#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_CCF_CI95_high	i_CCF_CI95_low	i_CCF_CI_high	i_CCF_CI_low	i_CCF_hat	i_CCF_mean	i_CCF_median	i_CCF_mode	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_CancerGermlineMut	i_CGC_CancerMolecularGenetics	i_CGC_CancerSomaticMut	i_CGC_CancerSyndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_ChrBand	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_OtherGermlineMut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_TissueType	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_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_ExAC_AC	i_ExAC_AN	i_ExAC_LQ	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_IS_SCNA	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_SCNA_NA	i_SCNA_NB	i_SCNA_q_hat	i_SCNA_tau	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_bcgsc	i_broad	i_build	i_cDNA_Change	i_ccds_id	i_clonal	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_GERP_NR	i_dbNSFP_GERP_RS	i_dbNSFP_GERP_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_folddegenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_hg18_pos1coor	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dna_fraction_in_tumor	i_entrez_gene_id	i_external_id_capture	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_hgsc	i_igv_bad	i_localAssembly_detected	i_min_val_count_KRAS	i_min_val_count_localAssembly	i_min_val_count_rna	i_min_val_count_targeted	i_n_alt_count	i_n_alt_count_KRAS	i_n_alt_count_full	i_n_alt_count_localAssembly	i_n_ref_count	i_n_ref_count_KRAS	i_n_ref_count_full	i_n_ref_count_localAssembly	i_passExAC	i_ploidy	i_pon_loglike	i_pon_pass_loglike	i_purity	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_KRAS	i_t_alt_count_full	i_t_alt_count_localAssembly	i_t_ref_count_KRAS	i_t_ref_count_full	i_t_ref_count_localAssembly	i_ucsc	i_validation_judgement_KRAS	i_validation_judgement_localAssembly	i_validation_judgement_rna	i_validation_judgement_targeted	i_validation_normal_alt_count_rna	i_validation_normal_alt_count_targeted	i_validation_normal_ref_count_rna	i_validation_normal_ref_count_targeted	i_validation_power_KRAS	i_validation_power_localAssembly	i_validation_power_rna	i_validation_power_targeted	i_validation_tumor_alt_count_rna	i_validation_tumor_alt_count_targeted	i_validation_tumor_ref_count_rna	i_validation_tumor_ref_count_targeted	t_alt_count	t_ref_count
PRC1	9055	broad.mit.edu	37	15	91527307	91527308	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			-	T	-	-		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr15:91527307_91527308insT	ENST00000361188.5	-	3	1418_1419	c.207_208insA	c.(205-210)atatccfs	p.S70fs	PRC1_ENST00000556129.1_5'UTR|PRC1-AS1_ENST00000554388.1_RNA|PRC1_ENST00000361919.3_Frame_Shift_Ins_p.S70fs|PRC1_ENST00000394249.3_Frame_Shift_Ins_p.S70fs|PRC1_ENST00000442656.2_Intron					protein regulator of cytokinesis 1											endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25	Lung NSC(78;0.0987)|all_lung(78;0.175)					TGACAGACGGATATGCTTTTGA	0.49																																						ENST00000361188.5	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000																										0				25						c.(205-210)atatccfs		protein regulator of cytokinesis 1																																				SO:0001589	frameshift_variant	9055	0	0					g.chr15:91527307_91527308insT	AF044588	CCDS32334.1, CCDS45352.1, CCDS45353.1, CCDS45353.2	15q26.1	2013-05-29		2006-07-07	ENSG00000198901	ENSG00000198901			9341	protein-coding gene	gene with protein product	"""anaphase spindle elongation 1 homolog (S. cerevisiae)"""	603484				9885575	Standard	NM_003981		Approved	ASE1	uc002bqm.4	O43663	OTTHUMG00000171685	ENST00000361188.5:c.208dupA	chr15.hg19:g.91527308_91527308dupT	ENSP00000354679:p.Ser70fs	1					PRC1-AS1_ENST00000554388.1_RNA|PRC1_ENST00000394249.3_Frame_Shift_Ins_p.S70fs|PRC1_ENST00000361919.3_Frame_Shift_Ins_p.S70fs|PRC1_ENST00000442656.2_Intron|PRC1_ENST00000556129.1_5'UTR	p.S70fs			2	4	6	2.035251				3	1418_1419	-	Lung NSC(78;0.0987)|all_lung(78;0.175)			Frame_Shift_Ins	INS	ENST00000361188.5	0	1	hg19	c.207_208insA	CCDS45352.1	1																																																																																								0.667160		TCGA-IB-A7LX-01A-12D-A36O-08	0.490	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	1	0	1		2	2		0	0	0	0	362	0	362	354	1	3.150000	-20.000000	1	0.550000	NM_003981		0	397	404	0	1227	1221	0	0	1	0	0	0	0	362	0	0	1.000000	9.992689e-01	0	0	0	35	0	397	1227
BDP1	55814	broad.mit.edu	37	5	70751780	70751798	+	Frame_Shift_Del	DEL	AATCCCCAGCGTGGACGGG	AATCCCCAGCGTGGACGGG	-	rs3748042	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:70751780_70751798delAATCCCCAGCGTGGACGGG	ENST00000358731.4	+	1	339_357	c.76_94delAATCCCCAGCGTGGACGGG	c.(76-96)aatccccagcgtggacgggagfs	p.NPQRGRE26fs	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	26	Interaction with ZBTB43.		N -> S (in dbSNP:rs3748042).		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		CACAGCTTCCAATCCCCAGCGTGGACGGGAGTCTCCCAG	0.68																																						ENST00000358731.4	0.870000	0.320000	7.100000e-01	4.300000e-01	0.560000	0.575410	0.560000	0.550000																										0				72						c.(76-96)aatccccagcgtggacgggagfs		B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB																																				SO:0001589	frameshift_variant	55814	0	0					g.chr5:70751780_70751798delAATCCCCAGCGTGGACGGG	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.76_94delAATCCCCAGCGTGGACGGG	chr5.hg19:g.70751780_70751798delAATCCCCAGCGTGGACGGG	ENSP00000351575:p.Asn26fs	1					BDP1_ENST00000380675.2_5'UTR	p.NPQRGRE26fs	NM_018429.2	NP_060899.2	1	2	3	1.889547	A6H8Y1	BDP1_HUMAN		1	339_357	+		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Frame_Shift_Del	DEL	ENST00000358731.4	0	1	hg19	c.76_94delAATCCCCAGCGTGGACGGG	CCDS43328.1	0																																																																																								0.646296		TCGA-IB-A7LX-01A-12D-A36O-08	0.680	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	1	0	1		13	2		0	0	0	1	32	0	32	33	1	3.150000	-19.996320	1	0.550000	NM_018429		0	14	17	0	104	107	0	0	1	0	0	0	0	32	0	0	0.699014	4.498035e-02	0	0	0	3	0	14	104
HIF1AN	55662	broad.mit.edu	37	10	102296374	102296374	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr10:102296374C>A	ENST00000299163.6	+	2	484	c.384C>A	c.(382-384)ttC>ttA	p.F128L	HIF1AN_ENST00000528044.1_3'UTR	NM_017902.2	NP_060372.2	Q9NWT6	HIF1N_HUMAN	hypoxia inducible factor 1, alpha subunit inhibitor	128					cellular response to hypoxia (GO:0071456)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|oxidation-reduction process (GO:0055114)|peptidyl-asparagine hydroxylation (GO:0042265)|peptidyl-aspartic acid hydroxylation (GO:0042264)|peptidyl-histidine hydroxylation (GO:0036138)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of vasculogenesis (GO:2001214)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ankyrin repeat binding (GO:0071532)|carboxylic acid binding (GO:0031406)|cofactor binding (GO:0048037)|iron ion binding (GO:0005506)|NF-kappaB binding (GO:0051059)|Notch binding (GO:0005112)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-asparagine 3-dioxygenase activity (GO:0036140)|peptidyl-histidine dioxygenase activity (GO:0036139)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(1)|prostate(2)|urinary_tract(1)	10		Colorectal(252;0.234)		Epithelial(162;6.75e-10)|all cancers(201;4.88e-08)		TTCATGAGTTCGTTGAGAAAC	0.418																																						ENST00000299163.6	0.310000	0.090000	2.500000e-01	1.400000e-01	0.190000	0.202123	0.190000	0.200000																										0				10						c.(382-384)ttC>ttA		hypoxia inducible factor 1, alpha subunit inhibitor							82.0	85.0	84.0					10																	102296374		2203	4300	6503	SO:0001583	missense	55662	0	0					g.chr10:102296374C>A	AK000622	CCDS7498.1	10q24	2008-12-18	2008-12-02		ENSG00000166135	ENSG00000166135	1.14.11.16		17113	protein-coding gene	gene with protein product	"""Peptide-aspartate beta-dioxygenase"""	606615				11641274	Standard	NM_017902		Approved	FLJ20615, DKFZp762F1811, FLJ22027, FIH1	uc001krj.4	Q9NWT6	OTTHUMG00000018911	ENST00000299163.6:c.384C>A	chr10.hg19:g.102296374C>A	ENSP00000299163:p.Phe128Leu	1					HIF1AN_ENST00000528044.1_3'UTR	p.F128L	NM_017902.2	NP_060372.2	2	2	4	2.372051	Q9NWT6	HIF1N_HUMAN		2	484	+		Colorectal(252;0.234)	D3DR69|Q5W147|Q969Q7|Q9NPV5	Missense_Mutation	SNP	ENST00000299163.6	1	0	hg19	c.384C>A	CCDS7498.1	0	.	.	.	.	.	.	.	.	.	.	C	24.1	4.497411	0.85069	.	.	ENSG00000166135	ENST00000533589;ENST00000299163;ENST00000442724	T;T	0.75589	-0.95;-0.95	5.6	-3.81	0.04294	5.6	-3.81	0.04294	.	3.236230	0.00682	N	0.000698	D	0.83348	0.5235	L	0.57130	1.785	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.72711	-0.4211	10	0.42905	T	0.14	-26.9035	12.1375	0.53979	0.0:0.3619:0.0:0.6381	.	128	Q9NWT6	HIF1N_HUMAN	L	21;128;161	ENSP00000433360:F21L;ENSP00000299163:F128L	ENSP00000299163:F128L	F	+	3	2	2	HIF1AN	102286364	102286364	1.000000	0.71417	0.931000	0.37212	0.916000	0.54674	1.676000	0.37565	-0.977000	0.03537	-1.154000	0.01816	TTC	0.709677		TCGA-IB-A7LX-01A-12D-A36O-08	0.418	HIF1AN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049865.5	1	0	1	2	2	2	2	0	0	0	0	98	98	98	97	1	3.150000	-3.023347	1	0.550000	NM_017902		0	13	13	0	375	366	0		1	0		0	0	98	0	0	0.999477	5.557056e-01	0	0	0	53	0	13	375
GPR158	57512	broad.mit.edu	37	10	25701403	25701403	+	Splice_Site	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr10:25701403G>T	ENST00000376351.3	+	4	1694		c.e4+1			NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158						protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						CAAAGCAAAGGTAAACCCAGG	0.433																																						ENST00000376351.3	0.760000	0.440000	6.800000e-01	5.100000e-01	0.590000	0.604385	0.590000	0.600000																										0				119						c.e4+1		G protein-coupled receptor 158							118.0	103.0	108.0					10																	25701403		2203	4300	6503	SO:0001630	splice_region_variant	57512	0	0					g.chr10:25701403G>T	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"""GPCR / Class C : Orphans"""	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.1335+1G>T	chr10.hg19:g.25701403G>T		1							NM_020752.2	NP_065803.2	1	2	3	1.868416	Q5T848	GP158_HUMAN		4	1694	+			Q6QR81|Q9ULT3	Splice_Site	SNP	ENST00000376351.3	1	1	hg19		CCDS31166.1	0	.	.	.	.	.	.	.	.	.	.	G	29.4	4.999869	0.93227	.	.	ENSG00000151025	ENST00000376351	.	.	.	6.16	6.16	0.99307	6.16	6.16	0.99307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	.	GPR158	25741409	25741409	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.252000	0.95491	2.937000	0.99478	0.650000	0.86243	.	0.647059		TCGA-IB-A7LX-01A-12D-A36O-08	0.433	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	1	0	1	2	2	2	2	0	0	0	0	123	123	123	122	1	3.150000	-20.000000	1	0.550000	XM_166110	Intron	0	46	44	0	312	299	0		1			0	0	123	0	0	1.000000	0	0	0	0	0	0	46	312
WAC	51322	broad.mit.edu	37	10	28878735	28878735	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr10:28878735G>T	ENST00000354911.4	+	5	613	c.452G>T	c.(451-453)cGa>cTa	p.R151L	WAC_ENST00000428935.1_Missense_Mutation_p.R106L|WAC_ENST00000347934.4_Missense_Mutation_p.R151L|WAC_ENST00000375646.1_Missense_Mutation_p.R106L|WAC_ENST00000375664.4_Missense_Mutation_p.R106L	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil	151	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						TACAATTGTCGAACAGAAGTT	0.318																																						ENST00000354911.4	0.300000	0.120000	2.600000e-01	1.600000e-01	0.200000	0.211863	0.200000	0.210000																										0				32						c.(451-453)cGa>cTa		WW domain containing adaptor with coiled-coil							84.0	92.0	89.0					10																	28878735		2203	4300	6503	SO:0001583	missense	51322	0	0					g.chr10:28878735G>T	AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"""WW domain-containing adaptor with coiled coil"""			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.452G>T	chr10.hg19:g.28878735G>T	ENSP00000346986:p.Arg151Leu	1					WAC_ENST00000347934.4_Missense_Mutation_p.R151L|WAC_ENST00000375664.4_Missense_Mutation_p.R106L|WAC_ENST00000375646.1_Missense_Mutation_p.R106L|WAC_ENST00000428935.1_Missense_Mutation_p.R106L	p.R151L	NM_016628.4	NP_057712.2	1	2	3	1.868416	Q9BTA9	WAC_HUMAN		5	613	+			A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Missense_Mutation	SNP	ENST00000354911.4	1	0	hg19	c.452G>T	CCDS7159.1	0	.	.	.	.	.	.	.	.	.	.	G	31	5.081695	0.94050	.	.	ENSG00000095787	ENST00000375664;ENST00000375646;ENST00000347934;ENST00000354911;ENST00000428935;ENST00000420266;ENST00000424454;ENST00000538000;ENST00000442148;ENST00000414108	D;D;D;D;D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59;-1.59;-1.59;-1.59;-1.59	5.24	4.33	0.51752	5.24	4.33	0.51752	WW/Rsp5/WWP (6);	0.000000	0.85682	D	0.000000	T	0.79009	0.4374	N	0.20304	0.555	0.80722	D	1	P;B;P	0.49447	0.811;0.447;0.924	P;B;P	0.49085	0.464;0.245;0.6	T	0.81284	-0.1002	10	0.52906	T	0.07	-5.4856	16.1738	0.81836	0.0:0.1336:0.8664:0.0	.	106;151;151	Q9BTA9-2;Q9BTA9-5;Q9BTA9	.;.;WAC_HUMAN	L	106;106;151;151;106;106;106;106;106;106	ENSP00000364816:R106L;ENSP00000364797:R106L;ENSP00000311106:R151L;ENSP00000346986:R151L;ENSP00000399706:R106L;ENSP00000404758:R106L;ENSP00000400848:R106L;ENSP00000415645:R106L	ENSP00000311106:R151L	R	+	2	0	0	WAC	28918741	28918741	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.567000	0.98161	1.315000	0.45114	0.563000	0.77884	CGA	0.647059		TCGA-IB-A7LX-01A-12D-A36O-08	0.318	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	1	0	1	2	2	2	2	0	0	0	0	142	142	142	138	1	3.150000	-3.100219	1	0.550000	NM_100264		0	20	20	0	437	426	0		1	0		0	0	142	0	0	0.999994	9.847569e-01	0	0	0	148	0	20	437
RHOBTB1	9886	broad.mit.edu	37	10	62648097	62648097	+	Missense_Mutation	SNP	G	G	T	rs151278163		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr10:62648097G>T	ENST00000337910.5	-	6	1666	c.1329C>A	c.(1327-1329)ttC>ttA	p.F443L	RHOBTB1_ENST00000357917.4_Missense_Mutation_p.F443L	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	443					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					TCCTCAAATCGAACATCTCGA	0.463																																						ENST00000337910.5	0.440000	0.170000	3.700000e-01	2.300000e-01	0.290000	0.305621	0.290000	0.280000																										0				23						c.(1327-1329)ttC>ttA		Rho-related BTB domain containing 1							134.0	118.0	123.0					10																	62648097		2203	4300	6503	SO:0001583	missense	9886	0	0					g.chr10:62648097G>T	AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"""BTB/POZ domain containing"""	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.1329C>A	chr10.hg19:g.62648097G>T	ENSP00000338671:p.Phe443Leu	1					RHOBTB1_ENST00000357917.4_Missense_Mutation_p.F443L	p.F443L	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	2	2	4	2.372051	O94844	RHBT1_HUMAN		6	1666	-	Prostate(12;0.0112)			Missense_Mutation	SNP	ENST00000337910.5	1	0	hg19	c.1329C>A	CCDS7261.1	0	.	.	.	.	.	.	.	.	.	.	G	6.234	0.411291	0.11812	.	.	ENSG00000072422	ENST00000357917;ENST00000337910	T;T	0.66460	-0.21;-0.21	5.71	2.11	0.27256	5.71	2.11	0.27256	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.73505	0.3595	M	0.64567	1.98	0.58432	D	0.999993	D	0.89917	1.0	D	0.97110	1.0	T	0.67639	-0.5619	10	0.16896	T	0.51	.	8.601	0.33745	0.7158:0.0:0.2842:0.0	.	443	O94844	RHBT1_HUMAN	L	443	ENSP00000350595:F443L;ENSP00000338671:F443L	ENSP00000338671:F443L	F	-	3	2	2	RHOBTB1	62318103	62318103	1.000000	0.71417	0.993000	0.49108	0.846000	0.48090	2.104000	0.41815	0.115000	0.18071	-0.793000	0.03317	TTC	0.709677		TCGA-IB-A7LX-01A-12D-A36O-08	0.463	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1	1	0	1	2	2	2	2	0	0	0	0	80	80	80	79	1	3.150000	-2.919542	1	0.550000			0	18	17	0	330	327	0		1	0		0	0	80	0	0	0.999982	3.159376e-01	0	0	0	21	0	18	330
FAS	355	broad.mit.edu	37	10	90773947	90773947	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr10:90773947C>A	ENST00000355740.2	+	9	968	c.748C>A	c.(748-750)Cga>Aga	p.R250R	FAS_ENST00000352159.4_3'UTR|FAS_ENST00000357339.2_Silent_p.R229R|FAS_ENST00000355279.2_3'UTR|RP11-399O19.9_ENST00000562983.1_RNA	NM_000043.4|NM_152871.2|NM_152872.2	NP_000034.1|NP_690610.1|NP_690611.1	P49327	FAS_HUMAN	Fas cell surface death receptor	0	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	AGGCTTTGTTCGAAAGAATGG	0.353																																						ENST00000355740.2	0.350000	0.150000	3.000000e-01	1.900000e-01	0.240000	0.252349	0.240000	0.240000																										0				18	GRCh37	CM961371	FAS	M		c.(748-750)Cga>Aga		Fas cell surface death receptor	Cerulenin(DB01034)|Orlistat(DB01083)						109.0	104.0	106.0					10																	90773947		2203	4300	6503	SO:0001819	synonymous_variant	355	1	121412	31				g.chr10:90773947C>A	M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11920	protein-coding gene	gene with protein product	"""TNF receptor superfamily member 6"""	134637	"""tumor necrosis factor receptor superfamily, member 6"", ""Fas (TNF receptor superfamily, member 6)"""	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355740.2:c.748C>A	chr10.hg19:g.90773947C>A		1					FAS_ENST00000355279.2_3'UTR|FAS_ENST00000352159.4_3'UTR|FAS_ENST00000357339.2_Silent_p.R229R|RP11-399O19.9_ENST00000562983.1_RNA	p.R250R	NM_000043.4|NM_152871.2|NM_152872.2	NP_000034.1|NP_690610.1|NP_690611.1	2	2	4	2.372051	P49327	FAS_HUMAN		9	968	+		Colorectal(252;0.0161)	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000355740.2	1	0	hg19	c.748C>A	CCDS7393.1	0																																																																																								0.709677		TCGA-IB-A7LX-01A-12D-A36O-08	0.353	FAS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049274.3	1	0	1	2	2	2	2	0	0	0	0	129	129	129	129	1	3.150000	-3.186713	1	0.550000			0	27	26	0	596	592	0		1	0		0	0	129	0	0	1.000000	6.293041e-01	0	1	0	47	0	27	596
DHX32	55760	broad.mit.edu	37	10	127569154	127569154	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr10:127569154G>T	ENST00000284690.3	-	1	730	c.240C>A	c.(238-240)atC>atA	p.I80I	DHX32_ENST00000284688.6_Silent_p.I80I	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	80	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				AAACAATCACGATTTGATTTT	0.318																																						ENST00000284690.3	0.360000	0.110000	2.900000e-01	1.600000e-01	0.220000	0.231810	0.220000	0.210000																										0				29						c.(238-240)atC>atA		DEAH (Asp-Glu-Ala-His) box polypeptide 32							77.0	74.0	75.0					10																	127569154		2203	4300	6503	SO:0001819	synonymous_variant	55760	0	0					g.chr10:127569154G>T		CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"""DEAH-boxes"""	16717	protein-coding gene	gene with protein product		607960	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"""	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.240C>A	chr10.hg19:g.127569154G>T		1					DHX32_ENST00000284688.6_Silent_p.I80I	p.I80I	NM_018180.2	NP_060650.2	2	2	4	2.357296	Q7L7V1	DHX32_HUMAN		1	730	-		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Silent	SNP	ENST00000284690.3	1	0	hg19	c.240C>A	CCDS7652.1	0																																																																																								0.709677		TCGA-IB-A7LX-01A-12D-A36O-08	0.318	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	1	0	1	2	2	2	2	0	0	0	0	84	84	84	83	1	3.150000	-3.805459	1	0.550000	NM_018180		0	13	13	0	325	319	0		1	0		0	0	84	0	0	0.999502	8.589719e-01	0	0	0	90	0	13	325
DNHD1	144132	broad.mit.edu	37	11	6593035	6593035	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:6593035G>A	ENST00000527990.2	+	41	14081	c.14081G>A	c.(14080-14082)aGt>aAt	p.S4694N	DNHD1_ENST00000254579.6_Missense_Mutation_p.S4694N			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4694					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CCGGGCACCAGTGACCTGCCA	0.637																																						ENST00000527990.2	1.000000	0.990000	1	9.900000e-01	0.990000	0.998724	0.990000	1.000000																										0				55						c.(14080-14082)aGt>aAt		dynein heavy chain domain 1							46.0	56.0	53.0					11																	6593035		2136	4246	6382	SO:0001583	missense	144132	0	0					g.chr11:6593035G>A	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.14081G>A	chr11.hg19:g.6593035G>A	ENSP00000436180:p.Ser4694Asn	1					DNHD1_ENST00000254579.6_Missense_Mutation_p.S4694N	p.S4694N			2	5	7	2.287299	Q96M86	DNHD1_HUMAN		41	14081	+		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	1	1	hg19	c.14081G>A	CCDS44532.1	1	.	.	.	.	.	.	.	.	.	.	G	1.262	-0.615437	0.03663	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000530197	T;T	0.26067	1.76;1.76	4.75	-5.17	0.02849	4.75	-5.17	0.02849	Dynein heavy chain (1);	1.578020	0.03032	N	0.152237	T	0.11922	0.0290	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.28490	-1.0042	10	0.12103	T	0.63	1.5404	9.9464	0.41611	0.1879:0.1309:0.6813:0.0	.	3782;747;4694	B0I1S4;Q9NSW8;Q96M86	.;.;DNHD1_HUMAN	N	4694;4694;962	ENSP00000254579:S4694N;ENSP00000436180:S4694N	ENSP00000254579:S4694N	S	+	2	0	0	DNHD1	6549611	6549611	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.007000	0.03667	-0.921000	0.03794	-0.165000	0.13383	AGT	0.701740		TCGA-IB-A7LX-01A-12D-A36O-08	0.637	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	1	0	1	2	2	2	2	0	0	0	0	66	66	66	65	1	3.150000	-20.000000	1	0.550000	NM_144666		0	46	45	0	150	145	0		1	1		0	0	66	0	0	1.000000	5.963972e-01	0	3	0	5	0	46	150
RPS13	6207	broad.mit.edu	37	11	17097027	17097027	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:17097027G>T	ENST00000525634.1	-	4	440	c.295C>A	c.(295-297)Cga>Aga	p.R99R	SNORD14A_ENST00000606526.1_RNA|AC116533.1_ENST00000408395.1_RNA|RPS13_ENST00000228140.2_Silent_p.R99R|RPS13_ENST00000526895.1_5'UTR|PIK3C2A_ENST00000531428.1_5'Flank|SNORD14B_ENST00000364533.1_RNA			P62277	RS13_HUMAN	ribosomal protein S13	99					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of RNA splicing (GO:0033119)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribosome (GO:0005840)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.R99*(1)|p.R99G(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)	5						AGATGCTTTCGAACAGCAACT	0.353																																						ENST00000525634.1	1.000000	0.140000	1	1.900000e-01	0.270000	0.429577	0.270000	0.250000																										2	Substitution - Missense(1)|Substitution - Nonsense(1)	p.R99*(1)|p.R99G(1)	haematopoietic_and_lymphoid_tissue(1)|lung(1)	5						c.(295-297)Cga>Aga		ribosomal protein S13							73.0	70.0	71.0					11																	17097027		2200	4294	6494	SO:0001819	synonymous_variant	6207	0	0					g.chr11:17097027G>T	X79239	CCDS7823.1	11p	2011-04-05			ENSG00000110700	ENSG00000110700		"""S ribosomal proteins"""	10386	protein-coding gene	gene with protein product	"""40S ribosomal protein S13"""	180476				8332508, 9582194	Standard	NM_001017		Approved	S13	uc001mmp.3	P62277	OTTHUMG00000165988	ENST00000525634.1:c.295C>A	chr11.hg19:g.17097027G>T		1					PIK3C2A_ENST00000531428.1_5'Flank|AC116533.1_ENST00000408395.1_RNA|SNORD14B_ENST00000364533.1_RNA|RPS13_ENST00000526895.1_5'UTR|SNORD14A_ENST00000606526.1_RNA|RPS13_ENST00000228140.2_Silent_p.R99R	p.R99R			2	5	7	2.287299	P62277	RS13_HUMAN		4	440	-			B2R549|P19116|Q02546|Q29200|Q498Y0	Silent	SNP	ENST00000525634.1	1	0	hg19	c.295C>A	CCDS7823.1	0																																																																																								0.701740		TCGA-IB-A7LX-01A-12D-A36O-08	0.353	RPS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387320.2	1	0	1	2	2	2	2	0	0	0	0	55	55	55	54	1	3.150000	-2.993735	1	0.550000	NM_001017		0	13	13	0	276	274	0		1	1		0	0	55	0	0	0.999545	1	0	2	0	5206	0	13	276
RAPSN	5913	broad.mit.edu	37	11	47469684	47469684	+	Missense_Mutation	SNP	C	C	A	rs150051760		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:47469684C>A	ENST00000298854.2	-	2	424	c.211G>T	c.(211-213)Gac>Tac	p.D71Y	RAPSN_ENST00000352508.3_Missense_Mutation_p.D71Y|RAPSN_ENST00000524487.1_Missense_Mutation_p.D71Y|RAPSN_ENST00000529341.1_Missense_Mutation_p.D71Y	NM_005055.4	NP_005046.2	Q13702	RAPSN_HUMAN	receptor-associated protein of the synapse	71					positive regulation of neuron apoptotic process (GO:0043525)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)	acetylcholine receptor binding (GO:0033130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(6)|ovary(2)	12						CGGGCCGTGTCGATCTGGACC	0.622																																						ENST00000298854.2	1.000000	0.120000	1	2.000000e-01	0.300000	0.422891	0.300000	0.270000																										0				12						c.(211-213)Gac>Tac		receptor-associated protein of the synapse							59.0	48.0	51.0					11																	47469684		2201	4297	6498	SO:0001583	missense	5913	0	0					g.chr11:47469684C>A		CCDS7936.1, CCDS7937.1	11p11.2	2009-04-28	2007-02-23		ENSG00000165917	ENSG00000165917		"""RING-type (C3HC4) zinc fingers"""	9863	protein-coding gene	gene with protein product	"""rapsyn"""	601592	"""receptor-associated protein of the synapse, 43kD"""			8812503	Standard	NM_005055		Approved	RNF205, CMS1D, CMS1E	uc001nfi.2	Q13702	OTTHUMG00000166891	ENST00000298854.2:c.211G>T	chr11.hg19:g.47469684C>A	ENSP00000298854:p.Asp71Tyr	1					RAPSN_ENST00000352508.3_Missense_Mutation_p.D71Y|RAPSN_ENST00000529341.1_Missense_Mutation_p.D71Y|RAPSN_ENST00000524487.1_Missense_Mutation_p.D71Y	p.D71Y	NM_005055.4	NP_005046.2	2	6	8	2.128606	Q13702	RAPSN_HUMAN		2	424	-			Q8TDF3|Q9BTD9	Missense_Mutation	SNP	ENST00000298854.2	1	0	hg19	c.211G>T	CCDS7936.1	0	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442798	0.63067	.	.	ENSG00000165917	ENST00000298854;ENST00000352508;ENST00000524487;ENST00000529341	D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53	4.72	4.72	0.59763	4.72	4.72	0.59763	Tetratricopeptide-like helical (1);Rapsyn, myristoylation/linker region, N-terminal (1);	0.047920	0.85682	D	0.000000	D	0.86772	0.6013	L	0.47716	1.5	0.58432	D	0.99999	P;D;D	0.89917	0.468;0.996;1.0	B;D;D	0.75484	0.339;0.92;0.986	D	0.87824	0.2640	10	0.59425	D	0.04	-53.4394	18.0701	0.89403	0.0:1.0:0.0:0.0	.	71;71;71	E9PK11;Q13702-2;Q13702	.;.;RAPSN_HUMAN	Y	71	ENSP00000298854:D71Y;ENSP00000298853:D71Y;ENSP00000435551:D71Y;ENSP00000431732:D71Y	ENSP00000298854:D71Y	D	-	1	0	0	RAPSN	47426260	47426260	1.000000	0.71417	0.998000	0.56505	0.691000	0.40173	5.569000	0.67391	2.334000	0.79466	0.557000	0.71058	GAC	0.681416		TCGA-IB-A7LX-01A-12D-A36O-08	0.622	RAPSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391726.1	1	0	0	2	2	2	2	0	0	0	0	44	44	44	44	1	3.150000	-10.377630	1	0.550000			0	7	7	0	129	125	0		1			0	0	44	0	0	0.979399	0	0	0	0	0	0	7	129
OR4C15	81309	broad.mit.edu	37	11	55322649	55322650	+	Missense_Mutation	DNP	TC	TC	AA			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:55322649_55322650TC>AA	ENST00000314644.2	+	1	867_868	c.867_868TC>AA	c.(865-870)gcTCtc>gcAAtc	p.L290I		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						GCTGGAAAGCTCTCTCCACCTG	0.436										HNSCC(20;0.049)																												ENST00000314644.2			0	0																														0				56						c.(865-867)gcT>gcA|c.(868-870)Ctc>Atc		olfactory receptor, family 4, subfamily C, member 15																																				SO:0001583	missense	81309	0	0					g.chr11:55322649T>A|g.chr11:55322650C>A	BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"""GPCR / Class A : Olfactory receptors"""	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	Exception_encountered	chr11.hg19:g.55322649_55322650delinsAA	ENSP00000324958:p.Leu290Ile		HNSCC(20;0.049)					p.A289A|p.L290I	NM_001001920.1	NP_001001920.1					Q8NGM1	OR4CF_HUMAN		1	867|868	+			Q6IFE2	Silent|Missense_Mutation	SNP	ENST00000314644.2	1	1	hg19	c.867T>A|c.868C>A	CCDS31501.1																										|5.02	|5.02	|0.67125																																												|0			|55079226																TCGA-IB-A7LX-01A-12D-A36O-08	0.436	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	1	0	0|1	2	2	2	2	0	0	0	0	147	147|149	147|149	146|148	1	3.150000	-20.000000	1	0.550000	NM_001001920		0	202|203	204|205	0	276	273|272	1		1			0	0	147|149	0	0	1.000000	0	0	0	0	0	0	202	276
OR8K3	219473	broad.mit.edu	37	11	56086466	56086466	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:56086466G>T	ENST00000312711.1	+	1	684	c.684G>T	c.(682-684)atG>atT	p.M228I		NM_001005202.1	NP_001005202.1	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K, member 3	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|ovary(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	40	Esophageal squamous(21;0.00448)					TTCTCAGGATGAATTCTGCTG	0.413																																						ENST00000312711.1	1.000000	0.120000	1	1.600000e-01	0.210000	0.364225	0.210000	0.200000																										0				40						c.(682-684)atG>atT		olfactory receptor, family 8, subfamily K, member 3							95.0	91.0	92.0					11																	56086466		2201	4295	6496	SO:0001583	missense	219473	0	0					g.chr11:56086466G>T	AB065541	CCDS31527.1	11q11	2012-08-09			ENSG00000181689	ENSG00000181689		"""GPCR / Class A : Olfactory receptors"""	15313	protein-coding gene	gene with protein product							Standard	NM_001005202		Approved		uc010rjf.2	Q8NH51	OTTHUMG00000166855	ENST00000312711.1:c.684G>T	chr11.hg19:g.56086466G>T	ENSP00000323555:p.Met228Ile	1						p.M228I	NM_001005202.1	NP_001005202.1	2	5	7	2.095029	Q8NH51	OR8K3_HUMAN		1	684	+	Esophageal squamous(21;0.00448)		Q6IFC4	Missense_Mutation	SNP	ENST00000312711.1	1	0	hg19	c.684G>T	CCDS31527.1	0	.	.	.	.	.	.	.	.	.	.	G	0.620	-0.821600	0.02755	.	.	ENSG00000181689	ENST00000312711	T	0.00021	9.03	4.28	2.37	0.29283	4.28	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	0.077917	0.56097	D	0.000035	T	0.00039	0.0001	N	0.02379	-0.575	0.09310	N	0.999998	B	0.19817	0.039	B	0.26969	0.075	T	0.02464	-1.1155	10	0.08599	T	0.76	.	9.6999	0.40180	0.1726:0.0:0.8274:0.0	.	228	Q8NH51	OR8K3_HUMAN	I	228	ENSP00000323555:M228I	ENSP00000323555:M228I	M	+	3	0	0	OR8K3	55843042	55843042	0.001000	0.12720	0.971000	0.41717	0.029000	0.11900	-0.140000	0.10342	0.542000	0.28846	0.471000	0.43371	ATG	0.675090		TCGA-IB-A7LX-01A-12D-A36O-08	0.413	OR8K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391602.1	1	0	1	2	2	2	2	0	0	0	0	112	112	112	111	1	3.150000	-4.239183	1	0.550000	NM_001005202		0	17	17	0	409	404	0		1			0	0	112	0	0	0.999963	0	0	0	0	0	0	17	409
EML3	256364	broad.mit.edu	37	11	62370095	62370095	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:62370095G>A	ENST00000394773.2	-	22	2850	c.2543C>T	c.(2542-2544)aCg>aTg	p.T848M	MTA2_ENST00000527204.1_5'Flank|EML3_ENST00000531557.1_Missense_Mutation_p.T631M|EML3_ENST00000529309.1_Silent_p.H811H|MTA2_ENST00000278823.2_5'Flank|EML3_ENST00000278845.4_Missense_Mutation_p.T849M|EML3_ENST00000494176.2_Silent_p.H783H	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	848						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						GTCGTCGTGCGTGAATCGGAC	0.746																																						ENST00000394773.2	1.000000	0.200000	1	3.700000e-01	0.630000	0.663491	0.630000	1.000000																										0				26						c.(2542-2544)aCg>aTg		echinoderm microtubule associated protein like 3							14.0	10.0	11.0					11																	62370095		2136	4209	6345	SO:0001583	missense	256364	0	0					g.chr11:62370095G>A	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"""WD repeat domain containing"""	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.2543C>T	chr11.hg19:g.62370095G>A	ENSP00000378254:p.Thr848Met	1					EML3_ENST00000529309.1_Silent_p.H811H|EML3_ENST00000494176.2_Silent_p.H783H|MTA2_ENST00000278823.2_5'Flank|EML3_ENST00000531557.1_Missense_Mutation_p.T631M|EML3_ENST00000278845.4_Missense_Mutation_p.T849M|MTA2_ENST00000527204.1_5'Flank	p.T848M	NM_153265.2	NP_694997.2	2	5	7	2.095029	Q32P44	EMAL3_HUMAN		22	2850	-			Q6ZQW7|Q8NA55	Missense_Mutation	SNP	ENST00000394773.2	0	1	hg19	c.2543C>T	CCDS8023.2	0	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.3|21.3	4.126410|4.126410	0.77549|0.77549	.|.	.|.	ENSG00000149499|ENSG00000149499	ENST00000394776|ENST00000439994;ENST00000394773;ENST00000278845;ENST00000531557	.|T;T;T;T	.|0.41400	.|2.28;1.52;1.0;1.0	4.96|4.96	4.96|4.96	0.65561|0.65561	4.96|4.96	4.96|4.96	0.65561|0.65561	.|WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	.|0.511488	.|0.19627	.|N	.|0.109775	T|T	0.54191|0.54191	0.1843|0.1843	L|L	0.39397|0.39397	1.21|1.21	0.80722|0.80722	D|D	1|1	.|D;P;D	.|0.76494	.|0.995;0.882;0.999	.|P;B;D	.|0.66351	.|0.832;0.325;0.943	T|T	0.50775|0.50775	-0.8788|-0.8788	5|10	.|0.42905	.|T	.|0.14	-32.5046|-32.5046	16.0654|16.0654	0.80867|0.80867	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|848;631;849	.|Q32P44;G3V195;B7WPE2	.|EMAL3_HUMAN;.;.	C|M	806|89;848;849;631	.|ENSP00000409611:T89M;ENSP00000378254:T848M;ENSP00000278845:T849M;ENSP00000433417:T631M	.|ENSP00000278845:T849M	R|T	-|-	1|2	0|0	0|0	EML3|EML3	62126671|62126671	62126671|62126671	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	3.027000|3.027000	0.49697|0.49697	2.472000|2.472000	0.83506|0.83506	0.462000|0.462000	0.41574|0.41574	CGC|ACG	0.675090		TCGA-IB-A7LX-01A-12D-A36O-08	0.746	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	0	0	0	2	2	2	2	0	0	0	0	11	11	11	10	1	3.150000	-9.647493	1	0.550000	NM_153265		0	4	1	0	36	34	0		0	0		0	0	11	0	0	0.859457	9.946877e-01	0	0	0	113	0	4	36
KDM2A	22992	broad.mit.edu	37	11	67012810	67012810	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:67012810C>A	ENST00000529006.2	+	14	2160	c.1714C>A	c.(1714-1716)Cga>Aga	p.R572R	KDM2A_ENST00000526258.1_3'UTR|KDM2A_ENST00000308783.5_Silent_p.R30R|KDM2A_ENST00000530342.1_Silent_p.R133R|KDM2A_ENST00000398645.2_Silent_p.R572R	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	572					histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						AGTGCGATGTCGAAAATGCAA	0.552																																						ENST00000529006.2	1.000000	0.120000	1	1.700000e-01	0.250000	0.388959	0.250000	0.230000																										0				36						c.(1714-1716)Cga>Aga		lysine (K)-specific demethylase 2A							83.0	90.0	88.0					11																	67012810		2126	4245	6371	SO:0001819	synonymous_variant	22992	0	0					g.chr11:67012810C>A	BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13606	protein-coding gene	gene with protein product	"""F-box protein FBL11"", ""jumonji C domain-containing histone demethylase 1A"""	605657	"""F-box and leucine-rich repeat protein 11"""	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.1714C>A	chr11.hg19:g.67012810C>A		1					KDM2A_ENST00000308783.5_Silent_p.R30R|KDM2A_ENST00000526258.1_3'UTR|KDM2A_ENST00000530342.1_Silent_p.R133R|KDM2A_ENST00000398645.2_Silent_p.R572R	p.R572R	NM_012308.2	NP_036440.1	2	5	7	2.095029	Q9Y2K7	KDM2A_HUMAN		14	2160	+			D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Silent	SNP	ENST00000529006.2	1	0	hg19	c.1714C>A	CCDS44657.1	0																																																																																								0.675090		TCGA-IB-A7LX-01A-12D-A36O-08	0.552	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	1	0	1	2	2	2	2	0	0	0	0	75	75	75	74	1	3.150000	-12.880610	1	0.550000	NM_012308		0	11	11	0	236	225	0		1	0		0	0	75	0	0	0.997992	9.606481e-01	0	0	0	121	0	11	236
C11orf30	56946	broad.mit.edu	37	11	76257216	76257216	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:76257216G>A	ENST00000529032.1	+	19	3649	c.3649G>A	c.(3649-3651)Gtt>Att	p.V1217I	C11orf30_ENST00000524767.1_Missense_Mutation_p.V1232I|C11orf30_ENST00000525038.1_Missense_Mutation_p.V1218I|C11orf30_ENST00000343878.3_Intron|C11orf30_ENST00000524490.1_Missense_Mutation_p.V1119I|C11orf30_ENST00000533248.1_Missense_Mutation_p.V1126I|C11orf30_ENST00000525919.1_Missense_Mutation_p.V1218I|C11orf30_ENST00000334736.3_Missense_Mutation_p.V1217I			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	1217					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						TCCATCCACTGTTGGCTCTTC	0.512																																						ENST00000529032.1	1.000000	0.130000	1	1.800000e-01	0.240000	0.387989	0.240000	0.210000																										0				60						c.(3649-3651)Gtt>Att		chromosome 11 open reading frame 30							87.0	89.0	88.0					11																	76257216		2200	4292	6492	SO:0001583	missense	56946	0	0					g.chr11:76257216G>A	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.3649G>A	chr11.hg19:g.76257216G>A	ENSP00000432327:p.Val1217Ile	1					C11orf30_ENST00000524767.1_Missense_Mutation_p.V1232I|C11orf30_ENST00000334736.3_Missense_Mutation_p.V1217I|C11orf30_ENST00000343878.3_Intron|C11orf30_ENST00000525038.1_Missense_Mutation_p.V1218I|C11orf30_ENST00000524490.1_Missense_Mutation_p.V1119I|C11orf30_ENST00000525919.1_Missense_Mutation_p.V1218I|C11orf30_ENST00000533248.1_Missense_Mutation_p.V1126I	p.V1217I			2	5	7	2.111242	Q7Z589	EMSY_HUMAN		19	3649	+			B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Missense_Mutation	SNP	ENST00000529032.1	1	1	hg19	c.3649G>A	CCDS8244.1	0	.	.	.	.	.	.	.	.	.	.	G	9.733	1.162780	0.21538	.	.	ENSG00000158636	ENST00000524490;ENST00000334736;ENST00000393457;ENST00000524767;ENST00000533248;ENST00000525919;ENST00000525038;ENST00000529032	.	.	.	6.06	3.0	0.34707	6.06	3.0	0.34707	.	0.499003	0.20569	N	0.089772	T	0.36166	0.0957	N	0.14661	0.345	0.80722	D	1	B;B;B;B;B;B	0.22346	0.068;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.20767	0.031;0.0;0.0;0.0;0.0;0.0	T	0.15150	-1.0447	9	0.27082	T	0.32	-1.8144	9.3812	0.38316	0.1312:0.119:0.7498:0.0	.	1126;1218;1232;1218;1119;1217	B7ZKT8;B7ZKU2;B7ZKU0;Q17RM7;E9PMC9;Q7Z589	.;.;.;.;.;EMSY_HUMAN	I	1119;1217;899;1232;1126;1218;1218;1217	.	ENSP00000334130:V1217I	V	+	1	0	0	C11orf30	75934864	75934864	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.038000	0.41184	1.580000	0.49851	0.650000	0.86243	GTT	0.678284		TCGA-IB-A7LX-01A-12D-A36O-08	0.512	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	1	0	1	2	2	2	2	0	0	0	0	95	95	95	95	1	3.150000	-4.221989	1	0.550000	NM_020193		0	15	14	0	326	322	0		1	0		0	0	95	0	0	0.999866	2.058821e-01	0	0	0	18	0	15	326
NOX4	50507	broad.mit.edu	37	11	89133524	89133524	+	Silent	SNP	A	A	G			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:89133524A>G	ENST00000263317.4	-	10	1108	c.870T>C	c.(868-870)ccT>ccC	p.P290P	NOX4_ENST00000424319.1_Silent_p.P266P|NOX4_ENST00000542487.1_Silent_p.P266P|NOX4_ENST00000531342.1_Intron|NOX4_ENST00000532825.1_Silent_p.P266P|NOX4_ENST00000413594.2_Silent_p.P311P|NOX4_ENST00000343727.5_Silent_p.P266P|NOX4_ENST00000534731.1_Silent_p.P290P|NOX4_ENST00000375979.3_Intron|NOX4_ENST00000527956.1_Silent_p.P266P|NOX4_ENST00000535633.1_Silent_p.P266P|NOX4_ENST00000527626.1_Silent_p.P124P|NOX4_ENST00000528341.1_Silent_p.P265P|NOX4_ENST00000525196.1_Intron			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	290	Ferric oxidoreductase.|Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				ACAGGCACAAAGGTCCAGAAA	0.398																																						ENST00000263317.4	0.320000	0.100000	2.600000e-01	1.400000e-01	0.190000	0.205018	0.190000	0.190000																										0				44						c.(868-870)ccT>ccC		NADPH oxidase 4							48.0	46.0	47.0					11																	89133524		2201	4299	6500	SO:0001819	synonymous_variant	50507	0	0					g.chr11:89133524A>G	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.870T>C	chr11.hg19:g.89133524A>G		1					NOX4_ENST00000535633.1_Silent_p.P266P|NOX4_ENST00000528341.1_Silent_p.P265P|NOX4_ENST00000542487.1_Silent_p.P266P|NOX4_ENST00000534731.1_Silent_p.P290P|NOX4_ENST00000531342.1_Intron|NOX4_ENST00000532825.1_Silent_p.P266P|NOX4_ENST00000527626.1_Silent_p.P124P|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000527956.1_Silent_p.P266P|NOX4_ENST00000424319.1_Silent_p.P266P|NOX4_ENST00000413594.2_Silent_p.P311P|NOX4_ENST00000343727.5_Silent_p.P266P|NOX4_ENST00000375979.3_Intron	p.P290P			0	2	2	1.592599	Q9NPH5	NOX4_HUMAN		10	1108	-		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Silent	SNP	ENST00000263317.4	1	1	hg19	c.870T>C	CCDS8285.1	0																																																																																								0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.398	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	1	0	1	2	2	2	2	0	0	0	0	78	78	78	82	1	3.150000	-4.718546	1	0.550000	NM_016931		0	11	10	0	199	188	0		1	0		0	0	78	0	0	0.997876	7.448056e-02	0	0	0	8	0	11	199
TAF1D	79101	broad.mit.edu	37	11	93472407	93472407	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			G	T	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:93472407G>T	ENST00000448108.2	-	2	714	c.64C>A	c.(64-66)Cga>Aga	p.R22R	C11orf54_ENST00000354421.3_5'Flank|C11orf54_ENST00000540113.1_5'Flank|C11orf54_ENST00000528099.1_5'Flank|C11orf54_ENST00000528288.1_5'Flank|C11orf54_ENST00000331239.4_5'Flank	NM_024116.3	NP_077021.1	Q9H5J8	TAF1D_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa	22					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(3)|prostate(1)|skin(2)	7						ACTCACCTTCGATTTGCAAGT	0.318																																						ENST00000448108.2	0.270000	0.080000	2.200000e-01	1.200000e-01	0.160000	0.175182	0.160000	0.160000																										0				7						c.(64-66)Cga>Aga		TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa							150.0	139.0	143.0					11																	93472407		2201	4298	6499	SO:0001819	synonymous_variant	79101	0	0					g.chr11:93472407G>T		CCDS8293.1	11q21	2012-05-30	2008-09-30	2008-09-30	ENSG00000166012	ENSG00000166012			28759	protein-coding gene	gene with protein product		612823	"""Josephin domain containing 3"""	JOSD3		15520167, 17318177	Standard	NM_024116		Approved	MGC5306, TAF(I)41	uc001pec.3	Q9H5J8	OTTHUMG00000167451	ENST00000448108.2:c.64C>A	chr11.hg19:g.93472407G>T		1					C11orf54_ENST00000354421.3_5'Flank|C11orf54_ENST00000528288.1_5'Flank|C11orf54_ENST00000528099.1_5'Flank|C11orf54_ENST00000540113.1_5'Flank|C11orf54_ENST00000331239.4_5'Flank	p.R22R	NM_024116.3	NP_077021.1	0	2	2	1.608709	Q9H5J8	TAF1D_HUMAN		2	714	-			Q6I9Y6	Silent	SNP	ENST00000448108.2	1	0	hg19	c.64C>A	CCDS8293.1	0																																																																																								0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.318	TAF1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394662.2	1	0	1	2	2	2	2	0	0	0	0	81	81	81	80	1	3.150000	-3.261399	1	0.550000	NM_024116		0	12	12	0	255	249	0		1	0		0	0	81	0	0	0.999053	9.973335e-01	0	0	0	218	0	12	255
TRIM29	23650	broad.mit.edu	37	11	119993732	119993732	+	Silent	SNP	C	C	A	rs137882673		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr11:119993732C>A	ENST00000341846.5	-	5	1786	c.1365G>T	c.(1363-1365)acG>acT	p.T455T	TRIM29_ENST00000541857.1_Silent_p.T188T|TRIM29_ENST00000524816.3_Silent_p.T21T|TRIM29_ENST00000528870.1_5'UTR|TRIM29_ENST00000525887.1_5'Flank|TRIM29_ENST00000529044.1_Silent_p.T194T	NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	455					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		CGAAGCTGTTCGTGTAGTTGT	0.577																																						ENST00000341846.5	0.230000	0.070000	1.900000e-01	1.000000e-01	0.140000	0.152847	0.140000	0.140000																										0				30						c.(1363-1365)acG>acT		tripartite motif containing 29							216.0	158.0	178.0					11																	119993732		2199	4295	6494	SO:0001819	synonymous_variant	23650	0	0					g.chr11:119993732C>A	AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"""Tripartite motif containing / Tripartite motif containing"""	17274	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM29"", ""ataxia-telangiectasia group D-associated protein"""	610658	"""tripartite motif-containing 29"""			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.1365G>T	chr11.hg19:g.119993732C>A		1					TRIM29_ENST00000528870.1_5'UTR|TRIM29_ENST00000524816.3_Silent_p.T21T|TRIM29_ENST00000541857.1_Silent_p.T188T|TRIM29_ENST00000529044.1_Silent_p.T194T|TRIM29_ENST00000525887.1_5'Flank	p.T455T	NM_012101.3	NP_036233.2	0	2	2	1.608709	Q14134	TRI29_HUMAN		5	1786	-		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	Q96AA9|Q9BZY7	Silent	SNP	ENST00000341846.5	1	0	hg19	c.1365G>T	CCDS8428.1	0	.	.	.	.	.	.	.	.	.	.	C	4.375	0.069135	0.08436	.	.	ENSG00000137699	ENST00000525327	.	.	.	4.12	-8.25	0.01025	4.12	-8.25	0.01025	.	.	.	.	.	.	.	.	.	.	.	0.18873	N	0.999985	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.2926	0.21069	0.0942:0.2723:0.4906:0.1429	.	.	.	.	X	48	.	.	E	-	1	0	0	TRIM29	119498942	119498942	0.000000	0.05858	0.001000	0.08648	0.690000	0.40134	-3.482000	0.00456	-4.073000	0.00076	-1.707000	0.00718	GAA	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.577	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	1	0	1	2	2	2	2	0	0	0	0	123	123	123	121	1	3.150000	-2.740996	1	0.550000	NM_012101		0	14	15	0	340	334	0		1	0		0	0	123	0	0	0.999743	9.999955e-01	0	0	0	572	0	14	340
UHRF1BP1L	23074	broad.mit.edu	37	12	100491190	100491190	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:100491190G>T	ENST00000279907.7	-	6	834	c.622C>A	c.(622-624)Cga>Aga	p.R208R	UHRF1BP1L_ENST00000356828.3_Silent_p.R208R	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	208								p.R208*(2)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						GTTATTAATCGAACAGGAGCA	0.343																																						ENST00000279907.7	0.300000	0.080000	2.400000e-01	1.200000e-01	0.170000	0.187931	0.170000	0.180000																										2	Substitution - Nonsense(2)	p.R208*(2)	large_intestine(2)	50						c.(622-624)Cga>Aga		UHRF1 binding protein 1-like							158.0	134.0	142.0					12																	100491190		2203	4299	6502	SO:0001819	synonymous_variant	23074	0	0					g.chr12:100491190G>T		CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.622C>A	chr12.hg19:g.100491190G>T		1					UHRF1BP1L_ENST00000356828.3_Silent_p.R208R	p.R208R	NM_015054.1	NP_055869.1	0	2	2	1.513293	A0JNW5	UH1BL_HUMAN		6	834	-			A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Silent	SNP	ENST00000279907.7	1	0	hg19	c.622C>A	CCDS31882.1	0																																																																																								0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.343	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	1	0	1	2	2	2	2	0	0	0	0	62	62	62	60	1	3.150000	-3.207791	1	0.550000	NM_001006947		0	10	10	0	200	196	0		1	0		0	0	62	0	0	0.996710	6.368889e-02	0	0	0	8	0	10	200
DRAM1	55332	broad.mit.edu	37	12	102295199	102295199	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:102295199C>A	ENST00000258534.8	+	3	769	c.330C>A	c.(328-330)gtC>gtA	p.V110V	DRAM1_ENST00000544152.1_Silent_p.V110V	NM_018370.2	NP_060840.2	Q8N682	DRAM1_HUMAN	DNA-damage regulated autophagy modulator 1	110					apoptotic process (GO:0006915)|autophagy (GO:0006914)|regulation of autophagy (GO:0010506)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12						TGGGCATTGTCGCCAATTTTC	0.428																																						ENST00000258534.8	0.350000	0.090000	2.800000e-01	1.400000e-01	0.200000	0.214106	0.200000	0.200000																										0				12						c.(328-330)gtC>gtA		DNA-damage regulated autophagy modulator 1							196.0	179.0	184.0					12																	102295199		1903	4115	6018	SO:0001819	synonymous_variant	55332	0	0					g.chr12:102295199C>A	BC018435, DA721965	CCDS41823.1	12q23.2	2014-02-12	2009-06-12		ENSG00000136048	ENSG00000136048			25645	protein-coding gene	gene with protein product	"""damage-regulated autophagy modulator"""	610776				16839881	Standard	NM_018370		Approved	FLJ11259, DRAM	uc001tix.3	Q8N682		ENST00000258534.8:c.330C>A	chr12.hg19:g.102295199C>A		1					DRAM1_ENST00000544152.1_Silent_p.V110V	p.V110V	NM_018370.2	NP_060840.2	0	2	2	1.513293	Q8N682	DRAM1_HUMAN		3	769	+			B7Z4T0|Q7L3E3|Q9NUN1	Silent	SNP	ENST00000258534.8	1	0	hg19	c.330C>A	CCDS41823.1	0																																																																																								0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.428	DRAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409195.1	1	0	1	2	2	2	2	0	0	0	0	78	78	78	77	1	3.150000	-3.299010	1	0.550000	NM_018370		0	9	9	0	158	156	0		1	0		0	0	78	0	0	0.994147	6.905539e-01	0	0	0	43	0	9	158
UBE3B	89910	broad.mit.edu	37	12	109945463	109945463	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:109945463G>T	ENST00000342494.3	+	15	2140	c.1545G>T	c.(1543-1545)ctG>ctT	p.L515L	UBE3B_ENST00000535900.1_3'UTR|UBE3B_ENST00000434735.2_Silent_p.L515L|UBE3B_ENST00000280774.5_Silent_p.L515L	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	515					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						TGGAATGCCTGAACAATGACA	0.522																																						ENST00000342494.3	0.220000	0.080000	1.900000e-01	1.100000e-01	0.140000	0.153688	0.140000	0.140000																										0				45						c.(1543-1545)ctG>ctT		ubiquitin protein ligase E3B							163.0	142.0	149.0					12																	109945463		2203	4300	6503	SO:0001819	synonymous_variant	89910	0	0					g.chr12:109945463G>T	BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.1545G>T	chr12.hg19:g.109945463G>T		1					UBE3B_ENST00000535900.1_3'UTR|UBE3B_ENST00000280774.5_Silent_p.L515L|UBE3B_ENST00000434735.2_Silent_p.L515L	p.L515L	NM_130466.3	NP_569733.2	0	2	2	1.513293	Q7Z3V4	UBE3B_HUMAN		15	2140	+			A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Silent	SNP	ENST00000342494.3	1	0	hg19	c.1545G>T	CCDS9129.1	0																																																																																								0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.522	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	1	0	1	2	2	2	2	0	0	0	0	152	152	152	151	1	3.150000	-3.064727	1	0.550000	NM_183415		0	20	19	0	474	471	0		1	0		0	0	152	0	0	0.999995	2.081888e-01	0	0	0	20	0	20	474
TBX5	6910	broad.mit.edu	37	12	114841631	114841631	+	Missense_Mutation	SNP	C	C	A	rs148195311		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:114841631C>A	ENST00000310346.4	-	2	739	c.73G>T	c.(73-75)Gat>Tat	p.D25Y	TBX5_ENST00000552726.1_5'UTR|TBX5_ENST00000349716.5_Intron|TBX5_ENST00000405440.2_Missense_Mutation_p.D25Y|TBX5_ENST00000526441.1_Missense_Mutation_p.D25Y	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	25				GFGLAHTPLEPDAKDLPCDSKPESALGAPSKSPSSPQAAFT QQ -> ALAGAHLWSLTQKTCLRFEPRARSGPPASPPGRPR SRLHPA (in Ref. 1; CAA70592). {ECO:0000305}.	apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		GGTTTCGAATCGCAGGGCAGG	0.706																																					NSCLC(152;1358 1980 4050 23898 40356)	ENST00000310346.4	0.400000	0.130000	3.300000e-01	1.800000e-01	0.240000	0.261411	0.240000	0.240000																										0				56						c.(73-75)Gat>Tat		T-box 5		C	TYR/ASP,,TYR/ASP,TYR/ASP	1,4405	2.1+/-5.4	0,1,2202	34.0	42.0	39.0		73,,73,73	5.3	0.6	12	dbSNP_134	39	0,8600		0,0,4300	no	missense,intron,missense,missense	TBX5	NM_000192.3,NM_080717.2,NM_080718.1,NM_181486.1	160,,160,160	0,1,6502	AA,AC,CC		0.0,0.0227,0.0077	possibly-damaging,,possibly-damaging,possibly-damaging	25/519,,25/350,25/519	114841631	1,13005	2203	4300	6503	SO:0001583	missense	6910	1	121398	30				g.chr12:114841631C>A	U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"""T-boxes"""	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.73G>T	chr12.hg19:g.114841631C>A	ENSP00000309913:p.Asp25Tyr	1					TBX5_ENST00000552726.1_5'UTR|TBX5_ENST00000405440.2_Missense_Mutation_p.D25Y|TBX5_ENST00000349716.5_Intron|TBX5_ENST00000526441.1_Missense_Mutation_p.D25Y	p.D25Y	NM_000192.3	NP_000183.2	0	2	2	1.513293	Q99593	TBX5_HUMAN		2	739	-	Medulloblastoma(191;0.163)|all_neural(191;0.178)		A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	ENST00000310346.4	1	0	hg19	c.73G>T	CCDS9173.1	0	.	.	.	.	.	.	.	.	.	.	C	23.4	4.413796	0.83449	2.27E-4	0.0	ENSG00000089225	ENST00000310346;ENST00000405440;ENST00000526441	D;D;D	0.88201	-2.35;-2.35;-2.31	5.31	5.31	0.75309	5.31	5.31	0.75309	.	0.307696	0.35615	N	0.003093	D	0.86764	0.6011	N	0.19112	0.55	0.46701	D	0.999163	P;P	0.49447	0.887;0.924	P;P	0.49012	0.598;0.594	D	0.88669	0.3194	10	0.62326	D	0.03	.	18.988	0.92780	0.0:1.0:0.0:0.0	.	25;25	Q99593-2;Q99593	.;TBX5_HUMAN	Y	25	ENSP00000309913:D25Y;ENSP00000384152:D25Y;ENSP00000433292:D25Y	ENSP00000309913:D25Y	D	-	1	0	0	TBX5	113326014	113326014	0.997000	0.39634	0.575000	0.28536	0.908000	0.53690	3.897000	0.56273	2.476000	0.83614	0.655000	0.94253	GAT	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.706	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	1	0	1	2	2	2	2	0	0	0	0	45	45	45	44	1	3.150000	-15.904110	1	0.550000	NM_080717		0	12	12	0	166	157	0		1			0	0	45	0	0	0.998929	0	0	0	0	0	0	12	166
CLIP1	6249	broad.mit.edu	37	12	122839066	122839066	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:122839066C>A	ENST00000540338.1	-	6	1282	c.1241G>T	c.(1240-1242)cGa>cTa	p.R414L	CLIP1_ENST00000361654.4_Missense_Mutation_p.R414L|CLIP1_ENST00000545889.1_Missense_Mutation_p.R115L|CLIP1_ENST00000537178.1_Missense_Mutation_p.R414L|CLIP1_ENST00000302528.7_Missense_Mutation_p.R414L|CLIP1_ENST00000358808.2_Missense_Mutation_p.R414L			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	414					microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		CACCATTGTTCGCAGCTGGTC	0.512																																						ENST00000540338.1	1.000000	0.090000	2.600000e-01	1.300000e-01	0.180000	0.237578	0.180000	0.180000																										0				60						c.(1240-1242)cGa>cTa		CAP-GLY domain containing linker protein 1							131.0	107.0	115.0					12																	122839066		2203	4300	6503	SO:0001583	missense	6249	0	0					g.chr12:122839066C>A		CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"""restin"""	179838	"""restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"""	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.1241G>T	chr12.hg19:g.122839066C>A	ENSP00000439093:p.Arg414Leu	1					CLIP1_ENST00000361654.4_Missense_Mutation_p.R414L|CLIP1_ENST00000545889.1_Missense_Mutation_p.R115L|CLIP1_ENST00000537178.1_Missense_Mutation_p.R414L|CLIP1_ENST00000302528.7_Missense_Mutation_p.R414L|CLIP1_ENST00000358808.2_Missense_Mutation_p.R414L	p.R414L			0	3	3	1.820111	P30622	CLIP1_HUMAN		6	1282	-	all_neural(191;0.0837)|Medulloblastoma(191;0.163)		A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	1	0	hg19	c.1241G>T	CCDS58285.1	0	.	.	.	.	.	.	.	.	.	.	C	31	5.083510	0.94050	.	.	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304;ENST00000537004	T;T;T;T;T;T;T	0.69040	2.38;0.45;0.45;0.44;0.48;-0.11;-0.37	5.84	5.84	0.93424	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.82116	0.4967	M	0.72118	2.19	0.80722	D	1	D;D;D;D;D	0.89917	0.995;1.0;0.996;0.989;0.993	P;D;D;D;P	0.76071	0.878;0.987;0.935;0.935;0.862	T	0.81402	-0.0949	10	0.52906	T	0.07	-7.3582	20.1346	0.98019	0.0:1.0:0.0:0.0	.	348;115;414;414;414	F6VGP8;F5H0N7;P30622-2;P30622-1;P30622	.;.;.;.;CLIP1_HUMAN	L	115;414;414;259;414;414;348;348	ENSP00000438743:R115L;ENSP00000303585:R414L;ENSP00000351665:R414L;ENSP00000445531:R414L;ENSP00000439093:R414L;ENSP00000437786:R348L;ENSP00000441409:R348L	ENSP00000303585:R414L	R	-	2	0	0	CLIP1	121405019	121405019	1.000000	0.71417	0.925000	0.36789	0.973000	0.67179	7.818000	0.86416	2.765000	0.95021	0.655000	0.94253	CGA	0.641648		TCGA-IB-A7LX-01A-12D-A36O-08	0.512	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	1	0	1	2	2	2	2	0	0	0	0	71	71	71	69	1	3.150000	-3.002067	1	0.550000	NM_002956		0	11	11	0	271	266	0		1	0		0	0	71	0	0	0.998258	6.345548e-01	0	1	0	52	0	11	271
PLEKHA5	54477	broad.mit.edu	37	12	19512436	19512436	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:19512436C>A	ENST00000299275.6	+	22	2947	c.2941C>A	c.(2941-2943)Caa>Aaa	p.Q981K	PLEKHA5_ENST00000543806.1_Missense_Mutation_p.Q963K|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.Q1147K|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.Q1044K|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.Q1039K|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.Q1039K|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.Q970K|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.Q739K|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.Q925K	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	981					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					AGAAATTGTTCAACTAAAAGA	0.383																																					Pancreas(196;329 2193 11246 14234 19524)	ENST00000299275.6	1.000000	0.170000	4.100000e-01	2.300000e-01	0.310000	0.344369	0.310000	0.290000																										0				35						c.(2941-2943)Caa>Aaa		pleckstrin homology domain containing, family A member 5							99.0	93.0	95.0					12																	19512436		2203	4300	6503	SO:0001583	missense	54477	0	0					g.chr12:19512436C>A	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.2941C>A	chr12.hg19:g.19512436C>A	ENSP00000299275:p.Gln981Lys	1					PLEKHA5_ENST00000424268.1_Missense_Mutation_p.Q970K|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.Q1147K|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.Q1044K|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.Q963K|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.Q1039K|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.Q739K|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.Q1039K|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.Q925K	p.Q981K	NM_019012.5	NP_061885.2	2	4	6	3.113844	Q9HAU0	PKHA5_HUMAN		22	2947	+	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)		A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	1	0	hg19	c.2941C>A	CCDS8682.1	0	.	.	.	.	.	.	.	.	.	.	C	12.07	1.828021	0.32329	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974;ENST00000538972	T;T;T;T;T;T;T;T;T;T;T	0.09073	3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02	4.75	4.75	0.60458	4.75	4.75	0.60458	.	1.239000	0.05720	N	0.597588	T	0.07818	0.0196	N	0.24115	0.695	0.09310	N	1	B;B;B;B;B;B;B;B	0.22146	0.065;0.024;0.014;0.011;0.003;0.02;0.014;0.024	B;B;B;B;B;B;B;B	0.18561	0.022;0.018;0.008;0.008;0.006;0.008;0.008;0.018	T	0.11916	-1.0568	10	0.42905	T	0.14	3.8378	9.1527	0.36973	0.0:0.9019:0.0:0.0981	.	1044;963;970;1142;925;1147;981;1039	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;Q9HAU0-5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;.;PKHA5_HUMAN;.	K	1044;1039;925;1143;1147;981;739;1039;970;963;936;262	ENSP00000325155:Q1044K;ENSP00000347560:Q1039K;ENSP00000352104:Q925K;ENSP00000404296:Q1147K;ENSP00000299275:Q981K;ENSP00000440611:Q739K;ENSP00000439673:Q1039K;ENSP00000400411:Q970K;ENSP00000439837:Q963K;ENSP00000440371:Q936K;ENSP00000443553:Q262K	ENSP00000299275:Q981K	Q	+	1	0	0	PLEKHA5	19403703	19403703	0.013000	0.17824	0.005000	0.12908	0.173000	0.22820	2.184000	0.42575	2.627000	0.88993	0.460000	0.39030	CAA	0.779951		TCGA-IB-A7LX-01A-12D-A36O-08	0.383	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	1	0	1	2	2	2	2	0	0	0	0	63	63	63	63	1	3.150000	-3.260106	1	0.550000	NM_019012		0	17	17	0	401	392	0		1	0		0	0	63	0	0	0.999960	9.999126e-01	0	0	0	370	0	17	401
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	ENST00000256078.4	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119		Dom	yes			Dom	yes		12	12p12.1	12p12.1	3845	Mis	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog				"""L, E, M, O"""	L, E, M, O			pancreatic, colorectal, lung, thyroid, AML, others	UBE2L3/KRAS(2)	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	25349						c.(34-36)gGt>gAt		Kirsten rat sarcoma viral oncogene homolog							91.0	81.0	85.0					12																	25398284		2203	4300	6503	SO:0001583	missense	3845	2	121404	44	Noonan syndrome;Cardiofaciocutaneous syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	g.chr12:25398284C>T	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	chr12.hg19:g.25398284C>T	ENSP00000256078:p.Gly12Asp	1	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)				KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	p.G12D	NM_033360.2	NP_203524.1	2	4	6	3.113844	P01116	RASK_HUMAN	OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)	2	98	-	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	1	1	hg19	c.35G>A	CCDS8703.1	1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	0	KRAS	25289551	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	0.779951		TCGA-IB-A7LX-01A-12D-A36O-08	0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	2	2	2	2	0	0	0	0	84	84	84	82	1	3.150000	-20.000000	1	0.550000	NM_033360		4367	230	225	3666	222	214	1	1	1	1	1	0	0	84	767	1	1.000000	1	1	26	210	20	282	230	222
STK38L	23012	broad.mit.edu	37	12	27461299	27461299	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:27461299C>A	ENST00000389032.3	+	4	383	c.214C>A	c.(214-216)Cgc>Agc	p.R72S	STK38L_ENST00000539577.1_Intron	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					ACAACACGCTCGCAAAGAAAC	0.368																																						ENST00000389032.3	1.000000	0.220000	4.100000e-01	2.700000e-01	0.330000	0.365460	0.330000	0.340000																										0				12						c.(214-216)Cgc>Agc		serine/threonine kinase 38 like							90.0	93.0	92.0					12																	27461299		2203	4300	6503	SO:0001583	missense	23012	0	0					g.chr12:27461299C>A	AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"""nuclear Dbf2-related 2"""	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.214C>A	chr12.hg19:g.27461299C>A	ENSP00000373684:p.Arg72Ser	1					STK38L_ENST00000539577.1_Intron	p.R72S	NM_015000.3	NP_055815.1	2	4	6	3.113844				4	383	+	Colorectal(261;0.0847)			Missense_Mutation	SNP	ENST00000389032.3	1	0	hg19	c.214C>A	CCDS31761.1	0	.	.	.	.	.	.	.	.	.	.	C	17.50	3.405421	0.62288	.	.	ENSG00000211455	ENST00000541191;ENST00000389032;ENST00000540996;ENST00000543246;ENST00000544969	T;T;T;T;T	0.49720	0.99;0.77;0.99;0.99;0.99	4.54	4.54	0.55810	4.54	4.54	0.55810	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.46639	0.1403	L	0.56199	1.76	0.80722	D	1	B	0.10296	0.003	B	0.12837	0.008	T	0.46331	-0.9199	10	0.51188	T	0.08	.	17.29	0.87153	0.0:1.0:0.0:0.0	.	72	Q9Y2H1	ST38L_HUMAN	S	72	ENSP00000437856:R72S;ENSP00000373684:R72S;ENSP00000443838:R72S;ENSP00000442253:R72S;ENSP00000440279:R72S	ENSP00000373684:R72S	R	+	1	0	0	STK38L	27352566	27352566	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.515000	0.60489	2.257000	0.74773	0.460000	0.39030	CGC	0.779951		TCGA-IB-A7LX-01A-12D-A36O-08	0.368	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	1	0	1	2	2	2	2	0	0	0	0	144	144	144	142	1	3.150000	-2.488282	0	0.550000	NM_015000		0	36	39	0	770	757	0		1	0		0	0	144	0	0	1.000000	9.916101e-01	0	0	0	159	0	36	770
CNTN1	1272	broad.mit.edu	37	12	41414201	41414201	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:41414201C>A	ENST00000551295.2	+	20	2599	c.2482C>A	c.(2482-2484)Cat>Aat	p.H828N	CNTN1_ENST00000347616.1_Missense_Mutation_p.H828N|CNTN1_ENST00000348761.2_Missense_Mutation_p.H817N|CNTN1_ENST00000550305.1_3'UTR	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	828	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.H828Y(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				GATATCTGTTCATTGGGAACA	0.294																																						ENST00000551295.2	1.000000	0.120000	1	1.700000e-01	0.230000	0.375333	0.230000	0.210000																										1	Substitution - Missense(1)	p.H828Y(1)	lung(1)	90						c.(2482-2484)Cat>Aat		contactin 1							53.0	57.0	55.0					12																	41414201		2203	4292	6495	SO:0001583	missense	1272	0	0					g.chr12:41414201C>A	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"", ""Endogenous ligands"""	2171	protein-coding gene	gene with protein product	"""glycoprotein gP135"""	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.2482C>A	chr12.hg19:g.41414201C>A	ENSP00000447006:p.His828Asn	1					CNTN1_ENST00000347616.1_Missense_Mutation_p.H828N|CNTN1_ENST00000348761.2_Missense_Mutation_p.H817N|CNTN1_ENST00000550305.1_3'UTR	p.H828N	NM_001843.3	NP_001834.2	2	2	4	2.117339	Q12860	CNTN1_HUMAN		20	2599	+	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	1	0	hg19	c.2482C>A	CCDS8737.1	0	.	.	.	.	.	.	.	.	.	.	C	11.19	1.566934	0.28003	.	.	ENSG00000018236	ENST00000551295;ENST00000347616;ENST00000348761	T;T;T	0.55760	0.5;0.5;0.5	5.75	3.58	0.41010	5.75	3.58	0.41010	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.366663	0.30639	N	0.009186	T	0.26268	0.0641	N	0.08118	0	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.15870	0.008;0.014	T	0.09292	-1.0681	10	0.35671	T	0.21	.	3.1624	0.06524	0.0:0.4877:0.2254:0.2869	.	817;828	Q12860-2;Q12860	.;CNTN1_HUMAN	N	828;828;817	ENSP00000447006:H828N;ENSP00000325660:H828N;ENSP00000261160:H817N	ENSP00000325660:H828N	H	+	1	0	0	CNTN1	39700468	39700468	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.154000	0.42291	1.583000	0.49898	-0.140000	0.14226	CAT	0.677650		TCGA-IB-A7LX-01A-12D-A36O-08	0.294	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	1	0	1	2	2	2	2	0	0	0	0	86	86	86	85	1	3.150000	-3.010795	1	0.550000	NM_001843		0	17	20	0	386	377	0		1	0		0	0	86	0	0	0.999963	1.883276e-02	0	0	0	5	0	17	386
SOCS2	8835	broad.mit.edu	37	12	93968645	93968645	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:93968645G>T	ENST00000340600.2	+	3	885	c.287G>T	c.(286-288)cGa>cTa	p.R96L	SOCS2_ENST00000551556.1_Missense_Mutation_p.R96L|SOCS2_ENST00000548537.1_3'UTR|SOCS2_ENST00000549122.1_Missense_Mutation_p.R96L|SOCS2_ENST00000549206.1_Missense_Mutation_p.R96L|SOCS2_ENST00000536696.2_Missense_Mutation_p.R96L	NM_001270468.1|NM_001270469.1|NM_001270471.1|NM_003877.4	NP_001257397.1|NP_001257398.1|NP_001257400.1|NP_003868.1	O14508	SOCS2_HUMAN	suppressor of cytokine signaling 2	96	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cellular response to hormone stimulus (GO:0032870)|growth hormone receptor signaling pathway (GO:0060396)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of signal transduction (GO:0009967)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of signal transduction (GO:0009966)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	growth hormone receptor binding (GO:0005131)|insulin-like growth factor receptor binding (GO:0005159)|JAK pathway signal transduction adaptor activity (GO:0008269)|SH3/SH2 adaptor activity (GO:0005070)	p.R96Q(1)		cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)	14						ACTAATCTTCGAATCGAATAC	0.378																																						ENST00000340600.2	0.280000	0.080000	2.200000e-01	1.200000e-01	0.160000	0.176061	0.160000	0.160000																										1	Substitution - Missense(1)	p.R96Q(1)	large_intestine(1)	14						c.(286-288)cGa>cTa		suppressor of cytokine signaling 2							83.0	78.0	80.0					12																	93968645		2203	4300	6503	SO:0001583	missense	8835	0	0					g.chr12:93968645G>T	AF037989	CCDS9047.1	12q	2013-02-14			ENSG00000120833	ENSG00000120833		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	19382	protein-coding gene	gene with protein product	"""STAT-induced STAT inhibitor-2"""	605117				9344848, 9266833	Standard	NM_003877		Approved	STATI2, SSI2, SOCS-2, SSI-2, CIS2, Cish2	uc031qjc.1	O14508		ENST00000340600.2:c.287G>T	chr12.hg19:g.93968645G>T	ENSP00000339428:p.Arg96Leu	1					SOCS2_ENST00000536696.2_Missense_Mutation_p.R96L|SOCS2_ENST00000548537.1_3'UTR|SOCS2_ENST00000549122.1_Missense_Mutation_p.R96L|SOCS2_ENST00000551556.1_Missense_Mutation_p.R96L|SOCS2_ENST00000549206.1_Missense_Mutation_p.R96L	p.R96L	NM_001270468.1|NM_001270469.1|NM_001270471.1|NM_003877.4	NP_001257397.1|NP_001257398.1|NP_001257400.1|NP_003868.1	0	2	2	1.513293	O14508	SOCS2_HUMAN		3	885	+			A8K3D1|O14542|O95102|Q9UKS5	Missense_Mutation	SNP	ENST00000340600.2	1	0	hg19	c.287G>T	CCDS9047.1	0	.	.	.	.	.	.	.	.	.	.	G	18.78	3.696989	0.68386	.	.	ENSG00000120833	ENST00000340600;ENST00000549206;ENST00000536696;ENST00000539385;ENST00000548091;ENST00000549122;ENST00000549887;ENST00000551556	D;D;D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52	5.84	5.84	0.93424	5.84	5.84	0.93424	SH2 motif (4);	0.055893	0.64402	D	0.000001	D	0.94830	0.8330	M	0.79343	2.45	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94707	0.7888	10	0.87932	D	0	-0.8535	20.1346	0.98019	0.0:0.0:1.0:0.0	.	96	O14508	SOCS2_HUMAN	L	96;96;96;44;96;96;96;96	ENSP00000339428:R96L;ENSP00000448815:R96L;ENSP00000442898:R96L;ENSP00000447902:R96L;ENSP00000447161:R96L;ENSP00000448611:R96L;ENSP00000449227:R96L	ENSP00000339428:R96L	R	+	2	0	0	SOCS2	92492776	92492776	1.000000	0.71417	0.966000	0.40874	0.239000	0.25481	9.531000	0.98054	2.765000	0.95021	0.655000	0.94253	CGA	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.378	SOCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407731.2	1	0	1	2	2	2	2	0	0	0	0	93	93	93	93	1	3.150000	-3.084451	1	0.550000			0	11	11	0	234	228	0		1	0		0	0	93	0	0	0.998211	1.162609e-01	0	0	0	12	0	11	234
RILPL2	196383	broad.mit.edu	37	12	123907604	123907604	+	Missense_Mutation	SNP	T	T	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr12:123907604T>A	ENST00000280571.8	-	3	888	c.592A>T	c.(592-594)Atc>Ttc	p.I198F		NM_145058.1	NP_659495.1	Q969X0	RIPL2_HUMAN	Rab interacting lysosomal protein-like 2	198					epithelial cell morphogenesis (GO:0003382)|intracellular protein transport (GO:0006886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|primary cilium (GO:0072372)	identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(2)|skin(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000546)|Epithelial(86;0.00179)|all cancers(50;0.0168)		TTTTTTATGATTGTCTTCTCC	0.507																																						ENST00000280571.8	1.000000	0.030000	1.400000e-01	5.000000e-02	0.090000	0.147092	0.090000	0.090000																										0				6						c.(592-594)Atc>Ttc		Rab interacting lysosomal protein-like 2							192.0	172.0	179.0					12																	123907604		2203	4300	6503	SO:0001583	missense	196383	0	0					g.chr12:123907604T>A	AB085763	CCDS9248.1	12q24.31	2007-11-27				ENSG00000150977			28787	protein-coding gene	gene with protein product		614093				14668488	Standard	NM_145058		Approved	MGC7036, FLJ30380, FLJ32372	uc001uey.1	Q969X0		ENST00000280571.8:c.592A>T	chr12.hg19:g.123907604T>A	ENSP00000280571:p.Ile198Phe	1						p.I198F	NM_145058.1	NP_659495.1	0	3	3	1.820111	Q969X0	RIPL2_HUMAN		3	888	-	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Missense_Mutation	SNP	ENST00000280571.8	0	1	hg19	c.592A>T	CCDS9248.1	0	.	.	.	.	.	.	.	.	.	.	T	13.79	2.342477	0.41498	.	.	ENSG00000150977	ENST00000280571	T	0.45668	0.89	5.0	3.85	0.44370	5.0	3.85	0.44370	.	0.229969	0.44688	D	0.000439	T	0.32224	0.0822	L	0.29908	0.895	0.38433	D	0.946505	P	0.49961	0.93	P	0.44860	0.462	T	0.14392	-1.0474	10	0.48119	T	0.1	.	8.3232	0.32140	0.0:0.0913:0.0:0.9087	.	198	Q969X0	RIPL2_HUMAN	F	198	ENSP00000280571:I198F	ENSP00000280571:I198F	I	-	1	0	0	RILPL2	122473557	122473557	0.981000	0.34729	0.610000	0.28997	0.063000	0.16089	1.962000	0.40442	0.858000	0.35431	0.533000	0.62120	ATC	0.641648		TCGA-IB-A7LX-01A-12D-A36O-08	0.507	RILPL2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		0	0	0	2	2	2	2	0	0	0	0	82	82	82	82	1	3.150000	-6.754241	1	0.550000	NM_145058		0	6	6	0	322	317	0		1	1		0	0	82	0	0	0.963650	5.462801e-01	0	2	0	89	0	6	322
WASF3	10810	broad.mit.edu	37	13	27239254	27239254	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr13:27239254C>A	ENST00000335327.5	+	4	401	c.223C>A	c.(223-225)Cgc>Agc	p.R75S	WASF3_ENST00000496788.1_3'UTR|WASF3_ENST00000361042.4_Missense_Mutation_p.R75S	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	75					actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		CAGAATTGATCGCCTTGCTGT	0.413																																						ENST00000335327.5	0.370000	0.100000	3.000000e-01	1.500000e-01	0.210000	0.227817	0.210000	0.200000																										0				22						c.(223-225)Cgc>Agc		WAS protein family, member 3							97.0	89.0	92.0					13																	27239254		2203	4300	6503	SO:0001583	missense	10810	0	0					g.chr13:27239254C>A	AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.223C>A	chr13.hg19:g.27239254C>A	ENSP00000335055:p.Arg75Ser	1					WASF3_ENST00000361042.4_Missense_Mutation_p.R75S|WASF3_ENST00000496788.1_3'UTR	p.R75S	NM_006646.5	NP_006637.2	2	2	4	2.350227	Q9UPY6	WASF3_HUMAN		4	401	+	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)	O94974|Q86VQ2	Missense_Mutation	SNP	ENST00000335327.5	1	0	hg19	c.223C>A	CCDS9318.1	0	.	.	.	.	.	.	.	.	.	.	C	28.9	4.956245	0.92726	.	.	ENSG00000132970	ENST00000361042;ENST00000335327	T;T	0.67523	-0.27;-0.27	5.64	5.64	0.86602	5.64	5.64	0.86602	.	0.052354	0.85682	D	0.000000	T	0.77343	0.4116	M	0.79805	2.47	0.80722	D	1	P;P	0.50156	0.932;0.498	P;B	0.49387	0.609;0.318	T	0.79259	-0.1877	10	0.51188	T	0.08	-23.1243	19.6999	0.96048	0.0:1.0:0.0:0.0	.	75;75	Q86VQ2;Q9UPY6	.;WASF3_HUMAN	S	75	ENSP00000354325:R75S;ENSP00000335055:R75S	ENSP00000335055:R75S	R	+	1	0	0	WASF3	26137254	26137254	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.320000	0.79064	2.659000	0.90383	0.650000	0.86243	CGC	0.709677		TCGA-IB-A7LX-01A-12D-A36O-08	0.413	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1	1	0	1	2	2	2	2	0	0	0	0	66	66	66	65	1	3.150000	-3.116152	1	0.550000			0	9	9	0	236	231	0		1	0		0	0	66	0	0	0.993916	3.210462e-02	0	0	0	7	0	9	236
FREM2	341640	broad.mit.edu	37	13	39452994	39452994	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr13:39452994G>T	ENST00000280481.7	+	23	9102	c.8886G>T	c.(8884-8886)gcG>gcT	p.A2962A		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2962			A -> V (in dbSNP:rs7996253).		cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AGACACAAGCGACCAGTTTTG	0.443																																						ENST00000280481.7	0.300000	0.100000	2.500000e-01	1.400000e-01	0.180000	0.197593	0.180000	0.200000																										0				148						c.(8884-8886)gcG>gcT		FRAS1 related extracellular matrix protein 2							157.0	144.0	148.0					13																	39452994		2203	4300	6503	SO:0001819	synonymous_variant	341640	0	0					g.chr13:39452994G>T	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.8886G>T	chr13.hg19:g.39452994G>T		1						p.A2962A	NM_207361.4	NP_997244.3	2	2	4	2.350227	Q5SZK8	FREM2_HUMAN		23	9102	+		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	1	0	hg19	c.8886G>T	CCDS31960.1	0																																																																																								0.709677		TCGA-IB-A7LX-01A-12D-A36O-08	0.443	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	1	0	1	2	2	2	2	0	0	0	0	110	110	110	110	1	3.150000	-2.980733	1	0.550000	NM_207361		0	15	15	0	439	430	0		1	0		0	0	110	0	0	0.999856	1.305232e-03	0	0	0	2	0	15	439
NHLRC3	387921	broad.mit.edu	37	13	39616292	39616292	+	Missense_Mutation	SNP	C	C	A	rs369490569		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr13:39616292C>A	ENST00000379600.3	+	4	758	c.436C>A	c.(436-438)Caa>Aaa	p.Q146K	NHLRC3_ENST00000470258.1_5'UTR|NHLRC3_ENST00000379599.2_Intron	NM_001012754.3	NP_001012772.1	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3	146						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|skin(2)	11		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		TGATCTTGTTCAAGTCTTGGG	0.338																																						ENST00000379600.3	0.370000	0.130000	3.100000e-01	1.800000e-01	0.240000	0.251497	0.240000	0.240000																										0				11						c.(436-438)Caa>Aaa		NHL repeat containing 3							111.0	107.0	109.0					13																	39616292		2203	4300	6503	SO:0001583	missense	387921	0	0					g.chr13:39616292C>A		CCDS31961.1, CCDS31962.1	13q13.3	2007-12-18			ENSG00000188811	ENSG00000188811			33751	protein-coding gene	gene with protein product							Standard	NM_001017370		Approved		uc001uxc.4	Q5JS37	OTTHUMG00000016765	ENST00000379600.3:c.436C>A	chr13.hg19:g.39616292C>A	ENSP00000368920:p.Gln146Lys	1					NHLRC3_ENST00000470258.1_5'UTR|NHLRC3_ENST00000379599.2_Intron	p.Q146K	NM_001012754.3	NP_001012772.1	2	2	4	2.350227	Q5JS37	NHLC3_HUMAN		4	758	+		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)	B2RTZ2|B4DTL0|Q69YI9	Missense_Mutation	SNP	ENST00000379600.3	1	0	hg19	c.436C>A	CCDS31961.1	0	.	.	.	.	.	.	.	.	.	.	C	9.802	1.180739	0.21787	.	.	ENSG00000188811	ENST00000379600	T	0.45276	0.9	5.3	5.3	0.74995	5.3	5.3	0.74995	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.48804	0.1520	L	0.42245	1.32	0.80722	D	1	P;D	0.56521	0.473;0.976	B;P	0.52343	0.056;0.696	T	0.36625	-0.9740	9	.	.	.	-10.6501	17.9281	0.88989	0.0:1.0:0.0:0.0	.	146;146	Q5JS37;B4DRC8	NHLC3_HUMAN;.	K	146	ENSP00000368920:Q146K	.	Q	+	1	0	0	NHLRC3	38514292	38514292	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.945000	0.56637	2.457000	0.83068	0.467000	0.42956	CAA	0.709677		TCGA-IB-A7LX-01A-12D-A36O-08	0.338	NHLRC3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044616.2	1	0	1	2	2	2	2	0	0	0	0	91	91	91	90	1	3.150000	-4.523921	1	0.550000	NM_001012754		0	17	15	0	384	377	0		1	0		0	0	91	0	0	0.999960	4.728714e-01	0	0	0	36	0	17	384
PCDH17	27253	broad.mit.edu	37	13	58298909	58298909	+	Silent	SNP	C	C	T	rs138830034	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr13:58298909C>T	ENST00000377918.3	+	4	2987	c.2961C>T	c.(2959-2961)taC>taT	p.Y987Y		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	987					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CTGAGACTTACGAAACTGTGA	0.413																																					Melanoma(72;952 1291 1619 12849 33676)	ENST00000377918.3	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000																										0				120						c.(2959-2961)taC>taT		protocadherin 17		C		0,4406		0,0,2203	107.0	103.0	104.0		2961	-0.3	1.0	13	dbSNP_134	104	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	PCDH17	NM_001040429.2		0,7,6496	TT,TC,CC		0.0814,0.0,0.0538		987/1160	58298909	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	27253	85	121410	52				g.chr13:58298909C>T	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.2961C>T	chr13.hg19:g.58298909C>T		1						p.Y987Y	NM_001040429.2	NP_001035519.1	2	2	4	2.350227	O14917	PCD17_HUMAN		4	2987	+		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	1	1	hg19	c.2961C>T	CCDS31986.1	1																																																																																								0.709677		TCGA-IB-A7LX-01A-12D-A36O-08	0.413	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	1	0	1	2	2	2	2	0	0	0	0	83	83	83	83	1	3.150000	-2.879461	1	0.550000	NM_001040429		0	97	96	0	203	201	1		1	0		0	0	83	0	0	1.000000	8.812058e-01	0	0	0	10	0	97	203
CUL4A	8451	broad.mit.edu	37	13	113887578	113887578	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr13:113887578C>A	ENST00000375440.4	+	6	684	c.600C>A	c.(598-600)atC>atA	p.I200I	CUL4A_ENST00000326335.4_Silent_p.I100I|CUL4A_ENST00000451881.1_Silent_p.I100I|CUL4A_ENST00000375441.3_Silent_p.I100I	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	200					cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|regulation of nucleotide-excision repair (GO:2000819)|regulation of protein metabolic process (GO:0051246)|somatic stem cell maintenance (GO:0035019)|viral process (GO:0016032)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|skin(1)	17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			TACTGCTGATCGAGCGCGAGA	0.512																																						ENST00000375440.4	0.320000	0.100000	2.600000e-01	1.400000e-01	0.190000	0.204745	0.190000	0.200000																										0				17						c.(598-600)atC>atA		cullin 4A							86.0	83.0	84.0					13																	113887578		2203	4300	6503	SO:0001819	synonymous_variant	8451	0	0					g.chr13:113887578C>A	U58090	CCDS9533.1, CCDS41908.1, CCDS73604.1	13q34	2011-05-24			ENSG00000139842	ENSG00000139842			2554	protein-coding gene	gene with protein product		603137				8681378	Standard	NM_001008895		Approved		uc021rmv.1	Q13619	OTTHUMG00000017384	ENST00000375440.4:c.600C>A	chr13.hg19:g.113887578C>A		1					CUL4A_ENST00000451881.1_Silent_p.I100I|CUL4A_ENST00000326335.4_Silent_p.I100I|CUL4A_ENST00000375441.3_Silent_p.I100I	p.I200I	NM_001008895.1	NP_001008895.1	2	2	4	2.350227	Q13619	CUL4A_HUMAN	all cancers(43;0.112)	6	684	+	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Silent	SNP	ENST00000375440.4	1	0	hg19	c.600C>A	CCDS41908.1	0																																																																																								0.709677		TCGA-IB-A7LX-01A-12D-A36O-08	0.512	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	1	0	1	2	2	2	2	0	0	0	0	83	83	83	83	1	3.150000	-3.216127	1	0.550000	NM_003589		0	13	13	0	370	365	0		1	0		0	0	83	0	0	0.999512	9.257780e-01	0	0	0	130	0	13	370
OR11H6	122748	broad.mit.edu	37	14	20692623	20692623	+	Missense_Mutation	SNP	G	G	T	rs367798181		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr14:20692623G>T	ENST00000315519.2	+	1	833	c.755G>T	c.(754-756)cGa>cTa	p.R252L		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	252						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		GGTGCTGGTCGAACTAAAGCT	0.483																																						ENST00000315519.2	1.000000	0.160000	4.100000e-01	2.100000e-01	0.290000	0.365046	0.290000	0.270000																										0				29						c.(754-756)cGa>cTa		olfactory receptor, family 11, subfamily H, member 6							110.0	94.0	99.0					14																	20692623		2203	4300	6503	SO:0001583	missense	122748	0	0					g.chr14:20692623G>T		CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"""GPCR / Class A : Olfactory receptors"""	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.755G>T	chr14.hg19:g.20692623G>T	ENSP00000319071:p.Arg252Leu	1						p.R252L	NM_001004480.1	NP_001004480.1	2	2	4	2.243649	Q8NGC7	O11H6_HUMAN	Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	1	833	+	all_cancers(95;0.00108)		Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	1	0	hg19	c.755G>T	CCDS32033.1	0	.	.	.	.	.	.	.	.	.	.	G	17.36	3.369552	0.61624	.	.	ENSG00000176219	ENST00000315519	T	0.00330	8.08	4.78	3.89	0.44902	4.78	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41500	D	0.000870	T	0.00666	0.0022	M	0.85462	2.755	0.09310	N	1	P	0.51449	0.945	P	0.56127	0.792	T	0.27673	-1.0067	10	0.72032	D	0.01	.	10.7593	0.46256	0.0939:0.0:0.9061:0.0	.	252	Q8NGC7	O11H6_HUMAN	L	252	ENSP00000319071:R252L	ENSP00000319071:R252L	R	+	2	0	0	OR11H6	19762463	19762463	0.000000	0.05858	0.878000	0.34440	0.949000	0.60115	0.442000	0.21628	1.223000	0.43536	0.471000	0.43371	CGA	0.695637		TCGA-IB-A7LX-01A-12D-A36O-08	0.483	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1	1	0	1	2	2	2	2	0	0	0	0	71	71	71	71	1	3.150000	-4.686283	1	0.550000			0	15	15	0	278	273	0		1			0	0	71	0	0	0.999866	0	0	0	0	0	0	15	278
TEP1	7011	broad.mit.edu	37	14	20841221	20841221	+	Silent	SNP	T	T	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr14:20841221T>C	ENST00000262715.5	-	48	6940	c.6900A>G	c.(6898-6900)caA>caG	p.Q2300Q	TEP1_ENST00000545983.1_Silent_p.Q638Q|TEP1_ENST00000556935.1_Silent_p.Q2192Q	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2300					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GTTCCCCAGCTTGATTTCCAG	0.522																																						ENST00000262715.5	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000																										0				96						c.(6898-6900)caA>caG		telomerase-associated protein 1							77.0	77.0	77.0					14																	20841221		2203	4300	6503	SO:0001819	synonymous_variant	7011	1	121412	34				g.chr14:20841221T>C		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.6900A>G	chr14.hg19:g.20841221T>C		1					TEP1_ENST00000556935.1_Silent_p.Q2192Q|TEP1_ENST00000545983.1_Silent_p.Q638Q	p.Q2300Q	NM_007110.4	NP_009041.2	2	2	4	2.243649	Q99973	TEP1_HUMAN	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	48	6940	-	all_cancers(95;0.00123)	all_lung(585;0.235)	A0AUV9	Silent	SNP	ENST00000262715.5	1	1	hg19	c.6900A>G	CCDS9548.1	1	.	.	.	.	.	.	.	.	.	.	T	8.134	0.783739	0.16189	.	.	ENSG00000129566	ENST00000553984	.	.	.	5.77	0.76	0.18442	5.77	0.76	0.18442	.	.	.	.	.	T	0.32041	0.0816	.	.	.	0.21719	N	0.999572	.	.	.	.	.	.	T	0.26849	-1.0091	4	.	.	.	-0.0235	7.2173	0.25967	0.0:0.4669:0.0:0.5331	.	.	.	.	G	7	.	.	S	-	1	0	0	TEP1	19911061	19911061	0.053000	0.20554	0.110000	0.21437	0.973000	0.67179	0.124000	0.15728	0.135000	0.18707	0.533000	0.62120	AGC	0.695637		TCGA-IB-A7LX-01A-12D-A36O-08	0.522	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	1	0	1	2	2	2	2	0	0	0	0	69	69	69	67	1	3.150000	-20.000000	1	0.550000	NM_007110		0	91	87	0	178	174	1		1	1		0	0	69	0	0	1.000000	9.999992e-01	0	21	0	24	0	91	178
AKAP6	9472	broad.mit.edu	37	14	33291486	33291486	+	Silent	SNP	C	C	T	rs371708448		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr14:33291486C>T	ENST00000280979.4	+	13	4637	c.4467C>T	c.(4465-4467)agC>agT	p.S1489S	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1489					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		AGTCACAAAGCGAAAAAGCGC	0.348													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20207	0.0		0.0	False		,,,				2504	0.0				Melanoma(49;821 1200 7288 13647 42351)	ENST00000280979.4	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000																										0				122						c.(4465-4467)agC>agT		A kinase (PRKA) anchor protein 6		C		1,4405	2.1+/-5.4	0,1,2202	73.0	70.0	71.0		4467	4.6	1.0	14		71	0,8600		0,0,4300	no	coding-synonymous	AKAP6	NM_004274.4		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		1489/2320	33291486	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9472	7	121390	38				g.chr14:33291486C>T	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.4467C>T	chr14.hg19:g.33291486C>T		1					AKAP6_ENST00000557272.1_Intron	p.S1489S	NM_004274.4	NP_004265.3	2	2	4	2.243649	Q13023	AKAP6_HUMAN	LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	13	4637	+	Breast(36;0.0388)|Prostate(35;0.15)		A7E242|A7E2D4|O15028	Silent	SNP	ENST00000280979.4	1	1	hg19	c.4467C>T	CCDS9644.1	1																																																																																								0.695637		TCGA-IB-A7LX-01A-12D-A36O-08	0.348	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	1	0	1	2	2	2	2	0	0	0	0	73	73	73	73	1	3.150000	-20.000000	1	0.550000	NM_004274		0	86	86	0	190	189	1		1			0	0	73	0	0	1.000000	0	0	0	0	0	0	86	190
ARID4A	5926	broad.mit.edu	37	14	58785281	58785281	+	Missense_Mutation	SNP	G	G	T	rs377075782		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr14:58785281G>T	ENST00000355431.3	+	6	669	c.296G>T	c.(295-297)cGa>cTa	p.R99L	ARID4A_ENST00000431317.2_Missense_Mutation_p.R99L|ARID4A_ENST00000348476.3_Missense_Mutation_p.R99L|ARID4A_ENST00000395168.3_Missense_Mutation_p.R99L	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	99					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						GGTGATGAGCGAACATTGAGA	0.378																																						ENST00000355431.3	1.000000	0.110000	3.100000e-01	1.500000e-01	0.210000	0.297157	0.210000	0.190000																										0				60						c.(295-297)cGa>cTa		AT rich interactive domain 4A (RBP1-like)							194.0	167.0	176.0					14																	58785281		2203	4300	6503	SO:0001583	missense	5926	0	0					g.chr14:58785281G>T	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"""-"""	9885	protein-coding gene	gene with protein product		180201	"""retinoblastoma-binding protein 1"""	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.296G>T	chr14.hg19:g.58785281G>T	ENSP00000347602:p.Arg99Leu	1					ARID4A_ENST00000431317.2_Missense_Mutation_p.R99L|ARID4A_ENST00000348476.3_Missense_Mutation_p.R99L|ARID4A_ENST00000395168.3_Missense_Mutation_p.R99L	p.R99L	NM_002892.3	NP_002883.3	2	2	4	2.243649	P29374	ARI4A_HUMAN		6	669	+			Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	1	0	hg19	c.296G>T	CCDS9732.1	0	.	.	.	.	.	.	.	.	.	.	G	25.2	4.610945	0.87258	.	.	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000445108;ENST00000431317	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11	5.78	5.78	0.91487	5.78	5.78	0.91487	Tudor domain (1);	0.041251	0.85682	D	0.000000	T	0.59622	0.2207	L	0.43923	1.385	0.53688	D	0.999977	D;D;D	0.76494	0.999;0.997;0.998	D;D;D	0.70935	0.971;0.954;0.97	T	0.59883	-0.7370	10	0.87932	D	0	-25.8845	20.0079	0.97439	0.0:0.0:1.0:0.0	.	99;99;99	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	L	99;99;99;62;99	ENSP00000347602:R99L;ENSP00000344556:R99L;ENSP00000378597:R99L;ENSP00000392567:R62L;ENSP00000397368:R99L	ENSP00000344556:R99L	R	+	2	0	0	ARID4A	57855034	57855034	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.001000	0.70685	2.722000	0.93159	0.655000	0.94253	CGA	0.695637		TCGA-IB-A7LX-01A-12D-A36O-08	0.378	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	1	0	1	2	2	2	2	0	0	0	0	73	73	73	71	1	3.150000	-3.158608	1	0.550000	NM_023001		0	14	12	0	358	353	0		1	0		0	0	73	0	0	0.999733	3.222530e-01	0	0	0	29	0	14	358
MAP3K9	4293	broad.mit.edu	37	14	71216711	71216711	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr14:71216711C>A	ENST00000554752.2	-	4	1088	c.1089G>T	c.(1087-1089)atG>atT	p.M363I	MAP3K9_ENST00000555993.2_Missense_Mutation_p.M363I|MAP3K9_ENST00000553414.1_Missense_Mutation_p.M57I|MAP3K9_ENST00000381250.4_Missense_Mutation_p.M363I|MAP3K9_ENST00000554146.1_Missense_Mutation_p.M100I	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	363	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		CGAGTTTGTTCATGGCCACTC	0.507																																					GBM(114;411 1587 13539 28235 50070)	ENST00000554752.2	1.000000	0.120000	3.500000e-01	1.700000e-01	0.240000	0.321530	0.240000	0.220000																										0				46						c.(1087-1089)atG>atT		mitogen-activated protein kinase kinase kinase 9							170.0	147.0	154.0					14																	71216711		2203	4300	6503	SO:0001583	missense	4293	0	0					g.chr14:71216711C>A	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.1089G>T	chr14.hg19:g.71216711C>A	ENSP00000451612:p.Met363Ile	1					MAP3K9_ENST00000553414.1_Missense_Mutation_p.M57I|MAP3K9_ENST00000554146.1_Missense_Mutation_p.M100I|MAP3K9_ENST00000381250.4_Missense_Mutation_p.M363I|MAP3K9_ENST00000555993.2_Missense_Mutation_p.M363I	p.M363I	NM_001284230.1	NP_001271159.1	2	2	4	2.243649	P80192	M3K9_HUMAN		4	1088	-			A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Missense_Mutation	SNP	ENST00000554752.2	1	0	hg19	c.1089G>T		0	.	.	.	.	.	.	.	.	.	.	C	21.9	4.221675	0.79464	.	.	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284	D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44	5.91	5.02	0.67125	5.91	5.02	0.67125	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81202	0.4773	N	0.05554	-0.025	0.50632	D	0.999885	B;B;B;B	0.29188	0.022;0.236;0.198;0.198	B;B;B;B	0.37989	0.032;0.262;0.113;0.171	T	0.78272	-0.2268	10	0.33141	T	0.24	.	14.5088	0.67769	0.0:0.9302:0.0:0.0698	.	100;363;363;57	G3V4P9;P80192;P80192-4;G3V347	.;M3K9_HUMAN;.;.	I	363;363;57;363;100;91	ENSP00000451612:M363I;ENSP00000451038:M57I;ENSP00000370649:M363I;ENSP00000451921:M100I	ENSP00000005198:M363I	M	-	3	0	0	MAP3K9	70286464	70286464	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.115000	0.31209	2.808000	0.96608	0.655000	0.94253	ATG	0.695637		TCGA-IB-A7LX-01A-12D-A36O-08	0.507	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2	1	0	1	2	2	2	2	0	0	0	0	68	68	68	68	1	3.150000	-3.196010	1	0.550000			0	14	13	0	316	308	0		1	0		0	0	68	0	0	0.999714	1.467250e-01	0	0	0	15	0	14	316
BATF	10538	broad.mit.edu	37	14	75989073	75989073	+	Silent	SNP	T	T	G			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			T	G	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr14:75989073T>G	ENST00000286639.6	+	1	306	c.48T>G	c.(46-48)ccT>ccG	p.P16P	BATF_ENST00000555504.1_Silent_p.P16P|BATF_ENST00000555795.1_Intron	NM_006399.3	NP_006390.1	Q16520	BATF_HUMAN	basic leucine zipper transcription factor, ATF-like	16					cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hematopoietic stem cell differentiation (GO:0060218)|isotype switching (GO:0045190)|lymphoid progenitor cell differentiation (GO:0002320)|myeloid dendritic cell differentiation (GO:0043011)|T-helper 17 cell differentiation (GO:0072539)|T-helper 17 cell lineage commitment (GO:0072540)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|ovary(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.028)		GCCGCTCTCCTCCCCCTGGCA	0.587																																						ENST00000286639.6	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000																										0				3						c.(46-48)ccT>ccG		basic leucine zipper transcription factor, ATF-like							82.0	75.0	77.0					14																	75989073		2203	4300	6503	SO:0001819	synonymous_variant	10538	0	0					g.chr14:75989073T>G	AF016898	CCDS9843.1	14q24	2013-01-10				ENSG00000156127		"""basic leucine zipper proteins"""	958	protein-coding gene	gene with protein product	"""activating transcription factor B"", ""SF-HT-activated gene 2"""	612476				8570175, 8630063	Standard	NM_006399		Approved	B-ATF, SFA-2, BATF1	uc001xrr.3	Q16520		ENST00000286639.6:c.48T>G	chr14.hg19:g.75989073T>G		1					BATF_ENST00000555795.1_Intron|BATF_ENST00000555504.1_Silent_p.P16P	p.P16P	NM_006399.3	NP_006390.1	2	2	4	2.243649	Q16520	BATF_HUMAN		1	306	+				Silent	SNP	ENST00000286639.6	1	1	hg19	c.48T>G	CCDS9843.1	1																																																																																								0.695637		TCGA-IB-A7LX-01A-12D-A36O-08	0.587	BATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413669.1	1	0	1	2	2	2	2	0	0	0	0	54	54	54	54	1	3.150000	-8.900294	1	0.550000	NM_006399		0	79	77	0	166	164	1		1	1		0	0	54	0	0	1.000000	1	0	44	0	47	0	79	166
ADAMTSL3	57188	broad.mit.edu	37	15	84683327	84683327	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr15:84683327G>C	ENST00000286744.5	+	24	4231	c.4007G>C	c.(4006-4008)aGa>aCa	p.R1336T	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R1336T	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	1336	Ig-like C2-type 3.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R1336I(1)		NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			TGGTTGAAGAGAGGAGGATCT	0.428																																						ENST00000286744.5	1.000000	0.190000	1	2.300000e-01	0.280000	0.431600	0.280000	0.270000																										1	Substitution - Missense(1)	p.R1336I(1)	endometrium(1)	130						c.(4006-4008)aGa>aCa		ADAMTS-like 3							217.0	190.0	199.0					15																	84683327		2203	4299	6502	SO:0001583	missense	57188	0	0					g.chr15:84683327G>C	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.4007G>C	chr15.hg19:g.84683327G>C	ENSP00000286744:p.Arg1336Thr	1					ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R1336T	p.R1336T	NM_207517.2	NP_997400.2	2	4	6	2.035251	P82987	ATL3_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.211)	24	4231	+			A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	1	1	hg19	c.4007G>C	CCDS10326.1	0	.	.	.	.	.	.	.	.	.	.	G	10.69	1.420685	0.25639	.	.	ENSG00000156218	ENST00000286744	T	0.27402	1.67	4.7	1.68	0.24146	4.7	1.68	0.24146	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.739929	0.11659	N	0.541996	T	0.15696	0.0378	N	0.17082	0.46	0.26572	N	0.973534	B;B	0.09022	0.001;0.002	B;B	0.12837	0.008;0.007	T	0.31280	-0.9949	10	0.22109	T	0.4	.	4.2489	0.10684	0.4199:0.1664:0.4137:0.0	.	1336;1336	P82987-2;P82987	.;ATL3_HUMAN	T	1336	ENSP00000286744:R1336T	ENSP00000286744:R1336T	R	+	2	0	0	ADAMTSL3	82474331	82474331	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	0.900000	0.28431	0.048000	0.15891	-0.266000	0.10368	AGA	0.667160		TCGA-IB-A7LX-01A-12D-A36O-08	0.428	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	1	0	1	2	2	2	2	0	0	0	0	182	182	182	179	1	3.150000	-5.808365	1	0.550000	NM_207517		0	35	34	0	593	581	0		1	0		0	0	182	0	0	1.000000	4.274176e-02	0	0	0	6	0	35	593
CPD	1362	broad.mit.edu	37	17	28747986	28747986	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:28747986C>A	ENST00000225719.4	+	3	1198	c.1122C>A	c.(1120-1122)atC>atA	p.I374I	CPD_ENST00000543464.2_Silent_p.I127I	NM_001304.4	NP_001295.2	O75976	CBPD_HUMAN	carboxypeptidase D	374	Carboxypeptidase-like 1.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metallocarboxypeptidase activity (GO:0004181)|serine-type carboxypeptidase activity (GO:0004185)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(13)|skin(5)|stomach(1)|urinary_tract(1)	36						AGTCTTTGATCACATTGATTG	0.393																																						ENST00000225719.4	1.000000	0.130000	3.700000e-01	1.900000e-01	0.260000	0.325280	0.260000	0.260000																										0				36						c.(1120-1122)atC>atA		carboxypeptidase D							107.0	98.0	101.0					17																	28747986		2203	4300	6503	SO:0001819	synonymous_variant	1362	0	0					g.chr17:28747986C>A	U65090	CCDS11257.1, CCDS56025.1	17q11.2	2012-02-10			ENSG00000108582	ENSG00000108582	3.4.17.22		2301	protein-coding gene	gene with protein product	"""metallocarboxypeptidase D"""	603102				9628828, 9355738	Standard	NM_001304		Approved	GP180	uc002hfb.2	O75976	OTTHUMG00000132797	ENST00000225719.4:c.1122C>A	chr17.hg19:g.28747986C>A		1					CPD_ENST00000543464.2_Silent_p.I127I	p.I374I	NM_001304.4	NP_001295.2	2	2	4	2.274668	O75976	CBPD_HUMAN		3	1198	+			B7Z7T9|B7ZAU4|F5GZH6|O15377|Q86SH9|Q86XE6	Silent	SNP	ENST00000225719.4	1	0	hg19	c.1122C>A	CCDS11257.1	0																																																																																								0.700100		TCGA-IB-A7LX-01A-12D-A36O-08	0.393	CPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256214.3	1	0	1	2	2	2	2	0	0	0	0	69	69	69	67	1	3.150000	-3.217508	1	0.550000	NM_001304		0	12	12	0	246	243	0		1	0		0	0	69	0	0	0.999118	9.087127e-01	0	0	0	88	0	12	246
CCL7	6354	broad.mit.edu	37	17	32597292	32597292	+	De_novo_Start_InFrame	SNP	A	A	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:32597292A>T	ENST00000378569.2	+	0	53				CCL7_ENST00000200307.4_Missense_Mutation_p.M5L|CCL7_ENST00000394630.3_De_novo_Start_InFrame|CCL7_ENST00000394627.1_De_novo_Start_InFrame	NM_006273.2	NP_006264.2	P80098	CCL7_HUMAN	chemokine (C-C motif) ligand 7						cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|cellular response to ethanol (GO:0071361)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|immune response (GO:0006955)|inflammatory response (GO:0006954)|monocyte chemotaxis (GO:0002548)|positive regulation of cell migration (GO:0030335)|positive regulation of natural killer cell chemotaxis (GO:2000503)|regulation of cell shape (GO:0008360)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)			autonomic_ganglia(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	7	Breast(3;0.00224)	Breast(31;0.151)|Ovarian(249;0.17)		BRCA - Breast invasive adenocarcinoma(366;0.155)		GTGGAAGCCCATGCCCTCACC	0.547																																						ENST00000378569.2	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000																										0				7								chemokine (C-C motif) ligand 7							71.0	59.0	63.0					17																	32597292		2203	4300	6503			6354	0	0					g.chr17:32597292A>T	AF043338	CCDS11278.1	17q11.2-q12	2013-02-25	2002-08-22	2002-08-23	ENSG00000108688	ENSG00000108688		"""Chemokine ligands"", ""Endogenous ligands"""	10634	protein-coding gene	gene with protein product	"""monocyte chemoattractant protein 3"", ""monocyte chemotactic protein 3"""	158106	"""small inducible cytokine A7 (monocyte chemotactic protein 3)"""	SCYA6, SCYA7		8461011	Standard	NM_006273		Approved	MCP-3, NC28, FIC, MARC, MCP3	uc002hhz.4	P80098	OTTHUMG00000132889		chr17.hg19:g.32597292A>T		1					CCL7_ENST00000394630.3_De_novo_Start_InFrame|CCL7_ENST00000394627.1_De_novo_Start_InFrame|CCL7_ENST00000200307.4_Missense_Mutation_p.M5L		NM_006273.2	NP_006264.2	2	2	4	2.274668	P80098	CCL7_HUMAN		0	53	+	Breast(3;0.00224)	Breast(31;0.151)|Ovarian(249;0.17)	Q569J6	Translation_Start_Site	SNP	ENST00000378569.2	1	0	hg19		CCDS11278.1	1	.	.	.	.	.	.	.	.	.	.	A	0.081	-1.184197	0.01620	.	.	ENSG00000108688	ENST00000378569;ENST00000394630;ENST00000394627	.	.	.	3.89	0.269	0.15631	3.89	0.269	0.15631	.	10.005000	0.00166	N	0.000004	T	0.18635	0.0447	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.12477	-1.0546	6	0.11182	T	0.66	.	5.9178	0.19065	0.5474:0.0:0.4526:0.0	.	.	.	.	L	5	.	ENSP00000367832:M5L	M	+	1	0	0	CCL7	29621405	29621405	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.026000	0.01434	-0.061000	0.13110	0.528000	0.53228	ATG	0.700100		TCGA-IB-A7LX-01A-12D-A36O-08	0.547	CCL7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256386.2	0	0	1	2	2	2	2	0	0	0	0	50	50	50	50	1	3.150000	-20.000000	1	0.550000	NM_006273		0	60	57	0	89	87	1		1			0	0	50	0	0	1.000000	0	0	0	0	0	0	60	89
AP2B1	163	broad.mit.edu	37	17	33954701	33954701	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:33954701C>A	ENST00000262325.7	+	9	1664	c.1111C>A	c.(1111-1113)Cga>Aga	p.R371R	AP2B1_ENST00000592545.1_Silent_p.R333R|AP2B1_ENST00000538556.1_Silent_p.R314R|AP2B1_ENST00000589344.1_Silent_p.R371R|AP2B1_ENST00000537622.2_Silent_p.R371R|AP2B1_ENST00000545922.2_3'UTR|AP2B1_ENST00000312678.8_Silent_p.R371R	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	371					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)	p.R371*(1)		NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		TGACTTTGTTCGAAAAGCTGT	0.443																																						ENST00000262325.7	1.000000	0.140000	3.700000e-01	1.900000e-01	0.260000	0.321758	0.260000	0.260000																										1	Substitution - Nonsense(1)	p.R371*(1)	large_intestine(1)	28						c.(1111-1113)Cga>Aga		adaptor-related protein complex 2, beta 1 subunit							123.0	115.0	117.0					17																	33954701		2203	4300	6503	SO:0001819	synonymous_variant	163	0	0					g.chr17:33954701C>A	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.1111C>A	chr17.hg19:g.33954701C>A		1					AP2B1_ENST00000589344.1_Silent_p.R371R|AP2B1_ENST00000538556.1_Silent_p.R314R|AP2B1_ENST00000312678.8_Silent_p.R371R|AP2B1_ENST00000592545.1_Silent_p.R333R|AP2B1_ENST00000545922.2_3'UTR|AP2B1_ENST00000537622.2_Silent_p.R371R	p.R371R	NM_001282.2	NP_001273.1	2	2	4	2.274668	P63010	AP2B1_HUMAN		9	1664	+		Ovarian(249;0.17)	A6NJP3|P21851|Q7Z451|Q96J19	Silent	SNP	ENST00000262325.7	1	0	hg19	c.1111C>A	CCDS32622.1	0																																																																																								0.700100		TCGA-IB-A7LX-01A-12D-A36O-08	0.443	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1	1	0	1	2	2	2	2	0	0	0	0	65	65	65	63	1	3.150000	-2.806910	1	0.550000			0	13	13	0	269	266	0		1	0		0	0	65	0	0	0.999535	9.989629e-01	0	0	0	246	0	13	269
TOP2A	7153	broad.mit.edu	37	17	38564239	38564239	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:38564239G>T	ENST00000423485.1	-	12	1638	c.1480C>A	c.(1480-1482)Cga>Aga	p.R494R		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	494	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	GAAGCTTCTCGAACATTGAGT	0.368																																						ENST00000423485.1	1.000000	0.140000	3.200000e-01	1.800000e-01	0.240000	0.304127	0.240000	0.230000																										0				39						c.(1480-1482)Cga>Aga		topoisomerase (DNA) II alpha 170kDa	Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)						90.0	88.0	89.0					17																	38564239		1803	4068	5871	SO:0001819	synonymous_variant	7153	0	0					g.chr17:38564239G>T		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.1480C>A	chr17.hg19:g.38564239G>T		1						p.R494R	NM_001067.3	NP_001058.2	2	2	4	2.267005	P11388	TOP2A_HUMAN	STAD - Stomach adenocarcinoma(5;0.00183)	12	1638	-		Breast(137;0.00328)	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	1	0	hg19	c.1480C>A	CCDS45672.1	0																																																																																								0.698997		TCGA-IB-A7LX-01A-12D-A36O-08	0.368	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1	1	0	1	2	2	2	2	0	0	0	0	102	102	102	101	1	3.150000	-3.071207	1	0.550000			0	21	21	0	469	466	0		1	0		0	0	102	0	0	0.999997	8.623733e-01	0	0	0	81	0	21	469
KRT28	162605	broad.mit.edu	37	17	38949428	38949428	+	Missense_Mutation	SNP	T	T	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:38949428T>A	ENST00000306658.7	-	7	1296	c.1231A>T	c.(1231-1233)Agc>Tgc	p.S411C		NM_181535.3	NP_853513.2			keratin 28											NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30		Breast(137;0.000301)				TTCCCAGGGCTTCCTGATCCA	0.313																																					Melanoma(19;789 869 15380 26882 39836)	ENST00000306658.7	1.000000	0.660000	1	7.500000e-01	0.860000	0.867460	0.860000	1.000000																										0				30						c.(1231-1233)Agc>Tgc		keratin 28							26.0	26.0	26.0					17																	38949428		2200	4300	6500	SO:0001583	missense	162605	0	0					g.chr17:38949428T>A	AK129827	CCDS11376.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000173908	ENSG00000173908		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30842	protein-coding gene	gene with protein product			"""keratin 25D"""	KRT25D		16831889	Standard	NM_181535		Approved		uc002hvh.1	Q7Z3Y7	OTTHUMG00000133365	ENST00000306658.7:c.1231A>T	chr17.hg19:g.38949428T>A	ENSP00000305263:p.Ser411Cys	1						p.S411C	NM_181535.3	NP_853513.2	2	2	4	2.267005				7	1296	-		Breast(137;0.000301)		Missense_Mutation	SNP	ENST00000306658.7	1	1	hg19	c.1231A>T	CCDS11376.1	1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.471242	0.43942	.	.	ENSG00000173908	ENST00000306658	D	0.83419	-1.72	5.35	0.343	0.16001	5.35	0.343	0.16001	.	0.768911	0.12060	N	0.503255	T	0.76586	0.4008	L	0.38175	1.15	0.22081	N	0.999376	P	0.35192	0.489	B	0.41299	0.353	T	0.66968	-0.5789	10	0.62326	D	0.03	.	7.4993	0.27509	0.0:0.4287:0.0:0.5713	.	411	Q7Z3Y7	K1C28_HUMAN	C	411	ENSP00000305263:S411C	ENSP00000305263:S411C	S	-	1	0	0	KRT28	36202954	36202954	0.023000	0.18921	0.940000	0.37924	0.992000	0.81027	-0.298000	0.08265	0.108000	0.17862	0.533000	0.62120	AGC	0.698997		TCGA-IB-A7LX-01A-12D-A36O-08	0.313	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	1	0	1	2	2	2	2	0	0	0	0	77	77	77	77	1	3.150000	-20.000000	1	0.550000	NM_181535		0	55	54	0	296	287	1		1			0	0	77	0	0	1.000000	0	0	0	0	0	0	55	296
CHD3	1107	broad.mit.edu	37	17	7794350	7794350	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:7794350C>A	ENST00000330494.7	+	4	627	c.477C>A	c.(475-477)ctC>ctA	p.L159L	CHD3_ENST00000358181.4_Silent_p.L159L|CHD3_ENST00000380358.4_Silent_p.L218L	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	159					centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				ACCACACGCTCACCAACTACA	0.527																																						ENST00000330494.7	0.300000	0.130000	2.500000e-01	1.600000e-01	0.200000	0.214279	0.200000	0.210000																										0				65						c.(475-477)ctC>ctA		chromodomain helicase DNA binding protein 3							160.0	137.0	145.0					17																	7794350		2203	4300	6503	SO:0001819	synonymous_variant	1107	0	0					g.chr17:7794350C>A	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"""Zinc fingers, PHD-type"""	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.477C>A	chr17.hg19:g.7794350C>A		1					CHD3_ENST00000358181.4_Silent_p.L159L|CHD3_ENST00000380358.4_Silent_p.L218L	p.L159L	NM_001005273.2	NP_001005273.1	1	2	3	1.950712	Q12873	CHD3_HUMAN		4	627	+		Prostate(122;0.202)	D3DTQ9|E9PG89|Q9Y4I0	Silent	SNP	ENST00000330494.7	1	0	hg19	c.477C>A	CCDS32554.1	0	.	.	.	.	.	.	.	.	.	.	C	9.430	1.085307	0.20390	.	.	ENSG00000170004	ENST00000452447	.	.	.	4.54	-3.21	0.05140	4.54	-3.21	0.05140	.	.	.	.	.	T	0.40222	0.1108	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34750	-0.9816	4	.	.	.	-15.2706	3.1578	0.06510	0.1046:0.1724:0.1951:0.5278	.	.	.	.	N	34	.	.	H	+	1	0	0	CHD3	7735075	7735075	0.764000	0.28473	0.974000	0.42286	0.988000	0.76386	-0.190000	0.09615	-0.301000	0.08882	-0.259000	0.10710	CAC	0.647059		TCGA-IB-A7LX-01A-12D-A36O-08	0.527	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	1	0	1	2	2	2	2	0	0	0	0	137	137	137	133	1	3.150000	-3.018473	1	0.550000	NM_001005273		0	25	24	0	535	529	0		1	0		0	0	137	0	0	1.000000	9.948179e-01	0	0	0	176	0	25	535
MYH10	4628	broad.mit.edu	37	17	8439125	8439125	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:8439125C>A	ENST00000269243.4	-	14	1838	c.1700G>T	c.(1699-1701)cGa>cTa	p.R567L	MYH10_ENST00000396239.1_Missense_Mutation_p.R567L|MYH10_ENST00000379980.4_Missense_Mutation_p.R583L|MYH10_ENST00000360416.3_Missense_Mutation_p.R577L	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	567	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						TTTTAATTGTCGAGGTTTCTG	0.368																																						ENST00000269243.4	0.250000	0.080000	2.000000e-01	1.100000e-01	0.150000	0.161897	0.150000	0.150000																										0				52						c.(1699-1701)cGa>cTa		myosin, heavy chain 10, non-muscle							85.0	85.0	85.0					17																	8439125		2203	4300	6503	SO:0001583	missense	4628	0	0					g.chr17:8439125C>A	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.1700G>T	chr17.hg19:g.8439125C>A	ENSP00000269243:p.Arg567Leu	1					MYH10_ENST00000360416.3_Missense_Mutation_p.R577L|MYH10_ENST00000396239.1_Missense_Mutation_p.R567L|MYH10_ENST00000379980.4_Missense_Mutation_p.R583L	p.R567L	NM_005964.3	NP_005955.3	1	2	3	1.950712	P35580	MYH10_HUMAN		14	1838	-			B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	1	0	hg19	c.1700G>T	CCDS11144.1	0	.	.	.	.	.	.	.	.	.	.	C	21.7	4.182476	0.78677	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	T;T;D;T	0.88509	-0.74;-0.74;-2.39;-0.74	5.29	5.29	0.74685	5.29	5.29	0.74685	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.94997	0.8381	M	0.90977	3.165	0.58432	D	0.99999	P;P;P	0.51057	0.941;0.928;0.941	P;P;P	0.56751	0.805;0.705;0.805	D	0.95680	0.8731	10	0.87932	D	0	.	19.1238	0.93374	0.0:1.0:0.0:0.0	.	576;577;567	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	L	567;577;567;583	ENSP00000269243:R567L;ENSP00000353590:R577L;ENSP00000379539:R567L;ENSP00000369315:R583L	ENSP00000269243:R567L	R	-	2	0	0	MYH10	8379850	8379850	0.401000	0.25303	0.999000	0.59377	0.542000	0.35054	3.206000	0.51098	2.752000	0.94435	0.557000	0.71058	CGA	0.647059		TCGA-IB-A7LX-01A-12D-A36O-08	0.368	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2	1	0	1	2	2	2	2	0	0	0	0	109	109	109	109	1	3.150000	-3.256806	1	0.550000			0	14	14	0	413	407	0		1	0		0	0	109	0	0	0.999739	5.657491e-02	0	0	0	11	0	14	413
HEATR6	63897	broad.mit.edu	37	17	58128258	58128258	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr17:58128258C>A	ENST00000184956.6	-	15	2386	c.2370G>T	c.(2368-2370)gcG>gcT	p.A790A	HEATR6_ENST00000585976.1_Intron	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	790							poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			CACAGGCGCTCGCCTGGAGAG	0.532																																						ENST00000184956.6	1.000000	0.110000	3.600000e-01	1.600000e-01	0.230000	0.323144	0.230000	0.220000																										0				44						c.(2368-2370)gcG>gcT		HEAT repeat containing 6							75.0	68.0	71.0					17																	58128258		2203	4300	6503	SO:0001819	synonymous_variant	63897	0	0					g.chr17:58128258C>A	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"""amplified in breast cancer 1"""					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.2370G>T	chr17.hg19:g.58128258C>A		1					HEATR6_ENST00000585976.1_Intron	p.A790A	NM_022070.4	NP_071353.4	2	2	4	2.231336	Q6AI08	HEAT6_HUMAN	BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)	15	2386	-	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Silent	SNP	ENST00000184956.6	1	0	hg19	c.2370G>T	CCDS11623.1	0																																																																																								0.694501		TCGA-IB-A7LX-01A-12D-A36O-08	0.532	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	1	0	1	2	2	2	2	0	0	0	0	55	55	55	53	1	3.150000	-2.802442	1	0.550000	NM_022070		0	10	10	0	235	234	0		1	0		0	0	55	0	0	0.996991	2.734309e-01	0	0	0	22	0	10	235
DSG2	1829	broad.mit.edu	37	18	29115333	29115333	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr18:29115333C>A	ENST00000261590.8	+	10	1590	c.1381C>A	c.(1381-1383)Caa>Aaa	p.Q461K		NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	461	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			TAGATATGTTCAAAATGGCAC	0.279																																						ENST00000261590.8	1.000000	0.120000	1	1.600000e-01	0.200000	0.350999	0.200000	0.190000																										0				49						c.(1381-1383)Caa>Aaa		desmoglein 2							44.0	42.0	43.0					18																	29115333		1805	4070	5875	SO:0001583	missense	1829	0	0					g.chr18:29115333C>A	Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"""Cadherins / Major cadherins"""	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.1381C>A	chr18.hg19:g.29115333C>A	ENSP00000261590:p.Gln461Lys	1						p.Q461K	NM_001943.3	NP_001934.2	0	3	3	1.685847	Q14126	DSG2_HUMAN	OV - Ovarian serous cystadenocarcinoma(10;0.0068)	10	1590	+			Q4KKU6	Missense_Mutation	SNP	ENST00000261590.8	1	0	hg19	c.1381C>A	CCDS42423.1	0	.	.	.	.	.	.	.	.	.	.	C	10.63	1.405016	0.25378	.	.	ENSG00000046604	ENST00000261590	T	0.59906	0.23	5.66	2.39	0.29439	5.66	2.39	0.29439	Cadherin (4);Cadherin-like (1);	1.115670	0.06754	N	0.780562	T	0.32971	0.0847	N	0.05554	-0.025	0.09310	N	1	B	0.17667	0.023	B	0.15052	0.012	T	0.14839	-1.0458	10	0.02654	T	1	.	8.9226	0.35621	0.4051:0.4015:0.1934:0.0	.	461	Q14126	DSG2_HUMAN	K	461	ENSP00000261590:Q461K	ENSP00000261590:Q461K	Q	+	1	0	0	DSG2	27369331	27369331	0.000000	0.05858	0.955000	0.39395	0.836000	0.47400	-0.080000	0.11339	0.663000	0.31027	0.462000	0.41574	CAA	0.626091		TCGA-IB-A7LX-01A-12D-A36O-08	0.279	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	1	0	1	2	2	2	2	0	0	0	0	170	170	170	169	1	3.150000	-3.210889	1	0.550000	NM_001943		0	22	22	0	468	461	0		1	0		0	0	170	0	0	0.999999	9.998950e-01	0	0	0	312	0	22	468
SLC14A2	8170	broad.mit.edu	37	18	43224013	43224013	+	Silent	SNP	G	G	T	rs149835341		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr18:43224013G>T	ENST00000255226.6	+	10	2055	c.1239G>T	c.(1237-1239)acG>acT	p.T413T	RP11-116O18.1_ENST00000590535.1_RNA|SLC14A2_ENST00000586448.1_Silent_p.T413T	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	413					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TGCTCCTGACGACAAACAACC	0.542																																						ENST00000255226.6	1.000000	0.080000	1	1.200000e-01	0.170000	0.321760	0.170000	0.160000																										0				63						c.(1237-1239)acG>acT		solute carrier family 14 (urea transporter), member 2							187.0	181.0	183.0					18																	43224013		2203	4300	6503	SO:0001819	synonymous_variant	8170	0	0					g.chr18:43224013G>T	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"""Solute carriers"""	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.1239G>T	chr18.hg19:g.43224013G>T		1					SLC14A2_ENST00000586448.1_Silent_p.T413T|RP11-116O18.1_ENST00000590535.1_RNA	p.T413T	NM_007163.3	NP_009094.3	0	3	3	1.685847	Q15849	UT2_HUMAN		10	2055	+			A8K8Q7|Q2TBD6|Q96PH5	Silent	SNP	ENST00000255226.6	1	0	hg19	c.1239G>T	CCDS11924.1	0																																																																																								0.626091		TCGA-IB-A7LX-01A-12D-A36O-08	0.542	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1	1	0	1	2	2	2	2	0	0	0	0	148	148	148	148	1	3.150000	-2.841885	1	0.550000			0	14	14	0	373	370	0		1			0	0	148	0	0	0.999753	0	0	0	0	0	0	14	373
ZNF491	126069	broad.mit.edu	37	19	11918032	11918032	+	Missense_Mutation	SNP	C	C	A	rs544465856		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:11918032C>A	ENST00000323169.5	+	3	1595	c.1264C>A	c.(1264-1266)Cgt>Agt	p.R422S	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(14)|lung(6)|ovary(2)|skin(1)	26						AGCCTTCATTCGTTCCAGTTA	0.333																																						ENST00000323169.5	0.320000	0.090000	2.600000e-01	1.300000e-01	0.180000	0.198787	0.180000	0.180000																										0				26						c.(1264-1266)Cgt>Agt		zinc finger protein 491							39.0	44.0	43.0					19																	11918032		2200	4297	6497	SO:0001583	missense	126069	0	0					g.chr19:11918032C>A	AK092110	CCDS12267.1	19p13.2	2013-01-08			ENSG00000177599	ENSG00000177599		"""Zinc fingers, C2H2-type"""	23706	protein-coding gene	gene with protein product							Standard	XM_005259730		Approved	FLJ34791	uc002mso.1	Q8N8L2	OTTHUMG00000156529	ENST00000323169.5:c.1264C>A	chr19.hg19:g.11918032C>A	ENSP00000313443:p.Arg422Ser	1					ZNF491_ENST00000492230.1_Intron	p.R422S	NM_152356.3	NP_689569.2	1	2	3	1.925710	Q8N8L2	ZN491_HUMAN		3	1595	+			Q3MJ35|Q8NAT8	Missense_Mutation	SNP	ENST00000323169.5	1	0	hg19	c.1264C>A	CCDS12267.1	0	.	.	.	.	.	.	.	.	.	.	c	0.278	-0.988536	0.02162	.	.	ENSG00000177599	ENST00000323169;ENST00000455048	T	0.60424	0.19	0.737	-0.437	0.12272	0.737	-0.437	0.12272	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32071	0.0817	N	0.13003	0.285	0.09310	N	1	B	0.20052	0.041	B	0.10450	0.005	T	0.14062	-1.0486	9	0.32370	T	0.25	.	2.3692	0.04326	0.2684:0.4281:0.0:0.3035	.	422	Q8N8L2	ZN491_HUMAN	S	422;394	ENSP00000313443:R422S	ENSP00000313443:R422S	R	+	1	0	0	ZNF491	11779032	11779032	0.000000	0.05858	0.002000	0.10522	0.085000	0.17905	-0.354000	0.07681	-0.163000	0.10946	-0.451000	0.05528	CGT	0.647059		TCGA-IB-A7LX-01A-12D-A36O-08	0.333	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	1	0	1	2	2	2	2	0	0	0	0	66	66	66	66	1	3.150000	-3.087178	1	0.550000	NM_152356		0	10	9	0	244	236	0		1	0		0	0	66	0	0	0.996451	0	0	0	0	1	0	10	244
PLVAP	83483	broad.mit.edu	37	19	17488061	17488061	+	Silent	SNP	G	G	T	rs370989890		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:17488061G>T	ENST00000252590.4	-	1	98	c.37C>A	c.(37-39)Cgg>Agg	p.R13R		NM_031310.1	NP_112600.1	Q9BX97	PLVAP_HUMAN	plasmalemma vesicle associated protein	13					MAPK cascade (GO:0000165)|positive regulation of cellular extravasation (GO:0002693)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CCCCCCGCCCGAGCGTAGGAC	0.652																																						ENST00000252590.4	1.000000	0.100000	1	1.400000e-01	0.210000	0.377920	0.210000	0.180000																										0				27						c.(37-39)Cgg>Agg		plasmalemma vesicle associated protein							62.0	68.0	66.0					19																	17488061		2203	4300	6503	SO:0001819	synonymous_variant	83483	0	0					g.chr19:17488061G>T	AF326591	CCDS32952.1	19p13.2	2008-07-17				ENSG00000130300			13635	protein-coding gene	gene with protein product	"""fenestrated-endothelial linked structure protein; PV-1 protein"""	607647				11401446	Standard	NM_031310		Approved	gp68, PV-1, PV1, FELS	uc002ngk.1	Q9BX97		ENST00000252590.4:c.37C>A	chr19.hg19:g.17488061G>T		1						p.R13R	NM_031310.1	NP_112600.1	2	4	6	2.114927	Q9BX97	PLVAP_HUMAN		1	98	-			Q86VP0|Q8N8Y0|Q8ND68|Q8TER8|Q9BZD5	Silent	SNP	ENST00000252590.4	1	0	hg19	c.37C>A	CCDS32952.1	0																																																																																								0.677650		TCGA-IB-A7LX-01A-12D-A36O-08	0.652	PLVAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463655.1	1	0	1	2	2	2	2	0	0	0	0	83	83	83	83	1	3.150000	-2.789037	1	0.550000	NM_031310		0	12	12	0	316	311	0		1	0		0	0	83	0	0	0.999076	9.514635e-01	0	0	0	138	0	12	316
ZNF99	7652	broad.mit.edu	37	19	22940990	22940990	+	Missense_Mutation	SNP	A	A	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:22940990A>C	ENST00000596209.1	-	4	1811	c.1721T>G	c.(1720-1722)tTt>tGt	p.F574C	ZNF99_ENST00000397104.3_Missense_Mutation_p.F483C	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	574					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				AGATTGCTTAAAAGCTTTGCC	0.368																																						ENST00000596209.1	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000																										0				124						c.(1720-1722)tTt>tGt		zinc finger protein 99							50.0	54.0	52.0					19																	22940990		2094	4233	6327	SO:0001583	missense	7652	0	0					g.chr19:22940990A>C	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1721T>G	chr19.hg19:g.22940990A>C	ENSP00000472969:p.Phe574Cys	1					ZNF99_ENST00000397104.3_Missense_Mutation_p.F483C	p.F574C	NM_001080409.2	NP_001073878.2	2	4	6	2.027318	A8MXY4	ZNF99_HUMAN		4	1811	-		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)	M0R335	Missense_Mutation	SNP	ENST00000596209.1	1	1	hg19	c.1721T>G	CCDS59369.1	1	.	.	.	.	.	.	.	.	.	.	-	10.29	1.308831	0.23821	.	.	ENSG00000213973	ENST00000397104	T	0.45668	0.89	1.44	0.101	0.14517	1.44	0.101	0.14517	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.63570	0.2522	M	0.88377	2.95	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.51348	-0.8717	9	0.66056	D	0.02	.	5.428	0.16438	0.7506:0.0:0.0:0.2493	.	483	A8MXY4	ZNF99_HUMAN	C	483	ENSP00000380293:F483C	ENSP00000380293:F483C	F	-	2	0	0	ZNF99	22732830	22732830	0.978000	0.34361	0.001000	0.08648	0.011000	0.07611	4.718000	0.61930	-0.219000	0.10003	0.163000	0.16589	TTT	0.664430		TCGA-IB-A7LX-01A-12D-A36O-08	0.368	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	1	0	1	2	2	2	2	0	0	0	0	104	104	104	103	1	3.150000	-20.000000	1	0.550000	XM_065124		0	114	112	0	177	175	1		1			0	0	104	0	0	1.000000	0	0	0	0	0	0	114	177
FCGBP	8857	broad.mit.edu	37	19	40433627	40433627	+	Silent	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:40433627G>A	ENST00000221347.6	-	2	649	c.642C>T	c.(640-642)gtC>gtT	p.V214V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	214	IgGFc-binding.					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)			TACTAGCTGTGACCTTTGACC	0.562																																						ENST00000221347.6	0.470000	0.180000	3.900000e-01	2.400000e-01	0.310000	0.323208	0.310000	0.300000																										0				165						c.(640-642)gtC>gtT		Fc fragment of IgG binding protein							73.0	71.0	72.0					19																	40433627		2203	4300	6503	SO:0001819	synonymous_variant	8857	0	0					g.chr19:40433627G>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.642C>T	chr19.hg19:g.40433627G>A		1						p.V214V	NM_003890.2	NP_003881.2	1	2	3	1.979295	Q9Y6R7	FCGBP_HUMAN	Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)	2	649	-	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		O95784	Silent	SNP	ENST00000221347.6	1	1	hg19	c.642C>T	CCDS12546.1	0																																																																																								0.647059		TCGA-IB-A7LX-01A-12D-A36O-08	0.562	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	1	0	1	2	2	2	2	0	0	0	0	83	83	83	82	1	3.150000	-19.989210	1	0.550000	NM_003890		0	18	18	0	252	248	0		1	0		0	0	83	0	0	0.999982	1.446437e-02	0	0	0	3	0	18	252
BLOC1S3	388552	broad.mit.edu	37	19	45682658	45682658	+	Missense_Mutation	SNP	A	A	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:45682658A>C	ENST00000433642.2	+	2	200	c.104A>C	c.(103-105)gAg>gCg	p.E35A	TRAPPC6A_ENST00000585934.1_5'Flank|AC005779.2_ENST00000593083.1_5'Flank|TRAPPC6A_ENST00000592647.1_5'Flank|TRAPPC6A_ENST00000006275.4_5'Flank|TRAPPC6A_ENST00000588062.1_5'Flank|BLOC1S3_ENST00000587722.1_Missense_Mutation_p.E35A	NM_212550.3	NP_997715.1	Q6QNY0	BL1S3_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 3	35					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|endosome to melanosome transport (GO:0035646)|eye development (GO:0001654)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of natural killer cell activation (GO:0032816)|post-Golgi vesicle-mediated transport (GO:0006892)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)	BLOC-1 complex (GO:0031083)|cytosol (GO:0005829)|transport vesicle (GO:0030133)				ovary(1)|skin(1)	2		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)		TCCTCGTCGGAGGAGGAGGAG	0.761									Hermansky-Pudlak syndrome																													ENST00000433642.2	1.000000	0.990000	1	9.900000e-01	0.990000	0.999957	0.990000	1.000000																										0				2						c.(103-105)gAg>gCg		biogenesis of lysosomal organelles complex-1, subunit 3							9.0	10.0	10.0					19																	45682658		2158	4240	6398	SO:0001583	missense	388552	6	119586	35	Hermansky-Pudlak syndrome	Familial Cancer Database	HPS, HPS1-8	g.chr19:45682658A>C	AY531266	CCDS12656.1	19q13.32	2012-08-01	2008-08-11			ENSG00000189114		"""Biogenesis of lysosomal organelles complex-1 subunits"""	20914	protein-coding gene	gene with protein product	"""BLOC-1 subunit 3"", ""Biogenesis of Lysosome-related Organelles complex-1 Subunit 3"", ""Hermansky-Pudlak syndrome 8"""	609762				15102850	Standard	NM_212550		Approved	BLOS3, HPS8	uc002pax.4	Q6QNY0		ENST00000433642.2:c.104A>C	chr19.hg19:g.45682658A>C	ENSP00000393840:p.Glu35Ala	1					BLOC1S3_ENST00000587722.1_Missense_Mutation_p.E35A|TRAPPC6A_ENST00000006275.4_5'Flank|TRAPPC6A_ENST00000592647.1_5'Flank|AC005779.2_ENST00000593083.1_5'Flank|TRAPPC6A_ENST00000585934.1_5'Flank|TRAPPC6A_ENST00000588062.1_5'Flank	p.E35A	NM_212550.3	NP_997715.1	1	2	3	1.979295	Q6QNY0	BL1S3_HUMAN		2	200	+		Ovarian(192;0.0728)|all_neural(266;0.112)	B2RXB8	Missense_Mutation	SNP	ENST00000433642.2	0	1	hg19	c.104A>C	CCDS12656.1	1	.	.	.	.	.	.	.	.	.	.	A	13.92	2.381951	0.42207	.	.	ENSG00000189114	ENST00000433642	.	.	.	2.93	1.77	0.24775	2.93	1.77	0.24775	.	0.624228	0.12947	N	0.426136	T	0.16642	0.0400	N	0.08118	0	0.26487	N	0.975019	B	0.28128	0.201	B	0.20767	0.031	T	0.13980	-1.0489	9	0.62326	D	0.03	.	6.2471	0.20825	0.7472:0.2528:0.0:0.0	.	35	Q6QNY0	BL1S3_HUMAN	A	35	.	ENSP00000393840:E35A	E	+	2	0	0	BLOC1S3	50374498	50374498	0.697000	0.27767	0.994000	0.49952	0.982000	0.71751	0.657000	0.24963	1.121000	0.41925	0.374000	0.22700	GAG	0.647059		TCGA-IB-A7LX-01A-12D-A36O-08	0.761	BLOC1S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457559.1	1	0	1	2	2	2	2	0	0	0	0	9	9	9	8	1	3.150000	-20.000000	1	0.550000	NM_212550		0	18	18	0	23	23	0		1	1		0	0	9	0	0	0.999998	9.874824e-01	0	5	0	8	0	18	23
ZNF256	10172	broad.mit.edu	37	19	58453311	58453311	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:58453311G>T	ENST00000282308.3	-	3	1061	c.865C>A	c.(865-867)Cac>Aac	p.H289N	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	289					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		ACTCCAGTGTGAATTCTTCGG	0.393																																					NSCLC(55;1313 1552 8040 11996)	ENST00000282308.3	0.270000	0.090000	2.200000e-01	1.300000e-01	0.170000	0.181201	0.170000	0.180000																										0				19						c.(865-867)Cac>Aac		zinc finger protein 256							92.0	88.0	89.0					19																	58453311		2203	4300	6503	SO:0001583	missense	10172	0	0					g.chr19:58453311G>T	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"""Zinc fingers, C2H2-type"", ""-"""	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.865C>A	chr19.hg19:g.58453311G>T	ENSP00000282308:p.His289Asn	1					ZNF256_ENST00000598928.1_3'UTR	p.H289N	NM_005773.2	NP_005764.2	1	2	3	1.990465	Q9Y2P7	ZN256_HUMAN		3	1061	-		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)	B2RA92|Q53Y85|Q9BV71	Missense_Mutation	SNP	ENST00000282308.3	1	0	hg19	c.865C>A	CCDS12966.1	0	.	.	.	.	.	.	.	.	.	.	.	23.0	4.368789	0.82463	.	.	ENSG00000152454	ENST00000282308	T	0.67345	-0.26	3.13	2.07	0.26955	3.13	2.07	0.26955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.81795	0.4898	M	0.89287	3.02	0.28223	N	0.926444	D	0.76494	0.999	D	0.73708	0.981	T	0.72047	-0.4408	9	0.87932	D	0	.	9.0328	0.36269	0.1174:0.0:0.8826:0.0	.	289	Q9Y2P7	ZN256_HUMAN	N	289	ENSP00000282308:H289N	ENSP00000282308:H289N	H	-	1	0	0	ZNF256	63145123	63145123	1.000000	0.71417	0.247000	0.24249	0.980000	0.70556	3.300000	0.51834	0.639000	0.30564	0.460000	0.39030	CAC	0.647059		TCGA-IB-A7LX-01A-12D-A36O-08	0.393	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1	1	0	1	2	2	2	2	0	0	0	0	153	153	153	152	1	3.150000	-4.132772	1	0.550000			0	17	17	0	441	437	0		1	0		0	0	153	0	0	0.999964	1.477809e-02	0	0	0	5	0	17	441
C19orf18	147685	broad.mit.edu	37	19	58477954	58477954	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:58477954C>A	ENST00000314391.3	-	4	416	c.315G>T	c.(313-315)tcG>tcT	p.S105S		NM_152474.4	NP_689687.1	Q8NEA5	CS018_HUMAN	chromosome 19 open reading frame 18	105						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)		AGGCTACGCTCGAAATTAAAA	0.348																																						ENST00000314391.3	0.290000	0.090000	2.400000e-01	1.300000e-01	0.170000	0.186858	0.170000	0.180000																										0				8						c.(313-315)tcG>tcT		chromosome 19 open reading frame 18							77.0	76.0	76.0					19																	58477954		2203	4300	6503	SO:0001819	synonymous_variant	147685	0	0					g.chr19:58477954C>A	BC033933	CCDS12967.1	19q13.43	2013-03-11			ENSG00000177025	ENSG00000177025			28642	protein-coding gene	gene with protein product						12477932	Standard	NM_152474		Approved	MGC41906	uc002qqv.3	Q8NEA5	OTTHUMG00000183450	ENST00000314391.3:c.315G>T	chr19.hg19:g.58477954C>A		1						p.S105S	NM_152474.4	NP_689687.1	1	2	3	1.990465	Q8NEA5	CS018_HUMAN		4	416	-		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		Silent	SNP	ENST00000314391.3	1	0	hg19	c.315G>T	CCDS12967.1	0																																																																																								0.647059		TCGA-IB-A7LX-01A-12D-A36O-08	0.348	C19orf18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466704.1	1	0	1	2	2	2	2	0	0	0	0	72	72	72	72	1	3.150000	-2.803158	1	0.550000	NM_152474		0	12	11	0	308	305	0		1	0		0	0	72	0	0	0.999094	0	0	0	0	1	0	12	308
ZNF606	80095	broad.mit.edu	37	19	58490276	58490276	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr19:58490276G>A	ENST00000341164.4	-	7	2392	c.1772C>T	c.(1771-1773)aCg>aTg	p.T591M	ZNF606_ENST00000536132.1_Missense_Mutation_p.T501M	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	591					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		TTTCTCTCCCGTGTGAGTTCT	0.418																																						ENST00000341164.4	0.250000	0.070000	2.000000e-01	1.100000e-01	0.150000	0.161239	0.150000	0.150000																										0				26						c.(1771-1773)aCg>aTg		zinc finger protein 606							90.0	88.0	89.0					19																	58490276		2203	4300	6503	SO:0001583	missense	80095	1	121412	29				g.chr19:58490276G>A	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"""Zinc fingers, C2H2-type"", ""-"""	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.1772C>T	chr19.hg19:g.58490276G>A	ENSP00000343617:p.Thr591Met	1					ZNF606_ENST00000536132.1_Missense_Mutation_p.T501M	p.T591M	NM_025027.3	NP_079303.2	1	2	3	1.990465	Q8WXB4	ZN606_HUMAN		7	2392	-		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	1	1	hg19	c.1772C>T	CCDS12968.1	0	.	.	.	.	.	.	.	.	.	.	G	14.81	2.647444	0.47258	.	.	ENSG00000166704	ENST00000341164;ENST00000536132	T;T	0.26373	1.74;1.74	4.91	4.91	0.64330	4.91	4.91	0.64330	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.134588	0.34676	N	0.003775	T	0.53530	0.1802	M	0.79926	2.475	0.46416	D	0.999034	D	0.89917	1.0	D	0.68765	0.96	T	0.58973	-0.7541	10	0.87932	D	0	.	17.3812	0.87405	0.0:0.0:1.0:0.0	.	591	Q8WXB4	ZN606_HUMAN	M	591;501	ENSP00000343617:T591M;ENSP00000445624:T501M	ENSP00000343617:T591M	T	-	2	0	0	ZNF606	63182088	63182088	0.994000	0.37717	0.995000	0.50966	0.976000	0.68499	2.147000	0.42226	2.706000	0.92434	0.561000	0.74099	ACG	0.647059		TCGA-IB-A7LX-01A-12D-A36O-08	0.418	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	0	0	1	2	2	2	2	1	1	1	0	116	116	116	113	1	3.150000	-2.695491	1	0.550000	NM_025027		0	13	12	0	387	377	0		1	0		1	0	116	0	0	0.999461	1.740299e-02	0	0	0	6	0	13	387
GPSM2	29899	broad.mit.edu	37	1	109428193	109428193	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:109428193C>A	ENST00000406462.2	+	3	822	c.49C>A	c.(49-51)Cgt>Agt	p.R17S	AKNAD1_ENST00000357393.4_Intron|GPSM2_ENST00000264126.3_Missense_Mutation_p.R17S			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	17					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		TTTTCATGTTCGTTACAGGTA	0.294																																						ENST00000406462.2	0.230000	0.100000	2.000000e-01	1.300000e-01	0.160000	0.170195	0.160000	0.160000																										0				14						c.(49-51)Cgt>Agt		G-protein signaling modulator 2							128.0	134.0	132.0					1																	109428193		2203	4295	6498	SO:0001583	missense	29899	0	0					g.chr1:109428193C>A	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"""Tetratricopeptide (TTC) repeat domain containing"""	29501	protein-coding gene	gene with protein product		609245	"""G-protein signalling modulator 2 (AGS3-like, C. elegans)"", ""deafness, autosomal recessive 82"""	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.49C>A	chr1.hg19:g.109428193C>A	ENSP00000385510:p.Arg17Ser	1					AKNAD1_ENST00000357393.4_Intron|GPSM2_ENST00000264126.3_Missense_Mutation_p.R17S	p.R17S			0	2	2	1.629647	P81274	GPSM2_HUMAN		3	822	+		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)	Q5T1N8|Q6IBL7|Q8N0Z5	Missense_Mutation	SNP	ENST00000406462.2	1	0	hg19	c.49C>A	CCDS792.2	0	.	.	.	.	.	.	.	.	.	.	C	18.06	3.538254	0.65085	.	.	ENSG00000121957	ENST00000406462;ENST00000435987;ENST00000264126;ENST00000435475;ENST00000446797	D;D;D	0.93189	-3.18;-2.38;-3.18	5.62	5.62	0.85841	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.78413	0.4279	N	0.03608	-0.345	0.39307	D	0.965015	P	0.43024	0.798	B	0.34779	0.189	D	0.84184	0.0441	10	0.46703	T	0.11	-5.4334	18.2007	0.89836	0.0:1.0:0.0:0.0	.	17	P81274	GPSM2_HUMAN	S	17	ENSP00000385510:R17S;ENSP00000408664:R17S;ENSP00000264126:R17S	ENSP00000264126:R17S	R	+	1	0	0	GPSM2	109229716	109229716	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.317000	0.65822	2.801000	0.96364	0.650000	0.86243	CGT	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.294	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	1	0	1	2	2	2	2	0	0	0	0	174	174	174	174	1	3.150000	-3.914346	1	0.550000	NM_013296		0	26	26	0	548	547	0		1	0		0	0	174	0	0	1.000000	2.066676e-01	0	0	0	18	0	26	548
PTCHD2	57540	broad.mit.edu	37	1	11561859	11561859	+	Silent	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:11561859C>T	ENST00000294484.6	+	2	948	c.810C>T	c.(808-810)caC>caT	p.H270H	PTCHD2_ENST00000389575.3_Silent_p.H270H	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	270					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CTCAGACGCACGCGCACTGGC	0.677																																						ENST00000294484.6	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000																										0				76						c.(808-810)caC>caT		patched domain containing 2							14.0	16.0	15.0					1																	11561859		2024	4164	6188	SO:0001819	synonymous_variant	57540	0	0					g.chr1:11561859C>T	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.810C>T	chr1.hg19:g.11561859C>T		1					PTCHD2_ENST00000389575.3_Silent_p.H270H	p.H270H	NM_020780.1	NP_065831.1	0	3	3	1.682210	Q9P2K9	PTHD2_HUMAN		2	948	+	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	Q5VTU9|Q9UJD6	Silent	SNP	ENST00000294484.6	1	1	hg19	c.810C>T	CCDS41247.1	1																																																																																								0.625234		TCGA-IB-A7LX-01A-12D-A36O-08	0.677	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	1	0	1	2	2	2	2	0	0	0	0	20	20	20	19	1	3.150000	-20.000000	1	0.550000	XM_052561		0	49	47	0	24	24	1		1			0	0	20	0	0	1.000000	0	0	0	0	0	0	49	24
PHTF1	10745	broad.mit.edu	37	1	114280825	114280825	+	Silent	SNP	G	G	T	rs78000844		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:114280825G>T	ENST00000369604.1	-	5	721	c.238C>A	c.(238-240)Cga>Aga	p.R80R	PHTF1_ENST00000369598.1_Silent_p.R80R|PHTF1_ENST00000357783.2_Silent_p.R80R|PHTF1_ENST00000393357.2_Silent_p.R80R|PHTF1_ENST00000447664.2_Silent_p.R80R|PHTF1_ENST00000369600.1_Intron|PHTF1_ENST00000369596.2_Intron			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	80					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AATACAACTCGAACAAGCCCC	0.358																																						ENST00000369604.1	0.310000	0.090000	2.500000e-01	1.300000e-01	0.180000	0.197590	0.180000	0.180000																										0				27						c.(238-240)Cga>Aga		putative homeodomain transcription factor 1							97.0	98.0	98.0					1																	114280825		2203	4300	6503	SO:0001819	synonymous_variant	10745	0	0					g.chr1:114280825G>T	AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.238C>A	chr1.hg19:g.114280825G>T		1					PHTF1_ENST00000393357.2_Silent_p.R80R|PHTF1_ENST00000447664.2_Silent_p.R80R|PHTF1_ENST00000369596.2_Intron|PHTF1_ENST00000357783.2_Silent_p.R80R|PHTF1_ENST00000369598.1_Silent_p.R80R|PHTF1_ENST00000369600.1_Intron	p.R80R			0	2	2	1.629647	Q9UMS5	PHTF1_HUMAN		5	721	-	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Silent	SNP	ENST00000369604.1	1	0	hg19	c.238C>A	CCDS861.1	0																																																																																								0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.358	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	1	0	1	2	2	2	2	0	0	0	0	85	85	85	85	1	3.150000	-4.545072	1	0.550000	NM_006608		0	11	11	0	207	203	0		1	0		0	0	85	0	0	0.998293	1.971210e-01	0	0	0	15	0	11	207
VPS13D	55187	broad.mit.edu	37	1	12383813	12383813	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:12383813C>A	ENST00000358136.3	+	35	8096	c.7966C>A	c.(7966-7968)Cgc>Agc	p.R2656S	VPS13D_ENST00000356315.4_Missense_Mutation_p.R2656S	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		GGATGATTGTCGCAAAGCTCT	0.383																																						ENST00000358136.3	1.000000	0.110000	1	1.500000e-01	0.200000	0.354122	0.200000	0.190000																										0				130						c.(7966-7968)Cgc>Agc		vacuolar protein sorting 13 homolog D (S. cerevisiae)							135.0	125.0	128.0					1																	12383813		2203	4300	6503	SO:0001583	missense	55187	0	0					g.chr1:12383813C>A	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.7966C>A	chr1.hg19:g.12383813C>A	ENSP00000350854:p.Arg2656Ser	1					VPS13D_ENST00000356315.4_Missense_Mutation_p.R2656S	p.R2656S	NM_015378.2	NP_056193.2	0	3	3	1.682210				35	8096	+	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		Missense_Mutation	SNP	ENST00000358136.3	1	0	hg19	c.7966C>A	CCDS30588.1	0	.	.	.	.	.	.	.	.	.	.	C	17.58	3.424276	0.62733	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.25749	1.78;1.78	5.61	5.61	0.85477	5.61	5.61	0.85477	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.073997	0.52532	D	0.000062	T	0.45216	0.1331	M	0.64404	1.975	0.80722	D	1	D;B;B	0.62365	0.991;0.388;0.442	D;B;B	0.64595	0.927;0.088;0.142	T	0.20806	-1.0264	10	0.08179	T	0.78	.	19.6336	0.95721	0.0:1.0:0.0:0.0	.	563;2656;2656	B1AJZ2;Q5THJ4-2;Q5THJ4	.;.;VP13D_HUMAN	S	2656	ENSP00000348666:R2656S;ENSP00000350854:R2656S	ENSP00000348666:R2656S	R	+	1	0	0	VPS13D	12306400	12306400	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.089000	0.64492	2.646000	0.89796	0.637000	0.83480	CGC	0.625234		TCGA-IB-A7LX-01A-12D-A36O-08	0.383	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	1	0	1	2	2	2	2	0	0	0	0	125	125	125	123	1	3.150000	-3.658427	1	0.550000	NM_015378		0	18	17	0	387	381	0		1	0		0	0	125	0	0	0.999981	3.254422e-01	0	0	0	24	0	18	387
SPAG17	200162	broad.mit.edu	37	1	118609502	118609502	+	Silent	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:118609502C>T	ENST00000336338.5	-	18	2471	c.2406G>A	c.(2404-2406)aaG>aaA	p.K802K		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	802						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ACCTATATTGCTTATGGGCTT	0.358																																						ENST00000336338.5	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000																										0				123						c.(2404-2406)aaG>aaA		sperm associated antigen 17							101.0	97.0	98.0					1																	118609502		2203	4300	6503	SO:0001819	synonymous_variant	200162	0	0					g.chr1:118609502C>T		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.2406G>A	chr1.hg19:g.118609502C>T		1						p.K802K	NM_206996.2	NP_996879.1	0	2	2	1.629647	Q6Q759	SPG17_HUMAN		18	2471	-	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	1	1	hg19	c.2406G>A	CCDS899.1	1																																																																																								0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.358	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	1	0	1	2	2	2	2	0	0	0	0	121	121	121	120	1	3.150000	-20.000000	1	0.550000	NM_206996		0	159	158	0	130	129	1		1			0	0	121	0	0	1.000000	0	0	0	0	0	0	159	130
THBS3	7059	broad.mit.edu	37	1	155170966	155170966	+	Silent	SNP	G	G	A	rs150820199	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:155170966G>A	ENST00000368378.3	-	12	1379	c.1359C>T	c.(1357-1359)aaC>aaT	p.N453N	RP11-263K19.4_ENST00000453136.1_RNA|RP11-263K19.4_ENST00000454348.1_RNA|RP11-263K19.4_ENST00000422665.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000541576.1_Intron|THBS3_ENST00000457183.2_Silent_p.N333N|RP11-263K19.4_ENST00000430312.1_RNA|THBS3_ENST00000486260.1_5'UTR|RP11-263K19.4_ENST00000436772.1_RNA|THBS3_ENST00000541990.1_De_novo_Start_OutOfFrame	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	453	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.N453N(1)		breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TCCCACACACGTTCCCATTCC	0.567																																						ENST00000368378.3	1.000000	0.030000	1	7.000000e-02	0.110000	0.303379	0.110000	0.090000																										1	Substitution - coding silent(1)	p.N453N(1)	endometrium(1)	48						c.(1357-1359)aaC>aaT		thrombospondin 3		G		1,4405	2.1+/-5.4	0,1,2202	204.0	165.0	178.0		1359	0.4	1.0	1	dbSNP_134	178	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	THBS3	NM_007112.3		0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231		453/957	155170966	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	7059	11	121412	43				g.chr1:155170966G>A	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.1359C>T	chr1.hg19:g.155170966G>A		1					RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000541990.1_De_novo_Start_OutOfFrame|THBS3_ENST00000486260.1_5'UTR|RP11-263K19.4_ENST00000422665.1_RNA|THBS3_ENST00000457183.2_Silent_p.N333N|RP11-263K19.4_ENST00000436772.1_RNA|RP11-263K19.4_ENST00000454348.1_RNA|THBS3_ENST00000541576.1_Intron|RP11-263K19.4_ENST00000430312.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA	p.N453N	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	0	9	9	2.571479	P49746	TSP3_HUMAN	Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)	12	1379	-	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		B1AVR8|B4DQ20|Q8WV34	Silent	SNP	ENST00000368378.3	0	1	hg19	c.1359C>T	CCDS1099.1	0																																																																																								0.728015		TCGA-IB-A7LX-01A-12D-A36O-08	0.567	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	0	0	0	2	2	2	2	0	0	0	0	112	112	112	111	1	3.150000	-2.825541	1	0.550000	NM_007112		0	8	8	0	480	475	0		1	1		0	0	112	0	0	0.989030	5.365262e-01	0	4	0	98	0	8	480
TPR	7175	broad.mit.edu	37	1	186304589	186304589	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:186304589G>T	ENST00000367478.4	-	34	5088	c.4792C>A	c.(4792-4794)Cgc>Agc	p.R1598S		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1598					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		GCAGTAATGCGAACATCCAAT	0.423			T	NTRK1	papillary thyroid																																	ENST00000367478.4	1.000000	0.140000	2.900000e-01	1.800000e-01	0.220000	0.261896	0.220000	0.230000				Dom	yes			Dom	yes		1	1q25	1q25	7175	T	translocated promoter region				E	E	NTRK1		papillary thyroid		0				123						c.(4792-4794)Cgc>Agc		translocated promoter region, nuclear basket protein							171.0	153.0	158.0					1																	186304589		1878	4112	5990	SO:0001583	missense	7175	0	0					g.chr1:186304589G>T	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.4792C>A	chr1.hg19:g.186304589G>T	ENSP00000356448:p.Arg1598Ser	1						p.R1598S	NM_003292.2	NP_003283.2	0	4	4	2.292661	P12270	TPR_HUMAN		34	5088	-		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	1	0	hg19	c.4792C>A	CCDS41446.1	0	.	.	.	.	.	.	.	.	.	.	G	29.2	4.989888	0.93106	.	.	ENSG00000047410	ENST00000367478	T	0.26518	1.73	5.14	5.14	0.70334	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.54498	0.1862	M	0.79805	2.47	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.53585	-0.8418	10	0.36615	T	0.2	.	18.9661	0.92697	0.0:0.0:1.0:0.0	.	1598	P12270	TPR_HUMAN	S	1598	ENSP00000356448:R1598S	ENSP00000356448:R1598S	R	-	1	0	0	TPR	184571212	184571212	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.065000	0.93941	2.545000	0.85829	0.650000	0.86243	CGC	0.704433		TCGA-IB-A7LX-01A-12D-A36O-08	0.423	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	1	0	1	2	2	2	2	0	0	0	0	155	155	155	155	1	3.150000	-2.881965	1	0.550000	NM_003292		0	25	24	0	591	583	0		1	0		0	0	155	0	0	1.000000	8.368645e-01	0	0	0	80	0	25	591
TROVE2	6738	broad.mit.edu	37	1	193046072	193046072	+	Silent	SNP	C	C	A	rs55932617	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:193046072C>A	ENST00000367446.3	+	5	1188	c.978C>A	c.(976-978)atC>atA	p.I326I	TROVE2_ENST00000367445.3_Silent_p.I326I|TROVE2_ENST00000432079.1_Silent_p.I51I|TROVE2_ENST00000367443.1_Silent_p.I326I|TROVE2_ENST00000367441.1_Silent_p.I326I|TROVE2_ENST00000367444.3_Silent_p.I326I|TROVE2_ENST00000416058.2_Silent_p.I51I|TROVE2_ENST00000460715.2_3'UTR|TROVE2_ENST00000400968.2_Silent_p.I326I	NM_004600.5	NP_004591.2	P10155	RO60_HUMAN	TROVE domain family, member 2	326	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				cilium morphogenesis (GO:0060271)|immune system development (GO:0002520)|response to UV (GO:0009411)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|U2 snRNA binding (GO:0030620)			biliary_tract(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|urinary_tract(1)	21						ATATTTTGATCGCATTAGAAA	0.338																																						ENST00000367446.3	1.000000	0.130000	3.300000e-01	1.800000e-01	0.240000	0.281234	0.240000	0.240000																										0				21						c.(976-978)atC>atA		TROVE domain family, member 2							91.0	83.0	86.0					1																	193046072		1868	4099	5967	SO:0001819	synonymous_variant	6738	0	0					g.chr1:193046072C>A	BC036658	CCDS41449.1, CCDS1379.1, CCDS41450.1, CCDS41450.2, CCDS53451.1	1q31	2014-08-06	2005-06-14	2005-06-14	ENSG00000116747	ENSG00000116747			11313	protein-coding gene	gene with protein product		600063	"""Sjogren syndrome antigen A2 (60kDa, ribonucleoprotein autoantigen SS-A/Ro)"""	SSA2		8188321	Standard	NM_001042369		Approved	Ro60	uc001gss.3	P10155	OTTHUMG00000035675	ENST00000367446.3:c.978C>A	chr1.hg19:g.193046072C>A		1					TROVE2_ENST00000367445.3_Silent_p.I326I|TROVE2_ENST00000416058.2_Silent_p.I51I|TROVE2_ENST00000432079.1_Silent_p.I51I|TROVE2_ENST00000400968.2_Silent_p.I326I|TROVE2_ENST00000367444.3_Silent_p.I326I|TROVE2_ENST00000460715.2_3'UTR|TROVE2_ENST00000367441.1_Silent_p.I326I|TROVE2_ENST00000367443.1_Silent_p.I326I	p.I326I	NM_004600.5	NP_004591.2	0	4	4	2.292661	P10155	RO60_HUMAN		5	1188	+			B2RBB9|Q5LJ98|Q5LJ99|Q5LJA0|Q86WL3|Q86WL4|Q92787|Q9H1W6	Silent	SNP	ENST00000367446.3	1	0	hg19	c.978C>A	CCDS1379.1	0																																																																																								0.704433		TCGA-IB-A7LX-01A-12D-A36O-08	0.338	TROVE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086688.1	1	0	1	2	2	2	2	0	0	0	0	71	71	71	71	1	3.150000	-2.966611	1	0.550000	NM_004600		0	14	14	0	312	306	0		1	0		0	0	71	0	0	0.999738	3.962869e-01	0	0	0	30	0	14	312
CRB1	23418	broad.mit.edu	37	1	197396927	197396927	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:197396927C>A	ENST00000367400.3	+	7	2607	c.2472C>A	c.(2470-2472)atC>atA	p.I824I	CRB1_ENST00000538660.1_Intron|CRB1_ENST00000367399.2_Silent_p.I712I|CRB1_ENST00000544212.1_Silent_p.I305I|CRB1_ENST00000535699.1_Silent_p.I755I|CRB1_ENST00000367397.1_Silent_p.I205I	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	824	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I824M(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						CGTGGAAAATCGAAAAGGGAG	0.373																																						ENST00000367400.3	1.000000	0.130000	3.400000e-01	1.800000e-01	0.250000	0.287006	0.250000	0.240000																										1	Substitution - Missense(1)	p.I824M(1)	lung(1)	132						c.(2470-2472)atC>atA		crumbs family member 1, photoreceptor morphogenesis associated							73.0	71.0	72.0					1																	197396927		2203	4300	6503	SO:0001819	synonymous_variant	23418	0	0					g.chr1:197396927C>A		CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"""crumbs (Drosophila) homolog 1"", ""crumbs homolog 1 (Drosophila)"""	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.2472C>A	chr1.hg19:g.197396927C>A		1					CRB1_ENST00000367399.2_Silent_p.I712I|CRB1_ENST00000544212.1_Silent_p.I305I|CRB1_ENST00000535699.1_Silent_p.I755I|CRB1_ENST00000538660.1_Intron|CRB1_ENST00000367397.1_Silent_p.I205I	p.I824I	NM_201253.2	NP_957705.1	0	4	4	2.292661	P82279	CRUM1_HUMAN		7	2607	+			A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Silent	SNP	ENST00000367400.3	1	0	hg19	c.2472C>A	CCDS1390.1	0																																																																																								0.704433		TCGA-IB-A7LX-01A-12D-A36O-08	0.373	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	1	0	0	2	2	2	2	0	0	0	0	73	73	73	73	1	3.150000	-4.390350	1	0.550000	NM_201253		0	13	13	0	284	281	0		1			0	0	73	0	0	0.999534	0	0	0	0	0	0	13	284
KDM5B	10765	broad.mit.edu	37	1	202724554	202724554	+	Missense_Mutation	SNP	C	C	A	rs76768289		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:202724554C>A	ENST00000367265.3	-	11	2547	c.1383G>T	c.(1381-1383)ttG>ttT	p.L461F	KDM5B_ENST00000367264.2_Missense_Mutation_p.L497F|KDM5B_ENST00000456180.1_5'UTR	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	461	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						GCATGTTGTTCAAATTCCAGC	0.378																																						ENST00000367265.3	1.000000	0.110000	2.600000e-01	1.500000e-01	0.200000	0.237404	0.200000	0.200000																										0				6						c.(1381-1383)ttG>ttT		lysine (K)-specific demethylase 5B							95.0	101.0	99.0					1																	202724554		2203	4300	6503	SO:0001583	missense	10765	23	121390	41				g.chr1:202724554C>A	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.1383G>T	chr1.hg19:g.202724554C>A	ENSP00000356234:p.Leu461Phe	1					KDM5B_ENST00000456180.1_5'UTR|KDM5B_ENST00000367264.2_Missense_Mutation_p.L497F	p.L461F	NM_006618.3	NP_006609.3	0	4	4	2.292661	Q9UGL1	KDM5B_HUMAN		11	2547	-			O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	0	1	hg19	c.1383G>T	CCDS30974.1	0	.	.	.	.	.	.	.	.	.	.	C	18.80	3.700822	0.68501	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	T;T;T	0.72505	-0.66;-0.66;-0.66	5.73	4.82	0.62117	5.73	4.82	0.62117	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	D	0.86351	0.5912	M	0.93328	3.405	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.91635	0.961;0.999	D	0.88022	0.2769	10	0.87932	D	0	-12.7178	9.1277	0.36826	0.0:0.7688:0.0:0.2312	.	497;461	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	F	461;303;497;303	ENSP00000356234:L461F;ENSP00000356233:L497F;ENSP00000235790:L303F	ENSP00000235790:L303F	L	-	3	2	2	KDM5B	200991177	200991177	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.022000	0.41030	1.425000	0.47237	0.655000	0.94253	TTG	0.704433		TCGA-IB-A7LX-01A-12D-A36O-08	0.378	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	0	0	1	2	2	2	2	0	0	0	0	127	127	127	125	1	3.150000	-1.828307	0	0.550000	NM_006618		0	18	16	0	487	472	0		1	0		0	0	127	0	0	0.999976	7.712277e-01	0	1	0	77	0	18	487
CNIH3	149111	broad.mit.edu	37	1	224868723	224868723	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:224868723C>A	ENST00000272133.3	+	2	1027	c.145C>A	c.(145-147)Cat>Aat	p.H49N		NM_152495.1	NP_689708.1	Q8TBE1	CNIH3_HUMAN	cornichon family AMPA receptor auxiliary protein 3	49					intracellular signal transduction (GO:0035556)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of membrane potential (GO:0042391)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendritic shaft (GO:0043198)|postsynaptic membrane (GO:0045211)	channel regulator activity (GO:0016247)			large_intestine(5)|lung(4)	9	Breast(184;0.218)			GBM - Glioblastoma multiforme(131;0.073)		CAATCCTGTTCATGCGGTAAG	0.483																																						ENST00000272133.3	1.000000	0.090000	2.400000e-01	1.300000e-01	0.180000	0.217597	0.180000	0.190000																										0				9						c.(145-147)Cat>Aat		cornichon family AMPA receptor auxiliary protein 3							121.0	117.0	118.0					1																	224868723		2203	4300	6503	SO:0001583	missense	149111	0	0					g.chr1:224868723C>A	AF070524	CCDS1544.1	1q42.12	2013-08-28	2013-08-28		ENSG00000143786	ENSG00000143786			26802	protein-coding gene	gene with protein product			"""cornichon homolog 3 (Drosophila)"""			8619474, 9110174	Standard	NM_152495		Approved	FLJ38993, CNIH-3	uc001hos.1	Q8TBE1	OTTHUMG00000037634	ENST00000272133.3:c.145C>A	chr1.hg19:g.224868723C>A	ENSP00000272133:p.His49Asn	1						p.H49N	NM_152495.1	NP_689708.1	0	4	4	2.292661	Q8TBE1	CNIH3_HUMAN		2	1027	+	Breast(184;0.218)			Missense_Mutation	SNP	ENST00000272133.3	1	0	hg19	c.145C>A	CCDS1544.1	0	.	.	.	.	.	.	.	.	.	.	C	7.784	0.710231	0.15239	.	.	ENSG00000143786	ENST00000272133	.	.	.	5.45	5.45	0.79879	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.24851	0.0603	N	0.00554	-1.385	0.80722	D	1	B	0.31705	0.336	B	0.39531	0.302	T	0.43734	-0.9373	9	0.02654	T	1	-24.8564	18.0599	0.89373	0.0:1.0:0.0:0.0	.	49	Q8TBE1	CNIH3_HUMAN	N	49	.	ENSP00000272133:H49N	H	+	1	0	0	CNIH3	222935346	222935346	0.997000	0.39634	0.970000	0.41538	0.845000	0.48019	5.322000	0.65852	2.573000	0.86826	0.643000	0.83706	CAT	0.704433		TCGA-IB-A7LX-01A-12D-A36O-08	0.483	CNIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091752.2	1	0	1	2	2	2	2	0	0	0	0	131	131	131	128	1	3.150000	-3.049391	1	0.550000	NM_152495		0	15	15	0	457	445	0		1	0		0	0	131	0	0	0.999851	3.651894e-01	0	0	0	38	0	15	457
RYR2	6262	broad.mit.edu	37	1	237995882	237995882	+	Missense_Mutation	SNP	A	A	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:237995882A>T	ENST00000366574.2	+	105	15156	c.14839A>T	c.(14839-14841)Agg>Tgg	p.R4947W	RYR2_ENST00000542537.1_Missense_Mutation_p.R4931W|RYR2_ENST00000360064.6_Missense_Mutation_p.R4953W	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4947					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GTATCAAGAAAGGTGTTGGGA	0.388																																						ENST00000366574.2	1.000000	0.130000	4.200000e-01	2.000000e-01	0.290000	0.327747	0.290000	0.270000																										0				586						c.(14839-14841)Agg>Tgg		ryanodine receptor 2 (cardiac)							93.0	89.0	90.0					1																	237995882		1860	4127	5987	SO:0001583	missense	6262	0	0					g.chr1:237995882A>T	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.14839A>T	chr1.hg19:g.237995882A>T	ENSP00000355533:p.Arg4947Trp	1					RYR2_ENST00000542537.1_Missense_Mutation_p.R4931W|RYR2_ENST00000360064.6_Missense_Mutation_p.R4953W	p.R4947W	NM_001035.2	NP_001026.2	0	4	4	2.292661	Q92736	RYR2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.00606)	105	15156	+	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	1	1	hg19	c.14839A>T	CCDS55691.1	0	.	.	.	.	.	.	.	.	.	.	A	17.22	3.333129	0.60853	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.97232	-4.3;-4.26;-4.29	5.16	4.0	0.46444	5.16	4.0	0.46444	.	0.000000	0.56097	D	0.000025	D	0.98460	0.9487	M	0.89968	3.075	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.98802	1.0740	10	0.87932	D	0	-17.2433	11.8212	0.52238	0.7051:0.2949:0.0:0.0	.	4947	Q92736	RYR2_HUMAN	W	4947;4953;4931	ENSP00000355533:R4947W;ENSP00000353174:R4953W;ENSP00000443798:R4931W	ENSP00000353174:R4953W	R	+	1	2	2	RYR2	236062505	236062505	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.605000	0.46283	0.932000	0.37266	0.533000	0.62120	AGG	0.704433		TCGA-IB-A7LX-01A-12D-A36O-08	0.388	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	0	0	1	2	2	2	2	0	0	0	0	33	33	33	32	1	3.150000	-4.539993	1	0.550000	NM_001035		0	8	8	0	155	154	0		1	0		0	0	33	0	0	0.989669	9.424743e-03	0	0	0	3	0	8	155
SDCCAG8	10806	broad.mit.edu	37	1	243507631	243507631	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:243507631C>A	ENST00000366541.3	+	12	1589	c.1471C>A	c.(1471-1473)Cag>Aag	p.Q491K	MIR4677_ENST00000584153.1_RNA|SDCCAG8_ENST00000355875.4_Missense_Mutation_p.Q448K|SDCCAG8_ENST00000343783.6_Missense_Mutation_p.Q346K	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	491	Sufficient for homodimerization. {ECO:0000250}.				establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		AATTAAAGATCAGGTAAGAGA	0.353																																						ENST00000366541.3	1.000000	0.530000	9.400000e-01	6.400000e-01	0.770000	0.785166	0.770000	1.000000																										0				29						c.(1471-1473)Cag>Aag		serologically defined colon cancer antigen 8							90.0	86.0	87.0					1																	243507631		2203	4300	6503	SO:0001583	missense	10806	0	0					g.chr1:243507631C>A	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.1471C>A	chr1.hg19:g.243507631C>A	ENSP00000355499:p.Gln491Lys	1					SDCCAG8_ENST00000355875.4_Missense_Mutation_p.Q448K|SDCCAG8_ENST00000343783.6_Missense_Mutation_p.Q346K|MIR4677_ENST00000584153.1_RNA	p.Q491K	NM_006642.3	NP_006633.1	0	4	4	2.225328	Q86SQ7	SDCG8_HUMAN	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	12	1589	+	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Missense_Mutation	SNP	ENST00000366541.3	1	1	hg19	c.1471C>A	CCDS31075.1	0	.	.	.	.	.	.	.	.	.	.	C	16.26	3.072404	0.55646	.	.	ENSG00000054282	ENST00000355875;ENST00000366541;ENST00000343783;ENST00000435549	T;T;T;T	0.57273	0.7;0.66;0.66;0.41	6.07	5.16	0.70880	6.07	5.16	0.70880	.	0.129373	0.52532	D	0.000063	T	0.39886	0.1095	L	0.29908	0.895	0.47245	D	0.999362	B;B	0.25441	0.075;0.126	B;B	0.28638	0.092;0.092	T	0.19614	-1.0300	10	0.15499	T	0.54	-7.4048	12.343	0.55105	0.1339:0.7375:0.1286:0.0	.	448;491	E9PFS7;Q86SQ7	.;SDCG8_HUMAN	K	448;491;346;271	ENSP00000348137:Q448K;ENSP00000355499:Q491K;ENSP00000341260:Q346K;ENSP00000410200:Q271K	ENSP00000341260:Q346K	Q	+	1	0	0	SDCCAG8	241574254	241574254	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	1.247000	0.32815	1.566000	0.49654	0.585000	0.79938	CAG	0.698997		TCGA-IB-A7LX-01A-12D-A36O-08	0.353	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	1	0	1	2	2	2	2	0	0	0	0	53	53	53	52	1	3.150000	-15.859720	1	0.550000	NM_006642		0	32	32	0	199	197	1		1	1		0	0	53	0	0	1.000000	9.703296e-01	0	9	0	29	0	32	199
OR2W5	441932	broad.mit.edu	37	1	247655339	247655339	+	RNA	SNP	A	A	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr1:247655339A>T	ENST00000522351.1	+	0	970							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			CCATGAAGAAACTTCTGGGGT	0.507																																						ENST00000522351.1	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000																										0				39								olfactory receptor, family 2, subfamily W, member 5							67.0	68.0	68.0					1																	247655339		2203	4300	6503			441932	0	0					g.chr1:247655339A>T			1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"""GPCR / Class A : Olfactory receptors"""	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		chr1.hg19:g.247655339A>T		1									0	4	4	2.225328	A6NFC9	OR2W5_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0188)	0	970	+	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	B9EH85	RNA	SNP	ENST00000522351.1	1	1	hg19			1																																																																																								0.698997		TCGA-IB-A7LX-01A-12D-A36O-08	0.507	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	0	0	1	2	2	2	2	0	0	0	0	97	97	97	96	1	3.150000	-20.000000	1	0.550000	NM_001004698		0	123	124	0	246	239	0		1			0	0	97	0	0	1.000000	0	0	0	0	0	0	123	246
CLDN8	9073	broad.mit.edu	37	21	31587596	31587596	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr21:31587596C>A	ENST00000399899.1	-	1	795	c.648G>T	c.(646-648)ccG>ccT	p.P216P	CLDN8_ENST00000286809.1_Silent_p.P216P	NM_199328.2	NP_955360.1	P56748	CLD8_HUMAN	claudin 8	216					calcium-independent cell-cell adhesion (GO:0016338)	basolateral plasma membrane (GO:0016323)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)	15						AGTAGACGCTCGGTGACTTCT	0.378																																						ENST00000399899.1			0	0																														0				15						c.(646-648)ccG>ccT		claudin 8							135.0	124.0	127.0					21																	31587596		2203	4300	6503	SO:0001819	synonymous_variant	9073	0	0					g.chr21:31587596C>A	AJ250711	CCDS13587.1	21q22.1	2008-07-31			ENSG00000156284	ENSG00000156284		"""Claudins"""	2050	protein-coding gene	gene with protein product		611231				9892664	Standard	NM_199328		Approved		uc002ynu.2	P56748	OTTHUMG00000081872	ENST00000399899.1:c.648G>T	chr21.hg19:g.31587596C>A							CLDN8_ENST00000286809.1_Silent_p.P216P	p.P216P	NM_199328.2	NP_955360.1					P56748	CLD8_HUMAN		1	795	-			D3DSE3|Q53EX7	Silent	SNP	ENST00000399899.1	1	0	hg19	c.648G>T	CCDS13587.1																																																																																											TCGA-IB-A7LX-01A-12D-A36O-08	0.378	CLDN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182260.1	1	0	1	2	2	2	2	0	0	0	0	128	128	128	126	1	3.150000	-2.595282	1	0.550000	NM_199328		0	25	24	0	478	470	0		1	0		0	0	128	0	0	1.000000	4.709011e-02	0	0	0	7	0	25	478
ITSN1	6453	broad.mit.edu	37	21	35147105	35147105	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr21:35147105C>A	ENST00000381318.3	+	13	1666	c.1378C>A	c.(1378-1380)Caa>Aaa	p.Q460K	ITSN1_ENST00000381285.4_Missense_Mutation_p.Q460K|ITSN1_ENST00000399352.1_Missense_Mutation_p.Q460K|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381291.4_Missense_Mutation_p.Q460K|ITSN1_ENST00000437442.2_Missense_Mutation_p.Q460K|ITSN1_ENST00000399355.2_Missense_Mutation_p.Q460K|ITSN1_ENST00000399367.3_Missense_Mutation_p.Q460K|ITSN1_ENST00000379960.5_Missense_Mutation_p.Q460K|ITSN1_ENST00000399326.3_Missense_Mutation_p.Q460K|ITSN1_ENST00000399338.4_Missense_Mutation_p.Q460K|ITSN1_ENST00000399349.1_Missense_Mutation_p.Q460K|ITSN1_ENST00000399353.1_Missense_Mutation_p.Q423K	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	460	KLERQ.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						ACTACTAAATCAAAGAAACAA	0.373																																						ENST00000381318.3	1.000000	0.120000	1	1.700000e-01	0.240000	0.408668	0.240000	0.230000																										0				67						c.(1378-1380)Caa>Aaa		intersectin 1 (SH3 domain protein)							78.0	78.0	78.0					21																	35147105		2203	4300	6503	SO:0001583	missense	6453	0	0					g.chr21:35147105C>A	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.1378C>A	chr21.hg19:g.35147105C>A	ENSP00000370719:p.Gln460Lys	1					ITSN1_ENST00000437442.2_Missense_Mutation_p.Q460K|ITSN1_ENST00000399355.2_Missense_Mutation_p.Q460K|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381291.4_Missense_Mutation_p.Q460K|ITSN1_ENST00000399353.1_Missense_Mutation_p.Q423K|ITSN1_ENST00000399338.4_Missense_Mutation_p.Q460K|ITSN1_ENST00000399352.1_Missense_Mutation_p.Q460K|ITSN1_ENST00000381285.4_Missense_Mutation_p.Q460K|ITSN1_ENST00000399367.3_Missense_Mutation_p.Q460K|ITSN1_ENST00000399326.3_Missense_Mutation_p.Q460K|ITSN1_ENST00000399349.1_Missense_Mutation_p.Q460K|ITSN1_ENST00000379960.5_Missense_Mutation_p.Q460K	p.Q460K	NM_003024.2	NP_003015.2	2	3	5	2.266323	Q15811	ITSN1_HUMAN		13	1666	+			A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	1	0	hg19	c.1378C>A	CCDS33545.1	0	.	.	.	.	.	.	.	.	.	.	C	17.68	3.450044	0.63290	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	T;T;T;T;T;T;T;T;T;T;T;T	0.49432	1.61;0.79;0.83;0.78;1.61;1.61;0.82;1.61;1.61;1.61;1.61;1.61	4.64	4.64	0.57946	4.64	4.64	0.57946	.	0.120389	0.56097	D	0.000021	T	0.49236	0.1545	M	0.68317	2.08	0.80722	D	1	B;B;B;B;B;P;B;B;B;B	0.34864	0.064;0.064;0.064;0.023;0.106;0.473;0.023;0.023;0.106;0.064	B;B;B;B;B;B;B;B;B;B	0.33121	0.039;0.039;0.039;0.005;0.084;0.158;0.005;0.005;0.084;0.039	T	0.56703	-0.7935	10	0.54805	T	0.06	.	17.8738	0.88818	0.0:1.0:0.0:0.0	.	423;423;423;460;460;460;460;460;460;423	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;.;ITSN1_HUMAN;.;.	K	423;460;460;460;460;460;460;460;460;460;460;460;460;460	ENSP00000382290:Q423K;ENSP00000370719:Q460K;ENSP00000370691:Q460K;ENSP00000370685:Q460K;ENSP00000382301:Q460K;ENSP00000382289:Q460K;ENSP00000382292:Q460K;ENSP00000382286:Q460K;ENSP00000382275:Q460K;ENSP00000387377:Q460K;ENSP00000382265:Q460K;ENSP00000369294:Q460K	ENSP00000369294:Q460K	Q	+	1	0	0	ITSN1	34068975	34068975	1.000000	0.71417	0.855000	0.33649	0.948000	0.59901	5.820000	0.69250	2.289000	0.77006	0.655000	0.94253	CAA	0.698997		TCGA-IB-A7LX-01A-12D-A36O-08	0.373	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	1	0	1	2	2	2	2	0	0	0	0	82	82	82	81	1	3.150000	-3.920832	1	0.550000	NM_003024		0	13	12	0	316	310	0		1	0		0	0	82	0	0	0.999492	7.013694e-01	0	0	0	60	0	13	316
DSCAM	1826	broad.mit.edu	37	21	41423897	41423897	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr21:41423897G>T	ENST00000400454.1	-	30	5650	c.5173C>A	c.(5173-5175)Cgg>Agg	p.R1725R		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1725					cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GTTCCCGGCCGAGCGTCTGAA	0.483																																					Melanoma(134;970 1778 1785 21664 32388)	ENST00000400454.1	1.000000	0.180000	1	2.200000e-01	0.290000	0.446621	0.290000	0.270000																										0				142						c.(5173-5175)Cgg>Agg		Down syndrome cell adhesion molecule							133.0	135.0	134.0					21																	41423897		1950	4151	6101	SO:0001819	synonymous_variant	1826	0	0					g.chr21:41423897G>T	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.5173C>A	chr21.hg19:g.41423897G>T		1						p.R1725R	NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	2	3	5	2.266323	O60469	DSCAM_HUMAN		30	5650	-		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)	O60468	Silent	SNP	ENST00000400454.1	1	0	hg19	c.5173C>A	CCDS42929.1	0																																																																																								0.698997		TCGA-IB-A7LX-01A-12D-A36O-08	0.483	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	1	0	1	2	2	2	2	0	0	0	0	122	122	122	121	1	3.150000	-2.870906	1	0.550000	NM_001389		0	27	27	0	516	503	0		1			0	0	122	0	0	1.000000	0	0	0	0	0	0	27	516
CACNG2	10369	broad.mit.edu	37	22	37098459	37098459	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr22:37098459C>T	ENST00000300105.6	-	1	1144	c.163G>A	c.(163-165)Gag>Aag	p.E55K	RP1-293L6.1_ENST00000430281.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	55					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						ATAACTTCCTCGTTCTTTTTG	0.517																																						ENST00000300105.6	1.000000	0.940000	1	9.900000e-01	0.990000	0.996954	0.990000	1.000000																										0				18						c.(163-165)Gag>Aag		calcium channel, voltage-dependent, gamma subunit 2							246.0	204.0	218.0					22																	37098459		2203	4300	6503	SO:0001583	missense	10369	0	0					g.chr22:37098459C>T	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"""Calcium channel subunits"""	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.163G>A	chr22.hg19:g.37098459C>T	ENSP00000300105:p.Glu55Lys	1					RP1-293L6.1_ENST00000430281.1_RNA	p.E55K	NM_006078.3	NP_006069.1	2	3	5	1.795983	Q9Y698	CCG2_HUMAN		1	1144	-			Q2M1M1|Q5TGT3|Q9UGZ7	Missense_Mutation	SNP	ENST00000300105.6	1	1	hg19	c.163G>A	CCDS13931.1	1	.	.	.	.	.	.	.	.	.	.	c	16.52	3.145171	0.57044	.	.	ENSG00000166862	ENST00000300105	T	0.37584	1.19	4.37	4.37	0.52481	4.37	4.37	0.52481	.	0.000000	0.85682	D	0.000000	T	0.22820	0.0551	N	0.12746	0.255	0.58432	D	0.999997	D	0.52996	0.957	P	0.44394	0.448	T	0.04281	-1.0963	10	0.06891	T	0.86	-10.3973	17.3494	0.87318	0.0:1.0:0.0:0.0	.	55	Q9Y698	CCG2_HUMAN	K	55	ENSP00000300105:E55K	ENSP00000300105:E55K	E	-	1	0	0	CACNG2	35428405	35428405	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.284000	0.78650	2.134000	0.65973	0.546000	0.68486	GAG	0.619128		TCGA-IB-A7LX-01A-12D-A36O-08	0.517	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2	1	0	1	2	2	2	2	0	0	0	0	133	133	133	130	1	3.150000	-5.967919	1	0.550000			0	113	112	0	322	318	1		1			0	0	133	0	0	1.000000	0	0	0	0	0	0	113	322
LGALS1	3956	broad.mit.edu	37	22	38075643	38075643	+	Missense_Mutation	SNP	G	G	A	rs375290542		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr22:38075643G>A	ENST00000215909.5	+	4	390	c.295G>A	c.(295-297)Gtc>Atc	p.V99I	LGALS1_ENST00000489315.1_3'UTR	NM_002305.3	NP_002296.1	P09382	LEG1_HUMAN	lectin, galactoside-binding, soluble, 1	99	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)|cellular response to glucose stimulus (GO:0071333)|cellular response to organic cyclic compound (GO:0071407)|multicellular organismal response to stress (GO:0033555)|myoblast differentiation (GO:0045445)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of neuron projection development (GO:0010977)|plasma cell differentiation (GO:0002317)|positive regulation of erythrocyte aggregation (GO:0034120)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	galactoside binding (GO:0016936)|lactose binding (GO:0030395)|poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(1)|lung(1)	3	Melanoma(58;0.0574)					CAACCTGACCGTCAAGCTGCC	0.567																																					Pancreas(23;406 890 14304 26016)	ENST00000215909.5	1.000000	0.800000	1	9.100000e-01	0.990000	0.971288	0.990000	1.000000																										0				3						c.(295-297)Gtc>Atc		lectin, galactoside-binding, soluble, 1		G	ILE/VAL	0,4406		0,0,2203	115.0	82.0	93.0		295	-0.1	1.0	22		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	LGALS1	NM_002305.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	99/136	38075643	1,13005	2203	4300	6503	SO:0001583	missense	3956	7	121412	44				g.chr22:38075643G>A		CCDS13954.1	22q13.1	2014-01-30	2008-07-25		ENSG00000100097	ENSG00000100097		"""Lectins, galactoside-binding"", ""Endogenous ligands"""	6561	protein-coding gene	gene with protein product	"""galectin 1"""	150570				1988031, 12271131	Standard	NM_002305		Approved	GBP	uc003atn.3	P09382	OTTHUMG00000150661	ENST00000215909.5:c.295G>A	chr22.hg19:g.38075643G>A	ENSP00000215909:p.Val99Ile	1					LGALS1_ENST00000489315.1_3'UTR	p.V99I	NM_002305.3	NP_002296.1	2	3	5	1.795983	P09382	LEG1_HUMAN		4	390	+	Melanoma(58;0.0574)		B2R5E8|Q9UDK5	Missense_Mutation	SNP	ENST00000215909.5	1	1	hg19	c.295G>A	CCDS13954.1	1	.	.	.	.	.	.	.	.	.	.	g	0.469	-0.885255	0.02511	0.0	1.16E-4	ENSG00000100097	ENST00000215909	T	0.04360	3.64	6.08	-0.0473	0.13844	6.08	-0.0473	0.13844	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.237165	0.42294	N	0.000737	T	0.03695	0.0105	L	0.31120	0.905	0.31764	N	0.632933	B	0.11235	0.004	B	0.19666	0.026	T	0.35051	-0.9804	10	0.19590	T	0.45	-0.9193	10.1288	0.42665	0.4005:0.0:0.5995:0.0	.	99	P09382	LEG1_HUMAN	I	99	ENSP00000215909:V99I	ENSP00000215909:V99I	V	+	1	0	0	LGALS1	36405589	36405589	0.451000	0.25705	0.997000	0.53966	0.127000	0.20565	0.715000	0.25822	-0.043000	0.13513	-1.057000	0.02308	GTC	0.619128		TCGA-IB-A7LX-01A-12D-A36O-08	0.567	LGALS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319482.1	1	0	1	2	2	2	2	0	0	0	0	71	71	71	71	1	3.150000	-4.275326	1	0.550000	NM_002305		0	50	50	0	159	155	1		1	1		0	0	71	0	0	1.000000	1	0	665	0	2015	0	50	159
MYCN	4613	broad.mit.edu	37	2	16086208	16086208	+	Silent	SNP	C	C	A	rs144531796	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:16086208C>A	ENST00000281043.3	+	3	1681	c.1384C>A	c.(1384-1386)Cgg>Agg	p.R462R		NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	462					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			TGAACACGCTCGGACTTGCTA	0.428			A		neuroblastoma																																	ENST00000281043.3	1.000000	0.150000	1	2.000000e-01	0.260000	0.379979	0.260000	0.240000				Dom	yes			Dom	yes		2	2p24.1	2p24.1	4613	A	"""v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"""				O	O			neuroblastoma		0				31						c.(1384-1386)Cgg>Agg		v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog							59.0	67.0	64.0					2																	16086208		2202	4300	6502	SO:0001819	synonymous_variant	4613	6	121406	42				g.chr2:16086208C>A	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"""Basic helix-loop-helix proteins"""	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.1384C>A	chr2.hg19:g.16086208C>A		1						p.R462R	NM_005378.4	NP_005369.2	2	6	8	2.087735	P04198	MYCN_HUMAN	GBM - Glioblastoma multiforme(3;0.000332)	3	1681	+	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		Q53XS5|Q6LDT9	Silent	SNP	ENST00000281043.3	1	0	hg19	c.1384C>A	CCDS1687.1	0																																																																																								0.673795		TCGA-IB-A7LX-01A-12D-A36O-08	0.428	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	1	0	1	2	2	2	2	0	0	0	0	117	117	117	117	1	3.150000	-2.522253	1	0.550000	NM_005378		0	21	22	0	411	400	0		1	0		0	0	117	0	0	0.999997	0	0	0	0	1	0	21	411
FAM49A	81553	broad.mit.edu	37	2	16743285	16743285	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:16743285G>T	ENST00000381323.3	-	6	643	c.423C>A	c.(421-423)ttC>ttA	p.F141L	FAM49A_ENST00000355549.2_Missense_Mutation_p.F141L|FAM49A_ENST00000406434.1_Missense_Mutation_p.F141L	NM_030797.3	NP_110424.1	Q9H0Q0	FA49A_HUMAN	family with sequence similarity 49, member A	141						intracellular (GO:0005622)		p.F141F(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|skin(3)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088)		GBM - Glioblastoma multiforme(3;0.00969)			TCAGCTCATCGAATCGAAGGG	0.453																																						ENST00000381323.3	1.000000	0.120000	1	1.800000e-01	0.260000	0.379540	0.260000	0.240000																										1	Substitution - coding silent(1)	p.F141F(1)	large_intestine(1)	23						c.(421-423)ttC>ttA		family with sequence similarity 49, member A							94.0	98.0	97.0					2																	16743285		2203	4300	6503	SO:0001583	missense	81553	0	0					g.chr2:16743285G>T	AK001942	CCDS1688.1	2p24.3	2008-02-05			ENSG00000197872	ENSG00000197872			25373	protein-coding gene	gene with protein product							Standard	NM_030797		Approved	DKFZP566A1524, FLJ11080	uc002rck.2	Q9H0Q0	OTTHUMG00000090615	ENST00000381323.3:c.423C>A	chr2.hg19:g.16743285G>T	ENSP00000370724:p.Phe141Leu	1					FAM49A_ENST00000355549.2_Missense_Mutation_p.F141L|FAM49A_ENST00000406434.1_Missense_Mutation_p.F141L	p.F141L	NM_030797.3	NP_110424.1	2	6	8	2.087735	Q9H0Q0	FA49A_HUMAN	GBM - Glioblastoma multiforme(3;0.00969)	6	643	-	Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088)		B3KNZ1|Q53QW2	Missense_Mutation	SNP	ENST00000381323.3	1	0	hg19	c.423C>A	CCDS1688.1	0	.	.	.	.	.	.	.	.	.	.	G	17.95	3.513807	0.64522	.	.	ENSG00000197872	ENST00000381323;ENST00000406434;ENST00000355549	T;T;T	0.57595	0.39;0.39;0.39	5.7	-3.83	0.04269	5.7	-3.83	0.04269	.	0.000000	0.85682	D	0.000000	T	0.71710	0.3372	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.74899	-0.3507	10	0.45353	T	0.12	-22.1984	13.5016	0.61459	0.6789:0.0:0.3211:0.0	.	141	Q9H0Q0	FA49A_HUMAN	L	141	ENSP00000370724:F141L;ENSP00000384771:F141L;ENSP00000347744:F141L	ENSP00000347744:F141L	F	-	3	2	2	FAM49A	16606766	16606766	0.005000	0.15991	0.957000	0.39632	0.494000	0.33585	-0.804000	0.04535	-0.587000	0.05890	-0.136000	0.14681	TTC	0.673795		TCGA-IB-A7LX-01A-12D-A36O-08	0.453	FAM49A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207203.2	1	0	1	2	2	2	2	0	0	0	0	71	71	71	71	1	3.150000	-3.343013	1	0.550000	NM_030797		0	11	11	0	224	221	0		1	0		0	0	71	0	0	0.998333	7.585464e-02	0	0	0	9	0	11	224
CHST10	9486	broad.mit.edu	37	2	101010109	101010109	+	Silent	SNP	T	T	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:101010109T>C	ENST00000264249.3	-	7	1054	c.669A>G	c.(667-669)agA>agG	p.R223R	CHST10_ENST00000409701.1_Silent_p.R223R|CHST10_ENST00000542617.1_Silent_p.R271R	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	223					carbohydrate biosynthetic process (GO:0016051)|cell adhesion (GO:0007155)|learning (GO:0007612)|long-term memory (GO:0007616)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	HNK-1 sulfotransferase activity (GO:0016232)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)	16						TCCTGTATTTTCTGATGATGC	0.483																																						ENST00000264249.3	1.000000	0.530000	1	6.000000e-01	0.690000	0.746654	0.690000	0.670000																										0				16						c.(667-669)agA>agG		carbohydrate sulfotransferase 10							145.0	146.0	146.0					2																	101010109		2203	4300	6503	SO:0001819	synonymous_variant	9486	0	0					g.chr2:101010109T>C	BC010441	CCDS2047.1	2q11.2	2008-02-05			ENSG00000115526	ENSG00000115526		"""Sulfotransferases, membrane-bound"""	19650	protein-coding gene	gene with protein product		606376				12080076	Standard	NM_004854		Approved	HNK-1ST	uc002tam.3	O43529	OTTHUMG00000130669	ENST00000264249.3:c.669A>G	chr2.hg19:g.101010109T>C		1					CHST10_ENST00000542617.1_Silent_p.R271R|CHST10_ENST00000409701.1_Silent_p.R223R	p.R223R	NM_004854.4	NP_004845.1	2	4	6	2.189758	O43529	CHSTA_HUMAN		7	1054	-			Q53T18	Silent	SNP	ENST00000264249.3	1	1	hg19	c.669A>G	CCDS2047.1	0																																																																																								0.685094		TCGA-IB-A7LX-01A-12D-A36O-08	0.483	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	1	0	1	2	2	2	2	0	0	0	0	150	150	150	150	1	3.150000	-20.000000	1	0.550000	NM_004854		0	68	64	0	464	458	0		1	0		0	0	150	0	0	1.000000	8.442364e-02	0	0	0	4	0	68	464
LRP2	4036	broad.mit.edu	37	2	170025143	170025143	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:170025143G>T	ENST00000263816.3	-	61	11826	c.11541C>A	c.(11539-11541)ttC>ttA	p.F3847L		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3847	LDL-receptor class A 34. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.F3847F(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	TTTTGCATTCGAACATAGTAG	0.428																																						ENST00000263816.3	1.000000	0.110000	1	1.700000e-01	0.240000	0.388524	0.240000	0.210000																										1	Substitution - coding silent(1)	p.F3847F(1)	large_intestine(1)	315						c.(11539-11541)ttC>ttA		low density lipoprotein receptor-related protein 2	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"						98.0	89.0	92.0					2																	170025143		2203	4300	6503	SO:0001583	missense	4036	0	0					g.chr2:170025143G>T		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.11541C>A	chr2.hg19:g.170025143G>T	ENSP00000263816:p.Phe3847Leu	1						p.F3847L	NM_004525.2	NP_004516.2	2	5	7	2.129539	P98164	LRP2_HUMAN		61	11826	-			O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	1	0	hg19	c.11541C>A	CCDS2232.1	0	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.6|25.6	4.656719|4.656719	0.88154|0.88154	.|.	.|.	ENSG00000081479|ENSG00000081479	ENST00000263816|ENST00000536293	D|.	0.98889|.	-5.21|.	5.82|5.82	-6.33|-6.33	0.01988|0.01988	5.82|5.82	-6.33|-6.33	0.01988|0.01988	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.79046|.	0.4380|.	M|M	0.85462|0.85462	2.755|2.755	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	D|.	0.83997|.	0.0341|.	10|.	0.72032|0.72032	D|D	0.01|0.01	.|.	17.3947|17.3947	0.87442|0.87442	0.8962:0.0:0.1038:0.0|0.8962:0.0:0.1038:0.0	.|.	3847|.	P98164|.	LRP2_HUMAN|.	L|X	3847|512	ENSP00000263816:F3847L|.	ENSP00000263816:F3847L|ENSP00000438157:S512X	F|S	-|-	3|2	2|0	2|0	LRP2|LRP2	169733389|169733389	169733389|169733389	0.971000|0.971000	0.33674|0.33674	0.855000|0.855000	0.33649|0.33649	0.823000|0.823000	0.46562|0.46562	0.340000|0.340000	0.19892|0.19892	-1.073000|-1.073000	0.03137|0.03137	-0.367000|-0.367000	0.07326|0.07326	TTC|TCG	0.678284		TCGA-IB-A7LX-01A-12D-A36O-08	0.428	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	1	0	1	2	2	2	2	0	0	0	0	64	64	64	62	1	3.150000	-4.333398	1	0.550000	NM_004525		0	10	9	0	223	218	0		1			0	0	64	0	0	0.996647	0	0	0	0	0	0	10	223
FASTKD1	79675	broad.mit.edu	37	2	170403116	170403116	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:170403116C>A	ENST00000453153.2	-	8	1659	c.1313G>T	c.(1312-1314)cGa>cTa	p.R438L	FASTKD1_ENST00000453929.2_Missense_Mutation_p.R438L	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	438					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						GGCTTCAATTCGGGATATCCC	0.413																																						ENST00000453153.2	1.000000	0.110000	1	1.600000e-01	0.220000	0.373971	0.220000	0.210000																										0				37						c.(1312-1314)cGa>cTa		FAST kinase domains 1							65.0	68.0	67.0					2																	170403116		2203	4300	6503	SO:0001583	missense	79675	0	0					g.chr2:170403116C>A	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1313G>T	chr2.hg19:g.170403116C>A	ENSP00000400513:p.Arg438Leu	1					FASTKD1_ENST00000453929.2_Missense_Mutation_p.R438L	p.R438L	NM_024622.3	NP_078898.3	2	5	7	2.129539	Q53R41	FAKD1_HUMAN		8	1659	-			Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	1	0	hg19	c.1313G>T	CCDS33318.1	0	.	.	.	.	.	.	.	.	.	.	C	18.33	3.600955	0.66332	.	.	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.25414	1.82;1.8	4.44	2.59	0.31030	4.44	2.59	0.31030	.	0.265024	0.35772	N	0.002992	T	0.37652	0.1011	L	0.59436	1.845	0.40632	D	0.981862	D;D	0.64830	0.994;0.99	P;P	0.60682	0.878;0.759	T	0.13255	-1.0516	10	0.56958	D	0.05	-29.0924	7.238	0.26079	0.0:0.6022:0.0:0.3978	.	438;438	Q53R41-2;Q53R41	.;FAKD1_HUMAN	L	438	ENSP00000400513:R438L;ENSP00000403229:R438L	ENSP00000400513:R438L	R	-	2	0	0	FASTKD1	170111362	170111362	0.678000	0.27586	0.245000	0.24217	0.899000	0.52679	1.083000	0.30815	0.585000	0.29608	0.563000	0.77884	CGA	0.678284		TCGA-IB-A7LX-01A-12D-A36O-08	0.413	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	1	0	1	2	2	2	2	0	0	0	0	65	65	65	64	1	3.150000	-3.222233	1	0.550000	NM_024622		0	13	13	0	309	302	0		1	0		0	0	65	0	0	0.999491	3.550350e-01	0	0	0	29	0	13	309
SF3B1	23451	broad.mit.edu	37	2	198265629	198265629	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:198265629T>C	ENST00000335508.6	-	18	2619	c.2528A>G	c.(2527-2529)aAa>aGa	p.K843R	SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	843					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TGCACCTACTTTGTTTGCCAA	0.348			Mis		myelodysplastic syndrome																																	ENST00000335508.6	1.000000	0.860000	1	9.700000e-01	0.990000	0.987063	0.990000	1.000000				Dom	yes			Dom	yes		2	2q33.1	2q33.1	23451	Mis	"""splicing factor 3b, subunit 1, 155kDa"""				L	L			myelodysplastic syndrome		0				633						c.(2527-2529)aAa>aGa		splicing factor 3b, subunit 1, 155kDa							84.0	83.0	84.0					2																	198265629		2203	4299	6502	SO:0001583	missense	23451	0	0					g.chr2:198265629T>C	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2528A>G	chr2.hg19:g.198265629T>C	ENSP00000335321:p.Lys843Arg	1					SF3B1_ENST00000462613.1_5'Flank	p.K843R	NM_012433.2	NP_036565.2	2	6	8	2.094740	O75533	SF3B1_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.246)	18	2619	-			E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	1	1	hg19	c.2528A>G	CCDS33356.1	1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.581538	0.65992	.	.	ENSG00000115524	ENST00000335508	T	0.65916	-0.18	5.77	5.77	0.91146	5.77	5.77	0.91146	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68412	0.2998	M	0.76433	2.335	0.80722	D	1	B	0.28082	0.2	B	0.36030	0.216	T	0.68447	-0.5406	10	0.52906	T	0.07	.	16.3948	0.83586	0.0:0.0:0.0:1.0	.	843	O75533	SF3B1_HUMAN	R	843	ENSP00000335321:K843R	ENSP00000335321:K843R	K	-	2	0	0	SF3B1	197973874	197973874	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.936000	0.87665	2.326000	0.78906	0.533000	0.62120	AAA	0.677650		TCGA-IB-A7LX-01A-12D-A36O-08	0.348	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2	1	0	1	2	2	2	2	0	0	0	0	78	78	78	78	1	3.150000	-20.000000	1	0.550000			0	65	65	0	241	239	1		1	1	1	0	0	78	577	0	1.000000	1	1	100	54	381	255	65	241
SF3B1	23451	broad.mit.edu	37	2	198266713	198266713	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:198266713C>T	ENST00000335508.6	-	15	2310	c.2219G>A	c.(2218-2220)gGa>gAa	p.G740E	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	740					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.G740E(1)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			ATTTACCTTTCCTCTGTGTTG	0.343			Mis		myelodysplastic syndrome																																	ENST00000335508.6	1.000000	0.990000	1	9.900000e-01	0.990000	0.999697	0.990000	1.000000				Dom	yes			Dom	yes		2	2q33.1	2q33.1	23451	Mis	"""splicing factor 3b, subunit 1, 155kDa"""				L	L			myelodysplastic syndrome		1	Substitution - Missense(1)	p.G740E(1)	haematopoietic_and_lymphoid_tissue(1)	633						c.(2218-2220)gGa>gAa		splicing factor 3b, subunit 1, 155kDa							87.0	83.0	85.0					2																	198266713		2203	4300	6503	SO:0001583	missense	23451	0	0					g.chr2:198266713C>T	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2219G>A	chr2.hg19:g.198266713C>T	ENSP00000335321:p.Gly740Glu	1					SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	p.G740E	NM_012433.2	NP_036565.2	2	6	8	2.094740	O75533	SF3B1_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.246)	15	2310	-			E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	1	1	hg19	c.2219G>A	CCDS33356.1	1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.036521	0.93630	.	.	ENSG00000115524	ENST00000335508	T	0.62364	0.03	5.58	5.58	0.84498	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.107844	0.64402	D	0.000005	T	0.76449	0.3989	M	0.83692	2.655	0.80722	D	1	D	0.55800	0.973	P	0.51974	0.686	T	0.80183	-0.1488	10	0.66056	D	0.02	.	19.5659	0.95393	0.0:1.0:0.0:0.0	.	740	O75533	SF3B1_HUMAN	E	740	ENSP00000335321:G740E	ENSP00000335321:G740E	G	-	2	0	0	SF3B1	197974958	197974958	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.359000	0.79477	2.619000	0.88677	0.563000	0.77884	GGA	0.677650		TCGA-IB-A7LX-01A-12D-A36O-08	0.343	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2	1	0	1	2	2	2	2	0	0	0	0	76	76	76	76	1	3.150000	-20.000000	1	0.550000			0	76	75	0	226	219	1		1	1	1	0	0	76	366	0	1.000000	1	1	157	42	347	125	76	226
ATIC	471	broad.mit.edu	37	2	216190751	216190751	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr2:216190751C>A	ENST00000236959.9	+	6	747	c.421C>A	c.(421-423)Cga>Aga	p.R141R	ATIC_ENST00000540518.1_Silent_p.R82R|ATIC_ENST00000435675.1_Silent_p.R140R	NM_004044.6	NP_004035.2	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	141					'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|dihydrofolate metabolic process (GO:0046452)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	IMP cyclohydrolase activity (GO:0003937)|phosphoribosylaminoimidazolecarboxamide formyltransferase activity (GO:0004643)|protein homodimerization activity (GO:0042803)	p.R141*(1)	ATIC/ALK(24)	large_intestine(2)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	8		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)	AAACCACGCTCGAGTGACAGT	0.483			T	ALK	ALCL																																	ENST00000236959.9	1.000000	0.120000	1	1.700000e-01	0.250000	0.374253	0.250000	0.210000				Dom	yes			Dom	yes		2	2q35	2q35	471	T	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase				L	L	ALK		ALCL	ATIC/ALK(24)	1	Substitution - Nonsense(1)	p.R141*(1)	large_intestine(1)	8						c.(421-423)Cga>Aga		5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)						102.0	93.0	96.0					2																	216190751		2203	4300	6503	SO:0001819	synonymous_variant	471	0	0					g.chr2:216190751C>A		CCDS2398.1	2q35	2010-04-27			ENSG00000138363	ENSG00000138363	2.1.2.3, 3.5.4.10		794	protein-coding gene	gene with protein product	"""phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase"""	601731				8567683, 9378707	Standard	NM_004044		Approved	PURH, AICARFT, IMPCHASE	uc002vex.4	P31939	OTTHUMG00000133023	ENST00000236959.9:c.421C>A	chr2.hg19:g.216190751C>A		1					ATIC_ENST00000540518.1_Silent_p.R82R|ATIC_ENST00000435675.1_Silent_p.R140R	p.R141R	NM_004044.6	NP_004035.2	2	6	8	2.094740	P31939	PUR9_HUMAN		6	747	+		Renal(323;0.229)	A8K202|E9PBU3|Q13856|Q53S28	Silent	SNP	ENST00000236959.9	1	0	hg19	c.421C>A	CCDS2398.1	0																																																																																								0.677650		TCGA-IB-A7LX-01A-12D-A36O-08	0.483	ATIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256610.1	1	0	1	2	2	2	2	0	0	0	0	70	70	70	68	1	3.150000	-3.221883	1	0.550000	NM_004044		0	11	11	0	238	232	0		1	0		0	0	70	0	0	0.998213	9.953872e-01	0	1	0	202	0	11	238
CPNE4	131034	broad.mit.edu	37	3	131283152	131283152	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:131283152G>C	ENST00000512055.1	-	15	3095	c.969C>G	c.(967-969)aaC>aaG	p.N323K	CPNE4_ENST00000511604.1_Missense_Mutation_p.N323K|CPNE4_ENST00000502818.1_Missense_Mutation_p.N341K|CPNE4_ENST00000512332.1_Missense_Mutation_p.N341K|CPNE4_ENST00000429747.1_Missense_Mutation_p.N323K			Q96A23	CPNE4_HUMAN	copine IV	323	VWFA.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						AGGAACAGCTGTTCCTGGGGT	0.433																																						ENST00000512055.1	1.000000	0.810000	1	9.200000e-01	0.990000	0.972263	0.990000	1.000000																										0				39						c.(967-969)aaC>aaG		copine IV							114.0	109.0	111.0					3																	131283152		2203	4300	6503	SO:0001583	missense	131034	0	0					g.chr3:131283152G>C	H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"""copine 8"""	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.969C>G	chr3.hg19:g.131283152G>C	ENSP00000421705:p.Asn323Lys	1					CPNE4_ENST00000512332.1_Missense_Mutation_p.N341K|CPNE4_ENST00000429747.1_Missense_Mutation_p.N323K|CPNE4_ENST00000502818.1_Missense_Mutation_p.N341K|CPNE4_ENST00000511604.1_Missense_Mutation_p.N323K	p.N323K			1	3	4	2.284976	Q96A23	CPNE4_HUMAN		15	3095	-			D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	1	1	hg19	c.969C>G	CCDS3072.1	1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.243726	0.58995	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818	T;T;T;T;T	0.54071	0.6;0.6;0.59;0.6;0.59	5.52	4.65	0.58169	5.52	4.65	0.58169	von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	T	0.67173	0.2865	L	0.58510	1.815	0.80722	D	1	D;P	0.76494	0.999;0.81	D;B	0.74023	0.982;0.313	T	0.65994	-0.6033	10	0.35671	T	0.21	-36.7038	14.6356	0.68686	0.07:0.0:0.93:0.0	.	341;323	Q96A23-2;Q96A23	.;CPNE4_HUMAN	K	323;323;341;323;341	ENSP00000421705:N323K;ENSP00000411904:N323K;ENSP00000424853:N341K;ENSP00000423811:N323K;ENSP00000421646:N341K	ENSP00000411904:N323K	N	-	3	2	2	CPNE4	132765842	132765842	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.441000	0.66569	1.350000	0.45770	-0.221000	0.12465	AAC	0.707602		TCGA-IB-A7LX-01A-12D-A36O-08	0.433	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	1	0	1	2	2	2	2	0	0	0	0	80	80	80	79	1	3.150000	-20.000000	1	0.550000	NM_130808		0	65	64	0	287	282	1		1	0		0	0	80	0	0	1.000000	3.852143e-01	0	0	0	7	0	65	287
GK5	256356	broad.mit.edu	37	3	141900367	141900367	+	Silent	SNP	G	G	T	rs9866012	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:141900367G>T	ENST00000392993.2	-	11	1135	c.984C>A	c.(982-984)gtC>gtA	p.V328V		NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	328					glycerol catabolic process (GO:0019563)		ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			kidney(1)|large_intestine(1)|lung(7)|urinary_tract(1)	10						CTAAGCATACGACTTCTTGCC	0.383																																						ENST00000392993.2	0.380000	0.130000	3.000000e-01	1.800000e-01	0.230000	0.253288	0.230000	0.240000																										0				10						c.(982-984)gtC>gtA		glycerol kinase 5 (putative)							113.0	107.0	109.0					3																	141900367		2203	4300	6503	SO:0001819	synonymous_variant	256356	0	0					g.chr3:141900367G>T	BX648681	CCDS33871.1	3q23	2014-02-12	2006-09-21		ENSG00000175066	ENSG00000175066		"""Glycerol kinases"""	28635	protein-coding gene	gene with protein product						12477932	Standard	NM_001039547		Approved	MGC40579	uc003euq.2	Q6ZS86	OTTHUMG00000133572	ENST00000392993.2:c.984C>A	chr3.hg19:g.141900367G>T		1						p.V328V	NM_001039547.2	NP_001034636.1	1	3	4	2.284976	Q6ZS86	GLPK5_HUMAN		11	1135	-			B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Silent	SNP	ENST00000392993.2	1	0	hg19	c.984C>A	CCDS33871.1	0																																																																																								0.707602		TCGA-IB-A7LX-01A-12D-A36O-08	0.383	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	1	0	1	2	2	2	2	0	0	0	0	105	105	105	104	1	3.150000	-2.721274	1	0.550000	NM_001039547		0	18	17	0	412	403	0		1	0		0	0	105	0	0	0.999979	4.667193e-01	0	0	0	35	0	18	412
C3orf20	84077	broad.mit.edu	37	3	14769996	14769996	+	Silent	SNP	C	C	A	rs144350421	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:14769996C>A	ENST00000253697.3	+	12	2193	c.1741C>A	c.(1741-1743)Cgg>Agg	p.R581R	C3orf20_ENST00000435614.1_Silent_p.R459R|C3orf20_ENST00000412910.1_Silent_p.R459R	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	581						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						AGAATTTGTTCGGTTCAAGAT	0.463																																						ENST00000253697.3	1.000000	0.150000	4.200000e-01	2.100000e-01	0.280000	0.370845	0.280000	0.260000																										0				40						c.(1741-1743)Cgg>Agg		chromosome 3 open reading frame 20							83.0	82.0	83.0					3																	14769996		2203	4300	6503	SO:0001819	synonymous_variant	84077	0	0					g.chr3:14769996C>A	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.1741C>A	chr3.hg19:g.14769996C>A		1					C3orf20_ENST00000435614.1_Silent_p.R459R|C3orf20_ENST00000412910.1_Silent_p.R459R	p.R581R	NM_032137.4	NP_115513.4	1	2	3	1.822614	Q8ND61	CC020_HUMAN		12	2193	+			Q7L0U6|Q8NCP2|Q9H0I7	Silent	SNP	ENST00000253697.3	1	0	hg19	c.1741C>A	CCDS33706.1	0																																																																																								0.635258		TCGA-IB-A7LX-01A-12D-A36O-08	0.463	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	1	0	1	2	2	2	2	0	0	0	0	89	89	89	87	1	3.150000	-2.842149	1	0.550000	NM_032137		0	13	13	0	204	201	0		1			0	0	89	0	0	0.999542	0	0	0	0	0	0	13	204
ATR	545	broad.mit.edu	37	3	142188288	142188288	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:142188288C>A	ENST00000350721.4	-	38	6564	c.6443G>T	c.(6442-6444)cGa>cTa	p.R2148L	ATR_ENST00000383101.3_Missense_Mutation_p.R2084L|RP11-383G6.3_ENST00000460977.1_RNA	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2148	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R2148Q(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						ATGACAAATTCGAGAGATCAA	0.343								Other conserved DNA damage response genes																														ENST00000350721.4	0.400000	0.150000	3.200000e-01	2.000000e-01	0.250000	0.271826	0.250000	0.240000																										1	Substitution - Missense(1)	p.R2148Q(1)	lung(1)	122						c.(6442-6444)cGa>cTa	Other conserved DNA damage response genes	ATR serine/threonine kinase							131.0	138.0	136.0					3																	142188288		2203	4300	6503	SO:0001583	missense	545	0	0					g.chr3:142188288C>A	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.6443G>T	chr3.hg19:g.142188288C>A	ENSP00000343741:p.Arg2148Leu	1					RP11-383G6.3_ENST00000460977.1_RNA|ATR_ENST00000383101.3_Missense_Mutation_p.R2084L	p.R2148L	NM_001184.3	NP_001175.2	1	3	4	2.284976	Q13535	ATR_HUMAN		38	6564	-			Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	1	0	hg19	c.6443G>T	CCDS3124.1	0	.	.	.	.	.	.	.	.	.	.	C	29.5	5.009379	0.93346	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.15256	2.44;2.58	5.15	5.15	0.70609	5.15	5.15	0.70609	PIK-related kinase (1);	0.126462	0.52532	D	0.000080	T	0.25494	0.0620	M	0.71871	2.18	0.80722	D	1	B	0.30068	0.267	B	0.28991	0.097	T	0.07404	-1.0774	10	0.87932	D	0	-3.8171	18.5955	0.91228	0.0:1.0:0.0:0.0	.	2148	Q13535	ATR_HUMAN	L	2148;2084	ENSP00000343741:R2148L;ENSP00000372581:R2084L	ENSP00000343741:R2148L	R	-	2	0	0	ATR	143670978	143670978	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.805000	0.86005	2.378000	0.81104	0.591000	0.81541	CGA	0.707602		TCGA-IB-A7LX-01A-12D-A36O-08	0.343	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	1	0	1	2	2	2	2	0	0	0	0	118	118	118	118	1	3.150000	-4.388978	1	0.550000	NM_001184		0	22	22	0	462	461	0		1	0		0	0	118	0	0	0.999999	5.986506e-01	0	0	0	43	0	22	462
ERICH6	131831	broad.mit.edu	37	3	150391782	150391782	+	Missense_Mutation	SNP	T	T	G			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:150391782T>G	ENST00000295910.6	-	11	1356	c.1304A>C	c.(1303-1305)aAg>aCg	p.K435T	FAM194A_ENST00000491361.1_Missense_Mutation_p.K289T	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						AGTCAGAAACTTGCTCCCATG	0.333																																						ENST00000295910.6	0.920000	0.530000	8.000000e-01	6.100000e-01	0.700000	0.711508	0.700000	0.710000																										0				38						c.(1303-1305)aAg>aCg									155.0	150.0	151.0					3																	150391782		2203	4300	6503	SO:0001583	missense	0	0	0					g.chr3:150391782T>G																												ENST00000295910.6:c.1304A>C	chr3.hg19:g.150391782T>G	ENSP00000295910:p.Lys435Thr	1					FAM194A_ENST00000491361.1_Missense_Mutation_p.K289T	p.K435T	NM_152394.3	NP_689607.2	1	3	4	2.284976				11	1356	-				Missense_Mutation	SNP	ENST00000295910.6	1	1	hg19	c.1304A>C	CCDS3151.2	0	.	.	.	.	.	.	.	.	.	.	T	17.11	3.306745	0.60305	.	.	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.12984	2.63;2.63	4.94	4.94	0.65067	4.94	4.94	0.65067	.	0.220254	0.31461	N	0.007604	T	0.25457	0.0619	L	0.45228	1.405	0.30174	N	0.801058	D	0.76494	0.999	D	0.79784	0.993	T	0.05131	-1.0904	10	0.46703	T	0.11	-12.9558	8.3833	0.32486	0.0:0.0893:0.0:0.9107	.	435	Q7L0X2	F194A_HUMAN	T	435;289;393	ENSP00000295910:K435T;ENSP00000419366:K289T	ENSP00000295910:K435T	K	-	2	0	0	FAM194A	151874472	151874472	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.661000	0.54503	2.053000	0.61076	0.533000	0.62120	AAG	0.707602		TCGA-IB-A7LX-01A-12D-A36O-08	0.333	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1	0	0	1	2	2	2	2	0	0	0	0	114	114	114	111	1	3.150000	-20.000000	1	0.550000			0	53	52	0	371	363	1		1			0	0	114	0	0	1.000000	0	0	0	0	0	0	53	371
IFT80	57560	broad.mit.edu	37	3	159998536	159998536	+	Missense_Mutation	SNP	C	C	A	rs550922501		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:159998536C>A	ENST00000326448.7	-	15	2015	c.1583G>T	c.(1582-1584)cGa>cTa	p.R528L	RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.R699L|IFT80_ENST00000496589.1_Missense_Mutation_p.R391L|IFT80_ENST00000483465.1_Missense_Mutation_p.R391L	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	528					bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CACTATAAATCGAGTATCTTG	0.348																																						ENST00000326448.7	0.370000	0.110000	2.900000e-01	1.500000e-01	0.210000	0.231830	0.210000	0.200000																										0				36						c.(1582-1584)cGa>cTa		intraflagellar transport 80							127.0	113.0	117.0					3																	159998536		2203	4299	6502	SO:0001583	missense	57560	0	0					g.chr3:159998536C>A	AB037795	CCDS3188.1, CCDS54668.1	3q25.33	2014-07-03	2014-07-03	2005-11-02	ENSG00000068885	ENSG00000068885		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29262	protein-coding gene	gene with protein product		611177	"""WD repeat domain 56"", ""intraflagellar transport 80 homolog (Chlamydomonas)"""	WDR56		10718198	Standard	NM_020800		Approved	KIAA1374	uc021xgq.1	Q9P2H3	OTTHUMG00000158953	ENST00000326448.7:c.1583G>T	chr3.hg19:g.159998536C>A	ENSP00000312778:p.Arg528Leu	1					RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.R699L|IFT80_ENST00000496589.1_Missense_Mutation_p.R391L|IFT80_ENST00000483465.1_Missense_Mutation_p.R391L	p.R528L	NM_020800.2	NP_065851.1	1	3	4	2.284976	Q9P2H3	IFT80_HUMAN	Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)	15	2015	-			B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Missense_Mutation	SNP	ENST00000326448.7	1	0	hg19	c.1583G>T	CCDS3188.1	0	.	.	.	.	.	.	.	.	.	.	C	15.47	2.843076	0.51057	.	.	ENSG00000068885	ENST00000326448;ENST00000483465;ENST00000496589	T;T;T	0.70164	2.32;-0.46;-0.46	5.59	5.59	0.84812	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.281880	0.24645	U	0.036780	T	0.64283	0.2584	M	0.65975	2.015	0.47659	D	0.999489	B	0.09022	0.002	B	0.06405	0.002	T	0.59511	-0.7441	10	0.33940	T	0.23	.	13.3036	0.60338	0.0:0.9182:0.0:0.0818	.	528	Q9P2H3	IFT80_HUMAN	L	528;391;391	ENSP00000312778:R528L;ENSP00000418196:R391L;ENSP00000420646:R391L	ENSP00000312778:R528L	R	-	2	0	0	IFT80	161481230	161481230	0.960000	0.32886	0.970000	0.41538	0.974000	0.67602	1.262000	0.32992	2.635000	0.89317	0.460000	0.39030	CGA	0.707602		TCGA-IB-A7LX-01A-12D-A36O-08	0.348	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	1	0	1	2	2	2	2	0	0	0	0	80	80	80	80	1	3.150000	-3.096837	1	0.550000	NM_020800		0	13	13	0	334	330	0		1	0		0	0	80	0	0	0.999521	5.624329e-01	0	0	0	48	0	13	334
SMC4	10051	broad.mit.edu	37	3	160132228	160132228	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:160132228C>A	ENST00000357388.3	+	9	1646	c.1195C>A	c.(1195-1197)Caa>Aaa	p.Q399K	SMC4_ENST00000462787.1_Missense_Mutation_p.Q399K|SMC4_ENST00000344722.5_Missense_Mutation_p.Q399K|SMC4_ENST00000469762.1_Missense_Mutation_p.Q374K|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000360111.2_Missense_Mutation_p.Q399K	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	399					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GGAAGATGTTCAAGTTAGAGA	0.289																																						ENST00000357388.3	0.380000	0.120000	3.000000e-01	1.700000e-01	0.230000	0.245974	0.230000	0.230000																										0				48						c.(1195-1197)Caa>Aaa		structural maintenance of chromosomes 4							39.0	40.0	39.0					3																	160132228		2203	4298	6501	SO:0001583	missense	10051	0	0					g.chr3:160132228C>A	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"""Structural maintenance of chromosomes proteins"""	14013	protein-coding gene	gene with protein product		605575	"""SMC4 (structural maintenance of chromosomes 4, yeast)-like 1"", ""SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"""	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.1195C>A	chr3.hg19:g.160132228C>A	ENSP00000349961:p.Gln399Lys	1					SMC4_ENST00000462787.1_Missense_Mutation_p.Q399K|SMC4_ENST00000469762.1_Missense_Mutation_p.Q374K|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000344722.5_Missense_Mutation_p.Q399K|SMC4_ENST00000360111.2_Missense_Mutation_p.Q399K	p.Q399K	NM_001002800.1	NP_001002800.1	1	3	4	2.284976	Q9NTJ3	SMC4_HUMAN	Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)	9	1646	+			A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Missense_Mutation	SNP	ENST00000357388.3	1	0	hg19	c.1195C>A	CCDS3189.1	0	.	.	.	.	.	.	.	.	.	.	C	6.676	0.493216	0.12702	.	.	ENSG00000113810	ENST00000357388;ENST00000360111;ENST00000392788;ENST00000469762;ENST00000489573;ENST00000462787;ENST00000344722	T;T;T;T;T;T	0.73152	-0.69;-0.72;-0.7;0.41;-0.72;-0.69	5.49	5.49	0.81192	5.49	5.49	0.81192	RecF/RecN/SMC (1);	0.163089	0.53938	D	0.000045	T	0.41282	0.1152	N	0.02765	-0.5	0.35709	D	0.816222	B;B;B;B	0.12013	0.0;0.001;0.0;0.005	B;B;B;B	0.14023	0.002;0.002;0.001;0.01	T	0.48399	-0.9039	10	0.05833	T	0.94	-13.6609	10.8952	0.47019	0.1516:0.7182:0.1301:0.0	.	399;374;374;399	Q9NTJ3-2;B3KXX5;E9PD53;Q9NTJ3	.;.;.;SMC4_HUMAN	K	399;399;399;374;399;399;399	ENSP00000349961:Q399K;ENSP00000353225:Q399K;ENSP00000417964:Q374K;ENSP00000420121:Q399K;ENSP00000420734:Q399K;ENSP00000341382:Q399K	ENSP00000341382:Q399K	Q	+	1	0	0	SMC4	161614922	161614922	1.000000	0.71417	1.000000	0.80357	0.487000	0.33371	3.146000	0.50631	2.583000	0.87209	0.650000	0.86243	CAA	0.707602		TCGA-IB-A7LX-01A-12D-A36O-08	0.289	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1	1	0	1	2	2	2	2	0	0	0	0	84	84	84	84	1	3.150000	-3.221883	1	0.550000			0	15	15	0	358	353	0		1	0		0	0	84	0	0	0.999866	7.318526e-01	0	0	0	63	0	15	358
MFN1	55669	broad.mit.edu	37	3	179069714	179069714	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:179069714C>A	ENST00000471841.1	+	3	265	c.139C>A	c.(139-141)Cga>Aga	p.R47R	MFN1_ENST00000263969.5_Silent_p.R47R|MFN1_ENST00000280653.7_Silent_p.R47R	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	47					mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R47*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			GGAACTTGATCGAATAGCCAC	0.353																																						ENST00000471841.1	0.330000	0.110000	2.600000e-01	1.500000e-01	0.200000	0.220622	0.200000	0.200000																										1	Substitution - Nonsense(1)	p.R47*(1)	large_intestine(1)	31						c.(139-141)Cga>Aga		mitofusin 1							117.0	114.0	115.0					3																	179069714		2203	4300	6503	SO:0001819	synonymous_variant	55669	0	0					g.chr3:179069714C>A	AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.139C>A	chr3.hg19:g.179069714C>A		1					MFN1_ENST00000263969.5_Silent_p.R47R|MFN1_ENST00000280653.7_Silent_p.R47R	p.R47R	NM_033540.2	NP_284941	1	3	4	2.284976	Q8IWA4	MFN1_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)	3	265	+	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Silent	SNP	ENST00000471841.1	1	0	hg19	c.139C>A	CCDS3228.1	0																																																																																								0.707602		TCGA-IB-A7LX-01A-12D-A36O-08	0.353	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	1	0	1	2	2	2	2	0	0	0	0	117	117	117	117	1	3.150000	-3.302474	1	0.550000	NM_017927		0	18	18	0	479	470	0		1	0		0	0	117	0	0	0.999979	6.098508e-01	0	0	0	54	0	18	479
ACTL6A	86	broad.mit.edu	37	3	179291168	179291168	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:179291168G>A	ENST00000429709.2	+	4	502	c.289G>A	c.(289-291)Gat>Aat	p.D97N	ACTL6A_ENST00000392662.1_Missense_Mutation_p.D55N|ACTL6A_ENST00000450518.2_Missense_Mutation_p.D55N	NM_004301.3	NP_004292.1	O96019	ACL6A_HUMAN	actin-like 6A	97					ATP-dependent chromatin remodeling (GO:0043044)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|nervous system development (GO:0007399)|neural retina development (GO:0003407)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|npBAF complex (GO:0071564)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	21	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			TGAAGACTGGGATAGTTTCCA	0.353																																						ENST00000429709.2	0.210000	0.050000	1.600000e-01	8.000000e-02	0.110000	0.134363	0.110000	0.120000																										0				21						c.(289-291)Gat>Aat		actin-like 6A							87.0	86.0	86.0					3																	179291168		2203	4300	6503	SO:0001583	missense	86	1	121412	27				g.chr3:179291168G>A	AK098691	CCDS3231.1, CCDS43174.1	3q26.33	2011-07-06			ENSG00000136518	ENSG00000136518		"""INO80 complex subunits"""	24124	protein-coding gene	gene with protein product	"""BAF complex 53 kDa subunit"", ""BRG1-associated factor"", ""actin-related protein 4"", ""INO80 complex subunit K"""	604958				9845365, 10380635	Standard	NM_004301		Approved	Actl6, BAF53A, Arp4, Baf53a, INO80K	uc003fjw.3	O96019	OTTHUMG00000157782	ENST00000429709.2:c.289G>A	chr3.hg19:g.179291168G>A	ENSP00000397552:p.Asp97Asn	1					ACTL6A_ENST00000392662.1_Missense_Mutation_p.D55N|ACTL6A_ENST00000450518.2_Missense_Mutation_p.D55N	p.D97N	NM_004301.3	NP_004292.1	1	3	4	2.284976	O96019	ACL6A_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)	4	502	+	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		B3KMN1|D3DNR9|Q8TAE5|Q9BVS8|Q9H0W6	Missense_Mutation	SNP	ENST00000429709.2	0	1	hg19	c.289G>A	CCDS3231.1	0	.	.	.	.	.	.	.	.	.	.	G	34	5.398826	0.96030	.	.	ENSG00000136518	ENST00000429709;ENST00000450518;ENST00000392662	D;D;D	0.95853	-3.83;-3.83;-3.83	5.28	5.28	0.74379	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.96439	0.8838	M	0.64260	1.97	0.80722	D	1	D	0.52996	0.957	P	0.53954	0.738	D	0.96821	0.9604	10	0.87932	D	0	.	19.2768	0.94034	0.0:0.0:1.0:0.0	.	97	O96019	ACL6A_HUMAN	N	97;55;55	ENSP00000397552:D97N;ENSP00000394014:D55N;ENSP00000376430:D55N	ENSP00000376430:D55N	D	+	1	0	0	ACTL6A	180773862	180773862	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.686000	0.98664	2.625000	0.88918	0.555000	0.69702	GAT	0.707602		TCGA-IB-A7LX-01A-12D-A36O-08	0.353	ACTL6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349599.1	0	0	0	2	2	2	2	0	0	0	0	144	144	144	143	1	3.150000	-3.068190	1	0.550000	NM_004301		0	13	13	0	607	593	0		1	1		0	0	144	0	0	0.999457	8.162320e-01	0	4	0	144	0	13	607
MCF2L2	23101	broad.mit.edu	37	3	182923997	182923997	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:182923997C>A	ENST00000328913.3	-	24	3015	c.2718G>T	c.(2716-2718)atG>atT	p.M906I	MCF2L2_ENST00000468976.1_5'UTR|MCF2L2_ENST00000473233.1_Missense_Mutation_p.M906I	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	906	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TTGAAAGTGTCATCAGCTATT	0.408																																						ENST00000328913.3	0.390000	0.130000	3.100000e-01	1.800000e-01	0.230000	0.254224	0.230000	0.240000																										0				72						c.(2716-2718)atG>atT		MCF.2 cell line derived transforming sequence-like 2							121.0	110.0	113.0					3																	182923997		2203	4300	6503	SO:0001583	missense	23101	0	0					g.chr3:182923997C>A	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"""Rho guanine nucleotide exchange factors"""	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.2718G>T	chr3.hg19:g.182923997C>A	ENSP00000328118:p.Met906Ile	1					MCF2L2_ENST00000468976.1_5'UTR|MCF2L2_ENST00000473233.1_Missense_Mutation_p.M906I	p.M906I	NM_015078.2	NP_055893	1	3	4	2.284976	Q86YR7	MF2L2_HUMAN	all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)	24	3015	-	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	1	0	hg19	c.2718G>T	CCDS3243.1	0	.	.	.	.	.	.	.	.	.	.	C	4.420	0.077657	0.08485	.	.	ENSG00000053524	ENST00000328913;ENST00000473233	T;T	0.11063	2.81;2.81	4.28	1.25	0.21368	4.28	1.25	0.21368	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	1.050980	0.07506	N	0.908130	T	0.08179	0.0204	L	0.29908	0.895	0.20975	N	0.999815	B	0.06786	0.001	B	0.04013	0.001	T	0.38112	-0.9676	10	0.56958	D	0.05	.	3.9497	0.09363	0.0:0.5782:0.1998:0.222	.	906	Q86YR7	MF2L2_HUMAN	I	906	ENSP00000328118:M906I;ENSP00000420070:M906I	ENSP00000328118:M906I	M	-	3	0	0	MCF2L2	184406691	184406691	0.023000	0.18921	0.360000	0.25837	0.118000	0.20060	0.077000	0.14738	0.553000	0.29044	0.563000	0.77884	ATG	0.707602		TCGA-IB-A7LX-01A-12D-A36O-08	0.408	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	1	0	1	2	2	2	2	0	0	0	0	79	79	79	79	1	3.150000	-4.050431	1	0.550000	NM_015078		0	16	16	0	367	362	0		1			0	0	79	0	0	0.999930	0	0	0	0	0	0	16	367
TP63	8626	broad.mit.edu	37	3	189612250	189612250	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:189612250C>A	ENST00000264731.3	+	14	2091	c.2002C>A	c.(2002-2004)Cgc>Agc	p.R668S	TP63_ENST00000354600.5_Missense_Mutation_p.R574S|TP63_ENST00000440651.2_Missense_Mutation_p.R664S|TP63_ENST00000449992.1_Missense_Mutation_p.R489S|TP63_ENST00000456148.1_Missense_Mutation_p.R570S|TP63_ENST00000382063.4_Missense_Mutation_p.R583S|TP63_ENST00000320472.5_3'UTR	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63	668	Transactivation inhibition.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		CATGGATGCTCGCCGCAATAA	0.542										HNSCC(45;0.13)																												ENST00000264731.3	0.460000	0.140000	3.600000e-01	2.000000e-01	0.270000	0.288450	0.270000	0.270000																										0				61						c.(2002-2004)Cgc>Agc		tumor protein p63							79.0	74.0	76.0					3																	189612250		2203	4300	6503	SO:0001583	missense	8626	0	0					g.chr3:189612250C>A	AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282			15979	protein-coding gene	gene with protein product		603273	"""tumor protein p73-like"", ""tumor protein p53-like"", ""tumor protein p53-competing protein"""	TP73L, TP53L, TP53CP		9774969, 9662378, 11181441, 11181451	Standard	NM_003722		Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000264731.3:c.2002C>A	chr3.hg19:g.189612250C>A	ENSP00000264731:p.Arg668Ser	1	HNSCC(45;0.13)				TP63_ENST00000440651.2_Missense_Mutation_p.R664S|TP63_ENST00000449992.1_Missense_Mutation_p.R489S|TP63_ENST00000456148.1_Missense_Mutation_p.R570S|TP63_ENST00000382063.4_Missense_Mutation_p.R583S|TP63_ENST00000320472.5_3'UTR|TP63_ENST00000354600.5_Missense_Mutation_p.R574S	p.R668S	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	1	3	4	2.284976	Q9H3D4	P63_HUMAN	Lung(62;3.33e-05)	14	2091	+	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	Missense_Mutation	SNP	ENST00000264731.3	1	0	hg19	c.2002C>A	CCDS3293.1	0	.	.	.	.	.	.	.	.	.	.	C	16.73	3.202877	0.58234	.	.	ENSG00000073282	ENST00000264731;ENST00000440651;ENST00000382063;ENST00000354600;ENST00000449992;ENST00000456148	D;D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62;-2.62;-2.62	5.91	5.91	0.95273	5.91	5.91	0.95273	.	0.108147	0.64402	D	0.000006	D	0.84701	0.5530	N	0.19112	0.55	0.80722	D	1	B;B;B	0.18968	0.028;0.028;0.032	B;B;B	0.20955	0.032;0.032;0.026	T	0.78620	-0.2133	9	.	.	.	-11.7075	19.2867	0.94077	0.0:1.0:0.0:0.0	.	489;574;668	Q9H3D4-10;Q9H3D4-2;Q9H3D4	.;.;P63_HUMAN	S	668;664;583;574;489;570	ENSP00000264731:R668S;ENSP00000394337:R664S;ENSP00000371495:R583S;ENSP00000346614:R574S;ENSP00000387839:R489S;ENSP00000389485:R570S	.	R	+	1	0	0	TP63	191094944	191094944	1.000000	0.71417	0.990000	0.47175	0.746000	0.42486	5.598000	0.67585	2.793000	0.96121	0.655000	0.94253	CGC	0.707602		TCGA-IB-A7LX-01A-12D-A36O-08	0.542	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	1	0	1	2	2	2	2	0	0	0	0	59	59	59	58	1	3.150000	-3.094281	1	0.550000	NM_003722		0	13	13	0	263	254	0		1	0		0	0	59	0	0	0.999462	1.400073e-01	0	0	0	13	0	13	263
JAGN1	84522	broad.mit.edu	37	3	9934901	9934901	+	Missense_Mutation	SNP	G	G	A	rs542419840		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:9934901G>A	ENST00000307768.4	+	2	561	c.392G>A	c.(391-393)cGc>cAc	p.R131H		NM_032492.3	NP_115881.3			jagunal homolog 1 (Drosophila)											breast(1)|central_nervous_system(1)|endometrium(4)|lung(3)|ovary(1)	10	Medulloblastoma(99;0.227)					CAGCTCTACCGCCATGGCAAG	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		22334	0.0		0.0	False		,,,				2504	0.001					ENST00000307768.4	1.000000	0.100000	2.700000e-01	1.400000e-01	0.180000	0.284895	0.180000	0.170000																										0				10						c.(391-393)cGc>cAc		jagunal homolog 1 (Drosophila)							239.0	150.0	180.0					3																	9934901		2203	4300	6503	SO:0001583	missense	84522	8	121412	40				g.chr3:9934901G>A	AK074760	CCDS2588.1	3p25.2	2010-03-23			ENSG00000171135	ENSG00000171135			26926	protein-coding gene	gene with protein product						12477932	Standard	NM_032492		Approved	GL009, FLJ14602	uc003btt.4	Q8N5M9	OTTHUMG00000128523	ENST00000307768.4:c.392G>A	chr3.hg19:g.9934901G>A	ENSP00000306106:p.Arg131His	1						p.R131H	NM_032492.3	NP_115881.3	1	2	3	1.822614				2	561	+	Medulloblastoma(99;0.227)			Missense_Mutation	SNP	ENST00000307768.4	1	1	hg19	c.392G>A	CCDS2588.1	0	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.014448|4.014448	0.75161|0.75161	.|.	.|.	ENSG00000171135|ENSG00000171135	ENST00000543379|ENST00000307768	.|.	.|.	.|.	5.73|5.73	3.76|3.76	0.43208|0.43208	5.73|5.73	3.76|3.76	0.43208|0.43208	.|.	.|0.054409	.|0.64402	.|D	.|0.000001	T|T	0.74099|0.74099	0.3672|0.3672	M|M	0.84082|0.84082	2.675|2.675	0.53005|0.53005	D|D	0.999963|0.999963	.|D	.|0.63880	.|0.993	.|P	.|0.55713	.|0.782	T|T	0.78671|0.78671	-0.2113|-0.2113	6|9	0.13853|0.66056	T|D	0.58|0.02	-22.0269|-22.0269	11.9619|11.9619	0.53013|0.53013	0.071:0.0:0.7989:0.13|0.071:0.0:0.7989:0.13	.|.	.|131	.|Q8N5M9	.|JAGN1_HUMAN	T|H	130|131	.|.	ENSP00000442889:A130T|ENSP00000306106:R131H	A|R	+|+	1|2	0|0	0|0	JAGN1|JAGN1	9909901|9909901	9909901|9909901	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.933000|0.933000	0.57130|0.57130	7.496000|7.496000	0.81526|0.81526	1.434000|1.434000	0.47414|0.47414	-0.339000|-0.339000	0.08088|0.08088	GCC|CGC	0.635258		TCGA-IB-A7LX-01A-12D-A36O-08	0.527	JAGN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250335.1	0	0	1	2	12	11	2	1	1	1	1	130	130	130	130	1	3.150000	-3.461198	1	0.550000	NM_032492		0	16	16	0	386	379	0		1	1		1	0	130	0	0	0.817874	7.515957e-01	0	17	0	317	0	16	386
RPL35A	6165	broad.mit.edu	37	3	197680900	197680900	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr3:197680900C>A	ENST00000464167.1	+	4	458	c.191C>A	c.(190-192)cCa>cAa	p.P64Q	RPL35A_ENST00000329092.8_3'UTR|RPL35A_ENST00000448864.1_Missense_Mutation_p.P64Q|IQCG_ENST00000480302.1_Intron|IQCG_ENST00000265239.6_Intron	NM_000996.2	NP_000987.2	P18077	RL35A_HUMAN	ribosomal protein L35a	64					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)|tRNA binding (GO:0000049)			lung(1)|prostate(1)|urinary_tract(1)	3	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;1.04e-23)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.182)		GGCGGCAAACCAAACAAAACC	0.453																																						ENST00000464167.1	0.410000	0.090000	3.000000e-01	1.400000e-01	0.210000	0.232034	0.210000	0.200000																										0				3						c.(190-192)cCa>cAa		ribosomal protein L35a							62.0	63.0	63.0					3																	197680900		2203	4300	6503	SO:0001583	missense	6165	0	0					g.chr3:197680900C>A	X52966	CCDS33930.1	3q29	2011-04-06			ENSG00000182899	ENSG00000182899		"""L ribosomal proteins"""	10345	protein-coding gene	gene with protein product		180468				1577483, 8786106	Standard	NM_000996		Approved	L35A	uc003fyr.3	P18077	OTTHUMG00000155386	ENST00000464167.1:c.191C>A	chr3.hg19:g.197680900C>A	ENSP00000419117:p.Pro64Gln	1					RPL35A_ENST00000329092.8_3'UTR|IQCG_ENST00000480302.1_Intron|IQCG_ENST00000265239.6_Intron|RPL35A_ENST00000448864.1_Missense_Mutation_p.P64Q	p.P64Q	NM_000996.2	NP_000987.2	1	3	4	2.284976	P18077	RL35A_HUMAN	Epithelial(36;1.04e-23)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	4	458	+	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Q08ES9|Q9BVN7	Missense_Mutation	SNP	ENST00000464167.1	1	0	hg19	c.191C>A	CCDS33930.1	0	.	.	.	.	.	.	.	.	.	.	C	16.31	3.087892	0.55968	.	.	ENSG00000182899	ENST00000464167;ENST00000448864;ENST00000442341	.	.	.	5.35	5.35	0.76521	5.35	5.35	0.76521	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	T	0.71367	0.3331	M	0.80616	2.505	0.80722	D	1	B	0.12630	0.006	B	0.24269	0.052	T	0.67906	-0.5549	9	0.31617	T	0.26	-21.202	19.1227	0.93369	0.0:1.0:0.0:0.0	.	64	P18077	RL35A_HUMAN	Q	64	.	ENSP00000387688:P64Q	P	+	2	0	0	RPL35A	199165297	199165297	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	7.755000	0.85180	2.530000	0.85305	0.558000	0.71614	CCA	0.707602		TCGA-IB-A7LX-01A-12D-A36O-08	0.453	RPL35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339788.1	1	0	0	2	2	2	2	0	0	0	0	45	45	45	44	1	3.150000	-3.079547	1	0.550000	NM_000996		0	8	8	0	214	215	0		1	1		0	0	45	0	0	0.989940	1	0	3	0	7282	0	8	214
SPATA5	166378	broad.mit.edu	37	4	123859326	123859326	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:123859326G>T	ENST00000274008.4	+	8	1449	c.1380G>T	c.(1378-1380)ccG>ccT	p.P460P	SPATA5_ENST00000422835.2_3'UTR	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	460					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						CACTTTGTCCGAAAAGAGAGG	0.353																																						ENST00000274008.4	1.000000	0.080000	1	1.200000e-01	0.170000	0.309474	0.170000	0.160000																										0				24						c.(1378-1380)ccG>ccT		spermatogenesis associated 5							145.0	145.0	145.0					4																	123859326		2203	4300	6503	SO:0001819	synonymous_variant	166378	0	0					g.chr4:123859326G>T	AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"""ATPases / AAA-type"""	18119	protein-coding gene	gene with protein product	"""ATPase family gene 2 homolog (S. cerevisiae)"""	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.1380G>T	chr4.hg19:g.123859326G>T		1					SPATA5_ENST00000422835.2_3'UTR	p.P460P	NM_145207.2	NP_660208.2	2	3	5	1.795702	Q8NB90	SPAT5_HUMAN		8	1449	+			C9JT97|Q86XW1|Q8NI20|Q8TDL7	Silent	SNP	ENST00000274008.4	1	0	hg19	c.1380G>T	CCDS3730.1	0																																																																																								0.621769		TCGA-IB-A7LX-01A-12D-A36O-08	0.353	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256714.2	1	0	1	2	2	2	2	0	0	0	0	116	116	116	114	1	3.150000	-3.056472	1	0.550000	NM_145207		0	14	14	0	367	362	0		1	0		0	0	116	0	0	0.999743	1.492716e-02	0	0	0	5	0	14	367
FAT4	79633	broad.mit.edu	37	4	126411862	126411862	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:126411862G>A	ENST00000394329.3	+	17	13898	c.13885G>A	c.(13885-13887)Gcc>Acc	p.A4629T	FAT4_ENST00000335110.5_Missense_Mutation_p.A2870T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4629					branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CAGCAGCATCGCCCCTTCGGA	0.512																																						ENST00000394329.3	1.000000	0.150000	1	2.100000e-01	0.300000	0.413185	0.300000	0.270000																										0				355						c.(13885-13887)Gcc>Acc		FAT atypical cadherin 4							75.0	73.0	74.0					4																	126411862		2203	4300	6503	SO:0001583	missense	79633	1	121412	29				g.chr4:126411862G>A	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.13885G>A	chr4.hg19:g.126411862G>A	ENSP00000377862:p.Ala4629Thr	1					FAT4_ENST00000335110.5_Missense_Mutation_p.A2870T	p.A4629T	NM_024582.4	NP_078858.4	2	3	5	1.795702	Q6V0I7	FAT4_HUMAN		17	13898	+			A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	1	1	hg19	c.13885G>A	CCDS3732.3	0	.	.	.	.	.	.	.	.	.	.	G	17.86	3.493760	0.64186	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	D;D	0.91945	-2.94;-2.39	4.95	4.95	0.65309	4.95	4.95	0.65309	.	0.000000	0.34110	U	0.004241	D	0.94807	0.8323	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.995;0.998	D	0.94547	0.7750	10	0.45353	T	0.12	.	17.186	0.86867	0.0:0.0:1.0:0.0	.	2870;4629;4628	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	T	4629;2870	ENSP00000377862:A4629T;ENSP00000335169:A2870T	ENSP00000335169:A2870T	A	+	1	0	0	FAT4	126631312	126631312	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	9.440000	0.97547	2.275000	0.75901	0.561000	0.74099	GCC	0.621769		TCGA-IB-A7LX-01A-12D-A36O-08	0.512	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	1	0	1	2	2	2	2	0	0	0	0	64	64	64	64	1	3.150000	-3.318043	1	0.550000	NM_024582		0	11	11	0	163	163	0		1	0		0	0	64	0	0	0.998503	4.268310e-02	0	0	0	5	0	11	163
NOP14	8602	broad.mit.edu	37	4	2958537	2958537	+	Splice_Site	SNP	C	C	A	rs536498261		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:2958537C>A	ENST00000314262.6	-	3	380	c.332G>T	c.(331-333)cGa>cTa	p.R111L	NOP14-AS1_ENST00000503709.1_RNA|NOP14_ENST00000398071.4_Splice_Site_p.R111L|NOP14_ENST00000502735.1_Splice_Site_p.R111L|NOP14_ENST00000416614.2_Splice_Site_p.R111L	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	111					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						CTCATGATGTCGCTGACAGAA	0.313																																						ENST00000314262.6	1.000000	0.110000	1	1.700000e-01	0.270000	0.422119	0.270000	0.230000																										0				30						c.(331-333)cGa>cTa		NOP14 nucleolar protein							80.0	76.0	77.0					4																	2958537		2203	4300	6503	SO:0001630	splice_region_variant	8602	0	0					g.chr4:2958537C>A	AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"""NOP14 homolog (S. cerevisiae)"""	611526	"""chromosome 4 open reading frame 9"", ""nucleolar protein 14"", ""nucleolar protein 14 homolog (yeast)"", ""NOP14 nucleolar protein homolog (yeast)"""	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.331-1G>T	chr4.hg19:g.2958537C>A		1					NOP14_ENST00000416614.2_Splice_Site_p.R111L|NOP14_ENST00000398071.4_Splice_Site_p.R111L|NOP14_ENST00000502735.1_Splice_Site_p.R111L|NOP14-AS1_ENST00000503709.1_RNA	p.R111L	NM_003703.1	NP_003694.1	1	3	4	2.081941	P78316	NOP14_HUMAN		3	380	-			D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Splice_Site	SNP	ENST00000314262.6	1	0	hg19	c.332G>T	CCDS33945.1	0	.	.	.	.	.	.	.	.	.	.	C	19.99	3.927925	0.73327	.	.	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137	T;T;T;T	0.35973	1.28;1.28;1.28;1.28	5.41	4.53	0.55603	5.41	4.53	0.55603	.	0.227351	0.39615	N	0.001308	T	0.54481	0.1861	M	0.80982	2.52	0.80722	D	1	P;P	0.51057	0.897;0.941	P;P	0.61658	0.892;0.856	T	0.57682	-0.7769	10	0.87932	D	0	-6.5327	6.3695	0.21473	0.0:0.6616:0.0:0.3384	.	111;111	E9PFK5;P78316	.;NOP14_HUMAN	L	111;111;111;111;10	ENSP00000405068:R111L;ENSP00000315674:R111L;ENSP00000427415:R111L;ENSP00000381146:R111L	ENSP00000315674:R111L	R	-	2	0	0	NOP14	2928335	2928335	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.917000	0.48821	1.199000	0.43173	0.655000	0.94253	CGA	0.664430		TCGA-IB-A7LX-01A-12D-A36O-08	0.313	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	1	0	1	2	2	2	2	0	0	0	0	46	46	46	45	1	3.150000	-10.603720	1	0.550000	NM_003703	Missense_Mutation	0	8	8	0	164	162	0		1	0		0	0	46	0	0	0.989394	7.497036e-01	0	0	0	56	0	8	164
GPR125	166647	broad.mit.edu	37	4	22389706	22389706	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:22389706C>A	ENST00000334304.5	-	19	3857	c.3588G>T	c.(3586-3588)acG>acT	p.T1196T	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	1196					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				CTTCCACGCTCGTTGGGACAT	0.517																																						ENST00000334304.5	1.000000	0.140000	1	1.800000e-01	0.230000	0.402285	0.230000	0.220000																										0				56						c.(3586-3588)acG>acT		G protein-coupled receptor 125							95.0	88.0	91.0					4																	22389706		2203	4300	6503	SO:0001819	synonymous_variant	166647	0	0					g.chr4:22389706C>A	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"""	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.3588G>T	chr4.hg19:g.22389706C>A		1					GPR125_ENST00000282943.5_5'UTR	p.T1196T	NM_145290.3	NP_660333.2	1	3	4	2.081941	Q8IWK6	GP125_HUMAN		19	3857	-		Breast(46;0.198)	Q6UXK9|Q86SQ5|Q8TC55	Silent	SNP	ENST00000334304.5	1	0	hg19	c.3588G>T	CCDS33964.1	0																																																																																								0.664430		TCGA-IB-A7LX-01A-12D-A36O-08	0.517	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3	1	0	1	2	2	2	2	0	0	0	0	188	188	188	185	1	3.150000	-2.774725	1	0.550000			0	25	25	0	534	528	0		1	0		0	0	188	0	0	1.000000	9.846938e-01	0	0	0	144	0	25	534
TBC1D1	23216	broad.mit.edu	37	4	38134830	38134830	+	Silent	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:38134830C>T	ENST00000261439.4	+	19	3613	c.3258C>T	c.(3256-3258)acC>acT	p.T1086T	TBC1D1_ENST00000407365.1_3'UTR|TBC1D1_ENST00000508802.1_Silent_p.T1077T	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	1086					membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						TAGAGAAAACCAACAGCAGCT	0.393																																						ENST00000261439.4	1.000000	0.160000	1	2.100000e-01	0.290000	0.427790	0.290000	0.260000																										0				36						c.(3256-3258)acC>acT		TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1							111.0	103.0	106.0					4																	38134830		2203	4300	6503	SO:0001819	synonymous_variant	23216	1	121412	28				g.chr4:38134830C>T	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.3258C>T	chr4.hg19:g.38134830C>T		1					TBC1D1_ENST00000508802.1_Silent_p.T1077T|TBC1D1_ENST00000407365.1_3'UTR	p.T1086T	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	2	2	4	1.763541	Q86TI0	TBCD1_HUMAN		19	3613	+			B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Silent	SNP	ENST00000261439.4	1	1	hg19	c.3258C>T	CCDS33972.1	0	.	.	.	.	.	.	.	.	.	.	C	9.867	1.197786	0.22037	.	.	ENSG00000065882	ENST00000510573	.	.	.	4.97	4.13	0.48395	4.97	4.13	0.48395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-27.4575	6.939	0.24483	0.2837:0.6293:0.0:0.087	.	.	.	.	X	774	.	.	Q	+	1	0	0	TBC1D1	37811225	37811225	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.306000	0.43673	1.445000	0.47624	0.655000	0.94253	CAA	0.613734		TCGA-IB-A7LX-01A-12D-A36O-08	0.393	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	0	0	0	2	2	2	2	0	0	0	0	81	81	81	81	1	3.150000	-3.017629	1	0.550000	NM_015173		0	15	15	0	222	220	0		1	1		0	0	81	0	0	0.999880	9.802797e-01	0	9	0	91	0	15	222
FRYL	285527	broad.mit.edu	37	4	48584630	48584630	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:48584630G>T	ENST00000503238.1	-	17	1869	c.1870C>A	c.(1870-1872)Cgt>Agt	p.R624S	FRYL_ENST00000537810.1_Missense_Mutation_p.R624S|FRYL_ENST00000358350.4_Missense_Mutation_p.R624S|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000506685.1_Missense_Mutation_p.R330S|FRYL_ENST00000507711.1_Missense_Mutation_p.R624S			O94915	FRYL_HUMAN	FRY-like	624					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						GTCACTTCACGAACAATAAAA	0.398																																						ENST00000503238.1	1.000000	0.090000	1	1.300000e-01	0.200000	0.357415	0.200000	0.180000																										0				91						c.(1870-1872)Cgt>Agt		FRY-like							122.0	112.0	115.0					4																	48584630		1864	4101	5965	SO:0001583	missense	285527	0	0					g.chr4:48584630G>T	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"""KIAA0826"", ""furry homolog-like (Drosophila)"""	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.1870C>A	chr4.hg19:g.48584630G>T	ENSP00000426064:p.Arg624Ser	1					FRYL_ENST00000506685.1_Missense_Mutation_p.R330S|FRYL_ENST00000507711.1_Missense_Mutation_p.R624S|FRYL_ENST00000537810.1_Missense_Mutation_p.R624S|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Missense_Mutation_p.R624S	p.R624S			2	2	4	1.763541	O94915	FRYL_HUMAN		17	1869	-			O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	1	0	hg19	c.1870C>A	CCDS43227.1	0	.	.	.	.	.	.	.	.	.	.	G	16.54	3.151439	0.57151	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711;ENST00000506685	T;T;T;T;T	0.64260	3.64;3.64;3.64;3.64;-0.09	5.63	5.63	0.86233	5.63	5.63	0.86233	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	U	0.000001	T	0.75459	0.3852	L	0.51422	1.61	0.80722	D	1	D;P	0.64830	0.994;0.869	D;P	0.74023	0.982;0.724	T	0.70872	-0.4754	10	0.34782	T	0.22	.	20.0499	0.97621	0.0:0.0:1.0:0.0	.	624;624	F2Z2S2;O94915	.;FRYL_HUMAN	S	624;624;624;624;330	ENSP00000426064:R624S;ENSP00000351113:R624S;ENSP00000441114:R624S;ENSP00000421584:R624S;ENSP00000425592:R330S	ENSP00000351113:R624S	R	-	1	0	0	FRYL	48279387	48279387	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.926000	0.63433	2.798000	0.96311	0.655000	0.94253	CGT	0.613734		TCGA-IB-A7LX-01A-12D-A36O-08	0.398	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2	1	0	1	2	2	2	2	0	0	0	0	77	77	77	76	1	3.150000	-3.808958	1	0.550000			0	9	9	0	206	203	0		1	0		0	0	77	0	0	0.994144	1.064061e-01	0	0	0	12	0	9	206
TMPRSS11D	9407	broad.mit.edu	37	4	68725370	68725370	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:68725370C>T	ENST00000283916.6	-	2	133	c.35G>A	c.(34-36)aGa>aAa	p.R12K	TMPRSS11D_ENST00000509584.1_Intron|UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11D_ENST00000545541.1_Intron	NM_004262.2	NP_004253.1	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	12					proteolysis (GO:0006508)|respiratory gaseous exchange (GO:0007585)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						ATTCAGAAATCTTGAAGTCGA	0.388																																						ENST00000283916.6	1.000000	0.890000	1	9.900000e-01	0.990000	0.991382	0.990000	1.000000																										0				23						c.(34-36)aGa>aAa		transmembrane protease, serine 11D							98.0	88.0	91.0					4																	68725370		2203	4300	6503	SO:0001583	missense	9407	0	0					g.chr4:68725370C>T	AB002134	CCDS3518.1	4q13.2	2010-04-13			ENSG00000153802	ENSG00000153802		"""Serine peptidases / Transmembrane"""	24059	protein-coding gene	gene with protein product	"""airway trypsin like protease"""	605369				9565616, 9070615	Standard	XM_005265710		Approved		uc003hdq.3	O60235	OTTHUMG00000129300	ENST00000283916.6:c.35G>A	chr4.hg19:g.68725370C>T	ENSP00000283916:p.Arg12Lys	1					TMPRSS11D_ENST00000545541.1_Intron|TMPRSS11D_ENST00000509584.1_Intron|UBA6-AS1_ENST00000500538.2_RNA	p.R12K	NM_004262.2	NP_004253.1	2	2	4	1.763541	O60235	TM11D_HUMAN		2	133	-			Q08AF6	Missense_Mutation	SNP	ENST00000283916.6	1	1	hg19	c.35G>A	CCDS3518.1	1	.	.	.	.	.	.	.	.	.	.	C	19.86	3.905995	0.72868	.	.	ENSG00000153802	ENST00000283916	D	0.88046	-2.33	5.19	5.19	0.71726	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000010	D	0.89529	0.6741	L	0.61387	1.9	0.80722	D	1	D	0.67145	0.996	P	0.54759	0.76	D	0.88677	0.3199	10	0.41790	T	0.15	.	14.0925	0.65000	0.0:1.0:0.0:0.0	.	12	O60235	TM11D_HUMAN	K	12	ENSP00000283916:R12K	ENSP00000283916:R12K	R	-	2	0	0	TMPRSS11D	68407965	68407965	1.000000	0.71417	0.997000	0.53966	0.591000	0.36615	1.993000	0.40747	2.704000	0.92352	0.563000	0.77884	AGA	0.613734		TCGA-IB-A7LX-01A-12D-A36O-08	0.388	TMPRSS11D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251430.3	1	0	1	2	2	2	2	0	0	0	0	67	67	67	66	1	3.150000	-20.000000	1	0.550000	NM_004262		0	66	66	0	188	186	1		1			0	0	67	0	0	1.000000	0	0	0	0	0	0	66	188
RPS3A	6189	broad.mit.edu	37	4	152021718	152021718	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr4:152021718C>A	ENST00000274065.4	+	2	224	c.144C>A	c.(142-144)ctC>ctA	p.L48L	SNORD73_ENST00000364394.1_RNA|RPS3A_ENST00000506126.1_Silent_p.L11L|RPS3A_ENST00000514682.1_Silent_p.L11L|RPS3A_ENST00000509736.1_Intron|RPS3A_ENST00000512690.1_Silent_p.L48L|RPS3A_ENST00000322686.6_Silent_p.L35L	NM_001006.4	NP_000997.1			ribosomal protein S3A											endometrium(1)|lung(1)|ovary(1)|pancreas(1)	4	all_hematologic(180;0.093)					GAAAGACGCTCGTCACCAGGA	0.393																																						ENST00000274065.4	1.000000	0.150000	1	2.100000e-01	0.280000	0.402755	0.280000	0.270000																										0				4						c.(142-144)ctC>ctA		ribosomal protein S3A							72.0	78.0	76.0					4																	152021718		2203	4300	6503	SO:0001819	synonymous_variant	6189	0	0					g.chr4:152021718C>A	X87373	CCDS3775.1	4q31.2-q31.3	2011-04-05			ENSG00000145425	ENSG00000145425		"""S ribosomal proteins"""	10421	protein-coding gene	gene with protein product		180478		MFTL		8647443, 1398113	Standard	NM_001006		Approved	S3A	uc003ilz.4	P61247	OTTHUMG00000161445	ENST00000274065.4:c.144C>A	chr4.hg19:g.152021718C>A		1					RPS3A_ENST00000322686.6_Silent_p.L35L|SNORD73_ENST00000364394.1_RNA|RPS3A_ENST00000506126.1_Silent_p.L11L|RPS3A_ENST00000512690.1_Silent_p.L48L|RPS3A_ENST00000509736.1_Intron|RPS3A_ENST00000514682.1_Silent_p.L11L	p.L48L	NM_001006.4	NP_000997.1	2	3	5	1.795702				2	224	+	all_hematologic(180;0.093)			Silent	SNP	ENST00000274065.4	1	0	hg19	c.144C>A	CCDS3775.1	0																																																																																								0.621769		TCGA-IB-A7LX-01A-12D-A36O-08	0.393	RPS3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364957.1	1	0	1	2	2	2	2	0	0	0	0	79	79	79	79	1	3.150000	-3.076017	1	0.550000			0	14	14	0	214	212	0		1	0		0	0	79	0	0	0.999768	1	0	0	0	3517	0	14	214
MCC	4163	broad.mit.edu	37	5	112720776	112720776	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:112720776G>T	ENST00000408903.3	-	2	719	c.304C>A	c.(304-306)Cga>Aga	p.R102R	CTD-2201G3.1_ENST00000416046.2_RNA	NM_001085377.1	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers	0					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		CTAATTTCTCGAACAAGCTGC	0.458																																						ENST00000408903.3	0.280000	0.090000	2.200000e-01	1.200000e-01	0.160000	0.177686	0.160000	0.170000																										0				42						c.(304-306)Cga>Aga		mutated in colorectal cancers							147.0	136.0	140.0					5																	112720776		1892	4121	6013	SO:0001819	synonymous_variant	4163	0	0					g.chr5:112720776G>T		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000408903.3:c.304C>A	chr5.hg19:g.112720776G>T		1					CTD-2201G3.1_ENST00000416046.2_RNA	p.R102R	NM_001085377.1	NP_001078846	1	2	3	1.889547	P23508	CRCM_HUMAN		2	719	-		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)	D3DT05|Q6ZR04	Silent	SNP	ENST00000408903.3	1	0	hg19	c.304C>A	CCDS43351.1	0																																																																																								0.646296		TCGA-IB-A7LX-01A-12D-A36O-08	0.458	MCC-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370839.1	1	0	1	2	2	2	2	0	0	0	0	116	116	116	116	1	3.150000	-3.267031	1	0.550000	NM_001085377		0	14	14	0	374	368	0		1	0		0	0	116	0	0	0.999738	3.704771e-02	0	0	0	8	0	14	374
MYOT	9499	broad.mit.edu	37	5	137219194	137219194	+	Missense_Mutation	SNP	T	T	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:137219194T>A	ENST00000239926.4	+	7	1312	c.938T>A	c.(937-939)gTc>gAc	p.V313D	RP11-381K20.2_ENST00000514616.1_RNA|MYOT_ENST00000515645.1_Missense_Mutation_p.V198D|MYOT_ENST00000509812.1_Intron|RP11-381K20.2_ENST00000508281.2_RNA|MYOT_ENST00000421631.2_Missense_Mutation_p.V129D	NM_006790.2	NP_006781	Q9UBF9	MYOTI_HUMAN	myotilin	313	Ig-like C2-type 1.|Necessary for interaction with ACTA1.|Necessary for interaction with FLNC.				muscle contraction (GO:0006936)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	structural constituent of muscle (GO:0008307)			cervix(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTTGAAGTAGTCAGAGCTTCA	0.443																																						ENST00000239926.4	0.940000	0.540000	8.300000e-01	6.300000e-01	0.720000	0.734723	0.720000	0.720000																										0				23						c.(937-939)gTc>gAc		myotilin							109.0	102.0	104.0					5																	137219194		2203	4300	6503	SO:0001583	missense	9499	0	0					g.chr5:137219194T>A	AF133820	CCDS4194.1, CCDS47268.1, CCDS75309.1	5q31.2	2014-09-17	2005-09-07	2005-09-07	ENSG00000120729	ENSG00000120729		"""Immunoglobulin superfamily / I-set domain containing"""	12399	protein-coding gene	gene with protein product		604103	"""titin immunoglobulin domain protein (myotilin)"", ""limb-girdle muscular dystrophy 1A (autosomal dominant)"""	TTID, LGMD1A, LGMD1		10486214, 10369880	Standard	NM_006790		Approved		uc003lbv.3	Q9UBF9	OTTHUMG00000129154	ENST00000239926.4:c.938T>A	chr5.hg19:g.137219194T>A	ENSP00000239926:p.Val313Asp	1					MYOT_ENST00000509812.1_Intron|RP11-381K20.2_ENST00000514616.1_RNA|MYOT_ENST00000515645.1_Missense_Mutation_p.V198D|MYOT_ENST00000421631.2_Missense_Mutation_p.V129D|RP11-381K20.2_ENST00000508281.2_RNA	p.V313D	NM_006790.2	NP_006781	1	2	3	1.889547	Q9UBF9	MYOTI_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)	7	1312	+			A0A4R6|B4DT79	Missense_Mutation	SNP	ENST00000239926.4	1	1	hg19	c.938T>A	CCDS4194.1	0	.	.	.	.	.	.	.	.	.	.	T	21.9	4.221755	0.79464	.	.	ENSG00000120729	ENST00000239926;ENST00000421631;ENST00000515645	T;T;T	0.72505	-0.66;-0.66;-0.66	5.08	5.08	0.68730	5.08	5.08	0.68730	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000032	D	0.88276	0.6393	H	0.95816	3.725	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	D	0.91887	0.5520	10	0.87932	D	0	.	15.1564	0.72746	0.0:0.0:0.0:1.0	.	313	Q9UBF9	MYOTI_HUMAN	D	313;129;198	ENSP00000239926:V313D;ENSP00000391185:V129D;ENSP00000426281:V198D	ENSP00000239926:V313D	V	+	2	0	0	MYOT	137247093	137247093	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.191000	0.72063	2.021000	0.59480	0.533000	0.62120	GTC	0.646296		TCGA-IB-A7LX-01A-12D-A36O-08	0.443	MYOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251219.2	1	0	1	2	2	2	2	0	0	0	0	85	85	85	85	1	3.150000	-19.998670	1	0.550000	NM_006790		0	45	44	0	242	235	1		1			0	0	85	0	0	1.000000	0	0	0	0	0	0	45	242
PCDHB14	56122	broad.mit.edu	37	5	140603942	140603942	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:140603942C>A	ENST00000239449.4	+	1	865	c.865C>A	c.(865-867)Cgt>Agt	p.R289S	PCDHB14_ENST00000515856.2_Missense_Mutation_p.R136S	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	289	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGAAGATATTCGTAAAACATT	0.378																																					Ovarian(141;50 1831 27899 33809 37648)	ENST00000239449.4	0.360000	0.100000	2.800000e-01	1.500000e-01	0.200000	0.218956	0.200000	0.210000																										0				49						c.(865-867)Cgt>Agt		protocadherin beta 14							43.0	47.0	46.0					5																	140603942		2201	4300	6501	SO:0001583	missense	56122	1	121402	31				g.chr5:140603942C>A	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.865C>A	chr5.hg19:g.140603942C>A	ENSP00000239449:p.Arg289Ser	1					PCDHB14_ENST00000515856.2_Missense_Mutation_p.R136S	p.R289S	NM_018934.2	NP_061757.1	1	2	3	1.889547	Q9Y5E9	PCDBE_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)	1	865	+			B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	1	0	hg19	c.865C>A	CCDS4256.1	0	.	.	.	.	.	.	.	.	.	.	-	6.356	0.433698	0.12045	.	.	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.50001	0.76;0.76	4.75	0.286	0.15710	4.75	0.286	0.15710	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.22282	0.0537	N	0.16602	0.42	0.09310	N	1	B	0.15141	0.012	B	0.15052	0.012	T	0.28396	-1.0045	9	0.02654	T	1	.	4.3959	0.11363	0.2528:0.4394:0.2343:0.0735	.	289	Q9Y5E9	PCDBE_HUMAN	S	136;289	ENSP00000444518:R136S;ENSP00000239449:R289S	ENSP00000239449:R289S	R	+	1	0	0	PCDHB14	140584126	140584126	0.000000	0.05858	0.078000	0.20375	0.873000	0.50193	-0.821000	0.04452	0.109000	0.17891	0.655000	0.94253	CGT	0.646296		TCGA-IB-A7LX-01A-12D-A36O-08	0.378	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	1	0	0	2	2	2	2	0	0	0	0	66	66	66	66	1	3.150000	-12.871820	1	0.550000	NM_018934		0	11	11	0	240	237	0		1	0		0	0	66	0	0	0.998331	3.963645e-01	0	0	0	29	0	11	240
TCERG1	10915	broad.mit.edu	37	5	145859431	145859431	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:145859431G>T	ENST00000296702.5	+	11	1814	c.1776G>T	c.(1774-1776)ccG>ccT	p.P592P	TCERG1_ENST00000394421.2_Silent_p.P571P	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	592					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACCCAACTCCGACAATGCTGT	0.323																																						ENST00000296702.5	0.350000	0.090000	2.700000e-01	1.400000e-01	0.190000	0.208096	0.190000	0.180000																										0				46						c.(1774-1776)ccG>ccT		transcription elongation regulator 1							44.0	45.0	45.0					5																	145859431		2203	4300	6503	SO:0001819	synonymous_variant	10915	0	0					g.chr5:145859431G>T	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"""transcription factor CA150"", ""co-activator of 150 kDa"", ""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"", ""TATA box-binding protein-associated factor 2S"""	605409	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"""	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.1776G>T	chr5.hg19:g.145859431G>T		1					TCERG1_ENST00000394421.2_Silent_p.P571P	p.P592P	NM_006706.3	NP_006697.2	1	2	3	1.889547	O14776	TCRG1_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)	11	1814	+		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	Q2NKN2|Q59EA1	Silent	SNP	ENST00000296702.5	1	0	hg19	c.1776G>T	CCDS4282.1	0																																																																																								0.646296		TCGA-IB-A7LX-01A-12D-A36O-08	0.323	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	1	0	1	2	2	2	2	0	0	0	0	51	51	51	51	1	3.150000	-3.110063	1	0.550000	NM_001040006		0	10	10	0	232	227	0		1	0		0	0	51	0	0	0.996725	5.719337e-01	0	0	0	44	0	10	232
SLU7	10569	broad.mit.edu	37	5	159839519	159839519	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:159839519C>A	ENST00000297151.4	-	6	965	c.578G>T	c.(577-579)cGa>cTa	p.R193L		NM_006425.4	NP_006416.3	O95391	SLU7_HUMAN	SLU7 splicing factor homolog (S. cerevisiae)	193					alternative mRNA splicing, via spliceosome (GO:0000380)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	pre-mRNA 3'-splice site binding (GO:0030628)|second spliceosomal transesterification activity (GO:0000386)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(4)|lung(6)|ovary(1)	20	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTTCAATGTTCGTTTTGCCTT	0.274																																						ENST00000297151.4	0.310000	0.090000	2.500000e-01	1.300000e-01	0.180000	0.194181	0.180000	0.180000																										0				20						c.(577-579)cGa>cTa		SLU7 splicing factor homolog (S. cerevisiae)							76.0	73.0	74.0					5																	159839519		2202	4298	6500	SO:0001583	missense	10569	0	0					g.chr5:159839519C>A	AF101074	CCDS4352.1	5q33.3	2010-04-13			ENSG00000164609	ENSG00000164609			16939	protein-coding gene	gene with protein product	zinc knuckle motif containing	605974				10197984, 15728250	Standard	NM_006425		Approved	9G8	uc003lyg.3	O95391	OTTHUMG00000130324	ENST00000297151.4:c.578G>T	chr5.hg19:g.159839519C>A	ENSP00000297151:p.Arg193Leu	1						p.R193L	NM_006425.4	NP_006416.3	1	2	3	1.889547	O95391	SLU7_HUMAN	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	6	965	-	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	D3DQK2|Q3LUJ0|Q3LUJ1|Q6RXQ5|Q96FM9	Missense_Mutation	SNP	ENST00000297151.4	1	0	hg19	c.578G>T	CCDS4352.1	0	.	.	.	.	.	.	.	.	.	.	C	24.6	4.554570	0.86231	.	.	ENSG00000164609	ENST00000297151	T	0.45668	0.89	5.68	4.81	0.61882	5.68	4.81	0.61882	Pre-mRNA splicing Prp18-interacting factor (1);	0.051383	0.85682	D	0.000000	T	0.57651	0.2068	M	0.75150	2.29	0.80722	D	1	P	0.51147	0.942	P	0.54140	0.743	T	0.64071	-0.6493	10	0.87932	D	0	-28.4394	14.4844	0.67606	0.0:0.9296:0.0:0.0704	.	193	O95391	SLU7_HUMAN	L	193	ENSP00000297151:R193L	ENSP00000297151:R193L	R	-	2	0	0	SLU7	159772097	159772097	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.749000	0.74883	1.403000	0.46800	0.650000	0.86243	CGA	0.646296		TCGA-IB-A7LX-01A-12D-A36O-08	0.274	SLU7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252673.1	1	0	1	2	2	2	2	0	0	0	0	79	79	79	76	1	3.150000	-2.920853	1	0.550000	NM_006425		0	13	13	0	318	307	0		1	0		0	0	79	0	0	0.999404	8.083668e-01	0	0	0	78	0	13	318
TSPAN17	26262	broad.mit.edu	37	5	176084641	176084641	+	Missense_Mutation	SNP	G	G	T	rs141018454		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:176084641G>T	ENST00000503045.1	+	9	927	c.872G>T	c.(871-873)cGa>cTa	p.R291L	TSPAN17_ENST00000508164.1_Missense_Mutation_p.R311L|TSPAN17_ENST00000515708.1_3'UTR|TSPAN17_ENST00000310032.8_Missense_Mutation_p.R314L|TSPAN17_ENST00000405525.2_3'UTR|TSPAN17_ENST00000298564.10_3'UTR			Q96FV3	TSN17_HUMAN	tetraspanin 17	166					establishment of protein localization to organelle (GO:0072594)|protein ubiquitination (GO:0016567)	integral component of membrane (GO:0016021)|ubiquitin ligase complex (GO:0000151)	enzyme binding (GO:0019899)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	13	all_cancers(89;0.00141)|Renal(175;0.000269)|Lung NSC(126;0.00814)|all_lung(126;0.0133)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ccacccagccgacatgttttc	0.537																																						ENST00000503045.1	0.350000	0.090000	2.700000e-01	1.300000e-01	0.190000	0.207878	0.190000	0.180000																										0				13						c.(871-873)cGa>cTa		tetraspanin 17							29.0	35.0	33.0					5																	176084641		2201	4300	6501	SO:0001583	missense	26262	12	121404	41				g.chr5:176084641G>T	AF174603	CCDS34298.1, CCDS47346.1, CCDS47346.2, CCDS54952.1	5q35.3	2013-02-14	2005-03-21	2005-03-21	ENSG00000048140	ENSG00000048140		"""Tetraspanins"""	13594	protein-coding gene	gene with protein product			"""F-box only protein 23, transmembrane 4 superfamily member 17"""	FBXO23, TM4SF17		10531035, 10531037	Standard	NM_012171		Approved	FBX23	uc003met.3	Q96FV3	OTTHUMG00000163230	ENST00000503045.1:c.872G>T	chr5.hg19:g.176084641G>T	ENSP00000425212:p.Arg291Leu	1					TSPAN17_ENST00000405525.2_3'UTR|TSPAN17_ENST00000515708.1_3'UTR|TSPAN17_ENST00000310032.8_Missense_Mutation_p.R314L|TSPAN17_ENST00000298564.10_3'UTR|TSPAN17_ENST00000508164.1_Missense_Mutation_p.R311L	p.R291L			1	2	3	1.889547	Q96FV3	TSN17_HUMAN	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	9	927	+	all_cancers(89;0.00141)|Renal(175;0.000269)|Lung NSC(126;0.00814)|all_lung(126;0.0133)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Q6NXF7|Q96S98|Q9UKB9	Missense_Mutation	SNP	ENST00000503045.1	1	0	hg19	c.872G>T		0	.	.	.	.	.	.	.	.	.	.	G	13.99	2.403196	0.42613	.	.	ENSG00000048140	ENST00000310032;ENST00000508164;ENST00000503045	T;T;T	0.17528	3.13;3.14;2.27	2.8	-5.59	0.02505	2.8	-5.59	0.02505	.	.	.	.	.	T	0.06142	0.0159	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33317	-0.9873	9	0.87932	D	0	.	0.7854	0.01047	0.235:0.3522:0.1684:0.2445	.	311	Q96FV3-4	.	L	314;311;291	ENSP00000309036:R314L;ENSP00000422053:R311L;ENSP00000425212:R291L	ENSP00000309036:R314L	R	+	2	0	0	TSPAN17	176017247	176017247	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-1.876000	0.01633	-1.978000	0.00993	-0.339000	0.08088	CGA	0.646296		TCGA-IB-A7LX-01A-12D-A36O-08	0.537	TSPAN17-008	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372215.1	1	0	1	2	2	2	2	0	0	0	0	54	54	54	54	1	3.150000	-3.282755	1	0.550000			0	9	9	0	211	207	0		1	0		0	0	54	0	0	0.994019	7.700399e-01	0	0	0	67	0	9	211
SKIV2L2	23517	broad.mit.edu	37	5	54718748	54718748	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:54718748G>T	ENST00000230640.5	+	26	3268	c.3014G>T	c.(3013-3015)cGa>cTa	p.R1005L	SKIV2L2_ENST00000545714.1_Missense_Mutation_p.R904L	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	1005					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				GAATTGCTTCGACAAATGTGT	0.383																																					Melanoma(2;92 134 23744 29976 33782)	ENST00000230640.5	0.300000	0.090000	2.400000e-01	1.300000e-01	0.180000	0.192450	0.180000	0.180000																										0				41						c.(3013-3015)cGa>cTa		superkiller viralicidic activity 2-like 2 (S. cerevisiae)							78.0	73.0	75.0					5																	54718748		2203	4300	6503	SO:0001583	missense	23517	0	0					g.chr5:54718748G>T	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 118"""		"""KIAA0052"""	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.3014G>T	chr5.hg19:g.54718748G>T	ENSP00000230640:p.Arg1005Leu	1					SKIV2L2_ENST00000545714.1_Missense_Mutation_p.R904L	p.R1005L	NM_015360.4	NP_056175.3	1	2	3	1.889547	P42285	SK2L2_HUMAN		26	3268	+		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Missense_Mutation	SNP	ENST00000230640.5	1	0	hg19	c.3014G>T	CCDS3967.1	0	.	.	.	.	.	.	.	.	.	.	G	26.0	4.694671	0.88830	.	.	ENSG00000039123	ENST00000230640;ENST00000545714	T;T	0.26373	1.74;1.74	5.79	5.79	0.91817	5.79	5.79	0.91817	DSH, C-terminal (1);	0.062767	0.64402	D	0.000008	T	0.69079	0.3071	H	0.97983	4.12	0.80722	D	1	D;D	0.71674	0.998;0.984	D;D	0.71414	0.973;0.921	T	0.81202	-0.1040	10	0.87932	D	0	-10.8717	20.0281	0.97530	0.0:0.0:1.0:0.0	.	904;1005	F5H7E2;P42285	.;SK2L2_HUMAN	L	1005;904	ENSP00000230640:R1005L;ENSP00000442583:R904L	ENSP00000230640:R1005L	R	+	2	0	0	SKIV2L2	54754505	54754505	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.434000	0.97515	2.727000	0.93392	0.655000	0.94253	CGA	0.646296		TCGA-IB-A7LX-01A-12D-A36O-08	0.383	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1	1	0	1	2	2	2	2	0	0	0	0	79	79	79	79	1	3.150000	-2.975620	1	0.550000			0	13	13	0	321	318	0		1	0		0	0	79	0	0	0.999531	9.695676e-01	0	0	0	147	0	13	321
RUFY1	80230	broad.mit.edu	37	5	178994482	178994482	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr5:178994482G>T	ENST00000319449.4	+	4	635	c.623G>T	c.(622-624)cGa>cTa	p.R208L	RUFY1_ENST00000377001.2_Missense_Mutation_p.R208L|RUFY1_ENST00000393438.2_Missense_Mutation_p.R100L|RUFY1_ENST00000437570.2_Missense_Mutation_p.R100L	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	208	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGAAGAGGCCGAGCGTGGCTT	0.403										HNSCC(44;0.11)																												ENST00000319449.4	0.350000	0.090000	2.700000e-01	1.300000e-01	0.190000	0.204208	0.190000	0.180000																										0				26						c.(622-624)cGa>cTa		RUN and FYVE domain containing 1							109.0	107.0	108.0					5																	178994482		2203	4300	6503	SO:0001583	missense	80230	0	0					g.chr5:178994482G>T	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"""Zinc fingers, FYVE domain containing"""	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.623G>T	chr5.hg19:g.178994482G>T	ENSP00000325594:p.Arg208Leu	1	HNSCC(44;0.11)				RUFY1_ENST00000393438.2_Missense_Mutation_p.R100L|RUFY1_ENST00000377001.2_Missense_Mutation_p.R208L|RUFY1_ENST00000437570.2_Missense_Mutation_p.R100L	p.R208L	NM_025158.4	NP_079434.3	1	2	3	1.889547	Q96T51	RUFY1_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	4	635	+	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Q59FF3|Q71S93|Q9H6I3	Missense_Mutation	SNP	ENST00000319449.4	1	0	hg19	c.623G>T	CCDS4445.2	0	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.271432|5.271432	0.95429|0.95429	.|.	.|.	ENSG00000176783|ENSG00000176783	ENST00000502984;ENST00000508609|ENST00000319449;ENST00000377001;ENST00000437570;ENST00000393438	.|T;T;T;T	.|0.19105	.|2.17;2.17;2.17;2.17	5.43|5.43	5.43|5.43	0.79202|0.79202	5.43|5.43	5.43|5.43	0.79202|0.79202	.|RUN (3);	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.56171	.|0.1967	M|M	0.88241|0.88241	2.94|2.94	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	.|T	.|0.63769	.|-0.6562	.|10	.|0.87932	.|D	.|0	-15.4094|-15.4094	19.6173|19.6173	0.95639|0.95639	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|208	.|Q96T51	.|RUFY1_HUMAN	X|L	166;19|208;208;100;100	.|ENSP00000325594:R208L;ENSP00000366200:R208L;ENSP00000390025:R100L;ENSP00000377087:R100L	.|ENSP00000325594:R208L	E|R	+|+	1|2	0|0	0|0	RUFY1|RUFY1	178927088|178927088	178927088|178927088	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.876000|0.876000	0.50452|0.50452	9.481000|9.481000	0.97933|0.97933	2.712000|2.712000	0.92718|0.92718	0.557000|0.557000	0.71058|0.71058	GAG|CGA	0.646296		TCGA-IB-A7LX-01A-12D-A36O-08	0.403	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	1	0	1	2	2	2	2	0	0	0	0	68	68	68	68	1	3.150000	-2.896596	1	0.550000	NM_001040451		0	9	9	0	215	213	0		1	0		0	0	68	0	0	0.994264	8.642011e-01	0	0	0	88	0	9	215
AIM1	202	broad.mit.edu	37	6	106968971	106968971	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:106968971G>T	ENST00000369066.3	+	2	3151	c.2664G>T	c.(2662-2664)ttG>ttT	p.L888F		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)		CCTGTGGTTTGAACAAAGAAC	0.478																																						ENST00000369066.3	1.000000	0.110000	1	1.500000e-01	0.210000	0.336034	0.210000	0.200000																										0				69						c.(2662-2664)ttG>ttT		absent in melanoma 1							80.0	85.0	84.0					6																	106968971		2203	4300	6503	SO:0001583	missense	202	0	0					g.chr6:106968971G>T	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.2664G>T	chr6.hg19:g.106968971G>T	ENSP00000358062:p.Leu888Phe	1						p.L888F	NM_001624.2	NP_001615	0	2	2	1.365333	Q9UMX9	S45A2_HUMAN	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	2	3151	+	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)	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	1	0	hg19	c.2664G>T	CCDS34506.1	0	.	.	.	.	.	.	.	.	.	.	G	11.12	1.546580	0.27652	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.72051	-0.62	5.99	0.198	0.15168	5.99	0.198	0.15168	.	1.843970	0.02402	N	0.080812	T	0.29256	0.0728	N	0.22421	0.69	0.18873	N	0.999986	B	0.31931	0.347	B	0.25759	0.063	T	0.25187	-1.0139	10	0.52906	T	0.07	.	0.6497	0.00824	0.4479:0.1681:0.2214:0.1625	.	888	Q9Y4K1	AIM1_HUMAN	F	1296;888	ENSP00000358062:L888F	ENSP00000285105:L1296F	L	+	3	2	2	AIM1	107075664	107075664	0.970000	0.33590	0.009000	0.14445	0.980000	0.70556	0.373000	0.20484	0.078000	0.16900	-0.345000	0.07892	TTG	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.478	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1	1	0	1	2	2	2	2	0	0	0	0	119	119	119	119	1	3.150000	-4.788704	1	0.550000			0	15	15	0	264	257	0		1	0		0	0	119	0	0	0.999863	2.318775e-01	0	0	0	16	0	15	264
RTN4IP1	84816	broad.mit.edu	37	6	107070789	107070789	+	Silent	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:107070789G>T	ENST00000369063.3	-	2	795	c.330C>A	c.(328-330)atC>atA	p.I110I	RTN4IP1_ENST00000539449.1_Silent_p.I110I	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1	110						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		CTTCTCCTTTGATTTTCACGT	0.413																																						ENST00000369063.3	1.000000	0.130000	1	1.800000e-01	0.240000	0.365482	0.240000	0.230000																										0				13						c.(328-330)atC>atA		reticulon 4 interacting protein 1							99.0	95.0	96.0					6																	107070789		2203	4300	6503	SO:0001819	synonymous_variant	84816	0	0					g.chr6:107070789G>T	AF336861	CCDS5056.1	6q21	2008-02-05			ENSG00000130347	ENSG00000130347			18647	protein-coding gene	gene with protein product		610502					Standard	NM_032730		Approved	NIMP	uc003prj.3	Q8WWV3	OTTHUMG00000015304	ENST00000369063.3:c.330C>A	chr6.hg19:g.107070789G>T		1					RTN4IP1_ENST00000539449.1_Silent_p.I110I	p.I110I	NM_032730.4	NP_116119.2	0	2	2	1.365333	Q8WWV3	RT4I1_HUMAN	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	2	795	-	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Q8N9B3|Q8WZ66|Q9BRA4	Silent	SNP	ENST00000369063.3	1	0	hg19	c.330C>A	CCDS5056.1	0																																																																																								0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.413	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1	1	0	1	2	2	2	2	0	0	0	0	93	93	93	93	1	3.150000	-5.935248	1	0.550000			0	16	15	0	237	235	0		1	0		0	0	93	0	0	0.999935	4.033831e-02	0	0	0	5	0	16	237
ROS1	6098	broad.mit.edu	37	6	117710875	117710875	+	Missense_Mutation	SNP	C	C	A	rs140178288	byFrequency	TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:117710875C>A	ENST00000368508.3	-	12	1595	c.1397G>T	c.(1396-1398)cGa>cTa	p.R466L	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.R475L	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	466					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		GTAAATGATTCGCTTGGCTTG	0.493			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																	ENST00000368508.3	1.000000	0.110000	1	1.700000e-01	0.250000	0.371014	0.250000	0.220000				Dom	yes			Dom	yes		6	6q22	6q22	6098	T	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)				"""O, E"""	O, E	GOPC, SDC4, SLC34A2, EZR, LRIG3		glioblastoma, NSCLC	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	0				162						c.(1396-1398)cGa>cTa		ROS proto-oncogene 1 , receptor tyrosine kinase							103.0	70.0	81.0					6																	117710875		2203	4300	6503	SO:0001583	missense	6098	0	0					g.chr6:117710875C>A	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.1397G>T	chr6.hg19:g.117710875C>A	ENSP00000357494:p.Arg466Leu	1					ROS1_ENST00000368507.3_Missense_Mutation_p.R475L|GOPC_ENST00000467125.1_Intron	p.R466L	NM_002944.2	NP_002935.2	0	2	2	1.365333	P08922	ROS1_HUMAN		12	1595	-		all_cancers(87;0.00846)|all_epithelial(87;0.0242)	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	1	0	hg19	c.1397G>T	CCDS5116.1	0	.	.	.	.	.	.	.	.	.	.	C	19.56	3.850642	0.71719	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	D;D	0.91631	-2.88;-2.88	5.82	4.94	0.65067	5.82	4.94	0.65067	.	0.112377	0.37348	N	0.002123	D	0.90253	0.6952	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.65684	0.937	D	0.88337	0.2972	10	0.31617	T	0.26	.	11.6854	0.51483	0.0:0.9193:0.0:0.0807	.	466	P08922	ROS1_HUMAN	L	466;475	ENSP00000357494:R466L;ENSP00000357493:R475L	ENSP00000357493:R475L	R	-	2	0	0	ROS1	117817568	117817568	1.000000	0.71417	0.976000	0.42696	0.482000	0.33219	4.212000	0.58514	2.755000	0.94549	0.561000	0.74099	CGA	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.493	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1	1	0	1	2	2	2	2	0	0	0	0	31	31	31	31	1	3.150000	-3.326195	1	0.550000			0	8	8	0	121	110	0		1	0		0	0	31	0	0	0.985806	1.475323e-02	0	0	0	3	0	8	121
MAP3K5	4217	broad.mit.edu	37	6	137113237	137113237	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:137113237C>G	ENST00000359015.4	-	1	419	c.59G>C	c.(58-60)gGc>gCc	p.G20A		NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	20					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		GGTGCAGAAGCCCGAGGGGGC	0.751																																						ENST00000359015.4	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000																										0				58						c.(58-60)gGc>gCc		mitogen-activated protein kinase kinase kinase 5							5.0	5.0	5.0					6																	137113237		1768	3460	5228	SO:0001583	missense	4217	0	0					g.chr6:137113237C>G	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6857	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 1"""	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.59G>C	chr6.hg19:g.137113237C>G	ENSP00000351908:p.Gly20Ala	1						p.G20A	NM_005923.3	NP_005914.1	2	8	10	4.331302	Q99683	M3K5_HUMAN		1	419	-	Colorectal(23;0.24)		A6NIA0|B4DGB2|Q5THN3|Q99461	Missense_Mutation	SNP	ENST00000359015.4	0	1	hg19	c.59G>C	CCDS5179.1	1	.	.	.	.	.	.	.	.	.	.	C	9.984	1.228890	0.22542	.	.	ENSG00000197442	ENST00000359015;ENST00000367768	T	0.68624	-0.34	3.56	1.67	0.24075	3.56	1.67	0.24075	.	0.634408	0.14920	N	0.290736	T	0.20170	0.0485	N	0.14661	0.345	0.18873	N	0.999985	B	0.13594	0.008	B	0.11329	0.006	T	0.29792	-1.0000	10	0.12103	T	0.63	.	7.361	0.26745	0.1664:0.7407:0.0:0.0929	.	20	Q99683	M3K5_HUMAN	A	20;100	ENSP00000351908:G20A	ENSP00000351908:G20A	G	-	2	0	0	MAP3K5	137154930	137154930	0.535000	0.26370	0.016000	0.15963	0.025000	0.11179	2.498000	0.45363	0.287000	0.22375	0.573000	0.79308	GGC	0.844398		TCGA-IB-A7LX-01A-12D-A36O-08	0.751	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1	1	0	1	2	2	2	2	0	0	0	0	11	11	11	11	1	3.150000	-20.000000	1	0.550000			0	36	34	0	34	34	0		1	1		0	0	11	0	0	1.000000	9.999725e-01	0	14	0	8	0	36	34
UTRN	7402	broad.mit.edu	37	6	144768443	144768443	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:144768443C>A	ENST00000367545.3	+	14	1711	c.1711C>A	c.(1711-1713)Cga>Aga	p.R571R		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	571	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.R571*(2)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TGTCAGTGTTCGACGTCTGGC	0.383																																						ENST00000367545.3	1.000000	0.120000	1	1.800000e-01	0.280000	0.432807	0.280000	0.230000																										2	Substitution - Nonsense(2)	p.R571*(2)	large_intestine(1)|breast(1)	148						c.(1711-1713)Cga>Aga		utrophin							118.0	104.0	109.0					6																	144768443		2203	4300	6503	SO:0001819	synonymous_variant	7402	0	0					g.chr6:144768443C>A	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.1711C>A	chr6.hg19:g.144768443C>A		1						p.R571R	NM_007124.2	NP_009055.2	3	4	7	2.292266	P46939	UTRO_HUMAN		14	1711	+		Ovarian(120;0.218)	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	1	0	hg19	c.1711C>A	CCDS34547.1	0																																																																																								0.701740		TCGA-IB-A7LX-01A-12D-A36O-08	0.383	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1	1	0	1	2	2	2	2	0	0	0	0	52	52	52	52	1	3.150000	-4.312080	1	0.550000			0	8	8	0	174	171	0		1	0		0	0	52	0	0	0.989141	1.025800e-01	0	0	0	11	0	8	174
IMPG1	3617	broad.mit.edu	37	6	76751711	76751711	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:76751711C>A	ENST00000369950.3	-	2	389	c.200G>T	c.(199-201)cGa>cTa	p.R67L	IMPG1_ENST00000369963.3_Intron	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				TCTTTTTGTTCGATGCTTTGC	0.363																																					Pancreas(37;839 1141 2599 26037)	ENST00000369950.3	1.000000	0.070000	2.600000e-01	1.100000e-01	0.150000	0.277952	0.150000	0.140000																										0				63						c.(199-201)cGa>cTa		interphotoreceptor matrix proteoglycan 1							162.0	154.0	156.0					6																	76751711		2203	4300	6503	SO:0001583	missense	3617	0	0					g.chr6:76751711C>A	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"""sialoprotein associated with cones and rods"""	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.200G>T	chr6.hg19:g.76751711C>A	ENSP00000358966:p.Arg67Leu	1					IMPG1_ENST00000369963.3_Intron	p.R67L	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2	0	2	2	1.369231				2	389	-		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)		Missense_Mutation	SNP	ENST00000369950.3	1	0	hg19	c.200G>T	CCDS4985.1	0	.	.	.	.	.	.	.	.	.	.	C	26.8	4.768403	0.90020	.	.	ENSG00000112706	ENST00000369950	T	0.79940	-1.32	6.07	5.21	0.72293	6.07	5.21	0.72293	.	0.125602	0.36591	N	0.002519	D	0.87877	0.6288	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.89118	0.3501	9	.	.	.	.	15.5075	0.75753	0.0:0.9339:0.0:0.0661	.	67	Q17R60	IMPG1_HUMAN	L	67	ENSP00000358966:R67L	.	R	-	2	0	0	IMPG1	76808431	76808431	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.573000	0.53856	1.581000	0.49865	0.655000	0.94253	CGA	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.363	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	1	0	1	2	2	2	2	0	0	0	0	131	131	131	131	1	3.150000	-3.065444	1	0.550000	NM_001563		0	12	12	0	290	283	0		1			0	0	131	0	0	0.999037	0	0	0	0	0	0	12	290
MAP3K4	4216	broad.mit.edu	37	6	161514029	161514029	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr6:161514029G>T	ENST00000392142.4	+	14	3437	c.3289G>T	c.(3289-3291)Gat>Tat	p.D1097Y	MAP3K4_ENST00000366920.2_Missense_Mutation_p.D1097Y|MAP3K4_ENST00000348824.7_Missense_Mutation_p.D1097Y|MAP3K4_ENST00000366919.2_Missense_Mutation_p.D1097Y	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1097					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		TCAAGGATTTGATTTTCTACA	0.348																																						ENST00000392142.4	1.000000	0.080000	2.800000e-01	1.200000e-01	0.170000	0.290527	0.170000	0.160000																										0				77						c.(3289-3291)Gat>Tat		mitogen-activated protein kinase kinase kinase 4							155.0	141.0	145.0					6																	161514029		2203	4300	6503	SO:0001583	missense	4216	0	0					g.chr6:161514029G>T	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.3289G>T	chr6.hg19:g.161514029G>T	ENSP00000375986:p.Asp1097Tyr	1					MAP3K4_ENST00000366919.2_Missense_Mutation_p.D1097Y|MAP3K4_ENST00000366920.2_Missense_Mutation_p.D1097Y|MAP3K4_ENST00000348824.7_Missense_Mutation_p.D1097Y	p.D1097Y	NM_005922.2	NP_005913	0	2	2	1.366277	Q9Y6R4	M3K4_HUMAN		14	3437	+		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	1	0	hg19	c.3289G>T	CCDS34565.1	0	.	.	.	.	.	.	.	.	.	.	G	23.5	4.421880	0.83559	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.72167	-0.63;-0.61;-0.61;-0.63	5.84	4.97	0.65823	5.84	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.76062	0.3935	L	0.51422	1.61	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;P;D;D	0.91635	0.998;0.898;0.999;0.999	T	0.80400	-0.1398	10	0.87932	D	0	-38.942	16.2904	0.82747	0.0:0.0:0.8664:0.1336	.	1097;87;1097;1097	F5H538;Q9P1M2;Q9Y6R4-2;Q9Y6R4	.;.;.;M3K4_HUMAN	Y	1097	ENSP00000355886:D1097Y;ENSP00000375986:D1097Y;ENSP00000355887:D1097Y;ENSP00000297332:D1097Y	ENSP00000297332:D1097Y	D	+	1	0	0	MAP3K4	161434019	161434019	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	1.461000	0.47929	0.655000	0.94253	GAT	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.348	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3	1	0	1	2	2	2	2	0	0	0	0	104	104	104	103	1	3.150000	-3.193374	1	0.550000			0	13	13	0	284	279	0		1	0		0	0	104	0	0	0.999523	3.591268e-01	0	0	0	27	0	13	284
PMPCB	9512	broad.mit.edu	37	7	102950912	102950912	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:102950912C>A	ENST00000249269.4	+	9	1182	c.1144C>A	c.(1144-1146)Caa>Aaa	p.Q382K	PMPCB_ENST00000420236.2_Missense_Mutation_p.Q277K|PMPCB_ENST00000428154.1_Missense_Mutation_p.Q382K	NM_004279.2	NP_004270.2	O75439	MPPB_HUMAN	peptidase (mitochondrial processing) beta	382					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(9)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						ACATGTTGTTCAAAAAGAATG	0.308																																						ENST00000249269.4	1.000000	0.120000	1	1.700000e-01	0.230000	0.366243	0.230000	0.220000																										0				21						c.(1144-1146)Caa>Aaa		peptidase (mitochondrial processing) beta							78.0	76.0	77.0					7																	102950912		2203	4300	6503	SO:0001583	missense	9512	0	0					g.chr7:102950912C>A	AF054182	CCDS5730.1	7q22.1	2007-07-30			ENSG00000105819	ENSG00000105819			9119	protein-coding gene	gene with protein product		603131				9653160	Standard	XM_005250717		Approved	MPPB, MPPP52	uc003vbl.3	O75439	OTTHUMG00000157205	ENST00000249269.4:c.1144C>A	chr7.hg19:g.102950912C>A	ENSP00000249269:p.Gln382Lys	1					PMPCB_ENST00000420236.2_Missense_Mutation_p.Q277K|PMPCB_ENST00000428154.1_Missense_Mutation_p.Q382K	p.Q382K	NM_004279.2	NP_004270.2	0	3	3	1.672992	O75439	MPPB_HUMAN		9	1182	+			O60416|Q96FV4	Missense_Mutation	SNP	ENST00000249269.4	1	0	hg19	c.1144C>A	CCDS5730.1	0	.	.	.	.	.	.	.	.	.	.	C	24.7	4.556733	0.86231	.	.	ENSG00000105819	ENST00000249269;ENST00000428154;ENST00000420236	T;T;T	0.06608	3.28;3.28;3.28	5.71	4.83	0.62350	5.71	4.83	0.62350	Peptidase M16, C-terminal (1);Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.30166	0.0756	M	0.89287	3.02	0.80722	D	1	P;D;D;D;D;D	0.89917	0.937;1.0;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.76071	0.839;0.985;0.985;0.985;0.985;0.987	T	0.18147	-1.0346	10	0.51188	T	0.08	.	14.8943	0.70633	0.0:0.931:0.0:0.069	.	277;277;382;373;382;382	E7ERZ4;B4DM90;A8K1E9;Q96CP5;O75439;G3V0E4	.;.;.;.;MPPB_HUMAN;.	K	382;382;277	ENSP00000249269:Q382K;ENSP00000390035:Q382K;ENSP00000410393:Q277K	ENSP00000249269:Q382K	Q	+	1	0	0	PMPCB	102738148	102738148	1.000000	0.71417	0.992000	0.48379	0.963000	0.63663	6.026000	0.70873	1.423000	0.47198	0.585000	0.79938	CAA	0.627792		TCGA-IB-A7LX-01A-12D-A36O-08	0.308	PMPCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347913.1	1	0	1	2	11	2	2	0	0	0	1	101	101	101	99	1	3.150000	-4.627886	1	0.550000	NM_004279		0	14	14	0	267	265	0		1	0		0	0	101	0	0	0.782532	9.813653e-01	0	0	0	129	0	14	267
LAMB4	22798	broad.mit.edu	37	7	107743496	107743496	+	Silent	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:107743496C>T	ENST00000388781.3	-	10	1256	c.1173G>A	c.(1171-1173)gcG>gcA	p.A391A	LAMB4_ENST00000414450.2_Silent_p.A391A|LAMB4_ENST00000205386.4_Silent_p.A391A|LAMB4_ENST00000418464.1_Silent_p.A391A|LAMB4_ENST00000388780.3_Silent_p.A391A	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	391	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						CACGAATGCACGCGTAGGGAT	0.577																																						ENST00000388781.3	1.000000	0.660000	1	8.200000e-01	0.990000	0.934200	0.990000	1.000000																										0				97						c.(1171-1173)gcG>gcA		laminin, beta 4							64.0	57.0	59.0					7																	107743496		2203	4300	6503	SO:0001819	synonymous_variant	22798	1	121408	33				g.chr7:107743496C>T	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.1173G>A	chr7.hg19:g.107743496C>T		1					LAMB4_ENST00000414450.2_Silent_p.A391A|LAMB4_ENST00000205386.4_Silent_p.A391A|LAMB4_ENST00000388780.3_Silent_p.A391A|LAMB4_ENST00000418464.1_Silent_p.A391A	p.A391A	NM_007356.2	NP_031382.2	0	3	3	1.672992	A4D0S4	LAMB4_HUMAN		10	1256	-			A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	1	1	hg19	c.1173G>A	CCDS34732.1	1																																																																																								0.627792		TCGA-IB-A7LX-01A-12D-A36O-08	0.577	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	1	0	1	2	2	2	2	0	0	0	0	34	34	34	34	1	3.150000	-20.000000	1	0.550000	XM_209857		0	22	22	0	78	75	1		1			0	0	34	0	0	0.999999	0	0	0	0	0	0	22	78
TSPAN33	340348	broad.mit.edu	37	7	128801559	128801559	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:128801559C>A	ENST00000289407.4	+	2	251	c.142C>A	c.(142-144)Cgg>Agg	p.R48R		NM_178562.3	NP_848657.1	Q86UF1	TSN33_HUMAN	tetraspanin 33	48					establishment of protein localization to plasma membrane (GO:0090002)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14						TGTCTACGCTCGGCTAATGAA	0.582																																						ENST00000289407.4	1.000000	0.110000	1	1.500000e-01	0.210000	0.349124	0.210000	0.200000																										0				14						c.(142-144)Cgg>Agg		tetraspanin 33							247.0	192.0	210.0					7																	128801559		2203	4300	6503	SO:0001819	synonymous_variant	340348	0	0					g.chr7:128801559C>A		CCDS5810.1	7q32.3	2013-02-14			ENSG00000158457	ENSG00000158457		"""Tetraspanins"""	28743	protein-coding gene	gene with protein product		610120				16213355, 16242907	Standard	XM_006715960		Approved	MGC50844, Penumbra	uc003vop.2	Q86UF1	OTTHUMG00000158420	ENST00000289407.4:c.142C>A	chr7.hg19:g.128801559C>A		1						p.R48R	NM_178562.3	NP_848657.1	0	3	3	1.672992	Q86UF1	TSN33_HUMAN		2	251	+				Silent	SNP	ENST00000289407.4	1	0	hg19	c.142C>A	CCDS5810.1	0																																																																																								0.627792		TCGA-IB-A7LX-01A-12D-A36O-08	0.582	TSPAN33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350983.1	1	0	1	2	2	2	2	0	0	0	0	92	92	92	91	1	3.150000	-2.890505	1	0.550000	NM_178562		0	13	13	0	275	271	0		1	0		0	0	92	0	0	0.999523	7.192633e-03	0	0	0	3	0	13	275
ZC3HC1	51530	broad.mit.edu	37	7	129658541	129658541	+	Missense_Mutation	SNP	C	C	A	rs374729873		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:129658541C>A	ENST00000358303.4	-	10	1556	c.1472G>T	c.(1471-1473)cGa>cTa	p.R491L	ZC3HC1_ENST00000481503.1_Missense_Mutation_p.R448L|RP11-306G20.1_ENST00000480018.1_RNA|RP11-306G20.1_ENST00000587038.1_RNA|ZC3HC1_ENST00000311873.5_Missense_Mutation_p.R470L|ZC3HC1_ENST00000360708.5_Missense_Mutation_p.R420L	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	491					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.R491Q(1)		endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					CCGAAATATTCGGAATACTTT	0.393																																					Melanoma(115;540 1606 16325 28853 48167)	ENST00000358303.4	1.000000	0.100000	1	1.400000e-01	0.190000	0.333253	0.190000	0.190000																										1	Substitution - Missense(1)	p.R491Q(1)	endometrium(1)	22						c.(1471-1473)cGa>cTa		zinc finger, C3HC-type containing 1							93.0	98.0	96.0					7																	129658541		2203	4300	6503	SO:0001583	missense	51530	0	0					g.chr7:129658541C>A	AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"""Zinc fingers, C3HC-type"""	29913	protein-coding gene	gene with protein product	"""nuclear interaction partner of ALK"""					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.1472G>T	chr7.hg19:g.129658541C>A	ENSP00000351052:p.Arg491Leu	1					RP11-306G20.1_ENST00000480018.1_RNA|ZC3HC1_ENST00000360708.5_Missense_Mutation_p.R420L|ZC3HC1_ENST00000311873.5_Missense_Mutation_p.R470L|ZC3HC1_ENST00000481503.1_Missense_Mutation_p.R448L|RP11-306G20.1_ENST00000587038.1_RNA	p.R491L	NM_016478.3	NP_057562.3	0	3	3	1.672992	Q86WB0	NIPA_HUMAN		10	1556	-	Melanoma(18;0.0435)		A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Missense_Mutation	SNP	ENST00000358303.4	1	0	hg19	c.1472G>T	CCDS34753.1	0	.	.	.	.	.	.	.	.	.	.	C	21.0	4.081950	0.76528	.	.	ENSG00000091732	ENST00000358303;ENST00000360708;ENST00000311873;ENST00000481503	T;T;T;T	0.54675	1.21;0.62;1.24;0.56	6.17	6.17	0.99709	6.17	6.17	0.99709	.	0.237648	0.36628	N	0.002486	T	0.71099	0.3300	M	0.62723	1.935	0.47737	D	0.9995	D;D;D	0.89917	1.0;0.974;0.987	D;P;P	0.77004	0.989;0.576;0.698	T	0.70651	-0.4813	10	0.66056	D	0.02	-8.1694	17.5987	0.88020	0.0:1.0:0.0:0.0	.	420;491;448	Q86WB0-3;Q86WB0;C9J0I9	.;NIPA_HUMAN;.	L	491;420;470;448	ENSP00000351052:R491L;ENSP00000353933:R420L;ENSP00000309301:R470L;ENSP00000418533:R448L	ENSP00000309301:R470L	R	-	2	0	0	ZC3HC1	129445777	129445777	1.000000	0.71417	1.000000	0.80357	0.384000	0.30261	3.871000	0.56077	2.941000	0.99782	0.655000	0.94253	CGA	0.627792		TCGA-IB-A7LX-01A-12D-A36O-08	0.393	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	1	0	1	2	2	2	2	0	0	0	0	88	88	88	86	1	3.150000	-3.027710	1	0.550000	NM_016478		0	13	12	0	304	299	0		1	0		0	0	88	0	0	0.999502	2.680249e-01	0	0	0	23	0	13	304
UBE2D4	51619	broad.mit.edu	37	7	43990227	43990227	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:43990227G>T	ENST00000222402.3	+	6	423	c.334G>T	c.(334-336)Gac>Tac	p.D112Y	UBE2D4_ENST00000394798.4_Missense_Mutation_p.D74Y|POLR2J4_ENST00000427076.1_RNA|RP5-1165K10.2_ENST00000454572.1_RNA	NM_015983.3	NP_057067.1	Q9Y2X8	UB2D4_HUMAN	ubiquitin-conjugating enzyme E2D 4 (putative)	112					protein K11-linked ubiquitination (GO:0070979)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|large_intestine(2)|lung(1)|pancreas(1)	5						GCTGCTCTGCGACCCCAACCC	0.562																																					Esophageal Squamous(27;401 815 16344 30604)	ENST00000222402.3	1.000000	0.160000	1	2.400000e-01	0.340000	0.484510	0.340000	0.300000																										0				5						c.(334-336)Gac>Tac		ubiquitin-conjugating enzyme E2D 4 (putative)							126.0	112.0	117.0					7																	43990227		2203	4300	6503	SO:0001583	missense	51619	0	0					g.chr7:43990227G>T	BC004104	CCDS5474.1	7p13	2005-08-11			ENSG00000078967	ENSG00000078967		"""Ubiquitin-conjugating enzymes E2"""	21647	protein-coding gene	gene with protein product						12690205	Standard	NM_015983		Approved	HBUCE1	uc003tja.2	Q9Y2X8	OTTHUMG00000128971	ENST00000222402.3:c.334G>T	chr7.hg19:g.43990227G>T	ENSP00000222402:p.Asp112Tyr	1					RP5-1165K10.2_ENST00000454572.1_RNA|POLR2J4_ENST00000427076.1_RNA|UBE2D4_ENST00000394798.4_Missense_Mutation_p.D74Y	p.D112Y	NM_015983.3	NP_057067.1	2	4	6	2.227293	Q9Y2X8	UB2D4_HUMAN		6	423	+			A4D1V0	Missense_Mutation	SNP	ENST00000222402.3	1	0	hg19	c.334G>T	CCDS5474.1	0	.	.	.	.	.	.	.	.	.	.	G	20.6	4.025689	0.75390	.	.	ENSG00000078967	ENST00000222402;ENST00000394798	T;T	0.73789	-0.78;-0.78	4.49	3.61	0.41365	4.49	3.61	0.41365	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.055533	0.64402	D	0.000002	D	0.86834	0.6028	M	0.90369	3.11	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.77557	0.976;0.99	D	0.87620	0.2509	10	0.87932	D	0	.	10.2569	0.43403	0.0996:0.0:0.9004:0.0	.	74;112	Q9UQL0;Q9Y2X8	.;UB2D4_HUMAN	Y	112;74	ENSP00000222402:D112Y;ENSP00000378277:D74Y	ENSP00000222402:D112Y	D	+	1	0	0	UBE2D4	43956752	43956752	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.286000	0.89916	0.885000	0.36088	0.655000	0.94253	GAC	0.694501		TCGA-IB-A7LX-01A-12D-A36O-08	0.562	UBE2D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250958.2	1	0	1	2	2	2	2	0	0	0	0	41	41	41	39	1	3.150000	-3.220448	1	0.550000	NM_015983		0	11	11	0	185	183	0		1	0		0	0	41	0	0	0.998390	6.120975e-01	0	0	0	35	0	11	185
DYNC1I1	1780	broad.mit.edu	37	7	95665004	95665004	+	Missense_Mutation	SNP	T	T	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:95665004T>A	ENST00000324972.6	+	13	1548	c.1355T>A	c.(1354-1356)gTc>gAc	p.V452D	DYNC1I1_ENST00000497626.1_3'UTR|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.V415D|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.V435D|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.V435D|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.V415D|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.V432D	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	452					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)			NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			ACGGGAGACGTCAATAACTTC	0.463																																						ENST00000324972.6	1.000000	0.570000	1	6.400000e-01	0.720000	0.769685	0.720000	0.730000																										0				54						c.(1354-1356)gTc>gAc		dynein, cytoplasmic 1, intermediate chain 1							323.0	260.0	282.0					7																	95665004		2203	4300	6503	SO:0001583	missense	1780	0	0					g.chr7:95665004T>A	AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"""Cytoplasmic dyneins"", ""WD repeat domain containing"""	2963	protein-coding gene	gene with protein product		603772	"""dynein, cytoplasmic, intermediate polypeptide 1"""	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.1355T>A	chr7.hg19:g.95665004T>A	ENSP00000320130:p.Val452Asp	1					DYNC1I1_ENST00000537881.1_Missense_Mutation_p.V415D|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.V432D|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.V435D|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.V435D|DYNC1I1_ENST00000497626.1_3'UTR|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.V415D	p.V452D	NM_004411.4	NP_004402.1	3	6	9	3.443848	O14576	DC1I1_HUMAN	STAD - Stomach adenocarcinoma(171;0.0957)	13	1548	+	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	1	1	hg19	c.1355T>A	CCDS5644.1	0	.	.	.	.	.	.	.	.	.	.	T	16.60	3.168707	0.57584	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	5.1	5.1	0.69264	5.1	5.1	0.69264	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.85673	0.5751	M	0.74546	2.27	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.997;0.996	D;D;D;D;D	0.78314	0.979;0.991;0.991;0.969;0.923	T	0.82631	-0.0362	10	0.11182	T	0.66	0.0118	15.3616	0.74478	0.0:0.0:0.0:1.0	.	435;432;435;452;415	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	D	435;452;415;432;415;435	ENSP00000392337:V435D;ENSP00000320130:V452D;ENSP00000438377:V415D;ENSP00000398118:V432D;ENSP00000352348:V415D;ENSP00000412444:V435D	ENSP00000320130:V452D	V	+	2	0	0	DYNC1I1	95502940	95502940	1.000000	0.71417	1.000000	0.80357	0.120000	0.20174	7.868000	0.87116	2.283000	0.76528	0.477000	0.44152	GTC	0.801806		TCGA-IB-A7LX-01A-12D-A36O-08	0.463	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	1	0	1	2	2	2	2	0	0	0	0	231	231	231	227	1	3.150000	-19.999790	1	0.550000	NM_004411		0	103	102	0	1111	1092	0		1	0		0	0	231	0	0	1.000000	0	0	0	0	1	0	103	1111
UBE3C	9690	broad.mit.edu	37	7	156961790	156961790	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr7:156961790C>A	ENST00000348165.5	+	3	529	c.169C>A	c.(169-171)Cga>Aga	p.R57R	UBE3C_ENST00000389103.4_Intron	NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	57	Cis-determinant of acceptor ubiquitin- binding.|IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		GTCATTTATTCGAGGCTATAG	0.363																																						ENST00000348165.5	1.000000	0.110000	1	1.600000e-01	0.230000	0.364627	0.230000	0.210000																										0				63						c.(169-171)Cga>Aga		ubiquitin protein ligase E3C							93.0	90.0	91.0					7																	156961790		2203	4300	6503	SO:0001819	synonymous_variant	9690	0	0					g.chr7:156961790C>A	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.169C>A	chr7.hg19:g.156961790C>A		1					UBE3C_ENST00000389103.4_Intron	p.R57R	NM_014671.2	NP_055486.2	0	3	3	1.671923	Q15386	UBE3C_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	3	529	+		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Silent	SNP	ENST00000348165.5	1	0	hg19	c.169C>A	CCDS34789.1	0																																																																																								0.626943		TCGA-IB-A7LX-01A-12D-A36O-08	0.363	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	1	0	1	2	2	2	2	0	0	0	0	65	65	65	65	1	3.150000	-2.926263	1	0.550000	NM_014671		0	12	12	0	238	236	0		1	0		0	0	65	0	0	0.999140	6.664925e-01	0	0	0	46	0	12	238
PPP1R3B	79660	broad.mit.edu	37	8	8998916	8998916	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr8:8998916G>T	ENST00000310455.3	-	2	396	c.246C>A	c.(244-246)ttC>ttA	p.F82L	PPP1R3B_ENST00000519699.1_Missense_Mutation_p.F82L|RP11-10A14.3_ENST00000520017.1_RNA|RP11-10A14.3_ENST00000522057.1_RNA	NM_001201329.1|NM_024607.3	NP_001188258.1|NP_078883.2	Q86XI6	PPR3B_HUMAN	protein phosphatase 1, regulatory subunit 3B	82					glycogen metabolic process (GO:0005977)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)	glycogen granule (GO:0042587)|intracellular membrane-bounded organelle (GO:0043231)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase regulator activity (GO:0019888)			endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	12				COAD - Colon adenocarcinoma(149;0.0717)|READ - Rectum adenocarcinoma(644;0.241)		GCGGGTCATCGAATTCCGAGA	0.532																																						ENST00000310455.3	0.220000	0.060000	1.700000e-01	9.000000e-02	0.120000	0.136422	0.120000	0.120000																										0				12						c.(244-246)ttC>ttA		protein phosphatase 1, regulatory subunit 3B							118.0	111.0	113.0					8																	8998916		2203	4300	6503	SO:0001583	missense	79660	0	0					g.chr8:8998916G>T	AK024067	CCDS5973.1	8p23.1	2012-04-17	2011-10-04		ENSG00000173281	ENSG00000173281		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14942	protein-coding gene	gene with protein product	"""PP1 subunit R4"", ""hepatic glycogen-targeting subunit, G(L)"""	610541	"""protein phosphatase 1, regulatory (inhibitor) subunit 3B"""			11948623, 17555403	Standard	NM_024607		Approved	GL, FLJ14005, PPP1R4	uc003wsn.4	Q86XI6	OTTHUMG00000129329	ENST00000310455.3:c.246C>A	chr8.hg19:g.8998916G>T	ENSP00000308318:p.Phe82Leu	1					RP11-10A14.3_ENST00000520017.1_RNA|RP11-10A14.3_ENST00000522057.1_RNA|PPP1R3B_ENST00000519699.1_Missense_Mutation_p.F82L	p.F82L	NM_001201329.1|NM_024607.3	NP_001188258.1|NP_078883.2	0	2	2	1.565375	Q86XI6	PPR3B_HUMAN		2	396	-			B3KTV3|Q9H812	Missense_Mutation	SNP	ENST00000310455.3	1	0	hg19	c.246C>A	CCDS5973.1	0	.	.	.	.	.	.	.	.	.	.	G	12.70	2.017814	0.35606	.	.	ENSG00000173281	ENST00000310455;ENST00000519699	T;T	0.43688	0.94;0.94	5.68	-8.12	0.01078	5.68	-8.12	0.01078	.	0.097783	0.64402	D	0.000001	T	0.30792	0.0776	L	0.51914	1.62	0.35771	D	0.820934	D	0.57571	0.98	P	0.46543	0.52	T	0.62464	-0.6849	10	0.09590	T	0.72	-25.5449	13.8132	0.63276	0.6793:0.0811:0.2396:0.0	.	82	Q86XI6	PPR3B_HUMAN	L	82	ENSP00000308318:F82L;ENSP00000428642:F82L	ENSP00000308318:F82L	F	-	3	2	2	PPP1R3B	9036326	9036326	0.005000	0.15991	0.630000	0.29268	0.844000	0.47949	-0.829000	0.04415	-1.404000	0.02050	-0.254000	0.11334	TTC	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.532	PPP1R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251472.1	1	0	1	2	11	3	2	1	1	1	1	117	117	117	117	1	3.150000	-3.046002	1	0.550000	NM_024607		0	11	11	0	306	303	0		1	0		1	0	117	0	0	0.573693	1.171865e-01	0	0	0	31	0	11	306
KCTD9	54793	broad.mit.edu	37	8	25296876	25296876	+	Silent	SNP	G	G	T	rs368385732		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr8:25296876G>T	ENST00000221200.4	-	6	638	c.418C>A	c.(418-420)Cga>Aga	p.R140R	KCTD9_ENST00000518067.1_5'UTR	NM_017634.3	NP_060104.2	Q7L273	KCTD9_HUMAN	potassium channel tetramerization domain containing 9	140	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein homooligomerization (GO:0051260)					breast(1)|endometrium(2)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)	12		all_cancers(63;0.0164)|Ovarian(32;0.000878)|all_epithelial(46;0.00542)|Breast(100;0.0164)|Hepatocellular(4;0.114)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Epithelial(17;2.39e-12)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0438)		TCAGGACTTCGGTCAATTAAG	0.368																																						ENST00000221200.4	0.210000	0.040000	1.600000e-01	6.000000e-02	0.100000	0.118473	0.100000	0.100000																										0				12						c.(418-420)Cga>Aga		potassium channel tetramerization domain containing 9							40.0	40.0	40.0					8																	25296876		2203	4299	6502	SO:0001819	synonymous_variant	54793	0	0					g.chr8:25296876G>T	BC021216	CCDS6048.1	8p21.1	2013-06-20	2013-06-20		ENSG00000104756	ENSG00000104756		"""BTB/POZ domain containing"""	22401	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 9"""			11483580	Standard	NM_017634		Approved	FLJ20038, BTBD27	uc003xeo.3	Q7L273	OTTHUMG00000099428	ENST00000221200.4:c.418C>A	chr8.hg19:g.25296876G>T		1					KCTD9_ENST00000518067.1_5'UTR	p.R140R	NM_017634.3	NP_060104.2	0	2	2	1.555864	Q7L273	KCTD9_HUMAN		6	638	-		all_cancers(63;0.0164)|Ovarian(32;0.000878)|all_epithelial(46;0.00542)|Breast(100;0.0164)|Hepatocellular(4;0.114)|Prostate(55;0.191)	Q6NUM8|Q9NXV4	Silent	SNP	ENST00000221200.4	1	1	hg19	c.418C>A	CCDS6048.1	0																																																																																								0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.368	KCTD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216890.1	1	0	1	2	2	2	2	0	0	0	0	73	73	73	73	1	3.150000	-2.614836	1	0.550000	NM_017634		0	6	6	0	206	201	0		1	0		0	0	73	0	0	0.962974	2.118032e-01	0	0	0	26	0	6	206
PREX2	80243	broad.mit.edu	37	8	68981315	68981315	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr8:68981315C>T	ENST00000288368.4	+	12	1664	c.1387C>T	c.(1387-1389)Cgc>Tgc	p.R463C	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	463	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.R463C(2)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						ATATAGATTTCGCTATGATGA	0.348																																						ENST00000288368.4	1.000000	0.990000	1	9.900000e-01	0.990000	1.000000	0.990000	1.000000																										2	Substitution - Missense(2)	p.R463C(2)	skin(2)	178						c.(1387-1389)Cgc>Tgc		phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2							76.0	71.0	73.0					8																	68981315		2203	4300	6503	SO:0001583	missense	80243	0	0					g.chr8:68981315C>T	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1387C>T	chr8.hg19:g.68981315C>T	ENSP00000288368:p.Arg463Cys	1					PREX2_ENST00000529398.1_3'UTR	p.R463C	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	1	2	3	1.925306	Q70Z35	PREX2_HUMAN		12	1664	+			B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	1	1	hg19	c.1387C>T	CCDS6201.1	1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.751767	0.89753	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.14391	2.51	5.72	4.84	0.62591	5.72	4.84	0.62591	DEP domain (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.34193	0.0889	L	0.60904	1.88	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.991;0.996	T	0.08576	-1.0715	10	0.87932	D	0	.	15.0201	0.71624	0.0:0.9317:0.0:0.0683	.	463;463;463	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	C	463	ENSP00000288368:R463C	ENSP00000288368:R463C	R	+	1	0	0	PREX2	69143869	69143869	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.566000	0.82347	1.559000	0.49555	0.650000	0.86243	CGC	0.641648		TCGA-IB-A7LX-01A-12D-A36O-08	0.348	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	1	0	1	2	2	2	2	0	0	0	0	51	51	51	50	1	3.150000	-11.491400	1	0.550000	NM_025170		0	74	74	0	122	122	1		1	0		0	0	51	0	0	1.000000	4.872542e-01	0	0	0	4	0	74	122
JPH1	56704	broad.mit.edu	37	8	75227735	75227735	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr8:75227735C>T	ENST00000342232.4	-	2	540	c.500G>A	c.(499-501)cGc>cAc	p.R167H		NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1	167					calcium ion transport into cytosol (GO:0060402)|muscle organ development (GO:0007517)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			CTGCTCGCTGCGCAGCGAGGC	0.721																																						ENST00000342232.4	1.000000	0.170000	5.900000e-01	2.700000e-01	0.400000	0.445188	0.400000	0.380000																										0				24						c.(499-501)cGc>cAc		junctophilin 1							13.0	13.0	13.0					8																	75227735		2125	4151	6276	SO:0001583	missense	56704	0	0					g.chr8:75227735C>T	AB042634	CCDS6217.1	8q21	2008-07-03			ENSG00000104369	ENSG00000104369			14201	protein-coding gene	gene with protein product		605266				10891348, 10949023	Standard	XM_005251273		Approved	JP-1	uc003yae.3	Q9HDC5	OTTHUMG00000164524	ENST00000342232.4:c.500G>A	chr8.hg19:g.75227735C>T	ENSP00000344488:p.Arg167His	1						p.R167H	NM_020647.2	NP_065698.1	1	2	3	1.925306	Q9HDC5	JPH1_HUMAN	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)	2	540	-	Breast(64;0.00576)		B2RTZ0	Missense_Mutation	SNP	ENST00000342232.4	1	1	hg19	c.500G>A	CCDS6217.1	0	.	.	.	.	.	.	.	.	.	.	C	33	5.214836	0.95104	.	.	ENSG00000104369	ENST00000342232	T	0.63913	-0.07	4.43	4.43	0.53597	4.43	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.80428	0.4621	M	0.82193	2.58	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.82824	-0.0266	10	0.49607	T	0.09	.	17.2378	0.87004	0.0:1.0:0.0:0.0	.	167	Q9HDC5	JPH1_HUMAN	H	167	ENSP00000344488:R167H	ENSP00000344488:R167H	R	-	2	0	0	JPH1	75390290	75390290	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.489000	0.81451	2.284000	0.76573	0.655000	0.94253	CGC	0.641648		TCGA-IB-A7LX-01A-12D-A36O-08	0.721	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379102.1	1	0	1	2	2	2	2	0	0	0	0	27	27	27	27	1	3.150000	-12.727030	1	0.550000			0	7	7	0	79	74	0		1	0		0	0	27	0	0	0.977793	1.332411e-01	0	1	0	6	0	7	79
CSMD3	114788	broad.mit.edu	37	8	113599442	113599442	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr8:113599442C>A	ENST00000297405.5	-	23	3982	c.3738G>T	c.(3736-3738)acG>acT	p.T1246T	CSMD3_ENST00000455883.2_Silent_p.T1142T|CSMD3_ENST00000343508.3_Silent_p.T1206T|CSMD3_ENST00000352409.3_Silent_p.T1246T	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1246	CUB 7. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CTTCATTATTCGTTGCAGATG	0.353										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																												ENST00000297405.5	0.420000	0.180000	3.600000e-01	2.300000e-01	0.290000	0.302985	0.290000	0.300000																										0				646						c.(3736-3738)acG>acT		CUB and Sushi multiple domains 3							113.0	108.0	110.0					8																	113599442		2203	4299	6502	SO:0001819	synonymous_variant	114788	0	0					g.chr8:113599442C>A	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3738G>T	chr8.hg19:g.113599442C>A		1	HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)				CSMD3_ENST00000352409.3_Silent_p.T1246T|CSMD3_ENST00000455883.2_Silent_p.T1142T|CSMD3_ENST00000343508.3_Silent_p.T1206T	p.T1246T	NM_198123.1	NP_937756.1	2	4	6	3.192915	Q7Z407	CSMD3_HUMAN		23	3982	-			Q96PZ3	Silent	SNP	ENST00000297405.5	1	0	hg19	c.3738G>T	CCDS6315.1	0																																																																																								0.785714		TCGA-IB-A7LX-01A-12D-A36O-08	0.353	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	1	0	1	2	18	2	2	0	0	0	1	124	124	124	124	1	3.150000	-3.079016	1	0.550000	NM_052900		0	25	24	0	628	622	0		1			0	0	124	0	0	0.885077	0	0	0	0	0	0	25	628
SLC24A2	25769	broad.mit.edu	37	9	19516253	19516253	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr9:19516253C>A	ENST00000341998.2	-	10	1945	c.1884G>T	c.(1882-1884)atG>atT	p.M628I	SLC24A2_ENST00000286344.3_Missense_Mutation_p.M611I	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	628					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)			endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		GGATTTTGTTCATTCGCCACT	0.502																																						ENST00000341998.2	1.000000	0.100000	1	1.400000e-01	0.190000	0.321835	0.190000	0.170000																										0				33						c.(1882-1884)atG>atT		solute carrier family 24 (sodium/potassium/calcium exchanger), member 2							136.0	127.0	130.0					9																	19516253		2203	4300	6503	SO:0001583	missense	25769	0	0					g.chr9:19516253C>A	AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"""Solute carriers"""	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.1884G>T	chr9.hg19:g.19516253C>A	ENSP00000344801:p.Met628Ile	1					SLC24A2_ENST00000286344.3_Missense_Mutation_p.M611I	p.M628I	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	0	3	3	1.727980	Q9UI40	NCKX2_HUMAN		10	1945	-			B7ZLL8|Q9NTN5|Q9NZQ4	Missense_Mutation	SNP	ENST00000341998.2	1	0	hg19	c.1884G>T	CCDS6493.1	0	.	.	.	.	.	.	.	.	.	.	C	26.2	4.710039	0.89018	.	.	ENSG00000155886	ENST00000341998;ENST00000286344	T;T	0.59502	0.26;0.26	5.07	5.07	0.68467	5.07	5.07	0.68467	Sodium/calcium exchanger membrane region (1);	0.000000	0.85682	D	0.000000	T	0.67392	0.2888	L	0.33753	1.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.985;1.0	T	0.65492	-0.6155	9	.	.	.	.	18.4603	0.90736	0.0:1.0:0.0:0.0	.	611;628	Q9UI40-2;Q9UI40	.;NCKX2_HUMAN	I	628;611	ENSP00000344801:M628I;ENSP00000286344:M611I	.	M	-	3	0	0	SLC24A2	19506253	19506253	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.771000	0.85420	2.351000	0.79841	0.655000	0.94253	ATG	0.629477		TCGA-IB-A7LX-01A-12D-A36O-08	0.502	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	1	0	1	2	2	2	2	0	0	0	0	152	152	152	152	1	3.150000	-3.036471	1	0.550000	NM_020344		0	17	17	0	400	397	0		1	0		0	0	152	0	0	0.999965	1.943403e-03	0	0	0	2	0	17	400
IKBKAP	8518	broad.mit.edu	37	9	111679935	111679935	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chr9:111679935C>A	ENST00000374647.5	-	9	1063	c.756G>T	c.(754-756)ttG>ttT	p.L252F	IKBKAP_ENST00000537196.1_5'UTR	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	252					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TAGATGCAATCAAACTGCCTG	0.373																																						ENST00000374647.5	0.230000	0.090000	1.900000e-01	1.200000e-01	0.150000	0.162125	0.150000	0.160000																										0				53						c.(754-756)ttG>ttT		inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein							163.0	165.0	164.0					9																	111679935		2203	4300	6503	SO:0001583	missense	8518	0	0					g.chr9:111679935C>A	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.756G>T	chr9.hg19:g.111679935C>A	ENSP00000363779:p.Leu252Phe	1					IKBKAP_ENST00000537196.1_5'UTR	p.L252F	NM_003640.3	NP_003631.2	0	2	2	1.589671	O95163	ELP1_HUMAN		9	1063	-			Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	1	0	hg19	c.756G>T	CCDS6773.1	0	.	.	.	.	.	.	.	.	.	.	C	21.0	4.081679	0.76528	.	.	ENSG00000070061	ENST00000374647	T	0.37752	1.18	5.29	5.29	0.74685	5.29	5.29	0.74685	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.61350	0.2340	M	0.85859	2.78	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.65150	-0.6238	10	0.59425	D	0.04	-0.7514	10.2761	0.43510	0.0:0.9096:0.0:0.0904	.	252	O95163	ELP1_HUMAN	F	252	ENSP00000363779:L252F	ENSP00000363779:L252F	L	-	3	2	2	IKBKAP	110719756	110719756	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.861000	0.48380	2.642000	0.89623	0.561000	0.74099	TTG	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.373	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1	1	0	1	2	2	2	2	0	0	0	0	159	159	159	158	1	3.150000	-3.959990	1	0.550000			0	22	22	0	491	483	0		1	0		0	0	159	0	0	0.999999	8.563759e-02	0	0	0	11	0	22	491
EGFL6	25975	broad.mit.edu	37	X	13645269	13645269	+	Silent	SNP	C	C	A	rs200962676		TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:13645269C>A	ENST00000361306.1	+	11	1682	c.1425C>A	c.(1423-1425)gtC>gtA	p.V475V	EGFL6_ENST00000380602.3_Silent_p.V476V	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	475	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						GAGACAAAGTCGGGAAACTTC	0.468																																						ENST00000361306.1	0.190000	0.060000	1.500000e-01	8.000000e-02	0.110000	0.121313	0.110000	0.110000																										0				23						c.(1423-1425)gtC>gtA		EGF-like-domain, multiple 6							113.0	103.0	106.0					X																	13645269		2203	4300	6503	SO:0001819	synonymous_variant	25975	0	0					g.chrX:13645269C>A	AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"""MAM and EGF domain containing"""	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.1425C>A	chrX.hg19:g.13645269C>A							EGFL6_ENST00000380602.3_Silent_p.V476V	p.V475V	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	0	1	1		Q8IUX8	EGFL6_HUMAN		11	1682	+			B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Silent	SNP	ENST00000361306.1	1	0	hg19	c.1425C>A	CCDS14155.1	0																																																																																								0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.468	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	1	0	1	2	2	2	2	0	0	0	0	76	76	76	74	1	3.150000	-2.917043	1	0.550000	NM_015507		0	12	12	0	180	176	0		1	0		0	0	76	0	0	0.999130	9.920691e-02	0	0	0	8	0	12	180
SLC9A6	10479	broad.mit.edu	37	X	135076969	135076969	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:135076969G>T	ENST00000370698.3	+	2	385	c.350G>T	c.(349-351)cGg>cTg	p.R117L	SLC9A6_ENST00000370701.1_Missense_Mutation_p.R65L|SLC9A6_ENST00000370695.4_Missense_Mutation_p.R117L	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6	117					axon extension (GO:0048675)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|dendrite extension (GO:0097484)|dendritic spine development (GO:0060996)|ion transport (GO:0006811)|neuron projection morphogenesis (GO:0048812)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon terminus (GO:0043679)|axonal spine (GO:0044308)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)	sodium:proton antiporter activity (GO:0015385)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(18)|ovary(2)|upper_aerodigestive_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CTTGTGCTTCGGTATGGCATT	0.428																																						ENST00000370698.3	0.100000	0.030000	8.000000e-02	4.000000e-02	0.050000	0.065579	0.050000	0.060000																										0				33						c.(349-351)cGg>cTg		solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6							227.0	171.0	190.0					X																	135076969		2203	4300	6503	SO:0001583	missense	10479	0	0					g.chrX:135076969G>T	AF030409	CCDS14654.1, CCDS44003.1, CCDS55504.1	Xq26.3	2013-05-22	2012-03-22		ENSG00000198689	ENSG00000198689		"""Solute carriers"""	11079	protein-coding gene	gene with protein product		300231	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 6"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 6"""			9507001	Standard	NM_001042537		Approved	NHE6, KIAA0267	uc004ezk.3	Q92581	OTTHUMG00000022498	ENST00000370698.3:c.350G>T	chrX.hg19:g.135076969G>T	ENSP00000359732:p.Arg117Leu						SLC9A6_ENST00000370695.4_Missense_Mutation_p.R117L|SLC9A6_ENST00000370701.1_Missense_Mutation_p.R65L	p.R117L	NM_006359.2	NP_006350.1	0	1	1		Q92581	SL9A6_HUMAN		2	385	+	Acute lymphoblastic leukemia(192;0.000127)		A6NIQ9|A8K160|B4DU30|B7ZAE0|Q3ZCW7|Q5JPP8|Q5JPP9|Q86VS0	Missense_Mutation	SNP	ENST00000370698.3	1	0	hg19	c.350G>T	CCDS14654.1	0	.	.	.	.	.	.	.	.	.	.	G	29.9	5.048396	0.93740	.	.	ENSG00000198689	ENST00000370701;ENST00000370698;ENST00000370695	T;T;T	0.09817	2.94;2.94;2.94	5.07	5.07	0.68467	5.07	5.07	0.68467	Cation/H+ exchanger (1);	0.658813	0.16648	N	0.205338	T	0.20210	0.0486	L	0.39692	1.235	0.80722	D	1	P;P;P	0.50443	0.871;0.701;0.935	P;P;P	0.53809	0.667;0.462;0.735	T	0.00728	-1.1591	10	0.66056	D	0.02	.	16.6984	0.85342	0.0:0.0:1.0:0.0	.	65;117;117	B4DU30;Q92581-2;Q92581	.;.;SL9A6_HUMAN	L	65;117;117	ENSP00000359735:R65L;ENSP00000359732:R117L;ENSP00000359729:R117L	ENSP00000359729:R117L	R	+	2	0	0	SLC9A6	134904635	134904635	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.361000	0.97122	2.234000	0.73211	0.544000	0.68410	CGG	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.428	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058450.1	1	0	1	2	2	2	2	0	0	0	0	78	78	78	77	1	3.150000	-2.220510	0	0.550000	NM_006359		0	14	14	0	399	396	0		1	0		0	0	78	0	0	0.999752	1.269711e-01	0	0	0	17	0	14	399
CD99	4267	broad.mit.edu	37	X	2632474	2632474	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			G	T	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:2632474G>T	ENST00000381192.3	+	2	261	c.79G>T	c.(79-81)Gat>Tat	p.D27Y	CD99_ENST00000381187.3_Missense_Mutation_p.D27Y|CD99_ENST00000482405.2_3'UTR|CD99_ENST00000381184.1_Missense_Mutation_p.D27Y	NM_001277710.1|NM_002414.3	NP_001264639.1|NP_002405.1	P14209	CD99_HUMAN	CD99 molecule	27					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11						TGGTGGTTTCGATTTATCCGA	0.294																																						ENST00000381192.3	0.110000	0.040000	9.000000e-02	5.000000e-02	0.070000	0.078151	0.070000	0.080000																										0				11						c.(79-81)Gat>Tat		CD99 molecule							227.0	208.0	214.0					X																	2632474		2203	4296	6499	SO:0001583	missense	4267	0	0					g.chrX:2632474G>T	M16279	CCDS14119.1, CCDS48071.1, CCDS75947.1	Xp22.32 and Yp11.3	2012-10-02	2006-03-28	2003-02-14	ENSG00000002586	ENSG00000002586		"""Pseudoautosomal regions / PAR1"", ""CD molecules"""	7082	protein-coding gene	gene with protein product		313470, 450000	"""antigen identified by monoclonal antibodies 12E7, F21 and O13"", ""CD99 antigen"""	MIC2			Standard	NM_001122898		Approved		uc004cqm.3	P14209	OTTHUMG00000021073	ENST00000381192.3:c.79G>T	chrX.hg19:g.2632474G>T	ENSP00000370588:p.Asp27Tyr						CD99_ENST00000381187.3_Missense_Mutation_p.D27Y|CD99_ENST00000381184.1_Missense_Mutation_p.D27Y|CD99_ENST00000482405.2_3'UTR	p.D27Y	NM_001277710.1|NM_002414.3	NP_001264639.1|NP_002405.1	0	1	1		P14209	CD99_HUMAN		2	261	+			A6NIW1|O00518|Q6ICV7	Missense_Mutation	SNP	ENST00000381192.3	1	0	hg19	c.79G>T	CCDS14119.1	0	.	.	.	.	.	.	.	.	.	.	g	9.633	1.136817	0.21123	.	.	ENSG00000002586	ENST00000381192;ENST00000381187;ENST00000381184;ENST00000449611	T;T;T;T	0.49432	1.28;0.78;1.28;1.28	1.14	1.14	0.20703	1.14	1.14	0.20703	.	0.162784	0.36932	U	0.002338	T	0.56499	0.1989	L	0.59436	1.845	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.993;0.993;0.993	T	0.37663	-0.9696	10	0.72032	D	0.01	.	5.2921	0.15733	0.0:0.0:1.0:0.0	.	27;27;27	A6NIW1;B2R932;P14209	.;.;CD99_HUMAN	Y	27;27;27;70	ENSP00000370588:D27Y;ENSP00000370582:D27Y;ENSP00000370579:D27Y;ENSP00000405544:D70Y	ENSP00000370579:D27Y	D	+	1	0	0	CD99	2642474	2642474	0.069000	0.21087	0.025000	0.17156	0.016000	0.09150	1.398000	0.34554	0.857000	0.35407	0.429000	0.28392	GAT	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.294	CD99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055624.1	1	0	1	2	2	2	2	0	0	0	0	296	296	296	295	1	3.150000	-3.651936	1	0.550000	NM_001122898		0	25	24	0	577	567	0		1	0		0	0	296	0	0	1.000000	1	0	0	0	866	0	25	577
CXorf21	80231	broad.mit.edu	37	X	30577624	30577624	+	Silent	SNP	A	A	G			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:30577624A>G	ENST00000378962.3	-	3	1171	c.849T>C	c.(847-849)atT>atC	p.I283I		NM_025159.2	NP_079435.1	Q9HAI6	CX021_HUMAN	chromosome X open reading frame 21	283										kidney(1)|large_intestine(3)|lung(13)|ovary(1)|stomach(1)|urinary_tract(1)	20						TAATTTCAGTAATTTCAGTTG	0.378																																						ENST00000378962.3	0.130000	0.010000	1.000000e-01	3.000000e-02	0.050000	0.069476	0.050000	0.060000																										0				20						c.(847-849)atT>atC		chromosome X open reading frame 21							78.0	68.0	71.0					X																	30577624		2202	4300	6502	SO:0001819	synonymous_variant	80231	0	0					g.chrX:30577624A>G	BC020611	CCDS14224.1	Xp21.3	2006-04-12			ENSG00000120280	ENSG00000120280			25667	protein-coding gene	gene with protein product						12477932	Standard	NM_025159		Approved	FLJ11577	uc004dcg.2	Q9HAI6	OTTHUMG00000021325	ENST00000378962.3:c.849T>C	chrX.hg19:g.30577624A>G								p.I283I	NM_025159.2	NP_079435.1	0	1	1		Q9HAI6	CX021_HUMAN		3	1171	-				Silent	SNP	ENST00000378962.3	0	1	hg19	c.849T>C	CCDS14224.1	0																																																																																								0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.378	CXorf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056164.1	0	0	0	2	2	2	2	0	0	0	0	53	53	53	53	1	3.150000	-7.304968	1	0.550000	NM_025159		0	4	4	0	124	121	0		1	0		0	0	53	0	0	0.885915	5.097955e-03	0	0	0	3	0	4	124
BRWD3	254065	broad.mit.edu	37	X	79939559	79939559	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:79939559G>T	ENST00000373275.4	-	37	4399	c.4183C>A	c.(4183-4185)Cgc>Agc	p.R1395S	BRWD3_ENST00000473691.1_Intron	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1395	Bromo 2. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						AATATTTGGCGAACATCCTTA	0.348																																						ENST00000373275.4	0.130000	0.030000	1.100000e-01	5.000000e-02	0.070000	0.085278	0.070000	0.080000																										0				87						c.(4183-4185)Cgc>Agc		bromodomain and WD repeat domain containing 3							89.0	84.0	85.0					X																	79939559		2202	4297	6499	SO:0001583	missense	254065	0	0					g.chrX:79939559G>T		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"""WD repeat domain containing"""	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.4183C>A	chrX.hg19:g.79939559G>T	ENSP00000362372:p.Arg1395Ser						BRWD3_ENST00000473691.1_Intron	p.R1395S	NM_153252.4	NP_694984	0	1	1		Q6RI45	BRWD3_HUMAN		37	4399	-			C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	1	0	hg19	c.4183C>A	CCDS14447.1	0	.	.	.	.	.	.	.	.	.	.	G	25.0	4.596937	0.87055	.	.	ENSG00000165288	ENST00000373275	T	0.29142	1.58	4.66	4.66	0.58398	4.66	4.66	0.58398	Bromodomain (6);	0.051438	0.85682	D	0.000000	T	0.64571	0.2610	M	0.91459	3.21	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.74671	-0.3587	9	.	.	.	0.4745	16.8308	0.85944	0.0:0.0:1.0:0.0	.	1395	Q6RI45	BRWD3_HUMAN	S	1395	ENSP00000362372:R1395S	.	R	-	1	0	0	BRWD3	79826215	79826215	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.298000	0.78815	2.149000	0.67028	0.502000	0.49764	CGC	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.348	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	1	0	1	2	2	2	2	0	0	0	0	37	37	37	35	1	3.150000	-4.155208	1	0.550000	NM_153252		0	11	12	0	242	241	0		1	0		0	0	37	0	0	0.998438	2.091063e-01	0	0	0	17	0	11	242
NAP1L3	4675	broad.mit.edu	37	X	92926869	92926869	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:92926869T>C	ENST00000373079.3	-	1	1698	c.1435A>G	c.(1435-1437)Aaa>Gaa	p.K479E	NAP1L3_ENST00000475430.2_Missense_Mutation_p.K472E|FAM133A_ENST00000322139.4_5'Flank|FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000332647.4_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	479					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						TAGATTGATTTCAGGATGACA	0.363																																						ENST00000373079.3	0.140000	0.020000	1.100000e-01	4.000000e-02	0.060000	0.078009	0.060000	0.070000																										0				34						c.(1435-1437)Aaa>Gaa		nucleosome assembly protein 1-like 3							70.0	62.0	65.0					X																	92926869		2203	4300	6503	SO:0001583	missense	4675	0	0					g.chrX:92926869T>C		CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.1435A>G	chrX.hg19:g.92926869T>C	ENSP00000362171:p.Lys479Glu						FAM133A_ENST00000538690.1_5'Flank|NAP1L3_ENST00000475430.2_Missense_Mutation_p.K472E|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000322139.4_5'Flank|FAM133A_ENST00000332647.4_5'Flank	p.K479E	NM_004538.5	NP_004529.2	0	1	1		Q99457	NP1L3_HUMAN		1	1698	-			B2RCM0|O60788	Missense_Mutation	SNP	ENST00000373079.3	0	1	hg19	c.1435A>G	CCDS14465.1	0	.	.	.	.	.	.	.	.	.	.	T	12.32	1.902300	0.33628	.	.	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.25912	1.77	3.42	3.42	0.39159	3.42	3.42	0.39159	.	0.053033	0.64402	D	0.000001	T	0.34774	0.0909	L	0.46947	1.48	0.09310	N	1	D	0.63046	0.992	D	0.64410	0.925	T	0.07385	-1.0775	10	0.62326	D	0.03	.	4.6798	0.12729	0.0:0.1434:0.0:0.8566	.	479	Q99457	NP1L3_HUMAN	E	479;472	ENSP00000362171:K479E	ENSP00000362171:K479E	K	-	1	0	0	NAP1L3	92813525	92813525	0.998000	0.40836	0.715000	0.30552	0.719000	0.41307	1.448000	0.35112	1.588000	0.49971	0.430000	0.28490	AAA	0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.363	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	0	0	1	2	2	2	2	0	0	0	0	22	22	22	22	1	3.150000	-8.153669	1	0.550000	NM_004538		0	5	5	0	132	131	0		1	0		0	0	22	0	0	0.937518	1.199328e-02	0	0	0	4	0	5	132
GABRE	2564	broad.mit.edu	37	X	151124313	151124313	+	Silent	SNP	C	C	A			TCGA-IB-A7LX-01A-12D-A36O-08	TCGA-IB-A7LX-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b42e059c-cdb8-4a32-83d3-298334042c3e	1ad317bb-1738-4a90-a9a5-17f34cb9357e	g.chrX:151124313C>A	ENST00000370328.3	-	7	857	c.804G>T	c.(802-804)acG>acT	p.T268T	GABRE_ENST00000370325.1_Silent_p.T268T|AF274855.1_ENST00000582865.1_RNA|GABRE_ENST00000483564.1_5'UTR|MIR224_ENST00000384889.1_RNA	NM_004961.3	NP_004952.2	P78334	GBRE_HUMAN	gamma-aminobutyric acid (GABA) A receptor, epsilon	268					gamma-aminobutyric acid signaling pathway (GO:0007214)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|skin(1)	27	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGAAGAAAATCGTCATGACCA	0.478																																						ENST00000370328.3	0.120000	0.030000	1.000000e-01	5.000000e-02	0.070000	0.079514	0.070000	0.080000																										0				27						c.(802-804)acG>acT		gamma-aminobutyric acid (GABA) A receptor, epsilon	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)						157.0	122.0	134.0					X																	151124313		2203	4300	6503	SO:0001819	synonymous_variant	2564	0	0					g.chrX:151124313C>A	Y09765	CCDS14703.1	Xq28	2012-06-22			ENSG00000102287	ENSG00000102287		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4085	protein-coding gene	gene with protein product	"""GABA(A) receptor, epsilon"""	300093				9039914, 9084408	Standard	NM_004961		Approved		uc004ffi.3	P78334	OTTHUMG00000024176	ENST00000370328.3:c.804G>T	chrX.hg19:g.151124313C>A							AF274855.1_ENST00000582865.1_RNA|GABRE_ENST00000370325.1_Silent_p.T268T|GABRE_ENST00000483564.1_5'UTR|MIR224_ENST00000384889.1_RNA	p.T268T	NM_004961.3	NP_004952.2	0	1	1		P78334	GBRE_HUMAN		7	857	-	Acute lymphoblastic leukemia(192;6.56e-05)		E7ET93|O15345|O15346|Q6PCD2|Q99520	Silent	SNP	ENST00000370328.3	1	0	hg19	c.804G>T	CCDS14703.1	0																																																																																								0.550000		TCGA-IB-A7LX-01A-12D-A36O-08	0.478	GABRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060903.1	1	0	1	2	2	2	2	0	0	0	0	73	73	73	73	1	3.150000	-3.911315	1	0.550000	NM_004961, NM_021990, NM_021984		0	15	16	0	348	346	0		1	0		0	0	73	0	0	0.999877	9.958631e-01	0	0	0	211	0	15	348
