.14661	0.345	0.49130	D	0.999752	D;D;D;D;D	0.89917	1.0;1.0;0.986;1.0;1.0	D;D;P;D;D	0.91635	0.999;0.988;0.455;0.998;0.997	T	0.54583	-0.8272	10	0.52906	T	0.07	-9.397	17.8508	0.88747	0.0:0.0:1.0:0.0	.	10;10;125;10;10	B4DXR2;Q504Z1;B1AN89;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	L	10;200;10;10;10;125;10;10;10	ENSP00000264211:P10L;ENSP00000383274:P10L;ENSP00000364071:P10L;ENSP00000364073:P10L;ENSP00000349386:P125L;ENSP00000364062:P10L;ENSP00000395381:P10L;ENSP00000396083:P10L	ENSP00000264211:P10L	P	-	2	0	EIF4G3	21201794	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.669000	0.74462	2.641000	0.89580	0.650000	0.86243	CCG		0.448	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760	Missense_Mutation	13	248	0	0	0	1	0	13	248				
TSSC2	650368	broad.mit.edu	37	11	3427759	3427759	+	RNA	SNP	C	C	T			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr11:3427759C>T	ENST00000529482.1	+	0	876									tumor suppressing subtransferable candidate 2 pseudogene																		TGTCTGCACACGTCCTGCAGT	0.612																																						ENST00000529482.1																			0																																																			0							g.chr11:3427759C>T			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427759C>T														0	876	+									RNA	SNP	ENST00000529482.1	37																																																																																						0.612	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			3	48	0	0	0	1	0	3	48				
KRT15	3866	broad.mit.edu	37	17	39673194	39673194	+	Missense_Mutation	SNP	G	G	A	rs201818657		TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr17:39673194G>A	ENST00000254043.3	-	3	4189	c.604C>T	c.(604-606)Cgc>Tgc	p.R202C	KRT15_ENST00000393981.3_Missense_Mutation_p.R37C|KRT15_ENST00000393974.3_Missense_Mutation_p.R37C|KRT15_ENST00000393976.2_Missense_Mutation_p.R202C	NM_002275.3	NP_002266	P19012	K1C15_HUMAN	keratin 15	202	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		Breast(137;0.000286)				ACGCCCTGGCGCAGGGCCAGC	0.597																																						ENST00000254043.3																			0				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						c.(604-606)Cgc>Tgc		keratin 15		G	CYS/ARG	0,4406		0,0,2203	72.0	74.0	73.0		604	4.9	1.0	17		73	1,8599		0,1,4299	yes	missense	KRT15	NM_002275.3	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	202/457	39673194	1,13005	2203	4300	6503	SO:0001583	missense	3866				epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton	g.chr17:39673194G>A		CCDS11398.1	17q21.2	2013-06-20			ENSG00000171346	ENSG00000171346		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6421	protein-coding gene	gene with protein product	"""keratin-15, basic"", ""keratin-15, beta"", ""type I cytoskeletal 15"", ""cytokeratin 15"""	148030				16831889	Standard	NM_002275		Approved	K15, CK15, K1CO	uc002hwy.3	P19012	OTTHUMG00000133435	ENST00000254043.3:c.604C>T	17.37:g.39673194G>A	ENSP00000254043:p.Arg202Cys					KRT15_ENST00000393981.3_Missense_Mutation_p.R37C|KRT15_ENST00000393974.3_Missense_Mutation_p.R37C|KRT15_ENST00000393976.2_Missense_Mutation_p.R202C	p.R202C	NM_002275.3	NP_002266.2	P19012	K1C15_HUMAN			3	4189	-		Breast(137;0.000286)	202			Coil 1B.|Rod.		B3KQY1|B3KRA2|E0CX14|Q53XV8|Q9BUG4	Missense_Mutation	SNP	ENST00000254043.3	37	c.604C>T	CCDS11398.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.250801	0.59212	0.0	1.16E-4	ENSG00000171346	ENST00000254043;ENST00000393974;ENST00000393976;ENST00000393981;ENST00000458290	D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91	4.86	4.86	0.63082	Filament (1);	0.000000	0.50627	D	0.000119	D	0.95526	0.8546	M	0.78916	2.43	0.80722	D	1	D;P;D	0.89917	1.0;0.928;0.989	D;P;P	0.87578	0.998;0.632;0.808	D	0.95614	0.8675	10	0.72032	D	0.01	.	13.1878	0.59691	0.0:0.0:0.8407:0.1593	.	37;202;202	A8MT21;B3KVF5;P19012	.;.;K1C15_HUMAN	C	202;37;202;37;37	ENSP00000254043:R202C;ENSP00000377544:R37C;ENSP00000377546:R202C;ENSP00000377550:R37C;ENSP00000409282:R37C	ENSP00000254043:R202C	R	-	1	0	KRT15	36926720	0.998000	0.40836	1.000000	0.80357	0.351000	0.29236	4.362000	0.59467	2.514000	0.84764	0.650000	0.86243	CGC		0.597	KRT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257301.1	NM_002275		4	111	0	0	0	1	0	4	111				
CHEK2P2	646096	broad.mit.edu	37	15	20488802	20488802	+	RNA	SNP	T	T	C			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr15:20488802T>C	ENST00000555186.1	+	0	285					NR_038836.1				checkpoint kinase 2 pseudogene 2																		TCATGAGAACTTTATGTGGAA	0.423																																						ENST00000555186.1																			0																																																			0							g.chr15:20488802T>C			15q11.1	2011-11-11			ENSG00000259156	ENSG00000259156			43578	pseudogene	pseudogene							Standard	NR_038836		Approved		uc001ytf.1		OTTHUMG00000171660		15.37:g.20488802T>C								NR_038836.1						0	285	+									RNA	SNP	ENST00000555186.1	37																																																																																						0.423	CHEK2P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000414654.1	NR_038836		4	112	0	0	0	1	0	4	112				
SPATA31A6	389730	broad.mit.edu	37	9	43627263	43627263	+	Missense_Mutation	SNP	C	C	T	rs559415564	byFrequency	TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr9:43627263C>T	ENST00000332857.6	-	4	1452	c.1424G>A	c.(1423-1425)cGc>cAc	p.R475H	SPATA31A6_ENST00000496386.1_5'Flank	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	475					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AAAGGGTTGGCGGTGGGACAG	0.527																																						ENST00000332857.6																			0											c.(1423-1425)cGc>cAc		SPATA31 subfamily A, member 6							103.0	117.0	113.0					9																	43627263		617	1533	2150	SO:0001583	missense	389730							g.chr9:43627263C>T		CCDS75837.1	9p11.2	2012-10-15	2012-10-12	2012-10-12	ENSG00000185775	ENSG00000185775			32006	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A6"""	FAM75A6		20850414	Standard	NM_001145196		Approved	OTTHUMG00000013224	uc011lrb.2	Q5VVP1	OTTHUMG00000013224	ENST00000332857.6:c.1424G>A	9.37:g.43627263C>T	ENSP00000329825:p.Arg475His						p.R475H	NM_001145196.1	NP_001138668.1					4	1452	-									Missense_Mutation	SNP	ENST00000332857.6	37	c.1424G>A	CCDS47973.1	.	.	.	.	.	.	.	.	.	.	C	0.370	-0.934478	0.02340	.	.	ENSG00000185775	ENST00000332857	T	0.06449	3.3	2.13	0.22	0.15279	.	1.217210	0.05894	N	0.628683	T	0.03053	0.0090	N	0.08118	0	0.09310	N	1	B	0.17465	0.022	B	0.11329	0.006	T	0.46414	-0.9193	10	0.15066	T	0.55	-0.2466	3.398	0.07313	0.1687:0.2738:0.5575:0.0	.	475	Q5VVP1	F75A6_HUMAN	H	475	ENSP00000329825:R475H	ENSP00000329825:R475H	R	-	2	0	FAM75A6	43567259	0.001000	0.12720	0.000000	0.03702	0.019000	0.09904	-1.478000	0.02329	0.056000	0.16144	-1.398000	0.01145	CGC		0.527	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196		215	332	0	0	0	1	0	215	332				
FCGBP	8857	broad.mit.edu	37	19	40357401	40357401	+	Silent	SNP	C	C	A			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr19:40357401C>A	ENST00000221347.6	-	34	15919	c.15912G>T	c.(15910-15912)acG>acT	p.T5304T		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	5304	VWFD 13. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TTGGAGTCAACGTCACCATCC	0.542																																						ENST00000221347.6																			0				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165						c.(15910-15912)acG>acT		Fc fragment of IgG binding protein							134.0	127.0	129.0					19																	40357401		2203	4300	6503	SO:0001819	synonymous_variant	8857					extracellular region	protein binding	g.chr19:40357401C>A	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.15912G>T	19.37:g.40357401C>A							p.T5304T	NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)		34	15919	-	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		5304			VWFD 13.		O95784	Silent	SNP	ENST00000221347.6	37	c.15912G>T	CCDS12546.1																																																																																				0.542	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		4	82	1	0	0.00909568	1	0.00964142	4	82				
ZNF814	730051	broad.mit.edu	37	19	58385546	58385546	+	Missense_Mutation	SNP	G	G	T	rs201682072		TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr19:58385546G>T	ENST00000435989.2	-	3	1446	c.1212C>A	c.(1210-1212)gaC>gaA	p.D404E	ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	404					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D404E(10)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						AATGTTTTTTGTCAGTGTGAA	0.393																																						ENST00000435989.2																			10	Substitution - Missense(10)	p.D404E(10)	urinary_tract(3)|kidney(3)|prostate(2)|NS(1)|skin(1)	NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						c.(1210-1212)gaC>gaA		zinc finger protein 814							117.0	93.0	100.0					19																	58385546		692	1591	2283	SO:0001583	missense	730051				regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding	g.chr19:58385546G>T		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.1212C>A	19.37:g.58385546G>T	ENSP00000410545:p.Asp404Glu					ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000595295.1_Intron	p.D404E	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN			3	1446	-			404					A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	c.1212C>A	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	11.12	1.545823	0.27652	.	.	ENSG00000204514	ENST00000435989;ENST00000376205	T	0.14640	2.49	2.33	-4.66	0.03329	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04363	0.0120	N	0.03177	-0.4	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.33574	-0.9863	9	0.54805	T	0.06	.	1.2175	0.01917	0.3897:0.3041:0.1331:0.1731	.	404	B7Z6K7	ZN814_HUMAN	E	404;266	ENSP00000410545:D404E	ENSP00000365378:D266E	D	-	3	2	ZNF814	63077358	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-1.489000	0.02306	-2.531000	0.00491	-1.292000	0.01352	GAC		0.393	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		6	21	1	0	0.0215528	1	0.022398	6	21				
LPHN3	23284	broad.mit.edu	37	4	62812714	62812714	+	Silent	SNP	G	G	A	rs35637502	byFrequency	TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr4:62812714G>A	ENST00000514591.1	+	15	2627	c.2298G>A	c.(2296-2298)acG>acA	p.T766T	LPHN3_ENST00000508946.1_Silent_p.T766T|LPHN3_ENST00000506720.1_Silent_p.T834T|LPHN3_ENST00000507625.1_Silent_p.T834T|LPHN3_ENST00000514157.1_Silent_p.T766T|LPHN3_ENST00000509896.1_Silent_p.T834T|LPHN3_ENST00000507164.1_Silent_p.T834T|LPHN3_ENST00000506746.1_Silent_p.T834T|LPHN3_ENST00000508693.1_Silent_p.T834T|LPHN3_ENST00000504896.1_Silent_p.T766T|LPHN3_ENST00000506700.1_Silent_p.T766T|LPHN3_ENST00000511324.1_Silent_p.T834T|LPHN3_ENST00000508078.1_3'UTR|LPHN3_ENST00000545650.1_Silent_p.T766T|LPHN3_ENST00000514996.1_Silent_p.T766T|LPHN3_ENST00000512091.2_Silent_p.T766T			Q9HAR2	LPHN3_HUMAN	latrophilin 3	753					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						AGTTGGGAACGGAAGCTTTGT	0.403													G|||	16	0.00319489	0.0113	0.0014	5008	,	,		16768	0.0		0.0	False		,,,				2504	0.0					ENST00000512091.1																			0				breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						c.(2296-2298)acG>acA		latrophilin 3		G		41,3731		0,41,1845	252.0	236.0	241.0		2298	-4.8	1.0	4	dbSNP_126	241	4,8236		0,4,4116	no	coding-synonymous	LPHN3	NM_015236.4		0,45,5961	AA,AG,GG		0.0485,1.087,0.3746		766/1470	62812714	45,11967	1886	4120	6006	SO:0001819	synonymous_variant	23284				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding	g.chr4:62812714G>A	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.2298G>A	4.37:g.62812714G>A						LPHN3_ENST00000507625.1_Silent_p.T834T|LPHN3_ENST00000514591.1_Silent_p.T766T|LPHN3_ENST00000514157.1_Silent_p.T766T|LPHN3_ENST00000506746.1_Silent_p.T834T|LPHN3_ENST00000545650.1_Silent_p.T766T|LPHN3_ENST00000508078.1_3'UTR|LPHN3_ENST00000504896.1_Silent_p.T766T|LPHN3_ENST00000511324.1_Silent_p.T834T|LPHN3_ENST00000507164.1_Silent_p.T834T|LPHN3_ENST00000514996.1_Silent_p.T766T|LPHN3_ENST00000509896.1_Silent_p.T834T|LPHN3_ENST00000506700.1_Silent_p.T766T|LPHN3_ENST00000508693.1_Silent_p.T834T|LPHN3_ENST00000508946.1_Silent_p.T766T|LPHN3_ENST00000506720.1_Silent_p.T834T	p.T766T			Q9HAR2	LPHN3_HUMAN			15	3045	+			753					E9PE04|O94867|Q9NWK5	Silent	SNP	ENST00000514591.1	37	c.2298G>A	CCDS54768.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	G	8.415	0.845025	0.16963	0.01087	4.85E-4	ENSG00000150471	ENST00000502815	.	.	.	5.51	-4.83	0.03161	.	.	.	.	.	T	0.27489	0.0675	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42565	-0.9444	4	.	.	.	.	0.4788	0.00544	0.3555:0.183:0.2523:0.2092	rs35637502	.	.	.	R	224	.	.	G	+	1	0	LPHN3	62495309	0.047000	0.20315	0.966000	0.40874	0.971000	0.66376	-0.197000	0.09518	-0.242000	0.09667	-0.455000	0.05494	GGA		0.403	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			9	246	0	0	0	1	0	9	246				
EFEMP1	2202	broad.mit.edu	37	2	56104979	56104979	+	Missense_Mutation	SNP	G	G	A			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr2:56104979G>A	ENST00000394555.2	-	6	1097	c.662C>T	c.(661-663)cCt>cTt	p.P221L	EFEMP1_ENST00000394554.1_Missense_Mutation_p.P221L|EFEMP1_ENST00000424836.2_Intron|EFEMP1_ENST00000355426.3_Missense_Mutation_p.P221L	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	221	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GCAATATGGAGGGATGGTACA	0.408																																					GBM(92;934 1319 7714 28760 40110)	ENST00000394555.2																			0				NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						c.(661-663)cCt>cTt		EGF containing fibulin-like extracellular matrix protein 1							200.0	187.0	191.0					2																	56104979		2203	4300	6503	SO:0001583	missense	2202				negative regulation of chondrocyte differentiation|peptidyl-tyrosine phosphorylation|regulation of transcription, DNA-dependent|visual perception	extracellular space|proteinaceous extracellular matrix	calcium ion binding|epidermal growth factor receptor activity|epidermal growth factor receptor binding|growth factor activity	g.chr2:56104979G>A	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"""Fibulins"""	3218	protein-coding gene	gene with protein product	"""fibulin 3"""	601548	"""fibrillin-like"", ""EGF-containing fibulin-like extracellular matrix protein 1"""	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.662C>T	2.37:g.56104979G>A	ENSP00000378058:p.Pro221Leu					EFEMP1_ENST00000424836.2_Intron|EFEMP1_ENST00000355426.3_Missense_Mutation_p.P221L|EFEMP1_ENST00000394554.1_Missense_Mutation_p.P221L	p.P221L	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)		6	1097	-			221			EGF-like 3; calcium-binding (Potential).		A8K3I4|B4DW75|D6W5D2|Q541U7	Missense_Mutation	SNP	ENST00000394555.2	37	c.662C>T	CCDS1857.1	.	.	.	.	.	.	.	.	.	.	G	12.77	2.037171	0.35893	.	.	ENSG00000115380	ENST00000394555;ENST00000394554;ENST00000405693;ENST00000355426	D;D;D	0.87966	-2.32;-2.32;-2.32	5.87	5.87	0.94306	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000006	D	0.85622	0.5739	L	0.52823	1.66	0.80722	D	1	B	0.24258	0.1	B	0.21151	0.033	T	0.80162	-0.1497	10	0.30854	T	0.27	.	20.2181	0.98305	0.0:0.0:1.0:0.0	.	221	Q12805	FBLN3_HUMAN	L	221;221;77;221	ENSP00000378058:P221L;ENSP00000378057:P221L;ENSP00000347596:P221L	ENSP00000347596:P221L	P	-	2	0	EFEMP1	55958483	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	4.855000	0.62925	2.785000	0.95823	0.655000	0.94253	CCT		0.408	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2			51	115	0	0	0	1	0	51	115				
PPARGC1A	10891	broad.mit.edu	37	4	23886556	23886556	+	Splice_Site	SNP	T	T	C			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr4:23886556T>C	ENST00000264867.2	-	2	174		c.e2-2		PPARGC1A_ENST00000509702.1_5'Flank|PPARGC1A_ENST00000507380.1_Splice_Site	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha						androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				AGCAGCACACTGCAGGAGGCA	0.388																																					Esophageal Squamous(29;694 744 13796 34866 44181)	ENST00000264867.2																			0				central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51						c.e2-2		peroxisome proliferator-activated receptor gamma, coactivator 1 alpha							44.0	41.0	42.0					4																	23886556		2203	4300	6503	SO:0001630	splice_region_variant	10891				androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription cofactor activity|transcription factor binding	g.chr4:23886556T>C	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"""RNA binding motif (RRM) containing"""	9237	protein-coding gene	gene with protein product		604517	"""peroxisome proliferative activated receptor, gamma, coactivator 1"", ""peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"""	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.55-2A>G	4.37:g.23886556T>C						PPARGC1A_ENST00000507380.1_Splice_Site		NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN			2	174	-		Breast(46;0.0503)						B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Splice_Site	SNP	ENST00000264867.2	37		CCDS3429.1	.	.	.	.	.	.	.	.	.	.	T	18.04	3.535509	0.64972	.	.	ENSG00000109819	ENST00000264867;ENST00000507380	.	.	.	6.07	6.07	0.98685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6288	0.85011	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PPARGC1A	23495654	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.336000	0.79245	2.326000	0.78906	0.533000	0.62120	.		0.388	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	Intron	12	32	0	0	0	1	0	12	32				
ARHGEF9	23229	broad.mit.edu	37	X	62863890	62863890	+	Missense_Mutation	SNP	T	T	C			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chrX:62863890T>C	ENST00000253401.6	-	9	2139	c.1339A>G	c.(1339-1341)Atg>Gtg	p.M447V	ARHGEF9_ENST00000374878.1_Missense_Mutation_p.M445V|ARHGEF9_ENST00000433323.2_Missense_Mutation_p.M174V|ARHGEF9_ENST00000374870.4_Missense_Mutation_p.M345V|ARHGEF9_ENST00000374872.1_Missense_Mutation_p.M426V|ARHGEF9_ENST00000437457.2_Missense_Mutation_p.M394V|ARHGEF9_ENST00000495564.1_5'UTR	NM_015185.2	NP_056000.1	O43307	ARHG9_HUMAN	Cdc42 guanine nucleotide exchange factor (GEF) 9	447					apoptotic signaling pathway (GO:0097190)|ion transmembrane transport (GO:0034220)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|skin(1)	35						CTCACAGTCATTGCAGCCTGC	0.358																																						ENST00000253401.6																			0				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|skin(1)	35						c.(1339-1341)Atg>Gtg		Cdc42 guanine nucleotide exchange factor (GEF) 9							144.0	122.0	129.0					X																	62863890		2203	4300	6503	SO:0001583	missense	23229				apoptosis|induction of apoptosis by extracellular signals|ion transmembrane transport|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol	Rho guanyl-nucleotide exchange factor activity	g.chrX:62863890T>C	AB007884	CCDS35315.1, CCDS55429.1, CCDS55430.1	Xq11.1	2013-01-10			ENSG00000131089	ENSG00000131089		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14561	protein-coding gene	gene with protein product	"""collybistin"""	300429				10559246, 9455477	Standard	NM_015185		Approved	KIAA0424, PEM-2	uc011mot.2	O43307	OTTHUMG00000021700	ENST00000253401.6:c.1339A>G	X.37:g.62863890T>C	ENSP00000253401:p.Met447Val					ARHGEF9_ENST00000437457.2_Missense_Mutation_p.M394V|ARHGEF9_ENST00000374870.4_Missense_Mutation_p.M345V|ARHGEF9_ENST00000374878.1_Missense_Mutation_p.M445V|ARHGEF9_ENST00000374872.1_Missense_Mutation_p.M426V|ARHGEF9_ENST00000433323.2_Missense_Mutation_p.M174V|ARHGEF9_ENST00000495564.1_5'UTR	p.M447V	NM_015185.2	NP_056000.1	O43307	ARHG9_HUMAN			9	2139	-			447					A8K1S8|B4DHC7|F8W7P8|Q5JSL6	Missense_Mutation	SNP	ENST00000253401.6	37	c.1339A>G	CCDS35315.1	.	.	.	.	.	.	.	.	.	.	T	11.28	1.591629	0.28357	.	.	ENSG00000131089	ENST00000253401;ENST00000374878;ENST00000437457;ENST00000374870;ENST00000433323;ENST00000374872	D;D;D;D;D;D	0.87103	-2.21;-2.21;-2.21;-2.21;-2.21;-2.21	5.56	4.37	0.52481	.	0.093109	0.64402	D	0.000001	T	0.77505	0.4140	N	0.22421	0.69	0.42558	D	0.993134	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.68500	-0.5392	10	0.32370	T	0.25	.	10.0998	0.42497	0.1523:0.0:0.0:0.8477	.	394;445;447;447	B4DHC7;B1AMR4;O43307;A8K1S8	.;.;ARHG9_HUMAN;.	V	447;445;394;345;174;426	ENSP00000253401:M447V;ENSP00000364012:M445V;ENSP00000399994:M394V;ENSP00000364004:M345V;ENSP00000404478:M174V;ENSP00000364006:M426V	ENSP00000253401:M447V	M	-	1	0	ARHGEF9	62780615	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.714000	0.54889	0.734000	0.32515	-0.422000	0.05995	ATG		0.358	ARHGEF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056937.1			4	22	0	0	0	1	0	4	22				
FGF9	2254	broad.mit.edu	37	13	22246172	22246172	+	Missense_Mutation	SNP	G	G	A			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr13:22246172G>A	ENST00000382353.5	+	1	651	c.121G>A	c.(121-123)Gaa>Aaa	p.E41K		NM_002010.2	NP_002001.1	P31371	FGF9_HUMAN	fibroblast growth factor 9	41					angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic digestive tract development (GO:0048566)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|male gonad development (GO:0008584)|male sex determination (GO:0030238)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoblast differentiation (GO:0001649)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein import into nucleus (GO:0006606)|regulation of timing of cell differentiation (GO:0048505)|signal transduction (GO:0007165)|substantia nigra development (GO:0021762)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|skin(2)	9		all_cancers(29;1.23e-20)|all_epithelial(30;9.83e-19)|all_lung(29;9.64e-17)|Lung SC(185;0.0262)|Breast(139;0.106)		all cancers(112;3.92e-05)|Epithelial(112;0.000166)|OV - Ovarian serous cystadenocarcinoma(117;0.00314)|Lung(94;0.163)		GGGTCAGTCCGAAGCAGGGGG	0.572																																					Melanoma(195;1939 2127 12623 13963 52730)	ENST00000382353.5																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|skin(2)	9						c.(121-123)Gaa>Aaa		fibroblast growth factor 9							70.0	75.0	74.0					13																	22246172		2203	4300	6503	SO:0001583	missense	2254				cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|male gonad development|positive regulation of cell division	extracellular space	growth factor activity|heparin binding	g.chr13:22246172G>A	D14838	CCDS9298.1	13q11-q12	2014-01-30	2013-06-18		ENSG00000102678	ENSG00000102678		"""Endogenous ligands"""	3687	protein-coding gene	gene with protein product	"""glia-activating factor"""	600921	"""fibroblast growth factor 9 (glia-activating factor)"""			8321227	Standard	NM_002010		Approved		uc001uog.2	P31371	OTTHUMG00000017412	ENST00000382353.5:c.121G>A	13.37:g.22246172G>A	ENSP00000371790:p.Glu41Lys						p.E41K	NM_002010.2	NP_002001.1	P31371	FGF9_HUMAN		all cancers(112;3.92e-05)|Epithelial(112;0.000166)|OV - Ovarian serous cystadenocarcinoma(117;0.00314)|Lung(94;0.163)	1	651	+		all_cancers(29;1.23e-20)|all_epithelial(30;9.83e-19)|all_lung(29;9.64e-17)|Lung SC(185;0.0262)|Breast(139;0.106)	41					A8K427|Q3SY32	Missense_Mutation	SNP	ENST00000382353.5	37	c.121G>A	CCDS9298.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.991386	0.54041	.	.	ENSG00000102678	ENST00000382353	T	0.76186	-1.0	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.63331	0.2502	N	0.22421	0.69	0.46279	D	0.998964	D	0.58620	0.983	B	0.39706	0.307	T	0.68704	-0.5338	10	0.48119	T	0.1	.	18.9133	0.92494	0.0:0.0:1.0:0.0	.	41	P31371	FGF9_HUMAN	K	41	ENSP00000371790:E41K	ENSP00000371790:E41K	E	+	1	0	FGF9	21144172	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.976000	0.70484	2.483000	0.83821	0.561000	0.74099	GAA		0.572	FGF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046002.2			6	107	0	0	0	1	0	6	107				
TRANK1	9881	broad.mit.edu	37	3	36873598	36873598	+	Silent	SNP	C	C	A			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr3:36873598C>A	ENST00000429976.2	-	21	7591	c.7344G>T	c.(7342-7344)ctG>ctT	p.L2448L	TRANK1_ENST00000428977.2_Silent_p.L1898L|TRANK1_ENST00000301807.6_Silent_p.L1898L	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2448							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						TCTTGCTAAACAGGAACTCCC	0.507																																						ENST00000301807.6																			0				NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						c.(5692-5694)ctG>ctT		tetratricopeptide repeat and ankyrin repeat containing 1							103.0	105.0	104.0					3																	36873598		1952	4153	6105	SO:0001819	synonymous_variant	9881				DNA repair		ATP binding|ATP-dependent DNA helicase activity|DNA binding	g.chr3:36873598C>A	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.7344G>T	3.37:g.36873598C>A						TRANK1_ENST00000428977.2_Silent_p.L1898L|TRANK1_ENST00000429976.2_Silent_p.L2448L	p.L1898L	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN			21	7591	-			2448					Q8N8K0	Silent	SNP	ENST00000429976.2	37	c.5694G>T	CCDS46789.2																																																																																				0.507	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		7	119	1	0	0.00198382	1	0.00214576	7	119				
SORT1	6272	broad.mit.edu	37	1	109867585	109867585	+	Missense_Mutation	SNP	T	T	G			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr1:109867585T>G	ENST00000256637.6	-	14	1828	c.1770A>C	c.(1768-1770)gaA>gaC	p.E590D	SORT1_ENST00000538502.1_Missense_Mutation_p.E453D	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN	sortilin 1	590					endocytosis (GO:0006897)|endosome to lysosome transport (GO:0008333)|endosome transport via multivesicular body sorting pathway (GO:0032509)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose import (GO:0046323)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|negative regulation of lipoprotein lipase activity (GO:0051005)|nerve growth factor signaling pathway (GO:0038180)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|plasma membrane to endosome transport (GO:0048227)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|vesicle organization (GO:0016050)	cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	enzyme binding (GO:0019899)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotensin receptor activity, non-G-protein coupled (GO:0030379)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		TCAGGAAAGATTCTGTGAAGC	0.463																																						ENST00000256637.6																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|prostate(1)|skin(1)	26						c.(1768-1770)gaA>gaC		sortilin 1							96.0	99.0	98.0					1																	109867585		2203	4300	6503	SO:0001583	missense	6272				endocytosis|endosome to lysosome transport|endosome transport via multivesicular body sorting pathway|glucose import|Golgi to endosome transport|induction of apoptosis by extracellular signals|myotube differentiation|negative regulation of apoptosis|negative regulation of lipoprotein lipase activity|neuropeptide signaling pathway|ossification|plasma membrane to endosome transport|regulation of gene expression|response to insulin stimulus|vesicle organization	cell surface|coated pit|early endosome|endoplasmic reticulum membrane|endosome membrane|Golgi cisterna membrane|integral to membrane|lysosomal membrane|microsome|nuclear membrane|perinuclear region of cytoplasm|plasma membrane	enzyme binding|nerve growth factor binding|nerve growth factor receptor activity|neurotensin receptor activity, non-G-protein coupled	g.chr1:109867585T>G	BC023542	CCDS798.1, CCDS55618.1	1p13.3	2008-05-14			ENSG00000134243	ENSG00000134243			11186	protein-coding gene	gene with protein product		602458					Standard	NM_002959		Approved	Gp95, NT3	uc001dxm.2	Q99523	OTTHUMG00000011999	ENST00000256637.6:c.1770A>C	1.37:g.109867585T>G	ENSP00000256637:p.Glu590Asp					SORT1_ENST00000538502.1_Missense_Mutation_p.E453D	p.E590D	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)	14	1828	-		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)	590					B4DWI3|C0JYZ0|Q8IZ49	Missense_Mutation	SNP	ENST00000256637.6	37	c.1770A>C	CCDS798.1	.	.	.	.	.	.	.	.	.	.	T	11.40	1.628451	0.28978	.	.	ENSG00000134243	ENST00000256637;ENST00000538502	T;T	0.21932	1.98;1.98	5.73	-2.64	0.06114	VPS10 (1);	0.518564	0.21655	N	0.071117	T	0.01061	0.0035	N	0.00879	-1.12	0.30728	N	0.747477	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38200	-0.9672	10	0.14656	T	0.56	-12.8366	2.9021	0.05709	0.1252:0.39:0.1291:0.3556	.	453;590	B4DWI3;Q99523	.;SORT_HUMAN	D	590;453	ENSP00000256637:E590D;ENSP00000438597:E453D	ENSP00000256637:E590D	E	-	3	2	SORT1	109669108	0.206000	0.23470	0.950000	0.38849	0.942000	0.58702	-0.518000	0.06267	-0.777000	0.04572	-0.466000	0.05196	GAA		0.463	SORT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033179.1	NM_002959		22	23	0	0	0	1	0	22	23				
PAPD7	11044	broad.mit.edu	37	5	6748612	6748612	+	Nonsense_Mutation	SNP	C	C	T			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr5:6748612C>T	ENST00000230859.6	+	8	874	c.745C>T	c.(745-747)Cag>Tag	p.Q249*		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	479					double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)			cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TGGCGCCATGCAGGTGAAGCA	0.542																																					NSCLC(7;212 333 5667 23379 46547)	ENST00000230859.6																			0				cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						c.(745-747)Cag>Tag		PAP associated domain containing 7							317.0	289.0	298.0					5																	6748612		2203	4300	6503	SO:0001587	stop_gained	11044				cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion	nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|SMC protein binding	g.chr5:6748612C>T	AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"""topoisomerase-related function protein 4-1"", ""polymerase (DNA-directed) sigma"", ""DNA polymerase kappa"", ""TUTase5"""	605198	"""polymerase (DNA directed) sigma"""	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.745C>T	5.37:g.6748612C>T	ENSP00000230859:p.Gln249*						p.Q249*	NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN			8	874	+			249					A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Nonsense_Mutation	SNP	ENST00000230859.6	37	c.745C>T	CCDS3871.1	.	.	.	.	.	.	.	.	.	.	C	37	6.480735	0.97603	.	.	ENSG00000112941	ENST00000230859	.	.	.	5.43	4.56	0.56223	.	0.120483	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	-10.7358	13.8039	0.63218	0.0:0.9267:0.0:0.0733	.	.	.	.	X	249	.	ENSP00000230859:Q249X	Q	+	1	0	PAPD7	6801612	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	5.483000	0.66838	1.286000	0.44565	0.561000	0.74099	CAG		0.542	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999		5	323	0	0	0	1	0	5	323				
ALMS1	7840	broad.mit.edu	37	2	73646386	73646386	+	Missense_Mutation	SNP	A	A	G			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr2:73646386A>G	ENST00000264448.6	+	3	697	c.586A>G	c.(586-588)Acg>Gcg	p.T196A	ALMS1_ENST00000409009.1_Missense_Mutation_p.T154A|ALMS1_ENST00000377715.1_Missense_Mutation_p.T196A	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	196					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GGGCATATTGACGCAATCAGA	0.428																																						ENST00000264448.6																			0				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						c.(586-588)Acg>Gcg		Alstrom syndrome 1							140.0	135.0	137.0					2																	73646386		1844	4099	5943	SO:0001583	missense	7840				G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole		g.chr2:73646386A>G	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.586A>G	2.37:g.73646386A>G	ENSP00000264448:p.Thr196Ala					ALMS1_ENST00000409009.1_Missense_Mutation_p.T154A|ALMS1_ENST00000377715.1_Missense_Mutation_p.T196A	p.T196A	NM_015120.4	NP_055935.4	Q8TCU4	ALMS1_HUMAN			3	697	+			196					Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	c.586A>G	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	4.218	0.039195	0.08148	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.13901	3.43;3.43;2.55	4.51	2.13	0.27403	.	0.882509	0.09434	N	0.802773	T	0.11196	0.0273	L	0.36672	1.1	0.09310	N	1	B;B	0.19331	0.035;0.035	B;B	0.17722	0.019;0.019	T	0.32903	-0.9889	10	0.51188	T	0.08	.	5.6663	0.17697	0.7722:0.0:0.2278:0.0	.	154;196	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	A	154;196;196	ENSP00000386627:T154A;ENSP00000264448:T196A;ENSP00000366944:T196A	ENSP00000264448:T196A	T	+	1	0	ALMS1	73499894	0.354000	0.24912	0.023000	0.16930	0.272000	0.26649	1.353000	0.34045	0.351000	0.24027	0.533000	0.62120	ACG		0.428	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		4	80	0	0	0	1	0	4	80				
FOXP2	93986	broad.mit.edu	37	7	114270018	114270018	+	Silent	SNP	G	G	A			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr7:114270018G>A	ENST00000393494.2	+	5	834	c.555G>A	c.(553-555)caG>caA	p.Q185Q	FOXP2_ENST00000393491.3_Silent_p.Q93Q|FOXP2_ENST00000393489.3_Silent_p.Q93Q|FOXP2_ENST00000378237.3_Silent_p.Q185Q|FOXP2_ENST00000390668.3_Silent_p.Q209Q|FOXP2_ENST00000403559.4_Silent_p.Q202Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393498.2_Silent_p.Q165Q|FOXP2_ENST00000350908.4_Silent_p.Q185Q|FOXP2_ENST00000393500.3_Silent_p.Q110Q|FOXP2_ENST00000408937.3_Silent_p.Q210Q|FOXP2_ENST00000360232.4_Silent_p.Q185Q			O15409	FOXP2_HUMAN	forkhead box P2	185	Gln-rich.				camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|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)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q210Q(2)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						agcagcaacagcagcagcagc	0.502																																						ENST00000393500.3																			2	Substitution - coding silent(2)	p.Q210Q(2)	lung(2)	breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						c.(328-330)caG>caA		forkhead box P2							48.0	44.0	45.0					7																	114270018		2197	4288	6485	SO:0001819	synonymous_variant	93986				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr7:114270018G>A	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.555G>A	7.37:g.114270018G>A						FOXP2_ENST00000378237.3_Silent_p.Q185Q|FOXP2_ENST00000350908.4_Silent_p.Q185Q|FOXP2_ENST00000390668.3_Silent_p.Q209Q|FOXP2_ENST00000393498.2_Silent_p.Q165Q|FOXP2_ENST00000360232.4_Silent_p.Q185Q|FOXP2_ENST00000408937.3_Silent_p.Q210Q|FOXP2_ENST00000403559.4_Silent_p.Q202Q|FOXP2_ENST00000393491.3_Silent_p.Q93Q|FOXP2_ENST00000393489.3_Silent_p.Q93Q|FOXP2_ENST00000393494.2_Silent_p.Q185Q	p.Q110Q			O15409	FOXP2_HUMAN			11	1150	+			185			Gln-rich.		A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Silent	SNP	ENST00000393494.2	37	c.330G>A	CCDS5760.1																																																																																				0.502	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		4	79	0	0	0	1	0	4	79				
TEX9	374618	broad.mit.edu	37	15	56657675	56657675	+	Splice_Site	SNP	G	G	C			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr15:56657675G>C	ENST00000352903.2	+	1	51	c.27G>C	c.(25-27)acG>acC	p.T9T	TEX9_ENST00000561221.2_Splice_Site_p.T9T|TEX9_ENST00000537232.1_5'UTR|TEX9_ENST00000558083.2_5'UTR	NM_198524.1	NP_940926.1	Q8N6V9	TEX9_HUMAN	testis expressed 9	9										cervix(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	14				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		TGTGTCTCACGGTCAGTTCAA	0.587																																						ENST00000561221.2																			0				cervix(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	14						c.e1+1		testis expressed 9							53.0	50.0	51.0					15																	56657675		2193	4292	6485	SO:0001630	splice_region_variant	374618							g.chr15:56657675G>C	BC028119	CCDS10157.1, CCDS66776.1	15q21.3	2007-03-13	2007-03-13		ENSG00000151575	ENSG00000151575			29585	protein-coding gene	gene with protein product			"""testis expressed sequence 9"""				Standard	XM_005254361		Approved		uc002adp.3	Q8N6V9	OTTHUMG00000132035	ENST00000352903.2:c.27+1G>C	15.37:g.56657675G>C						TEX9_ENST00000352903.2_Splice_Site_p.T9_splice|TEX9_ENST00000537232.1_5'UTR|TEX9_ENST00000558083.2_5'UTR	p.T9_splice			Q8N6V9	TEX9_HUMAN		all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)	1	32	+			9					B4DH73	Splice_Site	SNP	ENST00000352903.2	37	c.27_splice	CCDS10157.1																																																																																				0.587	TEX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255048.2	NM_198524	Silent	11	43	0	0	0	1	0	11	43				
MUC5AC	4586	broad.mit.edu	37	11	1157545	1157545	+	Missense_Mutation	SNP	C	C	T	rs540223217		TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr11:1157545C>T	ENST00000356191.2	+	12	716	c.716C>T	c.(715-717)aCg>aTg	p.T239M				P98088	MUC5A_HUMAN	mucin 5AC, oligomeric mucus/gel-forming	242	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|extracellular fibril organization (GO:0043206)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|fibril (GO:0043205)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)		AGAAGATGGACGACCCCACGG	0.627													C|||	1	0.000199681	0.0	0.0	5008	,	,		16798	0.0		0.001	False		,,,				2504	0.0					ENST00000356191.2																			0				NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203						c.(715-717)aCg>aTg		mucin 5AC, oligomeric mucus/gel-forming							23.0	22.0	22.0					11																	1157545		871	1985	2856	SO:0001583	missense	4586							g.chr11:1157545C>T	AJ001402, AJ298317		11p15.5	2007-04-23	2006-03-14		ENSG00000215182	ENSG00000215182		"""Mucins"""	7515	protein-coding gene	gene with protein product		158373	"""mucin 5, subtypes A and C, tracheobronchial/gastric"""			7826332, 9588204	Standard	XM_006709945		Approved	MUC5	uc001lsz.3	P98088	OTTHUMG00000154270	ENST00000356191.2:c.716C>T	11.37:g.1157545C>T	ENSP00000348519:p.Thr239Met						p.T239M						BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)	12	716	+		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)						O60460|O76065|Q13792|Q14425|Q658Q1|Q7M4S5|Q8N4M9|Q8WWQ3|Q8WWQ4|Q8WWQ5	Missense_Mutation	SNP	ENST00000356191.2	37	c.716C>T		.	.	.	.	.	.	.	.	.	.	c	4.137	0.023738	0.08006	.	.	ENSG00000215182	ENST00000356191	T	0.18502	2.21	3.1	-1.55	0.08558	.	.	.	.	.	T	0.20373	0.0490	.	.	.	.	.	.	.	.	.	.	.	.	T	0.33523	-0.9865	5	0.62326	D	0.03	.	8.2681	0.31827	0.0:0.3675:0.0:0.6325	.	.	.	.	M	239	ENSP00000348519:T239M	ENSP00000348519:T239M	T	+	2	0	MUC5AC	1147545	0.271000	0.24162	0.985000	0.45067	0.205000	0.24178	-0.640000	0.05440	-0.474000	0.06862	0.290000	0.19541	ACG		0.627	MUC5AC-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_001130382		5	25	0	0	0	1	0	5	25				
AOAH	313	broad.mit.edu	37	7	36561718	36561718	+	Missense_Mutation	SNP	A	A	G			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr7:36561718A>G	ENST00000258749.5	-	20	1925	c.1526T>C	c.(1525-1527)aTa>aCa	p.I509T	AOAH_ENST00000538464.1_Missense_Mutation_p.I231T|AOAH_ENST00000431169.1_Missense_Mutation_p.I509T|AOAH_ENST00000535891.1_Missense_Mutation_p.I477T	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	509					inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|lipopolysaccharide metabolic process (GO:0008653)|negative regulation of inflammatory response (GO:0050728)	extracellular region (GO:0005576)	acyloxyacyl hydrolase activity (GO:0050528)|catalytic activity (GO:0003824)|lipoprotein lipase activity (GO:0004465)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(21)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	41						CCACTCCTGTATGACTGCAGG	0.582																																						ENST00000431169.1																			0				NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(21)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	41						c.(1525-1527)aTa>aCa		acyloxyacyl hydrolase (neutrophil)							83.0	67.0	73.0					7																	36561718		2203	4300	6503	SO:0001583	missense	313				inflammatory response|lipid metabolic process	extracellular region	acyloxyacyl hydrolase activity|lipoprotein lipase activity	g.chr7:36561718A>G	BC025698	CCDS5448.1, CCDS55102.1, CCDS75584.1	7p14-p12	2014-03-14			ENSG00000136250	ENSG00000136250	3.1.1.77		548	protein-coding gene	gene with protein product		102593				1883828	Standard	NM_001637		Approved		uc022abu.1	P28039	OTTHUMG00000023566	ENST00000258749.5:c.1526T>C	7.37:g.36561718A>G	ENSP00000258749:p.Ile509Thr					AOAH_ENST00000538464.1_Missense_Mutation_p.I231T|AOAH_ENST00000535891.1_Missense_Mutation_p.I477T|AOAH_ENST00000258749.5_Missense_Mutation_p.I509T	p.I509T	NM_001177506.1	NP_001170977.1	P28039	AOAH_HUMAN			20	1826	-			509					A4D1Y5|B7Z490|Q53F13	Missense_Mutation	SNP	ENST00000258749.5	37	c.1526T>C	CCDS5448.1	.	.	.	.	.	.	.	.	.	.	A	12.90	2.076474	0.36662	.	.	ENSG00000136250	ENST00000538464;ENST00000535891;ENST00000258749;ENST00000431169;ENST00000544647	T;T;T;T	0.13778	2.56;2.56;2.56;2.56	4.92	-5.53	0.02552	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);	1.826510	0.02655	N	0.106906	T	0.11024	0.0269	.	.	.	0.09310	N	1	B;B;B	0.22003	0.0;0.063;0.001	B;B;B	0.19666	0.002;0.026;0.005	T	0.21415	-1.0246	9	0.33940	T	0.23	.	12.815	0.57660	0.7364:0.0:0.2636:0.0	.	477;509;509	B7Z490;C9J8T1;P28039	.;.;AOAH_HUMAN	T	231;477;509;509;509	ENSP00000439283:I231T;ENSP00000441101:I477T;ENSP00000258749:I509T;ENSP00000405683:I509T	ENSP00000258749:I509T	I	-	2	0	AOAH	36528243	0.000000	0.05858	0.000000	0.03702	0.874000	0.50279	-1.782000	0.01772	-1.561000	0.01684	0.379000	0.24179	ATA		0.582	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637		5	52	0	0	0	1	0	5	52				
TMEM171	134285	broad.mit.edu	37	5	72419573	72419573	+	Missense_Mutation	SNP	C	C	G			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr5:72419573C>G	ENST00000454765.2	+	2	846	c.373C>G	c.(373-375)Ctc>Gtc	p.L125V	TMEM171_ENST00000287773.5_Missense_Mutation_p.L125V			Q8WVE6	TM171_HUMAN	transmembrane protein 171	125						integral component of membrane (GO:0016021)				endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|stomach(1)	15		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;1.87e-54)|Lung(70;0.115)		AAGCGGCATGCTCATCAGCGT	0.587																																					NSCLC(112;638 2280 27369 30736)	ENST00000454765.2																			0				endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|stomach(1)	15						c.(373-375)Ctc>Gtc		transmembrane protein 171							126.0	128.0	127.0					5																	72419573		2203	4300	6503	SO:0001583	missense	134285					integral to membrane		g.chr5:72419573C>G	BC018083	CCDS4017.1, CCDS54869.1	5q13.2	2008-02-05			ENSG00000157111	ENSG00000157111			27031	protein-coding gene	gene with protein product						12477932	Standard	NM_173490		Approved	PRP2	uc003kcm.2	Q8WVE6	OTTHUMG00000131269	ENST00000454765.2:c.373C>G	5.37:g.72419573C>G	ENSP00000415030:p.Leu125Val					TMEM171_ENST00000287773.5_Missense_Mutation_p.L125V	p.L125V			Q8WVE6	TM171_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;1.87e-54)|Lung(70;0.115)	2	846	+		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)	125					Q8N0S1|Q8TDT7	Missense_Mutation	SNP	ENST00000454765.2	37	c.373C>G	CCDS4017.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.499064	0.44455	.	.	ENSG00000157111	ENST00000454765;ENST00000287773	T;T	0.36878	1.23;1.23	5.34	4.47	0.54385	.	0.000000	0.64402	D	0.000008	T	0.37265	0.0997	L	0.36672	1.1	0.37748	D	0.925874	P;P	0.42961	0.795;0.795	P;P	0.47528	0.549;0.549	T	0.41980	-0.9478	10	0.72032	D	0.01	-26.4583	12.2163	0.54408	0.0:0.8575:0.0:0.1425	.	125;125	Q8WVE6-2;Q8WVE6	.;TM171_HUMAN	V	125	ENSP00000415030:L125V;ENSP00000287773:L125V	ENSP00000287773:L125V	L	+	1	0	TMEM171	72455329	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	2.791000	0.47829	1.262000	0.44165	-0.463000	0.05309	CTC		0.587	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490		6	122	0	0	0	1	0	6	122				
LOC150776	150776	broad.mit.edu	37	2	132275379	132275379	+	RNA	SNP	C	C	G	rs142886923	byFrequency	TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr2:132275379C>G	ENST00000438378.2	+	0	1652					NR_026922.1																						CCGCACAGACCTGGTTAGCCC	0.582																																						ENST00000438378.2																			0																																																			0							g.chr2:132275379C>G																													2.37:g.132275379C>G								NR_026922.1						0	1652	+									RNA	SNP	ENST00000438378.2	37																																																																																						0.582	AC093838.4-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000331819.7			19	32	0	0	0	1	0	19	32				
ABLIM1	3983	broad.mit.edu	37	10	116207677	116207677	+	Missense_Mutation	SNP	G	G	A	rs549919699	byFrequency	TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr10:116207677G>A	ENST00000277895.5	-	15	1794	c.1697C>T	c.(1696-1698)aCg>aTg	p.T566M	ABLIM1_ENST00000369266.3_Missense_Mutation_p.T243M|ABLIM1_ENST00000533213.2_Missense_Mutation_p.T506M|ABLIM1_ENST00000392952.3_Missense_Mutation_p.T243M|ABLIM1_ENST00000369252.4_Missense_Mutation_p.T506M|ABLIM1_ENST00000369253.2_Missense_Mutation_p.T189M	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	566					axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		CCAGTGGTCCGTCTCAATCTT	0.542													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18602	0.0		0.0	False		,,,				2504	0.0					ENST00000369252.4																			0				breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30						c.(1516-1518)aCg>aTg		actin binding LIM protein 1							131.0	109.0	116.0					10																	116207677		2203	4300	6503	SO:0001583	missense	3983				axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding	g.chr10:116207677G>A	AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.1697C>T	10.37:g.116207677G>A	ENSP00000277895:p.Thr566Met					ABLIM1_ENST00000392952.3_Missense_Mutation_p.T243M|ABLIM1_ENST00000369253.2_Missense_Mutation_p.T189M|ABLIM1_ENST00000277895.5_Missense_Mutation_p.T566M|ABLIM1_ENST00000533213.2_Missense_Mutation_p.T506M|ABLIM1_ENST00000369266.3_Missense_Mutation_p.T243M	p.T506M	NM_001003407.1|NM_001003408.1	NP_001003407.1|NP_001003408.1	O14639	ABLM1_HUMAN		Epithelial(162;0.0132)|all cancers(201;0.0383)	15	1818	-		Colorectal(252;0.0373)|Breast(234;0.231)	566					A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Missense_Mutation	SNP	ENST00000277895.5	37	c.1517C>T	CCDS7590.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.45|12.45	1.942603|1.942603	0.34283|0.34283	.|.	.|.	ENSG00000099204|ENSG00000099204	ENST00000392955|ENST00000336585;ENST00000369252;ENST00000392952;ENST00000369257;ENST00000369267;ENST00000533213;ENST00000369262;ENST00000369263;ENST00000369266;ENST00000369256;ENST00000277895;ENST00000369253	.|T;T;T;T	.|0.30182	.|1.54;1.54;1.54;1.54	5.83|5.83	4.93|4.93	0.64822|0.64822	.|.	.|0.446133	.|0.24516	.|N	.|0.037856	T|T	0.42899|0.42899	0.1223|0.1223	L|L	0.41492|0.41492	1.28|1.28	0.43777|0.43777	D|D	0.996306|0.996306	.|B;D;P;B;P;P;B	.|0.71674	.|0.354;0.998;0.896;0.158;0.911;0.863;0.119	.|B;P;P;B;P;B;B	.|0.61722	.|0.124;0.893;0.635;0.066;0.614;0.205;0.018	T|T	0.17592|0.17592	-1.0364|-1.0364	5|10	.|0.35671	.|T	.|0.21	.|.	14.9035|14.9035	0.70699|0.70699	0.0685:0.0:0.9315:0.0|0.0685:0.0:0.9315:0.0	.|.	.|506;534;566;243;536;490;189	.|F8W8M4;A6NKJ2;O14639;O14639-5;B3KVH2;C9K0X4;O14639-4	.|.;.;ABLM1_HUMAN;.;.;.;.	W|M	440|566;506;243;189;534;506;634;490;243;490;634;318	.|ENSP00000358256:T506M;ENSP00000376679:T243M;ENSP00000433629:T506M;ENSP00000358270:T243M	.|ENSP00000277895:T634M	R|T	-|-	1|2	2|0	ABLIM1|ABLIM1	116197667|116197667	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	4.419000|4.419000	0.59835|0.59835	1.471000|1.471000	0.48121|0.48121	-0.136000|-0.136000	0.14681|0.14681	CGG|ACG		0.542	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			27	60	0	0	0	1	0	27	60				
RBM44	375316	broad.mit.edu	37	2	238737984	238737984	+	Missense_Mutation	SNP	T	T	A			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr2:238737984T>A	ENST00000409864.1	+	13	2982	c.2728T>A	c.(2728-2730)Tca>Aca	p.S910T	RBM44_ENST00000316997.4_Missense_Mutation_p.S910T			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	909						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		AGAATATACATCACCACTTTC	0.348																																						ENST00000316997.4																			0				breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						c.(2728-2730)Tca>Aca		RNA binding motif protein 44							111.0	108.0	109.0					2																	238737984		1828	4084	5912	SO:0001583	missense	375316						nucleotide binding|RNA binding	g.chr2:238737984T>A	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"""RNA binding motif (RRM) containing"""	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.2728T>A	2.37:g.238737984T>A	ENSP00000386727:p.Ser910Thr					RBM44_ENST00000409864.1_Missense_Mutation_p.S910T	p.S910T	NM_001080504.2	NP_001073973.2	Q6ZP01	RBM44_HUMAN		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)	13	2860	+		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)	909					A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	c.2728T>A	CCDS46554.1	.	.	.	.	.	.	.	.	.	.	T	10.85	1.466584	0.26335	.	.	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.25749	1.78;1.78	4.58	0.719	0.18208	.	.	.	.	.	T	0.28665	0.0710	L	0.47716	1.5	0.09310	N	1	D	0.55172	0.97	P	0.54346	0.749	T	0.11591	-1.0581	9	0.36615	T	0.2	-2.1053	3.8554	0.08973	0.0:0.222:0.1902:0.5879	.	909	Q6ZP01	RBM44_HUMAN	T	910	ENSP00000321179:S910T;ENSP00000386727:S910T	ENSP00000321179:S910T	S	+	1	0	RBM44	238402723	0.000000	0.05858	0.007000	0.13788	0.878000	0.50629	-0.114000	0.10757	0.215000	0.20761	0.450000	0.29827	TCA		0.348	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		7	53	0	0	0	1	0	7	53				
GRIA1	2890	broad.mit.edu	37	5	153144159	153144159	+	Silent	SNP	G	G	A	rs535451229		TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr5:153144159G>A	ENST00000285900.5	+	12	2332	c.1989G>A	c.(1987-1989)acG>acA	p.T663T	GRIA1_ENST00000521843.2_Silent_p.T594T|GRIA1_ENST00000448073.4_Silent_p.T673T|GRIA1_ENST00000518783.1_Silent_p.T673T|GRIA1_ENST00000340592.5_Silent_p.T663T|GRIA1_ENST00000518142.1_Silent_p.T583T	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	663					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	CCTACGGGACGCTGGAAGCAG	0.502													G|||	1	0.000199681	0.0	0.0	5008	,	,		20910	0.001		0.0	False		,,,				2504	0.0					ENST00000285900.5																			0				NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81						c.(1987-1989)acG>acA		glutamate receptor, ionotropic, AMPA 1	Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)						99.0	83.0	88.0					5																	153144159		2203	4300	6503	SO:0001819	synonymous_variant	0				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding	g.chr5:153144159G>A		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.1989G>A	5.37:g.153144159G>A						GRIA1_ENST00000518783.1_Silent_p.T673T|GRIA1_ENST00000340592.5_Silent_p.T663T|GRIA1_ENST00000521843.2_Silent_p.T594T|GRIA1_ENST00000518142.1_Silent_p.T583T|GRIA1_ENST00000448073.4_Silent_p.T673T	p.T663T	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		12	2332	+		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	663					B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Silent	SNP	ENST00000285900.5	37	c.1989G>A	CCDS4322.1																																																																																				0.502	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			18	41	0	0	0	1	0	18	41				
FAM111A	63901	broad.mit.edu	37	11	58920765	58920765	+	Missense_Mutation	SNP	G	G	A			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr11:58920765G>A	ENST00000528737.1	+	5	4442	c.1624G>A	c.(1624-1626)Ggc>Agc	p.G542S	FAM111A_ENST00000420244.1_Missense_Mutation_p.G542S|FAM111A_ENST00000533703.1_Missense_Mutation_p.G542S|FAM111A_ENST00000531147.1_Missense_Mutation_p.G542S|FAM111A_ENST00000361723.3_Missense_Mutation_p.G542S			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	542	Interaction with SV40 large T antigen.				defense response to virus (GO:0051607)|DNA replication (GO:0006260)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_epithelial(135;0.139)				TGGGGCTTCCGGCTCCCCTGT	0.413																																						ENST00000528737.1																			0				breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22						c.(1624-1626)Ggc>Agc		family with sequence similarity 111, member A							104.0	109.0	107.0					11																	58920765		2201	4295	6496	SO:0001583	missense	63901				proteolysis		serine-type endopeptidase activity	g.chr11:58920765G>A	AK092953	CCDS7973.1	11q12.1	2014-03-13				ENSG00000166801			24725	protein-coding gene	gene with protein product		615292				11572484, 23996431, 23684011	Standard	NM_022074		Approved	FLJ22794, KIAA1895	uc001nnq.3	Q96PZ2		ENST00000528737.1:c.1624G>A	11.37:g.58920765G>A	ENSP00000434435:p.Gly542Ser					FAM111A_ENST00000531147.1_Missense_Mutation_p.G542S|FAM111A_ENST00000361723.3_Missense_Mutation_p.G542S|FAM111A_ENST00000533703.1_Missense_Mutation_p.G542S|FAM111A_ENST00000420244.1_Missense_Mutation_p.G542S	p.G542S			Q96PZ2	F111A_HUMAN			5	4442	+		all_epithelial(135;0.139)	542					A8K5Y8|Q5RKS9|Q5XKM2|Q68DK9|Q6IPR7|Q9H5Y1	Missense_Mutation	SNP	ENST00000528737.1	37	c.1624G>A	CCDS7973.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.407432	0.83230	.	.	ENSG00000166801	ENST00000528737;ENST00000420244;ENST00000361723;ENST00000533703;ENST00000531147	D;D;D;D;D	0.99121	-5.45;-5.45;-5.45;-5.45;-5.45	5.57	5.57	0.84162	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.062017	0.64402	D	0.000007	D	0.99345	0.9770	M	0.87381	2.88	0.42735	D	0.993722	D	0.89917	1.0	D	0.97110	1.0	D	0.99293	1.0899	10	0.87932	D	0	-12.6521	16.8262	0.85931	0.0:0.0:1.0:0.0	.	542	Q96PZ2	F111A_HUMAN	S	542	ENSP00000434435:G542S;ENSP00000406683:G542S;ENSP00000355264:G542S;ENSP00000433154:G542S;ENSP00000431631:G542S	ENSP00000355264:G542S	G	+	1	0	FAM111A	58677341	1.000000	0.71417	0.998000	0.56505	0.494000	0.33585	4.629000	0.61290	2.791000	0.96007	0.655000	0.94253	GGC		0.413	FAM111A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393975.1	NM_022074		4	148	0	0	0	1	0	4	148				
FOXP2	93986	broad.mit.edu	37	7	114270000	114270000	+	Silent	SNP	G	G	A			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr7:114270000G>A	ENST00000393494.2	+	5	816	c.537G>A	c.(535-537)caG>caA	p.Q179Q	FOXP2_ENST00000393491.3_Silent_p.Q87Q|FOXP2_ENST00000393489.3_Silent_p.Q87Q|FOXP2_ENST00000378237.3_Silent_p.Q179Q|FOXP2_ENST00000390668.3_Silent_p.Q203Q|FOXP2_ENST00000403559.4_Silent_p.Q196Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393498.2_Silent_p.Q159Q|FOXP2_ENST00000350908.4_Silent_p.Q179Q|FOXP2_ENST00000393500.3_Silent_p.Q104Q|FOXP2_ENST00000408937.3_Silent_p.Q204Q|FOXP2_ENST00000360232.4_Silent_p.Q179Q			O15409	FOXP2_HUMAN	forkhead box P2	179	Gln-rich.				camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|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)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q204Q(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						agcaacaacagcagcagcagc	0.498																																						ENST00000393500.3																			1	Substitution - coding silent(1)	p.Q204Q(1)	lung(1)	breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						c.(310-312)caG>caA		forkhead box P2							41.0	38.0	39.0					7																	114270000		2199	4282	6481	SO:0001819	synonymous_variant	93986				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr7:114270000G>A	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.537G>A	7.37:g.114270000G>A						FOXP2_ENST00000378237.3_Silent_p.Q179Q|FOXP2_ENST00000350908.4_Silent_p.Q179Q|FOXP2_ENST00000390668.3_Silent_p.Q203Q|FOXP2_ENST00000393498.2_Silent_p.Q159Q|FOXP2_ENST00000360232.4_Silent_p.Q179Q|FOXP2_ENST00000408937.3_Silent_p.Q204Q|FOXP2_ENST00000403559.4_Silent_p.Q196Q|FOXP2_ENST00000393491.3_Silent_p.Q87Q|FOXP2_ENST00000393489.3_Silent_p.Q87Q|FOXP2_ENST00000393494.2_Silent_p.Q179Q|AC020606.1_ENST00000580664.1_RNA	p.Q104Q			O15409	FOXP2_HUMAN			11	1132	+			179			Gln-rich.		A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Silent	SNP	ENST00000393494.2	37	c.312G>A	CCDS5760.1																																																																																				0.498	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		4	70	0	0	0	1	0	4	70				
ATP6V1C2	245973	broad.mit.edu	37	2	10917819	10917820	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr2:10917819_10917820delAG	ENST00000272238.4	+	11	1043_1044	c.934_935delAG	c.(934-936)agafs	p.R312fs	ATP6V1C2_ENST00000381661.3_Intron	NM_001039362.1	NP_001034451.1	Q8NEY4	VATC2_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2	312					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of Wnt signaling pathway (GO:0030177)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|protein dimerization activity (GO:0046983)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		GCAGACCGACAGAGAGAGAGAG	0.604																																					NSCLC(188;1042 2136 10807 16813 47705)	ENST00000272238.4																			0				endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						c.(934-936)afs		ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2																																				SO:0001589	frameshift_variant	245973				ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting V-type ATPase, V1 domain		g.chr2:10917819_10917820delAG	AY039759	CCDS1674.1, CCDS42653.1	2p25.1	2010-04-21	2006-01-13		ENSG00000143882	ENSG00000143882		"""ATPases / V-type"""	18264	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal 42kD, V1 subunit C isoform 2"", ""ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C isoform 2"""			12384298	Standard	XR_426949		Approved	VMA5, ATP6C2	uc002ras.3	Q8NEY4	OTTHUMG00000090459	ENST00000272238.4:c.934_935delAG	2.37:g.10917829_10917830delAG	ENSP00000272238:p.Arg312fs					ATP6V1C2_ENST00000381661.3_Intron	p.R312fs	NM_001039362.1	NP_001034451.1	Q8NEY4	VATC2_HUMAN		Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)	11	1043_1044	+	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)		312					Q96EL8	Frame_Shift_Del	DEL	ENST00000272238.4	37	c.934_935delAG	CCDS42653.1																																																																																				0.604	ATP6V1C2-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323555.1	NM_144583		8	110						8	110	---	---	---	---
FAM53A	152877	broad.mit.edu	37	4	1657001	1657001	+	Frame_Shift_Del	DEL	C	C	-	rs561741907	byFrequency	TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr4:1657001delC	ENST00000308132.6	-	4	778	c.586delG	c.(586-588)gacfs	p.D196fs	FAM53A_ENST00000472884.2_Frame_Shift_Del_p.D196fs|FAM53A_ENST00000489363.1_Frame_Shift_Del_p.D196fs|FAM53A_ENST00000461064.1_Frame_Shift_Del_p.D196fs	NM_001174070.1	NP_001167541.1	Q6NSI3	FA53A_HUMAN	family with sequence similarity 53, member A	196						nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		all_epithelial(65;0.206)|Breast(71;0.212)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)			TCGCTGCTGTCCACGAAGCCG	0.746																																						ENST00000308132.6																			0				breast(2)|central_nervous_system(2)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						c.(586-588)acfs		family with sequence similarity 53, member A							3.0	4.0	4.0					4																	1657001		1683	3598	5281	SO:0001589	frameshift_variant	152877					nucleus		g.chr4:1657001delC	BC070112	CCDS33939.1, CCDS75091.1	4p16.3	2005-08-09			ENSG00000174137	ENSG00000174137			31860	protein-coding gene	gene with protein product							Standard	NM_001013622		Approved	DNTNP	uc021xkl.1	Q6NSI3	OTTHUMG00000159855	ENST00000308132.6:c.586delG	4.37:g.1657001delC	ENSP00000310057:p.Asp196fs					FAM53A_ENST00000461064.1_Frame_Shift_Del_p.D196fs|FAM53A_ENST00000489363.1_Frame_Shift_Del_p.D196fs|FAM53A_ENST00000472884.2_Frame_Shift_Del_p.D196fs	p.D196fs	NM_001174070.1	NP_001167541.1	Q6NSI3	FA53A_HUMAN	OV - Ovarian serous cystadenocarcinoma(23;0.0145)		4	778	-		all_epithelial(65;0.206)|Breast(71;0.212)	196					Q6ZUL5	Frame_Shift_Del	DEL	ENST00000308132.6	37	c.586delG	CCDS33939.1																																																																																				0.746	FAM53A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359224.1	NM_001013622		2	4						2	4	---	---	---	---
MSH5	4439	broad.mit.edu	37	6	31709057	31709058	+	Frame_Shift_Ins	INS	-	-	AG			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr6:31709057_31709058insAG	ENST00000375755.3	+	3	551_552	c.265_266insAG	c.(265-267)cagfs	p.Q89fs	MSH5-SAPCD1_ENST00000493662.2_Frame_Shift_Ins_p.Q89fs|MSH5_ENST00000534153.4_Frame_Shift_Ins_p.Q89fs|MSH5_ENST00000375740.3_Frame_Shift_Ins_p.Q89fs|MSH5_ENST00000375742.3_Frame_Shift_Ins_p.Q89fs|MSH5_ENST00000375750.3_Frame_Shift_Ins_p.Q89fs|MSH5_ENST00000482280.1_3'UTR|CLIC1_ENST00000395892.1_5'Flank|MSH5_ENST00000375703.3_Frame_Shift_Ins_p.Q89fs	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	89					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						CAAGCTTCTCCAGAGAGGTGGG	0.5								Direct reversal of damage;Mismatch excision repair (MMR)																														ENST00000493662.2																			0											c.(265-267)gagfs																																						SO:0001589	frameshift_variant	0							g.chr6:31709057_31709058insAG	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"""mutS (E. coli) homolog 5"", ""mutS homolog 5 (E. coli)"""			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.270_271dupAG	6.37:g.31709062_31709063dupAG	ENSP00000364908:p.Gln89fs					MSH5_ENST00000375703.3_Frame_Shift_Ins_p.E89fs|MSH5_ENST00000375740.3_Frame_Shift_Ins_p.E89fs|MSH5_ENST00000375742.3_Frame_Shift_Ins_p.E89fs|MSH5_ENST00000375750.3_Frame_Shift_Ins_p.E89fs|MSH5_ENST00000375755.3_Frame_Shift_Ins_p.E89fs|MSH5_ENST00000534153.4_Frame_Shift_Ins_p.E89fs|MSH5_ENST00000482280.1_3'UTR	p.E89fs							3	321_322	+								B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Frame_Shift_Ins	INS	ENST00000375755.3	37	c.265_266insAG	CCDS4720.1																																																																																				0.500	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4			28	125						28	125	---	---	---	---
CHST15	51363	broad.mit.edu	37	10	125780846	125780852	+	Frame_Shift_Del	DEL	GCTGCAG	GCTGCAG	-			TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr10:125780846_125780852delGCTGCAG	ENST00000346248.5	-	6	1909_1915	c.1267_1273delCTGCAGC	c.(1267-1275)ctgcagctgfs	p.LQL423fs	CHST15_ENST00000435907.1_Frame_Shift_Del_p.LQL423fs|CHST15_ENST00000421115.1_Frame_Shift_Del_p.LQL423fs	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	423					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hexose biosynthetic process (GO:0019319)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						TTTTCAAACAGCTGCAGTGCTTCTGTC	0.473																																						ENST00000346248.5																			0				endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						c.(1267-1275)tgfs		carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15																																				SO:0001589	frameshift_variant	51363				hexose biosynthetic process	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity	g.chr10:125780846_125780852delGCTGCAG	AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	2.8.2.33	"""Sulfotransferases, membrane-bound"""	18137	protein-coding gene	gene with protein product	"""B cell RAG associated protein"", ""N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"""	608277				9628581, 9754571, 11572857	Standard	NM_014863		Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.1267_1273delCTGCAGC	10.37:g.125780846_125780852delGCTGCAG	ENSP00000333947:p.Leu423fs					CHST15_ENST00000421115.1_Frame_Shift_Del_p.LQL423fs|CHST15_ENST00000435907.1_Frame_Shift_Del_p.LQL423fs	p.LQL423fs	NM_001270764.1|NM_015892.3	NP_001257693.1|NP_056976.2	Q7LFX5	CHSTF_HUMAN			6	1909_1915	-			423					O60338|O60474|Q86VM4	Frame_Shift_Del	DEL	ENST00000346248.5	37	c.1267_1273delCTGCAGC	CCDS7638.1																																																																																				0.473	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1	NM_015892		12	24						12	24	---	---	---	---
BAIAP2L2	80115	broad.mit.edu	37	22	38482353	38482394	+	In_Frame_Del	DEL	TGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	TGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	-	rs371997714|rs66500630|rs113792005|rs376182024|rs541462698|rs369923129|rs553799224	byFrequency	TCGA-J4-A67N-01A-11D-A30E-08	TCGA-J4-A67N-10A-01D-A30H-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07d2982-6313-4e21-a0a1-cf713daff114	f73b4226-3788-4704-acae-67420da417dd	g.chr22:38482353_38482394delTGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	ENST00000381669.3	-	12	1466_1507	c.1322_1363delTAGCACCCTCGGAGTACTGGGATGGCCAGTCCCGCTCCCGCA	c.(1321-1365)atagcaccctcggagtactgggatggccagtcccgctcccgcacc>acc	p.IAPSEYWDGQSRSR441del	SLC16A8_ENST00000469516.1_5'Flank	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	441					filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)			large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					CGGCTTGGGGTGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTATGGAGTTGCC	0.674														708	0.141374	0.0272	0.2291	5008	,	,		20774	0.0565		0.1918	False		,,,				2504	0.2689					ENST00000381669.3																			0				large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8						c.(1321-1365)acc>a		BAI1-associated protein 2-like 2				138,3818		23,92,1863						2.2	0.8		dbSNP_130	20	1131,6525		291,549,2988	no	coding	BAIAP2L2	NM_025045.4		314,641,4851	A1A1,A1R,RR		14.7727,3.4884,10.9283				1269,10343				SO:0001651	inframe_deletion	80115				filopodium assembly|signal transduction		cytoskeletal adaptor activity|SH3 domain binding	g.chr22:38482353_38482394delTGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1322_1363delTAGCACCCTCGGAGTACTGGGATGGCCAGTCCCGCTCCCGCA	22.37:g.38482353_38482394delTGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	ENSP00000371085:p.Ile441_Arg454del						p.IAPSEYWDGQSRSRT441del	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN			12	1466_1507	-	Melanoma(58;0.045)		441					B0QYE2|Q96BG7	In_Frame_Del	DEL	ENST00000381669.3	37	c.1322_1363delTAGCACCCTCGGAGTACTGGGATGGCCAGTCCCGCTCCCGCA	CCDS43018.1																																																																																				0.674	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045		4	6						4	6	---	---	---	---
