#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
KIAA1614	57710	broad.mit.edu	37	1	180907822	180907822	+	Missense_Mutation	SNP	G	G	A			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr1:180907822G>A	ENST00000367588.4	+	6	2948	c.2893G>A	c.(2893-2895)Gga>Aga	p.G965R	KIAA1614_ENST00000367587.1_Missense_Mutation_p.G586R	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	965	Ser-rich.									NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						GACAGGGTCAGGATCTGGAGG	0.582																																						ENST00000367588.4																			0				NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						c.(2893-2895)Gga>Aga		KIAA1614							69.0	76.0	74.0					1																	180907822		2150	4274	6424	SO:0001583	missense	57710							g.chr1:180907822G>A	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.2893G>A	1.37:g.180907822G>A	ENSP00000356560:p.Gly965Arg		Somatic				KIAA1614_ENST00000367587.1_Missense_Mutation_p.G586R	p.G965R	NM_020950.1	NP_066001.1	WXS	Illumina GAIIx	Phase_I	Q5VZ46	K1614_HUMAN			6	2948	+			965			Ser-rich.		Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	37	c.2893G>A	CCDS41442.1	.	.	.	.	.	.	.	.	.	.	G	7.261	0.605282	0.14002	.	.	ENSG00000135835	ENST00000367588;ENST00000367587	T;T	0.23147	2.49;1.92	4.6	-1.38	0.09027	.	1.213900	0.06011	N	0.649433	T	0.14485	0.0350	N	0.22421	0.69	0.25192	N	0.990126	B;B	0.09022	0.001;0.002	B;B	0.08055	0.001;0.003	T	0.32666	-0.9898	9	0.51188	T	0.08	0.306	1.2026	0.01888	0.329:0.3688:0.1216:0.1806	.	586;965	Q5VZ46-2;Q5VZ46	.;K1614_HUMAN	R	965;586	ENSP00000356560:G965R;ENSP00000356559:G586R	ENSP00000356559:G586R	G	+	1	0	KIAA1614	179174445	0.000000	0.05858	0.001000	0.08648	0.048000	0.14542	0.153000	0.16323	-0.083000	0.12618	0.561000	0.74099	GGA		0.582	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		3	49	3	49	---	---	---	---
IARS2	55699	broad.mit.edu	37	1	220273972	220273972	+	Silent	SNP	T	T	C			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr1:220273972T>C	ENST00000302637.5	+	3	635	c.531T>C	c.(529-531)gcT>gcC	p.A177A	IARS2_ENST00000366922.1_Silent_p.A105A	NM_018060.3	NP_060530.3	Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	177					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	ATCTTTCAGCTATGGAAATTA	0.348																																						ENST00000366922.1																			0				NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51						c.(313-315)gcT>gcC		isoleucyl-tRNA synthetase 2, mitochondrial	L-Isoleucine(DB00167)						54.0	60.0	58.0					1																	220273972		2203	4300	6503	SO:0001819	synonymous_variant	55699				isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity	g.chr1:220273972T>C	AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	6.1.1.5	"""Aminoacyl tRNA synthetases / Class I"""	29685	protein-coding gene	gene with protein product	"""isoleucine tRNA ligase 2, mitochondrial"""	612801					Standard	NM_018060		Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000302637.5:c.531T>C	1.37:g.220273972T>C			Somatic				IARS2_ENST00000302637.5_Silent_p.A177A	p.A105A			WXS	Illumina GAIIx	Phase_I	Q9NSE4	SYIM_HUMAN		GBM - Glioblastoma multiforme(131;0.0554)	3	646	+			177					B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	Silent	SNP	ENST00000302637.5	37	c.315T>C	CCDS1523.1																																																																																				0.348	IARS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018060		19	28	19	28	---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125547651	125547651	+	Silent	SNP	G	G	A			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr2:125547651G>A	ENST00000431078.1	+	18	3286	c.2922G>A	c.(2920-2922)gtG>gtA	p.V974V		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	974	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GCAAGTGTGTGGAGAAGCACA	0.557																																						ENST00000431078.1																			0				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176						c.(2920-2922)gtG>gtA		contactin associated protein-like 5							62.0	70.0	67.0					2																	125547651		2107	4223	6330	SO:0001819	synonymous_variant	129684				cell adhesion|signal transduction	integral to membrane	receptor binding	g.chr2:125547651G>A	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2922G>A	2.37:g.125547651G>A			Somatic					p.V974V	NM_130773.2	NP_570129.1	WXS	Illumina GAIIx	Phase_I	Q8WYK1	CNTP5_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.248)	18	3286	+			974			EGF-like 2.		Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	37	c.2922G>A	CCDS46401.1																																																																																				0.557	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			16	22	16	22	---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152322042	152322042	+	Missense_Mutation	SNP	A	A	C			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr2:152322042A>C	ENST00000243326.5	+	29	6491	c.6008A>C	c.(6007-6009)aAt>aCt	p.N2003T	RIF1_ENST00000453091.2_Missense_Mutation_p.N2003T|RIF1_ENST00000428287.2_Missense_Mutation_p.N2003T|RIF1_ENST00000430328.2_Missense_Mutation_p.N2003T|RIF1_ENST00000444746.2_Missense_Mutation_p.N2003T			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		GATGGAGGAAATGATGTATCT	0.368																																						ENST00000243326.5																			0				NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97						c.(6007-6009)aAt>aCt		RAP1 interacting factor homolog (yeast)							56.0	57.0	57.0					2																	152322042		2203	4300	6503	SO:0001583	missense	55183				cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding	g.chr2:152322042A>C	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.6008A>C	2.37:g.152322042A>C	ENSP00000243326:p.Asn2003Thr		Somatic				RIF1_ENST00000428287.2_Missense_Mutation_p.N2003T|RIF1_ENST00000444746.2_Missense_Mutation_p.N2003T|RIF1_ENST00000453091.2_Missense_Mutation_p.N2003T|RIF1_ENST00000430328.2_Missense_Mutation_p.N2003T	p.N2003T			WXS	Illumina GAIIx	Phase_I	Q5UIP0	RIF1_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0429)	29	6491	+						Interaction with condensed chromosomes in telophase.		A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	c.6008A>C	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	A	10.50	1.368755	0.24771	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.10668	2.87;2.85;2.85;2.87;2.85	5.6	-5.4	0.02656	.	1.269580	0.04585	N	0.395690	T	0.06781	0.0173	N	0.14661	0.345	0.09310	N	1	B;B	0.19706	0.022;0.038	B;B	0.15870	0.01;0.014	T	0.36529	-0.9744	10	0.19147	T	0.46	0.7654	13.8987	0.63790	0.7105:0.0:0.2895:0.0	.	2003;2003	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	T	2003	ENSP00000390181:N2003T;ENSP00000414615:N2003T;ENSP00000415691:N2003T;ENSP00000243326:N2003T;ENSP00000416123:N2003T	ENSP00000243326:N2003T	N	+	2	0	RIF1	152030288	0.130000	0.22417	0.000000	0.03702	0.001000	0.01503	0.438000	0.21559	-1.231000	0.02557	-0.917000	0.02746	AAT		0.368	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			8	15	8	15	---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33686339	33686339	+	Missense_Mutation	SNP	A	A	G			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr3:33686339A>G	ENST00000468888.2	-	8	818	c.772T>C	c.(772-774)Tca>Cca	p.S258P	CLASP2_ENST00000480013.1_Missense_Mutation_p.S25P|CLASP2_ENST00000539981.1_Missense_Mutation_p.S31P|CLASP2_ENST00000359576.5_Missense_Mutation_p.S258P|CLASP2_ENST00000307312.7_5'UTR|CLASP2_ENST00000333778.6_Missense_Mutation_p.S35P|CLASP2_ENST00000313350.6_Missense_Mutation_p.S31P|CLASP2_ENST00000461133.3_Missense_Mutation_p.S25P|CLASP2_ENST00000487200.1_Missense_Mutation_p.S31P|CLASP2_ENST00000399362.4_Missense_Mutation_p.S258P|CLASP2_ENST00000482896.1_5'UTR			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	25					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						TTGAAGGCTGATGCAGCTGAT	0.438																																						ENST00000399362.4																			0				breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						c.(772-774)Tca>Cca		cytoplasmic linker associated protein 2							98.0	93.0	94.0					3																	33686339		1954	4157	6111	SO:0001583	missense	23122							g.chr3:33686339A>G	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.772T>C	3.37:g.33686339A>G	ENSP00000419974:p.Ser258Pro		Somatic				CLASP2_ENST00000480013.1_Missense_Mutation_p.S25P|CLASP2_ENST00000359576.5_Missense_Mutation_p.S258P|CLASP2_ENST00000307312.7_5'UTR|CLASP2_ENST00000333778.6_Missense_Mutation_p.S35P|CLASP2_ENST00000487200.1_Missense_Mutation_p.S31P|CLASP2_ENST00000461133.3_Missense_Mutation_p.S25P|CLASP2_ENST00000313350.6_Missense_Mutation_p.S31P|CLASP2_ENST00000482896.1_5'UTR|CLASP2_ENST00000539981.1_Missense_Mutation_p.S31P|CLASP2_ENST00000468888.2_Missense_Mutation_p.S258P	p.S258P	NM_015097.2	NP_055912.2	WXS	Illumina GAIIx	Phase_I	B2RTR1	B2RTR1_HUMAN			8	1125	-			258					Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	37	c.772T>C		.	.	.	.	.	.	.	.	.	.	A	18.42	3.619070	0.66787	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576;ENST00000539981;ENST00000480013;ENST00000461133;ENST00000313350;ENST00000487200;ENST00000333778;ENST00000485378;ENST00000496954	T;T;T	0.22336	1.96;1.99;1.99	5.97	5.97	0.96955	.	0.213930	0.41097	D	0.000957	T	0.35566	0.0936	L	0.43923	1.385	0.80722	D	1	B;D;D;P	0.60575	0.104;0.988;0.973;0.718	B;P;P;P	0.59825	0.04;0.864;0.786;0.528	T	0.04693	-1.0933	10	0.72032	D	0.01	-15.2732	15.0245	0.71659	1.0:0.0:0.0:0.0	.	35;31;31;258	E7ENG2;B3KR06;O75122-2;F5H604	.;.;.;.	P	258;258;258;31;25;25;31;31;35;31;25	ENSP00000419974:S258P;ENSP00000382297:S258P;ENSP00000352581:S258P	ENSP00000324364:S31P	S	-	1	0	CLASP2	33661343	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.812000	0.62613	2.285000	0.76669	0.477000	0.44152	TCA		0.438	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		2	10	2	10	---	---	---	---
C6	729	broad.mit.edu	37	5	41154017	41154017	+	Missense_Mutation	SNP	C	C	T	rs545743707		TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr5:41154017C>T	ENST00000263413.3	-	15	2449	c.2185G>A	c.(2185-2187)Gag>Aag	p.E729K	C6_ENST00000337836.5_Missense_Mutation_p.E729K	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	729	C5b-binding domain.|CCP 2.|Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				CAAGTTAGCTCAATGGATTCA	0.478													C|||	1	0.000199681	0.0	0.0	5008	,	,		20228	0.0		0.0	False		,,,				2504	0.001					ENST00000263413.3																			0				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96						c.(2185-2187)Gag>Aag		complement component 6							121.0	106.0	111.0					5																	41154017		2203	4300	6503	SO:0001583	missense	729				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding	g.chr5:41154017C>T	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.2185G>A	5.37:g.41154017C>T	ENSP00000263413:p.Glu729Lys		Somatic				C6_ENST00000337836.5_Missense_Mutation_p.E729K	p.E729K	NM_001115131.1	NP_001108603.2	WXS	Illumina GAIIx	Phase_I	P13671	CO6_HUMAN			15	2449	-		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)	729			C5b-binding domain.|Sushi 2.			Missense_Mutation	SNP	ENST00000263413.3	37	c.2185G>A	CCDS3936.1	.	.	.	.	.	.	.	.	.	.	C	4.300	0.054913	0.08291	.	.	ENSG00000039537	ENST00000337836;ENST00000263413	T;T	0.63913	-0.07;-0.07	5.46	2.27	0.28462	Complement control module (2);Sushi/SCR/CCP (3);	0.518334	0.22969	N	0.053446	T	0.43590	0.1254	L	0.38175	1.15	0.39503	D	0.968231	B	0.16166	0.016	B	0.19666	0.026	T	0.23797	-1.0178	10	0.06236	T	0.91	-16.6662	8.1735	0.31268	0.0:0.2625:0.6213:0.1162	.	729	P13671	CO6_HUMAN	K	729	ENSP00000338861:E729K;ENSP00000263413:E729K	ENSP00000263413:E729K	E	-	1	0	C6	41189774	0.921000	0.31238	0.999000	0.59377	0.866000	0.49608	0.288000	0.18939	1.290000	0.44636	-0.315000	0.08773	GAG		0.478	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			17	48	17	48	---	---	---	---
GTF2E2	2961	broad.mit.edu	37	8	30437879	30437879	+	Missense_Mutation	SNP	A	A	C			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr8:30437879A>C	ENST00000355904.4	-	7	960	c.678T>G	c.(676-678)gaT>gaG	p.D226E		NM_002095.4	NP_002086.1	P29084	T2EB_HUMAN	general transcription factor IIE, polypeptide 2, beta 34kDa	226					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIE complex (GO:0005673)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(542;0.113)|Kidney(114;0.135)		CGTCCATGGAATCTACAGTGA	0.373																																						ENST00000355904.4																			0				endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						c.(676-678)gaT>gaG		general transcription factor IIE, polypeptide 2, beta 34kDa							139.0	127.0	131.0					8																	30437879		2203	4300	6503	SO:0001583	missense	2961				regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIE complex	DNA binding|protein binding	g.chr8:30437879A>C	BC030572	CCDS6078.1	8p12	2010-03-23	2002-08-29		ENSG00000197265	ENSG00000197265		"""General transcription factors"""	4651	protein-coding gene	gene with protein product		189964	"""general transcription factor IIE, polypeptide 2 (beta subunit, 34kD)"""			1956404	Standard	NM_002095		Approved	TFIIE-B, FE, TF2E2	uc003xig.3	P29084	OTTHUMG00000163934	ENST00000355904.4:c.678T>G	8.37:g.30437879A>C	ENSP00000348168:p.Asp226Glu		Somatic					p.D226E	NM_002095.4	NP_002086.1	WXS	Illumina GAIIx	Phase_I	P29084	T2EB_HUMAN		KIRC - Kidney renal clear cell carcinoma(542;0.113)|Kidney(114;0.135)	7	960	-			226					D3DSV2|Q9H2B9	Missense_Mutation	SNP	ENST00000355904.4	37	c.678T>G	CCDS6078.1	.	.	.	.	.	.	.	.	.	.	A	12.13	1.847039	0.32606	.	.	ENSG00000197265	ENST00000355904	T	0.34667	1.35	5.74	2.05	0.26809	.	0.088679	0.85682	D	0.000000	T	0.25754	0.0627	L	0.43152	1.355	0.58432	D	0.999996	B	0.22080	0.064	B	0.24541	0.054	T	0.05370	-1.0889	10	0.27785	T	0.31	-11.4784	5.6309	0.17510	0.7005:0.145:0.1546:0.0	.	226	P29084	T2EB_HUMAN	E	226	ENSP00000348168:D226E	ENSP00000348168:D226E	D	-	3	2	GTF2E2	30557421	1.000000	0.71417	0.997000	0.53966	0.484000	0.33280	2.084000	0.41625	0.109000	0.17891	-0.316000	0.08728	GAT		0.373	GTF2E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376459.2	NM_002095		28	59	28	59	---	---	---	---
MTDH	92140	broad.mit.edu	37	8	98657100	98657100	+	Silent	SNP	G	G	A			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr8:98657100G>A	ENST00000336273.3	+	1	694	c.366G>A	c.(364-366)ctG>ctA	p.L122L	MTDH_ENST00000519934.1_Silent_p.L99L	NM_178812.3	NP_848927.2	Q86UE4	LYRIC_HUMAN	metadherin	122	Interaction with BCCIP.|Interaction with RELA.				lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of angiogenesis (GO:0045766)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)	double-stranded RNA binding (GO:0003725)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			GGAAGAAACTGTCCGAGAAGC	0.672																																						ENST00000336273.3																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32						c.(364-366)ctG>ctA		metadherin							13.0	15.0	15.0					8																	98657100		1864	3765	5629	SO:0001819	synonymous_variant	92140				lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity	g.chr8:98657100G>A	AF411226	CCDS6274.1	8q22.1	2014-07-14			ENSG00000147649	ENSG00000147649			29608	protein-coding gene	gene with protein product	"""astrocyte elevated gene 1"""	610323				15093543	Standard	NM_178812		Approved	LYRIC, 3D3, AEG-1	uc003yhz.3	Q86UE4	OTTHUMG00000164692	ENST00000336273.3:c.366G>A	8.37:g.98657100G>A			Somatic				MTDH_ENST00000519934.1_Silent_p.L99L	p.L122L	NM_178812.3	NP_848927.2	WXS	Illumina GAIIx	Phase_I	Q86UE4	LYRIC_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;0.178)		1	694	+	Breast(36;2.56e-06)		122			Interaction with BCCIP.|Interaction with RELA.		Q05DH2|Q52QU9|Q6PK07|Q8TCX3	Silent	SNP	ENST00000336273.3	37	c.366G>A	CCDS6274.1	.	.	.	.	.	.	.	.	.	.	G	9.251	1.040768	0.19669	.	.	ENSG00000147649	ENST00000522313	.	.	.	5.19	-5.58	0.02512	.	.	.	.	.	T	0.20251	0.0487	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.32295	-0.9912	4	.	.	.	9.1422	4.9844	0.14182	0.0631:0.2786:0.2848:0.3736	.	.	.	.	Y	27	.	.	C	+	2	0	MTDH	98726276	0.000000	0.05858	0.002000	0.10522	0.922000	0.55478	-0.272000	0.08560	-0.696000	0.05098	0.591000	0.81541	TGT		0.672	MTDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379772.2			3	8	3	8	---	---	---	---
POLD3	10714	broad.mit.edu	37	11	74303721	74303721	+	Nonsense_Mutation	SNP	T	T	G			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr11:74303721T>G	ENST00000263681.2	+	1	147	c.18T>G	c.(16-18)taT>taG	p.Y6*	POLD3_ENST00000532784.1_3'UTR|POLD3_ENST00000532497.1_De_novo_Start_OutOfFrame|POLD3_ENST00000527458.1_De_novo_Start_InFrame	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	6					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					ACCAGCTTTATCTGGAAAATA	0.622																																						ENST00000263681.2																			0				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18						c.(16-18)taT>taG		polymerase (DNA-directed), delta 3, accessory subunit							30.0	30.0	30.0					11																	74303721		2200	4293	6493	SO:0001587	stop_gained	10714				base-excision repair|DNA strand elongation involved in DNA replication|DNA synthesis involved in DNA repair|mismatch repair|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	delta DNA polymerase complex|nucleoplasm	DNA-directed DNA polymerase activity|protein binding	g.chr11:74303721T>G	D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"""DNA polymerases"""	20932	protein-coding gene	gene with protein product	"""DNA polymerase delta subunit p66"", ""Pol delta C subunit (p66)"", ""protein phosphatase 1, regulatory subunit 128"""	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.18T>G	11.37:g.74303721T>G	ENSP00000263681:p.Tyr6*		Somatic				POLD3_ENST00000532784.1_3'UTR|POLD3_ENST00000532497.1_De_novo_Start_OutOfFrame|POLD3_ENST00000527458.1_De_novo_Start_InFrame	p.Y6*	NM_006591.2	NP_006582.1	WXS	Illumina GAIIx	Phase_I	Q15054	DPOD3_HUMAN			1	147	+	Breast(11;3.21e-06)		6					B7ZAI6|Q32MZ9|Q32N00	Nonsense_Mutation	SNP	ENST00000263681.2	37	c.18T>G	CCDS8233.1	.	.	.	.	.	.	.	.	.	.	T	37	6.436986	0.97568	.	.	ENSG00000077514	ENST00000263681;ENST00000538052	.	.	.	4.95	1.15	0.20763	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.1631	6.1859	0.20498	0.0:0.3796:0.0:0.6204	.	.	.	.	X	6	.	ENSP00000263681:Y6X	Y	+	3	2	POLD3	73981369	0.998000	0.40836	0.998000	0.56505	0.963000	0.63663	0.181000	0.16880	0.365000	0.24400	0.533000	0.62120	TAT		0.622	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1	NM_006591		9	11	9	11	---	---	---	---
BIRC2	329	broad.mit.edu	37	11	102248361	102248361	+	Missense_Mutation	SNP	C	C	G			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr11:102248361C>G	ENST00000227758.2	+	7	2900	c.1501C>G	c.(1501-1503)Cag>Gag	p.Q501E	BIRC2_ENST00000527910.1_3'UTR|BIRC2_ENST00000530675.1_Missense_Mutation_p.Q452E|BIRC2_ENST00000532672.1_Missense_Mutation_p.Q480E	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	Q13490	BIRC2_HUMAN	baculoviral IAP repeat containing 2	501	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein K48-linked ubiquitination (GO:1902524)|positive regulation of protein K63-linked ubiquitination (GO:1902523)|positive regulation of protein monoubiquitination (GO:1902527)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription, DNA-templated (GO:0006355)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		ACAAAAAACACAGATACCTTT	0.333																																						ENST00000227758.2																			0				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						c.(1501-1503)Cag>Gag		baculoviral IAP repeat containing 2							67.0	77.0	74.0					11																	102248361		2203	4297	6500	SO:0001583	missense	329				cell surface receptor linked signaling pathway|cellular component disassembly involved in apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination	CD40 receptor complex|cytosol|internal side of plasma membrane	protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding	g.chr11:102248361C>G	L49431	CCDS8316.1, CCDS58169.1	11q22	2011-01-25	2011-01-25		ENSG00000110330	ENSG00000110330		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	590	protein-coding gene	gene with protein product	"""NFR2-TRAF signalling complex protein"", ""apoptosis inhibitor 1"""	601712	"""baculoviral IAP repeat-containing 2"""	API1		8552191, 8548810	Standard	NM_001166		Approved	cIAP1, hiap-2, MIHB, RNF48, c-IAP1	uc010ruq.3	Q13490	OTTHUMG00000167325	ENST00000227758.2:c.1501C>G	11.37:g.102248361C>G	ENSP00000227758:p.Gln501Glu		Somatic				BIRC2_ENST00000527910.1_3'UTR|BIRC2_ENST00000530675.1_Missense_Mutation_p.Q452E|BIRC2_ENST00000532672.1_Missense_Mutation_p.Q480E	p.Q501E	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	WXS	Illumina GAIIx	Phase_I	Q13490	BIRC2_HUMAN	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)	7	2900	+	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	501			CARD.		B4E026|Q16516|Q4TTG0	Missense_Mutation	SNP	ENST00000227758.2	37	c.1501C>G	CCDS8316.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.523607	0.64747	.	.	ENSG00000110330	ENST00000530675;ENST00000533742;ENST00000227758;ENST00000541741;ENST00000532672;ENST00000531259	T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05	5.83	5.83	0.93111	DEATH-like (2);Caspase Recruitment (3);	0.106971	0.64402	D	0.000003	T	0.34048	0.0884	M	0.72479	2.2	0.58432	D	0.999996	B	0.27498	0.18	B	0.38500	0.275	T	0.10132	-1.0643	10	0.15952	T	0.53	-22.1291	20.1316	0.98000	0.0:1.0:0.0:0.0	.	501	Q13490	BIRC2_HUMAN	E	452;163;501;501;480;36	ENSP00000431723:Q452E;ENSP00000433851:Q163E;ENSP00000227758:Q501E;ENSP00000434979:Q480E;ENSP00000436741:Q36E	ENSP00000227758:Q501E	Q	+	1	0	BIRC2	101753571	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.931000	0.63469	2.766000	0.95052	0.650000	0.86243	CAG		0.333	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166		12	19	12	19	---	---	---	---
ISLR	3671	broad.mit.edu	37	15	74467265	74467265	+	Silent	SNP	C	C	T			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr15:74467265C>T	ENST00000249842.3	+	2	423	c.66C>T	c.(64-66)ccC>ccT	p.P22P	RP11-665J16.1_ENST00000561647.1_RNA|ISLR_ENST00000395118.1_Silent_p.P22P	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	22	LRRNT.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						GCCCTGAGCCCTGCGACTGTG	0.627																																						ENST00000249842.3																			0				central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						c.(64-66)ccC>ccT		immunoglobulin superfamily containing leucine-rich repeat							49.0	45.0	46.0					15																	74467265		2198	4297	6495	SO:0001819	synonymous_variant	3671				cell adhesion	extracellular region		g.chr15:74467265C>T	AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"""Immunoglobulin superfamily / I-set domain containing"""	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.66C>T	15.37:g.74467265C>T			Somatic				RP11-665J16.1_ENST00000561647.1_RNA|ISLR_ENST00000395118.1_Silent_p.P22P	p.P22P	NM_005545.3	NP_005536.1	WXS	Illumina GAIIx	Phase_I	O14498	ISLR_HUMAN			2	423	+			22			LRRNT.			Silent	SNP	ENST00000249842.3	37	c.66C>T	CCDS10260.1																																																																																				0.627	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545		13	34	13	34	---	---	---	---
MYO15A	51168	broad.mit.edu	37	17	18023607	18023607	+	Missense_Mutation	SNP	C	C	T			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr17:18023607C>T	ENST00000205890.5	+	2	1831	c.1493C>T	c.(1492-1494)cCa>cTa	p.P498L		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	498					inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					GTGCCCCTGCCACCCTCTCTG	0.642																																						ENST00000205890.5																			0				breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99						c.(1492-1494)cCa>cTa		myosin XVA							36.0	44.0	41.0					17																	18023607		2045	4178	6223	SO:0001583	missense	51168				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity	g.chr17:18023607C>T	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.1493C>T	17.37:g.18023607C>T	ENSP00000205890:p.Pro498Leu		Somatic					p.P498L	NM_016239.3	NP_057323.3	WXS	Illumina GAIIx	Phase_I	Q9UKN7	MYO15_HUMAN			2	1831	+	all_neural(463;0.228)		498			Myosin head-like.		B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	c.1493C>T	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.368143	0.82463	.	.	ENSG00000091536	ENST00000205890	T	0.43294	0.95	5.1	5.1	0.69264	.	.	.	.	.	T	0.55893	0.1949	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.59820	-0.7382	9	0.72032	D	0.01	.	18.1103	0.89533	0.0:1.0:0.0:0.0	.	498	Q9UKN7	MYO15_HUMAN	L	498	ENSP00000205890:P498L	ENSP00000205890:P498L	P	+	2	0	MYO15A	17964332	0.996000	0.38824	0.752000	0.31206	0.802000	0.45316	3.626000	0.54245	2.374000	0.81015	0.561000	0.74099	CCA		0.642	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		17	37	17	37	---	---	---	---
MED13	9969	broad.mit.edu	37	17	60060259	60060259	+	Missense_Mutation	SNP	T	T	A			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr17:60060259T>A	ENST00000397786.2	-	16	3181	c.3105A>T	c.(3103-3105)aaA>aaT	p.K1035N		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1035					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AATTTTCATATTTGACTGAAC	0.507																																						ENST00000397786.2																			0				breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						c.(3103-3105)aaA>aaT		mediator complex subunit 13							84.0	85.0	85.0					17																	60060259		1945	4133	6078	SO:0001583	missense	9969				androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding	g.chr17:60060259T>A	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.3105A>T	17.37:g.60060259T>A	ENSP00000380888:p.Lys1035Asn		Somatic					p.K1035N	NM_005121.2	NP_005112.2	WXS	Illumina GAIIx	Phase_I	Q9UHV7	MED13_HUMAN			16	3181	-			1035					B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	c.3105A>T	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.294136	0.60086	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.75704	-0.96	5.84	4.77	0.60923	.	0.000000	0.85682	D	0.000000	D	0.82273	0.5001	M	0.68952	2.095	0.58432	D	0.999995	D	0.76494	0.999	D	0.78314	0.991	T	0.82102	-0.0623	10	0.66056	D	0.02	-0.9803	7.6878	0.28550	0.0:0.2281:0.0:0.7719	.	1035	Q9UHV7	MED13_HUMAN	N	1035;1034	ENSP00000380888:K1035N	ENSP00000262436:K1034N	K	-	3	2	MED13	57415041	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	0.587000	0.23909	1.049000	0.40321	0.533000	0.62120	AAA		0.507	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		17	37	17	37	---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5416266	5416266	+	Missense_Mutation	SNP	G	G	T			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr18:5416266G>T	ENST00000341928.2	-	13	1958	c.1618C>A	c.(1618-1620)Cca>Aca	p.P540T	EPB41L3_ENST00000542146.1_Intron|EPB41L3_ENST00000400111.3_Intron|EPB41L3_ENST00000342933.3_Missense_Mutation_p.P540T|EPB41L3_ENST00000540638.2_Intron|EPB41L3_ENST00000544123.1_Intron|EPB41L3_ENST00000427684.2_Intron|EPB41L3_ENST00000542652.2_Intron	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	540	Spectrin--actin-binding. {ECO:0000255}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						TCATAACCTGGCAGTTTGCAG	0.582																																						ENST00000341928.2																			0				breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						c.(1618-1620)Cca>Aca		erythrocyte membrane protein band 4.1-like 3							79.0	80.0	79.0					18																	5416266		2203	4300	6503	SO:0001583	missense	23136				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity	g.chr18:5416266G>T	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.1618C>A	18.37:g.5416266G>T	ENSP00000343158:p.Pro540Thr		Somatic				EPB41L3_ENST00000540638.2_Intron|EPB41L3_ENST00000544123.1_Intron|EPB41L3_ENST00000542146.1_Intron|EPB41L3_ENST00000342933.3_Missense_Mutation_p.P540T|EPB41L3_ENST00000400111.3_Intron|EPB41L3_ENST00000542652.2_Intron|EPB41L3_ENST00000427684.2_Intron	p.P540T	NM_012307.2	NP_036439.2	WXS	Illumina GAIIx	Phase_I	Q9Y2J2	E41L3_HUMAN			13	1958	-			540			Spectrin--actin-binding (Potential).		B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	c.1618C>A	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	0.096	-1.159027	0.01686	.	.	ENSG00000082397	ENST00000341928;ENST00000342933	T;T	0.80214	-1.35;-1.35	4.82	-1.84	0.07809	.	0.638768	0.15562	N	0.255889	T	0.61337	0.2339	L	0.36672	1.1	0.09310	N	1	B	0.17667	0.023	B	0.14023	0.01	T	0.42050	-0.9474	10	0.12430	T	0.62	.	2.1753	0.03860	0.3175:0.4115:0.1339:0.1371	.	540	Q9Y2J2	E41L3_HUMAN	T	540	ENSP00000343158:P540T;ENSP00000341138:P540T	ENSP00000343158:P540T	P	-	1	0	EPB41L3	5406266	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.135000	0.10420	-0.474000	0.06862	-0.300000	0.09419	CCA		0.582	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		25	73	25	73	---	---	---	---
ATP5A1	498	broad.mit.edu	37	18	43666432	43666432	+	Missense_Mutation	SNP	T	T	C			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr18:43666432T>C	ENST00000398752.6	-	9	1326	c.1205A>G	c.(1204-1206)aAa>aGa	p.K402R	ATP5A1_ENST00000593152.2_Missense_Mutation_p.K352R|ATP5A1_ENST00000590665.1_Missense_Mutation_p.K380R|ATP5A1_ENST00000282050.2_Missense_Mutation_p.K402R	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	402					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						GCGGATACCTTTGTAGAACAA	0.408																																						ENST00000593152.2																			0				breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						c.(1054-1056)aAa>aGa		ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle							72.0	66.0	68.0					18																	43666432		2203	4300	6503	SO:0001583	missense	498				ATP hydrolysis coupled proton transport|embryo development|lipid metabolic process|negative regulation of endothelial cell proliferation|respiratory electron transport chain	mitochondrial matrix|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism	g.chr18:43666432T>C	D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	823	protein-coding gene	gene with protein product		164360	"""ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2"", ""ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"""	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.1205A>G	18.37:g.43666432T>C	ENSP00000381736:p.Lys402Arg		Somatic				ATP5A1_ENST00000590665.1_Missense_Mutation_p.K380R|ATP5A1_ENST00000398752.6_Missense_Mutation_p.K402R|ATP5A1_ENST00000282050.2_Missense_Mutation_p.K402R	p.K352R	NM_001257335.1	NP_001244264.1	WXS	Illumina GAIIx	Phase_I	P25705	ATPA_HUMAN			9	1594	-			402					A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Missense_Mutation	SNP	ENST00000398752.6	37	c.1055A>G	CCDS11927.1	.	.	.	.	.	.	.	.	.	.	T	17.26	3.345062	0.61073	.	.	ENSG00000152234	ENST00000282050;ENST00000398752;ENST00000542290	T;T	0.77098	-1.07;-1.07	4.66	4.66	0.58398	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.70701	0.3254	L	0.37630	1.12	0.51233	D	0.999911	B	0.15719	0.014	B	0.28991	0.097	T	0.65450	-0.6165	10	0.26408	T	0.33	-17.2407	14.1672	0.65486	0.0:0.0:0.0:1.0	.	402	P25705	ATPA_HUMAN	R	402;402;352	ENSP00000282050:K402R;ENSP00000381736:K402R	ENSP00000282050:K402R	K	-	2	0	ATP5A1	41920430	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.037000	0.88933	1.744000	0.51775	0.456000	0.33151	AAA		0.408	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046		10	20	10	20	---	---	---	---
C19orf44	84167	broad.mit.edu	37	19	16620545	16620545	+	Missense_Mutation	SNP	A	A	G			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr19:16620545A>G	ENST00000221671.3	+	5	1541	c.1385A>G	c.(1384-1386)aAc>aGc	p.N462S	C19orf44_ENST00000594035.1_Missense_Mutation_p.N462S|CTD-3222D19.2_ENST00000409035.1_Intron	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	462										endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						CCCATGGTGAACACAGTCAGC	0.547																																						ENST00000221671.3																			0				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						c.(1384-1386)aAc>aGc		chromosome 19 open reading frame 44							79.0	77.0	78.0					19																	16620545		2203	4300	6503	SO:0001583	missense	84167							g.chr19:16620545A>G	AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.1385A>G	19.37:g.16620545A>G	ENSP00000221671:p.Asn462Ser		Somatic				C19orf44_ENST00000594035.1_Missense_Mutation_p.N462S|CTD-3222D19.2_ENST00000409035.1_Intron	p.N462S	NM_032207.2	NP_115583.1	WXS	Illumina GAIIx	Phase_I	Q9H6X5	CS044_HUMAN			5	1541	+			462					Q8N6Y7	Missense_Mutation	SNP	ENST00000221671.3	37	c.1385A>G	CCDS12345.1	.	.	.	.	.	.	.	.	.	.	A	0.016	-1.518151	0.00967	.	.	ENSG00000105072	ENST00000221671	.	.	.	4.03	-0.04	0.13873	.	0.840154	0.10733	N	0.640416	T	0.07863	0.0197	N	0.00972	-1.085	0.09310	N	1	B;B;B	0.12013	0.002;0.001;0.005	B;B;B	0.06405	0.001;0.0;0.002	T	0.35724	-0.9777	9	0.11794	T	0.64	0.0456	3.9404	0.09325	0.2676:0.1838:0.5486:0.0	.	462;135;462	Q9H6X5;B4DN63;Q9H6X5-2	CS044_HUMAN;.;.	S	462	.	ENSP00000221671:N462S	N	+	2	0	C19orf44	16481545	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.172000	0.16704	-0.263000	0.09378	-0.417000	0.06048	AAC		0.547	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207		20	33	20	33	---	---	---	---
RSPH6A	81492	broad.mit.edu	37	19	46303813	46303813	+	Missense_Mutation	SNP	G	G	A			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr19:46303813G>A	ENST00000221538.3	-	5	1949	c.1807C>T	c.(1807-1809)Cac>Tac	p.H603Y	RSPH6A_ENST00000600188.1_Missense_Mutation_p.H339Y|RSPH6A_ENST00000597055.1_Missense_Mutation_p.H603Y	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	603	Glu-rich.					intracellular (GO:0005622)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						GGTGCCAGGTGCATGATTTCT	0.667																																						ENST00000221538.3																			0				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						c.(1807-1809)Cac>Tac		radial spoke head 6 homolog A (Chlamydomonas)							49.0	44.0	46.0					19																	46303813		2203	4298	6501	SO:0001583	missense	81492					intracellular		g.chr19:46303813G>A	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"""radial spokehead-like 1"""	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.1807C>T	19.37:g.46303813G>A	ENSP00000221538:p.His603Tyr		Somatic				RSPH6A_ENST00000597055.1_Missense_Mutation_p.H603Y|RSPH6A_ENST00000600188.1_Missense_Mutation_p.H339Y	p.H603Y	NM_030785.3	NP_110412.1	WXS	Illumina GAIIx	Phase_I	Q9H0K4	RSH6A_HUMAN			5	1949	-			603			Glu-rich.		Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	37	c.1807C>T	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	G	10.96	1.499623	0.26861	.	.	ENSG00000104941	ENST00000221538	T	0.15952	2.38	5.03	2.81	0.32909	.	0.324218	0.36932	N	0.002324	T	0.23611	0.0571	L	0.45581	1.43	0.09310	N	1	D	0.61080	0.989	P	0.55055	0.767	T	0.05784	-1.0864	10	0.29301	T	0.29	-1.8314	10.4857	0.44719	0.0:0.0:0.6589:0.3411	.	603	Q9H0K4	RSH6A_HUMAN	Y	603	ENSP00000221538:H603Y	ENSP00000221538:H603Y	H	-	1	0	RSPH6A	50995653	0.803000	0.28956	0.844000	0.33320	0.224000	0.24922	0.527000	0.22987	0.787000	0.33731	0.555000	0.69702	CAC		0.667	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1			12	36	12	36	---	---	---	---
HELQ	113510	broad.mit.edu	37	4	84375053	84375060	+	Frame_Shift_Del	DEL	TAAAGCTA	TAAAGCTA	-	rs199666920		TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr4:84375053_84375060delTAAAGCTA	ENST00000295488.3	-	2	498_505	c.336_343delTAGCTTTA	c.(334-345)gatagctttactfs	p.SFT113fs	MRPS18C_ENST00000295491.4_5'Flank|HELQ_ENST00000440639.2_5'UTR|MRPS18C_ENST00000507349.1_5'Flank|MRPS18C_ENST00000507019.1_5'Flank|HELQ_ENST00000510985.1_Frame_Shift_Del_p.SFT113fs	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	113					double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						GAGTTTTCAGTAAAGCTATCATAGTCAC	0.375								Other identified genes with known or suspected DNA repair function																														ENST00000295488.3																			0				breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						c.(334-345)gatagctttactfs	Other identified genes with known or suspected DNA repair function	helicase, POLQ-like																																				SO:0001589	frameshift_variant	113510						ATP binding|ATP-dependent helicase activity|nucleic acid binding	g.chr4:84375053_84375060delTAAAGCTA	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.336_343delTAGCTTTA	4.37:g.84375053_84375060delTAAAGCTA	ENSP00000295488:p.Ser113fs		Somatic				HELQ_ENST00000510985.1_Frame_Shift_Del_p.SFT113fs|HELQ_ENST00000440639.2_5'UTR	p.SFT113fs	NM_133636.2	NP_598375	WXS	Illumina GAIIx	Phase_I	Q8TDG4	HELQ_HUMAN			2	498_505	-			113					Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Frame_Shift_Del	DEL	ENST00000295488.3	37	c.336_343delTAGCTTTA	CCDS3603.1																																																																																				0.375	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		27	135	27	135	---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78593154	78593155	+	Frame_Shift_Ins	INS	-	-	T			TCGA-J4-8198-01A-11D-2260-08	TCGA-J4-8198-10A-01D-2260-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	686d289d-fcb7-456e-833f-11f3b2d5a361	5050d3e5-3b45-4d06-b454-7ccd753837dc	g.chr12:78593154_78593155insT	ENST00000397909.2	+	37	6731_6732	c.6558_6559insT	c.(6559-6561)tttfs	p.F2187fs	NAV3_ENST00000536525.2_Frame_Shift_Ins_p.F2165fs|NAV3_ENST00000228327.6_Frame_Shift_Ins_p.F2165fs|NAV3_ENST00000541270.1_Frame_Shift_Ins_p.F17fs|NAV3_ENST00000266692.7_Frame_Shift_Ins_p.F1988fs			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2187						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CAGTGAAAGGCTTTTTAGGCAG	0.302										HNSCC(70;0.22)																												ENST00000397909.2																			0				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						c.(6559-6561)tttfs		neuron navigator 3																																				SO:0001589	frameshift_variant	89795					nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity	g.chr12:78593154_78593155insT	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.6563dupT	12.37:g.78593159_78593159dupT	ENSP00000381007:p.Phe2187fs	HNSCC(70;0.22)	Somatic				NAV3_ENST00000536525.2_Frame_Shift_Ins_p.F2165fs|NAV3_ENST00000541270.1_Frame_Shift_Ins_p.F17fs|NAV3_ENST00000228327.6_Frame_Shift_Ins_p.F2165fs|NAV3_ENST00000266692.7_Frame_Shift_Ins_p.F1988fs	p.F2187fs			WXS	Illumina GAIIx	Phase_I	Q8IVL0	NAV3_HUMAN			37	6731_6732	+			2187					Q8NFW7|Q9Y2E7	Frame_Shift_Ins	INS	ENST00000397909.2	37	c.6558_6559insT																																																																																					0.302	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		8	92	8	92	---	---	---	---
