#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	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_dbSNPPopFreq	i_dbSNP_AF	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
GRIK3	2899	hgsc.bcm.edu	37	1	37356579	37356579	+	Silent	SNP	G	G	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr1:37356579G>T	ENST00000373091.3	-	2	250	c.234C>A	c.(232-234)acC>acA	p.T78T	GRIK3_ENST00000373093.4_Silent_p.T78T	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	78					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CATAGGTCAAGGTTGTGTTGG	0.547																																					p.T78T		Atlas-SNP	.											.	GRIK3	195	.	0			c.C234A						.						299.0	234.0	256.0					1																	37356579		2203	4300	6503	SO:0001819	synonymous_variant	2899	exon2			GGTCAAGGTTGTG	U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.234C>A	chr1.hg19:g.37356579G>T		54.0	0.0		128.0	41.0	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Silent	SNP	ENST00000373091.3	hg19	CCDS416.1																																																																																			.	.		0.547	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831	
C8A	731	hgsc.bcm.edu	37	1	57378219	57378219	+	Silent	SNP	C	C	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr1:57378219C>T	ENST00000361249.3	+	10	1620	c.1524C>T	c.(1522-1524)ccC>ccT	p.P508P		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	508	EGF-like.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						ATGGGGTGCCCATCCTCGAGG	0.612																																					p.P508P		Atlas-SNP	.											.	C8A	103	.	0			c.C1524T						.						83.0	85.0	84.0					1																	57378219		2203	4300	6503	SO:0001819	synonymous_variant	731	exon10			GGTGCCCATCCTC	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"""Complement system"""	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.1524C>T	chr1.hg19:g.57378219C>T		229.0	0.0		490.0	122.0	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Silent	SNP	ENST00000361249.3	hg19	CCDS606.1																																																																																			.	.		0.612	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562	
PYCR2	29920	hgsc.bcm.edu	37	1	226109910	226109910	+	Silent	SNP	C	C	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr1:226109910C>T	ENST00000343818.6	-	3	460	c.312G>A	c.(310-312)gtG>gtA	p.V104V	PYCR2_ENST00000478402.1_5'UTR|RP4-559A3.7_ENST00000432920.2_Silent_p.V104V	NM_013328.2	NP_037460.2	Q96C36	P5CR2_HUMAN	pyrroline-5-carboxylate reductase family, member 2	104					L-proline biosynthetic process (GO:0055129)	cytoplasm (GO:0005737)	pyrroline-5-carboxylate reductase activity (GO:0004735)			kidney(1)|lung(3)	4	Breast(184;0.197)				L-Proline(DB00172)	GCACCTTCTCCACAGAGCTGA	0.607																																					p.V104V		Atlas-SNP	.											.	PYCR2	13	.	0			c.G312A						.						78.0	63.0	68.0					1																	226109910		2203	4300	6503	SO:0001819	synonymous_variant	29920	exon3			CTTCTCCACAGAG	AF151351	CCDS31043.1, CCDS73039.1	1q42.13	2008-02-05			ENSG00000143811	ENSG00000143811			30262	protein-coding gene	gene with protein product						12477932	Standard	NM_013328		Approved	P5CR2	uc001hpq.4	Q96C36	OTTHUMG00000037506	ENST00000343818.6:c.312G>A	chr1.hg19:g.226109910C>T		45.0	0.0		69.0	12.0	NM_013328	A8K798|Q7Z515|Q9Y5J4	Silent	SNP	ENST00000343818.6	hg19	CCDS31043.1																																																																																			.	.		0.607	PYCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091314.1	NM_013328	
TARBP1	6894	hgsc.bcm.edu	37	1	234534263	234534263	+	Missense_Mutation	SNP	T	T	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr1:234534263T>A	ENST00000040877.1	-	26	4107	c.4108A>T	c.(4108-4110)Att>Ttt	p.I1370F	TARBP1_ENST00000483404.1_Intron	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1370					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			TCATCTTCAATAAGGCCTGAA	0.328																																					p.I1370F		Atlas-SNP	.											.	TARBP1	111	.	0			c.A4108T						.						76.0	78.0	77.0					1																	234534263		2203	4300	6503	SO:0001583	missense	6894	exon26			CTTCAATAAGGCC		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"""tRNA methyltransferase 3 homolog (S. cerevisiae)"""	605052	"""Tar (HIV-1) RNA binding protein 1"""			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.4108A>T	chr1.hg19:g.234534263T>A	ENSP00000040877:p.Ile1370Phe	50.0	0.0		93.0	12.0	NM_005646	Q9H581	Missense_Mutation	SNP	ENST00000040877.1	hg19	CCDS1601.1	.	.	.	.	.	.	.	.	.	.	T	15.19	2.760815	0.49468	.	.	ENSG00000059588	ENST00000040877	T	0.05996	3.36	5.85	-2.13	0.07144	.	1.014850	0.07850	N	0.964479	T	0.05640	0.0148	N	0.22421	0.69	0.18873	N	0.999986	B	0.26744	0.158	B	0.28232	0.087	T	0.42699	-0.9436	10	0.54805	T	0.06	-11.8186	11.4584	0.50195	0.0:0.515:0.0:0.485	.	1370	Q13395	TARB1_HUMAN	F	1370	ENSP00000040877:I1370F	ENSP00000040877:I1370F	I	-	1	0	TARBP1	232600886	0.014000	0.17966	0.013000	0.15412	0.976000	0.68499	0.287000	0.18920	-0.718000	0.04949	0.528000	0.53228	ATT	.	.		0.328	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
PAPOLG	64895	hgsc.bcm.edu	37	2	61014655	61014655	+	Silent	SNP	C	C	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr2:61014655C>T	ENST00000238714.3	+	15	1545	c.1296C>T	c.(1294-1296)taC>taT	p.Y432Y		NM_022894.3	NP_075045.2	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma	432					mRNA polyadenylation (GO:0006378)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	35	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)			GCAACAATTACGTATCAATGT	0.279																																					p.Y432Y	GBM(183;1497 2932 21839 46797)	Atlas-SNP	.											.	PAPOLG	66	.	0			c.C1296T						.						60.0	60.0	60.0					2																	61014655		2203	4300	6503	SO:0001819	synonymous_variant	64895	exon15			CAATTACGTATCA	AC012498	CCDS1863.1	2p16.1	2008-02-08			ENSG00000115421	ENSG00000115421	2.7.7.19		14982	protein-coding gene	gene with protein product							Standard	NM_022894		Approved	FLJ12972	uc002sai.3	Q9BWT3	OTTHUMG00000129419	ENST00000238714.3:c.1296C>T	chr2.hg19:g.61014655C>T		143.0	0.0		262.0	25.0	NM_022894	B2RBH4|Q59G05|Q969N1|Q9H8L2|Q9HAD0	Silent	SNP	ENST00000238714.3	hg19	CCDS1863.1																																																																																			.	.		0.279	PAPOLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251577.3	NM_022894	
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105892080	105892080	+	Silent	SNP	G	G	C			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr2:105892080G>C	ENST00000393359.2	-	8	2028	c.1602C>G	c.(1600-1602)acC>acG	p.T534T	TGFBRAP1_ENST00000258449.1_Silent_p.T534T			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	534					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						CTAAGCAGTAGGTAAGAAAAT	0.453																																					p.T534T	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C1602G						.						146.0	133.0	137.0					2																	105892080		2203	4300	6503	SO:0001819	synonymous_variant	9392	exon8			GCAGTAGGTAAGA	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.1602C>G	chr2.hg19:g.105892080G>C		138.0	0.0		174.0	26.0	NM_004257	A8K5R7|D3DVJ8|O60466	Silent	SNP	ENST00000393359.2	hg19	CCDS2067.1																																																																																			.	.		0.453	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257	
TMEM87B	84910	hgsc.bcm.edu	37	2	112813302	112813302	+	Missense_Mutation	SNP	A	A	C			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr2:112813302A>C	ENST00000283206.4	+	1	503	c.134A>C	c.(133-135)gAg>gCg	p.E45A		NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	45						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						GCGGTCCCTGAGCTCGGGCTC	0.726																																					p.E45A		Atlas-SNP	.											.	TMEM87B	52	.	0			c.A134C						.						13.0	15.0	15.0					2																	112813302		2180	4273	6453	SO:0001583	missense	84910	exon1			TCCCTGAGCTCGG	AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.134A>C	chr2.hg19:g.112813302A>C	ENSP00000283206:p.Glu45Ala	260.0	0.0		210.0	24.0	NM_032824	A8K2M9|Q1RLN2|Q53R54	Missense_Mutation	SNP	ENST00000283206.4	hg19	CCDS33275.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	16.99|16.99	3.275356|3.275356	0.59649|0.59649	.|.	.|.	ENSG00000153214|ENSG00000153214	ENST00000283206|ENST00000452614	.|.	.|.	.|.	3.81|3.81	2.51|2.51	0.30379|0.30379	.|.	0.073488|.	0.51477|.	D|.	0.000085|.	T|.	0.49508|.	0.1561|.	L|L	0.50333|0.50333	1.59|1.59	0.34714|0.34714	D|D	0.728045|0.728045	D;B|.	0.71674|.	0.998;0.11|.	D;B|.	0.78314|.	0.991;0.026|.	T|.	0.57694|.	-0.7767|.	9|.	0.66056|.	D|.	0.02|.	-12.6993|-12.6993	5.8903|5.8903	0.18909|0.18909	0.7658:0.0:0.0:0.2342|0.7658:0.0:0.0:0.2342	.|.	45;45|.	Q96K49-2;Q96K49|.	.;TM87B_HUMAN|.	A|C	45|2	.|.	ENSP00000283206:E45A|.	E|X	+|+	2|3	0|0	TMEM87B|TMEM87B	112529773|112529773	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.833000|0.833000	0.47200|0.47200	1.812000|1.812000	0.38952|0.38952	1.495000|1.495000	0.48549|0.48549	0.370000|0.370000	0.22315|0.22315	GAG|TGA	.	.		0.726	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824	
PDE1A	5136	hgsc.bcm.edu	37	2	183129067	183129067	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr2:183129067G>A	ENST00000410103.1	-	3	259	c.176C>T	c.(175-177)gCg>gTg	p.A59V	PDE1A_ENST00000435564.1_Missense_Mutation_p.A59V|PDE1A_ENST00000536095.1_5'UTR|PDE1A_ENST00000351439.5_Missense_Mutation_p.A43V|PDE1A_ENST00000358139.2_Missense_Mutation_p.A59V|PDE1A_ENST00000409365.1_Missense_Mutation_p.A43V|PDE1A_ENST00000331935.6_Missense_Mutation_p.A59V|PDE1A_ENST00000456212.1_Missense_Mutation_p.A59V	NM_001003683.2	NP_001003683.1	P54750	PDE1A_HUMAN	phosphodiesterase 1A, calmodulin-dependent	59					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of smooth muscle cell apoptotic process (GO:0034391)|regulation of smooth muscle cell proliferation (GO:0048660)|signal transduction (GO:0007165)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2)	35			OV - Ovarian serous cystadenocarcinoma(117;0.061)		Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	CACAGATGCCGCATATTCAAT	0.373																																					p.A63V		Atlas-SNP	.											.	PDE1A	184	.	0			c.C188T						.						118.0	111.0	113.0					2																	183129067		2202	4300	6502	SO:0001583	missense	5136	exon3			GATGCCGCATATT		CCDS2285.1, CCDS33344.1, CCDS58741.1, CCDS74612.1	2q32.1	2008-03-18			ENSG00000115252	ENSG00000115252	3.1.4.17	"""Phosphodiesterases"""	8774	protein-coding gene	gene with protein product		171890				8557689, 11342109	Standard	NM_005019		Approved		uc010zfq.2	P54750	OTTHUMG00000132596	ENST00000410103.1:c.176C>T	chr2.hg19:g.183129067G>A	ENSP00000387037:p.Ala59Val	78.0	0.0		198.0	36.0	NM_001258312	D3DPG5|Q86VZ0|Q9C0K8|Q9C0K9|Q9C0L0|Q9C0L1|Q9C0L2|Q9C0L3|Q9C0L4|Q9UFX3	Missense_Mutation	SNP	ENST00000410103.1	hg19	CCDS33344.1	.	.	.	.	.	.	.	.	.	.	G	34	5.336813	0.95758	.	.	ENSG00000115252	ENST00000435564;ENST00000409365;ENST00000331935;ENST00000351439;ENST00000410103;ENST00000358139;ENST00000456212	T;T;T;T;T;T;T	0.73575	-0.76;-0.72;-0.76;-0.72;-0.74;-0.74;-0.76	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.85265	0.5657	M	0.66297	2.02	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.999	D;D;D	0.91635	0.943;0.999;0.975	T	0.82866	-0.0245	10	0.37606	T	0.19	.	18.8374	0.92168	0.0:0.0:1.0:0.0	.	59;43;59	P54750;P54750-2;P54750-4	PDE1A_HUMAN;.;.	V	59;43;59;43;59;59;59	ENSP00000410309:A59V;ENSP00000386767:A43V;ENSP00000331574:A59V;ENSP00000309269:A43V;ENSP00000387037:A59V;ENSP00000350858:A59V;ENSP00000408874:A59V	ENSP00000331574:A59V	A	-	2	0	PDE1A	182837312	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.057000	0.93889	2.861000	0.98227	0.655000	0.94253	GCG	.	.		0.373	PDE1A-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334356.1		
USP37	57695	hgsc.bcm.edu	37	2	219374706	219374706	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr2:219374706G>A	ENST00000258399.3	-	11	1433	c.1021C>T	c.(1021-1023)Cag>Tag	p.Q341*	USP37_ENST00000418019.1_Nonsense_Mutation_p.Q341*|USP37_ENST00000415516.1_Nonsense_Mutation_p.Q269*|USP37_ENST00000454775.1_Nonsense_Mutation_p.Q341*	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	341	USP.				G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		ACCTACCCCTGCAGTTGCTGC	0.383																																					p.Q341X		Atlas-SNP	.											.	USP37	76	.	0			c.C1021T						.						95.0	96.0	95.0					2																	219374706		2203	4300	6503	SO:0001587	stop_gained	57695	exon11			ACCCCTGCAGTTG	AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913		"""Ubiquitin-specific peptidases"""	20063	protein-coding gene	gene with protein product			"""ubiquitin specific protease 37"""			12838346	Standard	NM_020935		Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000258399.3:c.1021C>T	chr2.hg19:g.219374706G>A	ENSP00000258399:p.Gln341*	73.0	0.0		126.0	50.0	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Nonsense_Mutation	SNP	ENST00000258399.3	hg19	CCDS2418.1	.	.	.	.	.	.	.	.	.	.	G	37	6.056772	0.97241	.	.	ENSG00000135913	ENST00000258399;ENST00000454775;ENST00000415516;ENST00000418019	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	20.0951	0.97834	0.0:0.0:1.0:0.0	.	.	.	.	X	341;341;269;341	.	ENSP00000258399:Q341X	Q	-	1	0	USP37	219082950	1.000000	0.71417	0.989000	0.46669	0.433000	0.31745	6.419000	0.73345	2.753000	0.94483	0.467000	0.42956	CAG	.	.		0.383	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935	
GPC1	2817	hgsc.bcm.edu	37	2	241405663	241405663	+	Missense_Mutation	SNP	C	C	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr2:241405663C>T	ENST00000264039.2	+	9	1881	c.1633C>T	c.(1633-1635)Ctc>Ttc	p.L545F	GPC1_ENST00000466624.1_3'UTR	NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	545					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|myelin assembly (GO:0032288)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|phototransduction, visible light (GO:0007603)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|retinoid metabolic process (GO:0001523)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|fibroblast growth factor binding (GO:0017134)|laminin binding (GO:0043236)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	9		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		CCTGCCCCTCCTCCTCTTCCT	0.642																																					p.L545F		Atlas-SNP	.											.	GPC1	32	.	0			c.C1633T						.						44.0	56.0	52.0					2																	241405663		2203	4300	6503	SO:0001583	missense	2817	exon9			CCCCTCCTCCTCT	AK095397	CCDS2534.1	2q35-q37	2008-02-05			ENSG00000063660	ENSG00000063660		"""Proteoglycans / Cell Surface : Glypicans"""	4449	protein-coding gene	gene with protein product	"""glypican proteoglycan 1"""	600395				7774946	Standard	NM_002081		Approved	glypican	uc002vyw.4	P35052	OTTHUMG00000133349	ENST00000264039.2:c.1633C>T	chr2.hg19:g.241405663C>T	ENSP00000264039:p.Leu545Phe	162.0	0.0		188.0	90.0	NM_002081	B3KTD1|Q53QM4	Missense_Mutation	SNP	ENST00000264039.2	hg19	CCDS2534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	4.553|4.553	0.102749|0.102749	0.08731|0.08731	.|.	.|.	ENSG00000063660|ENSG00000063660	ENST00000264039|ENST00000420138	T|.	0.50277|.	0.75|.	4.05|4.05	-0.0157|-0.0157	0.13975|0.13975	.|.	26.672600|.	0.00550|.	U|.	0.000260|.	T|T	0.36496|0.36496	0.0969|0.0969	L|L	0.54323|0.54323	1.7|1.7	0.09310|0.09310	N|N	1|1	B|.	0.23377|.	0.084|.	B|.	0.27170|.	0.077|.	T|T	0.32534|0.32534	-0.9903|-0.9903	10|5	0.20519|.	T|.	0.43|.	-11.8264|-11.8264	2.7386|2.7386	0.05247|0.05247	0.3445:0.347:0.0:0.3084|0.3445:0.347:0.0:0.3084	.|.	545|.	P35052|.	GPC1_HUMAN|.	F|L	545|584	ENSP00000264039:L545F|.	ENSP00000264039:L545F|.	L|P	+|+	1|2	0|0	GPC1|GPC1	241054336|241054336	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.014000|0.014000	0.08584|0.08584	0.187000|0.187000	0.16998|0.16998	0.004000|0.004000	0.14682|0.14682	-0.345000|-0.345000	0.07892|0.07892	CTC|CCT	.	.		0.642	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
ITPR1	3708	hgsc.bcm.edu	37	3	4699862	4699862	+	Missense_Mutation	SNP	A	A	G			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr3:4699862A>G	ENST00000443694.2	+	10	1006	c.1006A>G	c.(1006-1008)Atg>Gtg	p.M336V	ITPR1_ENST00000456211.2_Missense_Mutation_p.M336V|ITPR1_ENST00000423119.2_Missense_Mutation_p.M351V|ITPR1_ENST00000302640.8_Missense_Mutation_p.M336V|ITPR1_ENST00000354582.6_Missense_Mutation_p.M351V|ITPR1_ENST00000357086.4_Missense_Mutation_p.M351V|ITPR1_ENST00000544951.1_Intron			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	351	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	CCAAGAAAAGATGGTATACTC	0.527																																					p.M351V		Atlas-SNP	.											.	ITPR1	659	.	0			c.A1051G						.						167.0	167.0	167.0					3																	4699862		1987	4161	6148	SO:0001583	missense	3708	exon13			GAAAAGATGGTAT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.1006A>G	chr3.hg19:g.4699862A>G	ENSP00000401671:p.Met336Val	48.0	0.0		77.0	30.0	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	A	11.55	1.672447	0.29693	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13;-2.13;-2.13	5.19	5.19	0.71726	MIR motif (2);MIR (2);	0.092352	0.85682	D	0.000000	T	0.73148	0.3550	N	0.03608	-0.345	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.0;0.004;0.001	T	0.68454	-0.5404	10	0.30078	T	0.28	.	15.0661	0.71996	1.0:0.0:0.0:0.0	.	336;351;351	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	V	351;336;351;351;351;336;336	ENSP00000306253:M336V;ENSP00000346595:M351V;ENSP00000405934:M351V;ENSP00000349597:M351V;ENSP00000397885:M336V;ENSP00000401671:M336V	ENSP00000306253:M336V	M	+	1	0	ITPR1	4674862	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.751000	0.62169	1.959000	0.56917	0.533000	0.62120	ATG	.	.		0.527	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
TACC3	10460	hgsc.bcm.edu	37	4	1746478	1746478	+	Silent	SNP	G	G	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr4:1746478G>A	ENST00000313288.4	+	15	2476	c.2370G>A	c.(2368-2370)caG>caA	p.Q790Q		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	790					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			GCAAGGCCCAGGCGGAAGCGT	0.672																																					p.Q790Q	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.G2370A						.						24.0	26.0	25.0					4																	1746478		2197	4298	6495	SO:0001819	synonymous_variant	10460	exon15			GGCCCAGGCGGAA	AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810			11524	protein-coding gene	gene with protein product		605303				17675670	Standard	NM_006342		Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.2370G>A	chr4.hg19:g.1746478G>A		66.0	0.0		128.0	66.0	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Silent	SNP	ENST00000313288.4	hg19	CCDS3352.1																																																																																			.	.		0.672	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2		
KLF3	51274	hgsc.bcm.edu	37	4	38696400	38696400	+	Missense_Mutation	SNP	G	G	C			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr4:38696400G>C	ENST00000261438.5	+	5	1034	c.729G>C	c.(727-729)aaG>aaC	p.K243N		NM_016531.5	NP_057615.3	P57682	KLF3_HUMAN	Kruppel-like factor 3 (basic)	243	Pro-rich.				cellular response to peptide (GO:1901653)|multicellular organismal development (GO:0007275)|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(5)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	18						AGCCTGGGAAGAGACCTTTAC	0.468																																					p.K243N		Atlas-SNP	.											KLF3,right_upper_lobe,carcinoma,0,1	KLF3	40	.	0			c.G729C						.						134.0	131.0	132.0					4																	38696400		2203	4300	6503	SO:0001583	missense	51274	exon5			TGGGAAGAGACCT	AF285837	CCDS3444.1	4p16.1-p15.2	2013-01-08			ENSG00000109787	ENSG00000109787		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	16516	protein-coding gene	gene with protein product	"""basic Kruppel-like factor"""	609392				18391014	Standard	NM_016531		Approved	BKLF	uc003gth.4	P57682	OTTHUMG00000097821	ENST00000261438.5:c.729G>C	chr4.hg19:g.38696400G>C	ENSP00000261438:p.Lys243Asn	64.0	0.0		105.0	8.0	NM_016531	Q6PIR1|Q86TN0|Q9P2X6	Missense_Mutation	SNP	ENST00000261438.5	hg19	CCDS3444.1	.	.	.	.	.	.	.	.	.	.	G	17.21	3.332441	0.60853	.	.	ENSG00000109787	ENST00000261438	T	0.57436	0.4	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.47266	0.1436	L	0.50333	1.59	0.80722	D	1	P	0.42827	0.791	B	0.34931	0.192	T	0.38908	-0.9639	10	0.18276	T	0.48	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	243	P57682	KLF3_HUMAN	N	243	ENSP00000261438:K243N	ENSP00000261438:K243N	K	+	3	2	KLF3	38372795	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.010000	0.40913	2.941000	0.99782	0.655000	0.94253	AAG	.	.		0.468	KLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215093.2		
CEP44	80817	hgsc.bcm.edu	37	4	175224920	175224920	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr4:175224920G>A	ENST00000503780.1	+	5	718	c.304G>A	c.(304-306)Gca>Aca	p.A102T	CEP44_ENST00000426172.1_Missense_Mutation_p.A102T|CEP44_ENST00000296519.4_Missense_Mutation_p.A102T|CEP44_ENST00000457424.2_Missense_Mutation_p.A102T	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	102						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)				endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						ATGTGGGTTTGCAGAATGGAA	0.313																																					p.A102T		Atlas-SNP	.											CEP44,NS,carcinoma,0,1	CEP44	35	.	0			c.G304A						.						74.0	77.0	76.0					4																	175224920		2201	4298	6499	SO:0001583	missense	80817	exon5			GGGTTTGCAGAAT	AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"""KIAA1712"""	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.304G>A	chr4.hg19:g.175224920G>A	ENSP00000423153:p.Ala102Thr	184.0	0.0		239.0	35.0	NM_001040157	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Missense_Mutation	SNP	ENST00000503780.1	hg19	CCDS34106.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.637284	0.87760	.	.	ENSG00000164118	ENST00000503780;ENST00000505124;ENST00000457424;ENST00000514712;ENST00000515299;ENST00000503053;ENST00000426172;ENST00000296519	T;T;T;T;T	0.58652	0.37;0.32;0.42;0.32;0.37	5.61	5.61	0.85477	.	0.122605	0.53938	D	0.000052	T	0.76033	0.3931	M	0.81942	2.565	0.42653	D	0.99345	D;D	0.76494	0.999;0.999	D;D	0.69479	0.964;0.964	T	0.78876	-0.2031	10	0.72032	D	0.01	.	14.8033	0.69932	0.0:0.0:0.8559:0.1441	.	102;102	Q9C0F1-2;Q9C0F1	.;CEP44_HUMAN	T	102	ENSP00000423153:A102T;ENSP00000389427:A102T;ENSP00000421128:A102T;ENSP00000408221:A102T;ENSP00000296519:A102T	ENSP00000296519:A102T	A	+	1	0	CEP44	175461495	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.531000	0.60602	2.804000	0.96469	0.650000	0.86243	GCA	.	.		0.313	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633	
TRIM23	373	hgsc.bcm.edu	37	5	64909990	64909990	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr5:64909990G>A	ENST00000231524.9	-	3	672	c.301C>T	c.(301-303)Cga>Tga	p.R101*	TRIM23_ENST00000274327.7_Nonsense_Mutation_p.R101*|TRIM23_ENST00000381018.3_Nonsense_Mutation_p.R101*	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	101					GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R101*(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		TTCTGCAGTCGTTCCAAAAGC	0.363																																					p.R101X		Atlas-SNP	.											TRIM23,colon,carcinoma,+1,1	TRIM23	73	.	1	Substitution - Nonsense(1)	ovary(1)	c.C301T						.						117.0	123.0	121.0					5																	64909990		2203	4300	6503	SO:0001587	stop_gained	373	exon3			GCAGTCGTTCCAA	L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	660	protein-coding gene	gene with protein product		601747	"""ADP-ribosylation factor domain protein 1, 64kDa"", ""tripartite motif-containing 23"""	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.301C>T	chr5.hg19:g.64909990G>A	ENSP00000231524:p.Arg101*	211.0	1.0		449.0	201.0	NM_033228	Q9BZY4|Q9BZY5	Nonsense_Mutation	SNP	ENST00000231524.9	hg19	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.618182	0.87359	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	.	.	.	5.25	3.45	0.39498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.9968	0.41905	0.0721:0.0:0.7895:0.1384	.	.	.	.	X	101	.	ENSP00000231524:R101X	R	-	1	2	TRIM23	64945746	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	4.087000	0.57671	0.589000	0.29677	0.585000	0.79938	CGA	.	.		0.363	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656	
GPR98	84059	hgsc.bcm.edu	37	5	90106981	90106981	+	Missense_Mutation	SNP	A	A	G			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr5:90106981A>G	ENST00000405460.2	+	74	16000	c.15904A>G	c.(15904-15906)Ata>Gta	p.I5302V	GPR98_ENST00000425867.2_Missense_Mutation_p.I963V	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5302	Calx-beta 34. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TCTTACCCTTATATTCCTAGA	0.413																																					p.I5302V		Atlas-SNP	.											.	GPR98	605	.	0			c.A15904G						.						72.0	69.0	70.0					5																	90106981		1881	4116	5997	SO:0001583	missense	84059	exon74			ACCCTTATATTCC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.15904A>G	chr5.hg19:g.90106981A>G	ENSP00000384582:p.Ile5302Val	123.0	0.0		169.0	38.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	0.022	-1.411693	0.01145	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.26223	1.75;1.75	5.36	0.117	0.14652	Na-Ca exchanger/integrin-beta4 (1);	0.483045	0.23918	N	0.043270	T	0.07052	0.0179	N	0.01874	-0.695	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.002	T	0.34254	-0.9836	9	.	.	.	.	4.9113	0.13823	0.6515:0.0:0.2233:0.1252	.	963;5302;963	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	V	5302;5302;963	ENSP00000384582:I5302V;ENSP00000392618:I963V	.	I	+	1	0	GPR98	90142737	0.444000	0.25649	0.001000	0.08648	0.345000	0.29048	1.084000	0.30828	-0.212000	0.10109	-0.274000	0.10170	ATA	.	.		0.413	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
PRR16	51334	hgsc.bcm.edu	37	5	120022106	120022106	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr5:120022106G>A	ENST00000407149.2	+	2	826	c.617G>A	c.(616-618)cGg>cAg	p.R206Q	PRR16_ENST00000379551.2_Missense_Mutation_p.R183Q|PRR16_ENST00000446965.1_Missense_Mutation_p.R136Q|PRR16_ENST00000505123.1_Missense_Mutation_p.R136Q			Q569H4	LARGN_HUMAN	proline rich 16	206	Pro-rich.				positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)					endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		GAACGAGTTCGGTTTAATGAA	0.473																																					p.R183Q		Atlas-SNP	.											PRR16,NS,carcinoma,+1,1	PRR16	71	.	0			c.G548A						.						70.0	71.0	71.0					5																	120022106		2203	4300	6503	SO:0001583	missense	51334	exon3			GAGTTCGGTTTAA	AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.617G>A	chr5.hg19:g.120022106G>A	ENSP00000385118:p.Arg206Gln	105.0	0.0		183.0	31.0	NM_016644	D3DSZ0|Q8IXY1|Q9NYI5	Missense_Mutation	SNP	ENST00000407149.2	hg19		.	.	.	.	.	.	.	.	.	.	G	29.5	5.014251	0.93404	.	.	ENSG00000184838	ENST00000407149;ENST00000379551;ENST00000509923;ENST00000505123;ENST00000446965	T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.83464	0.5260	M	0.69823	2.125	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.83343	-0.0007	9	.	.	.	-0.0429	17.8787	0.88833	0.0:0.0:1.0:0.0	.	206;183	Q569H4;Q569H4-3	PRR16_HUMAN;.	Q	206;183;136;136;136	ENSP00000385118:R206Q;ENSP00000368869:R183Q;ENSP00000421256:R136Q;ENSP00000423446:R136Q;ENSP00000405491:R136Q	.	R	+	2	0	PRR16	120050005	1.000000	0.71417	0.974000	0.42286	0.995000	0.86356	9.388000	0.97237	2.505000	0.84491	0.650000	0.86243	CGG	.	.		0.473	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644	
AFF4	27125	hgsc.bcm.edu	37	5	132270588	132270588	+	Missense_Mutation	SNP	C	C	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr5:132270588C>T	ENST00000265343.5	-	3	548	c.169G>A	c.(169-171)Gga>Aga	p.G57R	AFF4_ENST00000378595.3_Missense_Mutation_p.G57R|AFF4_ENST00000491831.1_5'UTR	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	57					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCGTAGTTTCCAAGCATACTC	0.313																																					p.G57R	Ovarian(126;889 1733 2942 10745 11605)	Atlas-SNP	.											.	AFF4	120	.	0			c.G169A						.						95.0	100.0	98.0					5																	132270588		2202	4300	6502	SO:0001583	missense	27125	exon3			AGTTTCCAAGCAT	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"""ALL1 fused gene from 5q31"""	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.169G>A	chr5.hg19:g.132270588C>T	ENSP00000265343:p.Gly57Arg	53.0	0.0		62.0	23.0	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	ENST00000265343.5	hg19	CCDS4164.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.776460	0.90195	.	.	ENSG00000072364	ENST00000265343;ENST00000378595;ENST00000421773	D;D;D	0.83419	-1.72;-1.72;-1.72	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.92296	0.7556	M	0.82193	2.58	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.92511	0.6016	10	0.87932	D	0	-11.5109	20.1802	0.98196	0.0:1.0:0.0:0.0	.	57;57;57	Q9UHB7-3;Q9UHB7-2;Q9UHB7	.;.;AFF4_HUMAN	R	57	ENSP00000265343:G57R;ENSP00000367858:G57R;ENSP00000395268:G57R	ENSP00000265343:G57R	G	-	1	0	AFF4	132298487	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.786000	0.85741	2.777000	0.95525	0.655000	0.94253	GGA	.	.		0.313	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423	
MDN1	23195	hgsc.bcm.edu	37	6	90513095	90513095	+	Missense_Mutation	SNP	A	A	G			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr6:90513095A>G	ENST00000369393.3	-	2	396	c.281T>C	c.(280-282)cTa>cCa	p.L94P	MDN1_ENST00000428876.1_Missense_Mutation_p.L94P			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	94					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.L94P(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CGACACACATAGCCGTTCATG	0.473																																					p.L94P		Atlas-SNP	.											MDN1,NS,carcinoma,0,1	MDN1	478	.	1	Substitution - Missense(1)	lung(1)	c.T281C						.						288.0	251.0	263.0					6																	90513095		2203	4300	6503	SO:0001583	missense	23195	exon2			ACACATAGCCGTT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.281T>C	chr6.hg19:g.90513095A>G	ENSP00000358400:p.Leu94Pro	83.0	0.0		49.0	2.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	A	15.99	2.995463	0.54147	.	.	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.30981	1.51;1.51;1.51	4.77	4.77	0.60923	.	0.000000	0.64402	D	0.000007	T	0.44850	0.1313	M	0.69823	2.125	0.80722	D	1	D;P	0.89917	1.0;0.604	D;B	0.91635	0.999;0.204	T	0.41662	-0.9496	10	0.42905	T	0.14	.	14.589	0.68351	1.0:0.0:0.0:0.0	.	94;94	Q6ZVV6;Q9NU22	.;MDN1_HUMAN	P	94	ENSP00000358400:L94P;ENSP00000413970:L94P;ENSP00000409664:L94P	ENSP00000358400:L94P	L	-	2	0	MDN1	90569816	1.000000	0.71417	0.998000	0.56505	0.897000	0.52465	8.727000	0.91480	1.917000	0.55516	0.254000	0.18369	CTA	.	.		0.473	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
TMEM168	64418	hgsc.bcm.edu	37	7	112407741	112407741	+	Silent	SNP	G	G	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr7:112407741G>T	ENST00000312814.6	-	5	2165	c.1605C>A	c.(1603-1605)tcC>tcA	p.S535S	TMEM168_ENST00000454074.1_Silent_p.S535S	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	535						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						GGGAACAAAAGGAACCATTCT	0.403																																					p.S535S		Atlas-SNP	.											.	TMEM168	84	.	0			c.C1605A						.						64.0	64.0	64.0					7																	112407741		2203	4300	6503	SO:0001819	synonymous_variant	64418	exon5			ACAAAAGGAACCA		CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.1605C>A	chr7.hg19:g.112407741G>T		26.0	0.0		63.0	17.0	NM_022484	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Silent	SNP	ENST00000312814.6	hg19	CCDS5757.1																																																																																			.	.		0.403	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484	
NOS3	4846	hgsc.bcm.edu	37	7	150696315	150696315	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr7:150696315G>A	ENST00000484524.1	+	8	994	c.994G>A	c.(994-996)Gcc>Acc	p.A332T	NOS3_ENST00000461406.1_Missense_Mutation_p.A126T|NOS3_ENST00000467517.1_Missense_Mutation_p.A332T|NOS3_ENST00000297494.3_Missense_Mutation_p.A332T	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCGCTGGTACGCCCTCCCGGC	0.642																																					p.A332T		Atlas-SNP	.											.	NOS3	131	.	0			c.G994A						.						61.0	68.0	66.0					7																	150696315		2201	4295	6496	SO:0001583	missense	4846	exon8			TGGTACGCCCTCC		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"""endothelial nitric oxide synthase"""	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.994G>A	chr7.hg19:g.150696315G>A	ENSP00000420215:p.Ala332Thr	42.0	0.0		61.0	9.0	NM_001160111	Q495E5	Missense_Mutation	SNP	ENST00000484524.1	hg19	CCDS55182.1	.	.	.	.	.	.	.	.	.	.	N	33	5.199781	0.94997	.	.	ENSG00000164867	ENST00000297494;ENST00000461406;ENST00000484524;ENST00000467517	T;T;T;T	0.35048	1.33;1.53;1.33;1.33	5.59	5.59	0.84812	Nitric oxide synthase, oxygenase domain (2);	0.000000	0.64402	D	0.000014	T	0.67078	0.2855	M	0.89353	3.025	0.54753	D	0.999985	D;D;D;D;D	0.89917	1.0;1.0;0.99;0.988;1.0	D;D;P;P;P	0.77004	0.989;0.989;0.812;0.699;0.868	T	0.73193	-0.4060	10	0.72032	D	0.01	-9.7199	17.0996	0.86645	0.0:0.0:1.0:0.0	.	332;332;332;126;332	A0S0A6;E9PFR2;A0S0A8;E7ESA7;P29474	.;.;.;.;NOS3_HUMAN	T	332;126;332;332	ENSP00000297494:A332T;ENSP00000417143:A126T;ENSP00000420215:A332T;ENSP00000420551:A332T	ENSP00000297494:A332T	A	+	1	0	NOS3	150327248	0.997000	0.39634	0.958000	0.39756	0.847000	0.48162	6.771000	0.74996	2.620000	0.88729	0.639000	0.83563	GCC	.	.		0.642	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603	
HGSNAT	138050	hgsc.bcm.edu	37	8	43054562	43054562	+	Silent	SNP	C	C	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr8:43054562C>T	ENST00000458501.2	+	18	1842	c.1842C>T	c.(1840-1842)caC>caT	p.H614H	HGSNAT_ENST00000297798.7_Silent_p.H318H|HGSNAT_ENST00000521576.1_Silent_p.H303H|HGSNAT_ENST00000379644.4_Silent_p.H586H			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	614					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lysosomal transport (GO:0007041)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	heparan-alpha-glucosaminide N-acetyltransferase activity (GO:0015019)|transferase activity, transferring acyl groups (GO:0016746)			cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			ATGTCGGCCACGAGGTGTTTG	0.463																																					p.H586H		Atlas-SNP	.											.	HGSNAT	85	.	0			c.C1758T						.						58.0	59.0	59.0					8																	43054562		2194	4295	6489	SO:0001819	synonymous_variant	138050	exon18			CGGCCACGAGGTG		CCDS47852.1	8p11.1	2011-11-16	2006-09-05	2006-08-16	ENSG00000165102	ENSG00000165102	2.3.1.78		26527	protein-coding gene	gene with protein product		610453	"""transmembrane protein 76"""	TMEM76		17033958, 16960811	Standard	NM_152419		Approved	FLJ32731, HGNAT	uc003xpx.4	Q68CP4	OTTHUMG00000164102	ENST00000458501.2:c.1842C>T	chr8.hg19:g.43054562C>T		60.0	0.0		99.0	16.0	NM_152419	B4E2V0	Silent	SNP	ENST00000458501.2	hg19																																																																																				.	.		0.463	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038	
PAG1	55824	hgsc.bcm.edu	37	8	81888977	81888977	+	Missense_Mutation	SNP	T	T	G			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr8:81888977T>G	ENST00000220597.4	-	9	1811	c.1101A>C	c.(1099-1101)aaA>aaC	p.K367N	PAG1_ENST00000523463.1_5'Flank	NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	367					epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			TGTTTGGAGTTTTTTCGAAGT	0.507																																					p.K367N		Atlas-SNP	.											.	PAG1	39	.	0			c.A1101C						.						89.0	88.0	89.0					8																	81888977		2203	4300	6503	SO:0001583	missense	55824	exon9			TGGAGTTTTTTCG	AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30						30043	protein-coding gene	gene with protein product	"""Csk-binding protein"", ""transmembrane adaptor protein PAG"""	605767	"""phosphoprotein associated with glycosphingolipid microdomains 1"""			10790433	Standard	XM_006716461		Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.1101A>C	chr8.hg19:g.81888977T>G	ENSP00000220597:p.Lys367Asn	66.0	0.0		217.0	93.0	NM_018440	A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	Missense_Mutation	SNP	ENST00000220597.4	hg19	CCDS6227.1	.	.	.	.	.	.	.	.	.	.	T	1.653	-0.513401	0.04200	.	.	ENSG00000076641	ENST00000220597	.	.	.	5.05	-2.67	0.06059	.	0.407548	0.27048	N	0.021190	T	0.23846	0.0577	L	0.53249	1.67	0.24613	N	0.993714	B	0.06786	0.001	B	0.09377	0.004	T	0.26467	-1.0102	9	0.07482	T	0.82	-26.5581	2.2185	0.03966	0.1011:0.2411:0.309:0.3488	.	367	Q9NWQ8	PAG1_HUMAN	N	367	.	ENSP00000220597:K367N	K	-	3	2	PAG1	82051532	0.012000	0.17670	0.083000	0.20561	0.050000	0.14768	-0.098000	0.11024	-0.241000	0.09681	-0.331000	0.08364	AAA	.	.		0.507	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	NM_018440	
C8orf33	65265	hgsc.bcm.edu	37	8	146278706	146278706	+	Nonsense_Mutation	SNP	C	C	T	rs376887084		TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr8:146278706C>T	ENST00000331434.6	+	4	541	c.427C>T	c.(427-429)Cga>Tga	p.R143*		NM_023080.2	NP_075568.1	Q9H7E9	CH033_HUMAN	chromosome 8 open reading frame 33	143										endometrium(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;9.1e-38)|all cancers(56;7.37e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.243)		TGGAGCAATCCGAACCCTGCG	0.527																																					p.R143X		Atlas-SNP	.											.	C8orf33	25	.	0			c.C427T						.	C	stop/ARG	1,4405		0,1,2202	91.0	104.0	100.0		427	1.6	0.0	8		100	0,8600		0,0,4300	no	stop-gained	C8orf33	NM_023080.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		143/230	146278706	1,13005	2203	4300	6503	SO:0001587	stop_gained	65265	exon4			GCAATCCGAACCC		CCDS34974.1	8q24.3	2012-04-11			ENSG00000182307	ENSG00000182307			26104	protein-coding gene	gene with protein product							Standard	NM_023080		Approved	FLJ20989	uc003zfc.4	Q9H7E9	OTTHUMG00000165256	ENST00000331434.6:c.427C>T	chr8.hg19:g.146278706C>T	ENSP00000330361:p.Arg143*	156.0	0.0		191.0	41.0	NM_023080	A6NGC0|Q96BT8	Nonsense_Mutation	SNP	ENST00000331434.6	hg19	CCDS34974.1	.	.	.	.	.	.	.	.	.	.	.	20.2	3.944224	0.73672	2.27E-4	0.0	ENSG00000182307	ENST00000331434	.	.	.	3.61	1.57	0.23409	.	0.229940	0.33610	N	0.004723	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.9088	3.7887	0.08710	0.2394:0.6277:0.0:0.1328	.	.	.	.	X	143	.	.	R	+	1	2	C8orf33	146249510	0.149000	0.22717	0.002000	0.10522	0.283000	0.27025	0.120000	0.15647	0.836000	0.34901	0.467000	0.42956	CGA	.	.		0.527	C8orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382995.1	NM_023080	
ANKRD26	22852	hgsc.bcm.edu	37	10	27313397	27313397	+	Missense_Mutation	SNP	T	T	G			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr10:27313397T>G	ENST00000376087.4	-	28	4229	c.4064A>C	c.(4063-4065)gAa>gCa	p.E1355A	ANKRD26_ENST00000376070.3_Missense_Mutation_p.E912A|ANKRD26_ENST00000436985.2_Missense_Mutation_p.E1371A	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1354					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TCTTTCTAATTCAACATTTTT	0.249																																					p.E1355A		Atlas-SNP	.											.	ANKRD26	179	.	0			c.A4064C						.						69.0	69.0	69.0					10																	27313397		1779	4044	5823	SO:0001583	missense	22852	exon28			TCTAATTCAACAT	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.4064A>C	chr10.hg19:g.27313397T>G	ENSP00000365255:p.Glu1355Ala	168.0	0.0		240.0	29.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	hg19	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	T	3.222	-0.159391	0.06544	.	.	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.77489	-1.1;-1.1;-1.1	4.89	3.73	0.42828	.	0.112806	0.36101	N	0.002799	T	0.57888	0.2084	N	0.17631	0.505	0.37940	D	0.932297	P;B;B	0.36144	0.539;0.404;0.004	B;B;B	0.30179	0.112;0.052;0.007	T	0.55418	-0.8144	10	0.21540	T	0.41	.	9.7359	0.40388	0.0:0.0:0.1824:0.8176	.	1355;1354;1371	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	A	912;1355;1371	ENSP00000365238:E912A;ENSP00000365255:E1355A;ENSP00000405112:E1371A	ENSP00000365238:E912A	E	-	2	0	ANKRD26	27353403	0.997000	0.39634	0.816000	0.32577	0.171000	0.22731	2.987000	0.49378	0.695000	0.31675	0.455000	0.32223	GAA	.	.		0.249	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
EED	8726	hgsc.bcm.edu	37	11	85977167	85977167	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr11:85977167G>A	ENST00000263360.6	+	8	1455	c.769G>A	c.(769-771)Gat>Aat	p.D257N	EED_ENST00000528180.1_Intron|EED_ENST00000351625.6_Missense_Mutation_p.D257N|EED_ENST00000327320.4_Missense_Mutation_p.D257N	NM_003797.3	NP_003788.2	O75530	EED_HUMAN	embryonic ectoderm development	257	Interaction with EZH2. {ECO:0000250}.|Required for interaction with the matrix protein MA of HIV-1.				negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K27 methylation (GO:0061087)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	21		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				CTGTGGTATGGATCATTCTCT	0.284																																					p.D257N		Atlas-SNP	.											.	EED	50	.	0			c.G769A						.						91.0	101.0	98.0					11																	85977167		2201	4290	6491	SO:0001583	missense	8726	exon8			GGTATGGATCATT	AF078933	CCDS8273.1, CCDS8274.1	11q14.2-q22.3	2013-01-10			ENSG00000074266	ENSG00000074266		"""WD repeat domain containing"""	3188	protein-coding gene	gene with protein product	"""WD protein associating with integrin cytoplasmic tails 1"""	605984				9765275, 9806832	Standard	NM_003797		Approved	WAIT-1, HEED	uc001pbp.3	O75530	OTTHUMG00000167209	ENST00000263360.6:c.769G>A	chr11.hg19:g.85977167G>A	ENSP00000263360:p.Asp257Asn	106.0	0.0		140.0	21.0	NM_003797	A8K7V5|O00149|Q6NTH2|Q7LDA5|Q7LDG8|Q86VV2|Q9UNY7	Missense_Mutation	SNP	ENST00000263360.6	hg19	CCDS8273.1	.	.	.	.	.	.	.	.	.	.	G	35	5.521067	0.96416	.	.	ENSG00000074266	ENST00000263360;ENST00000351625;ENST00000327320;ENST00000533228;ENST00000534564	T;T;D	0.88975	0.89;0.89;-2.45	5.36	5.36	0.76844	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	0.95875	0.8657	M	0.91038	3.17	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96137	0.9097	9	.	.	.	-15.7044	19.4599	0.94912	0.0:0.0:1.0:0.0	.	257;257;257	O75530-3;O75530-2;O75530	.;.;EED_HUMAN	N	257;257;257;50;6	ENSP00000263360:D257N;ENSP00000338186:D257N;ENSP00000315587:D257N	.	D	+	1	0	EED	85654815	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.629000	0.98417	2.671000	0.90904	0.563000	0.77884	GAT	.	.		0.284	EED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393733.1	NM_003797	
PLEKHA5	54477	hgsc.bcm.edu	37	12	19467760	19467760	+	Intron	SNP	G	G	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr12:19467760G>T	ENST00000299275.6	+	13	1851				PLEKHA5_ENST00000355397.3_Intron|PLEKHA5_ENST00000317589.4_Intron|PLEKHA5_ENST00000538714.1_Intron|PLEKHA5_ENST00000543806.1_Nonsense_Mutation_p.E512*|PLEKHA5_ENST00000539256.1_Intron|PLEKHA5_ENST00000424268.1_Nonsense_Mutation_p.E512*|PLEKHA5_ENST00000359180.3_Intron|PLEKHA5_ENST00000429027.2_Nonsense_Mutation_p.E684*	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5						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)					GAAAGAAAATGAACCTATTAT	0.398																																					p.E684X	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.G2050T						.						131.0	110.0	117.0					12																	19467760		692	1591	2283	SO:0001627	intron_variant	54477	exon16			GAAAATGAACCTA	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.1846-5736G>T	chr12.hg19:g.19467760G>T		49.0	0.0		103.0	17.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Nonsense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	G	40	8.316369	0.98757	.	.	ENSG00000052126	ENST00000542828;ENST00000429027;ENST00000424268;ENST00000543806	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	18.9962	0.92813	0.0:0.0:1.0:0.0	.	.	.	.	X	685;684;512;512	.	ENSP00000400411:E512X	E	+	1	0	PLEKHA5	19359027	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.080000	0.94040	2.487000	0.83934	0.643000	0.83706	GAA	.	.		0.398	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	
BCDIN3D	144233	hgsc.bcm.edu	37	12	50236870	50236870	+	Start_Codon_SNP	SNP	T	T	G			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr12:50236870T>G	ENST00000333924.4	-	1	42	c.1A>C	c.(1-3)Atg>Ctg	p.M1L	BCDIN3D-AS1_ENST00000549124.1_RNA|BCDIN3D-AS1_ENST00000548872.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	1					miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)	p.M1L(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						GGCACCGCCATTAGCCTCAAC	0.662																																					p.M1L		Atlas-SNP	.											BCDIN3D,NS,carcinoma,0,1	BCDIN3D	20	.	1	Substitution - Missense(1)	kidney(1)	c.A1C						.						32.0	30.0	31.0					12																	50236870		2177	4254	6431	SO:0001582	initiator_codon_variant	144233	exon1			CCGCCATTAGCCT		CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.1A>C	chr12.hg19:g.50236870T>G	ENSP00000335201:p.Met1Leu	144.0	0.0		130.0	23.0	NM_181708	A8K829	Missense_Mutation	SNP	ENST00000333924.4	hg19	CCDS8790.1	.	.	.	.	.	.	.	.	.	.	T	16.26	3.074142	0.55646	.	.	ENSG00000186666	ENST00000333924	T	0.40476	1.03	6.08	4.92	0.64577	.	0.325555	0.35040	N	0.003488	T	0.35038	0.0918	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.15350	-1.0440	9	0.87932	D	0	.	9.5459	0.39279	0.1566:0.0:0.0:0.8434	.	1	Q7Z5W3	BN3D2_HUMAN	L	1	ENSP00000335201:M1L	ENSP00000335201:M1L	M	-	1	0	BCDIN3D	48523137	1.000000	0.71417	0.833000	0.33012	0.037000	0.13140	4.713000	0.61895	1.094000	0.41399	-0.468000	0.05107	ATG	.	.		0.662	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708	Missense_Mutation
PARPBP	55010	hgsc.bcm.edu	37	12	102569312	102569312	+	Silent	SNP	C	C	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr12:102569312C>T	ENST00000358383.5	+	7	918	c.873C>T	c.(871-873)ggC>ggT	p.G291G	PARPBP_ENST00000541394.1_Silent_p.G368G|PARPBP_ENST00000392911.2_Silent_p.G210G|PARPBP_ENST00000543784.1_Intron|PARPBP_ENST00000378128.3_Intron|PARPBP_ENST00000327680.2_Silent_p.G210G|PARPBP_ENST00000535811.1_Intron			Q9NWS1	PARI_HUMAN	PARP1 binding protein	291					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(8)|urinary_tract(2)	11						TGATTAAAGGCCAAAACAGCA	0.353																																					p.G291G		Atlas-SNP	.											.	PARPBP	40	.	0			c.C873T						.						106.0	108.0	107.0					12																	102569312		2203	4300	6503	SO:0001819	synonymous_variant	55010	exon7			TAAAGGCCAAAAC	AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"""PARP-1 binding protein"""	613687	"""chromosome 12 open reading frame 48"""	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.873C>T	chr12.hg19:g.102569312C>T		105.0	0.0		166.0	52.0	NM_017915	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Silent	SNP	ENST00000358383.5	hg19	CCDS9090.2																																																																																			.	.		0.353	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915	
NBEA	26960	hgsc.bcm.edu	37	13	35883674	35883674	+	Missense_Mutation	SNP	A	A	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr13:35883674A>T	ENST00000400445.3	+	36	6382	c.5848A>T	c.(5848-5850)Aac>Tac	p.N1950Y	NBEA_ENST00000310336.4_Missense_Mutation_p.N1950Y|NBEA_ENST00000379939.2_Missense_Mutation_p.N1947Y|NBEA_ENST00000540320.1_Missense_Mutation_p.N1950Y	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1950					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GGAATGGCAAAACTCTATTCA	0.313																																					p.N1950Y		Atlas-SNP	.											.	NBEA	340	.	0			c.A5848T						.						75.0	68.0	70.0					13																	35883674		1861	4120	5981	SO:0001583	missense	26960	exon36			TGGCAAAACTCTA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.5848A>T	chr13.hg19:g.35883674A>T	ENSP00000383295:p.Asn1950Tyr	132.0	0.0		174.0	40.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.293074	0.80914	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.54479	0.57;0.58;0.58;0.57	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.71039	0.3293	M	0.71206	2.165	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.79784	0.978;0.993	T	0.73164	-0.4069	10	0.51188	T	0.08	.	15.3088	0.74014	1.0:0.0:0.0:0.0	.	1950;1947	Q8NFP9;Q5T321	NBEA_HUMAN;.	Y	1950;1950;1947;1950;577	ENSP00000440951:N1950Y;ENSP00000383295:N1950Y;ENSP00000369271:N1947Y;ENSP00000308534:N1950Y	ENSP00000308534:N1950Y	N	+	1	0	NBEA	34781674	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.730000	0.91510	2.029000	0.59856	0.533000	0.62120	AAC	.	.		0.313	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
COL4A1	1282	hgsc.bcm.edu	37	13	110835413	110835413	+	Missense_Mutation	SNP	C	C	G			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr13:110835413C>G	ENST00000375820.4	-	28	2143	c.2022G>C	c.(2020-2022)agG>agC	p.R674S		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	674	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			GCAGGCCTGGCCTTCCTGGGG	0.627																																					p.R674S		Atlas-SNP	.											.	COL4A1	372	.	0			c.G2022C						.																																			SO:0001583	missense	1282	exon28			GCCTGGCCTTCCT	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.2022G>C	chr13.hg19:g.110835413C>G	ENSP00000364979:p.Arg674Ser	88.0	0.0		71.0	16.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.289361	0.40494	.	.	ENSG00000187498	ENST00000375820	D	0.93307	-3.2	4.7	1.89	0.25635	.	0.290655	0.33691	N	0.004649	D	0.88149	0.6359	N	0.11064	0.09	0.80722	D	1	D	0.61697	0.99	P	0.62885	0.908	T	0.82194	-0.0578	10	0.09084	T	0.74	.	5.5931	0.17311	0.1543:0.5906:0.0:0.2551	.	674	P02462	CO4A1_HUMAN	S	674	ENSP00000364979:R674S	ENSP00000364979:R674S	R	-	3	2	COL4A1	109633414	0.651000	0.27340	0.997000	0.53966	0.954000	0.61252	0.201000	0.17276	0.484000	0.27630	0.561000	0.74099	AGG	.	.		0.627	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
DYNC1H1	1778	hgsc.bcm.edu	37	14	102472421	102472421	+	Missense_Mutation	SNP	A	A	G			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr14:102472421A>G	ENST00000360184.4	+	27	5794	c.5630A>G	c.(5629-5631)gAc>gGc	p.D1877G		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1877	AAA 1. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GGTGTTCAGGACAAACTGGTC	0.473																																					p.D1877G		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A5630G						.						110.0	112.0	112.0					14																	102472421		2203	4300	6503	SO:0001583	missense	1778	exon27			TTCAGGACAAACT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.5630A>G	chr14.hg19:g.102472421A>G	ENSP00000348965:p.Asp1877Gly	65.0	0.0		43.0	18.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	a	23.7	4.445647	0.84101	.	.	ENSG00000197102	ENST00000360184	T	0.09163	3.01	6.06	6.06	0.98353	.	0.046426	0.85682	D	0.000000	T	0.15912	0.0383	N	0.20881	0.62	0.80722	D	1	P	0.50272	0.933	P	0.57679	0.825	T	0.16660	-1.0395	10	0.12103	T	0.63	.	16.6165	0.84917	1.0:0.0:0.0:0.0	.	1877	Q14204	DYHC1_HUMAN	G	1877	ENSP00000348965:D1877G	ENSP00000348965:D1877G	D	+	2	0	DYNC1H1	101542174	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.233000	0.72320	2.323000	0.78572	0.529000	0.55759	GAC	.	.		0.473	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
HCN4	10021	hgsc.bcm.edu	37	15	73635757	73635757	+	Missense_Mutation	SNP	C	C	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr15:73635757C>T	ENST00000261917.3	-	2	2171	c.1178G>A	c.(1177-1179)cGc>cAc	p.R393H	RP11-272D12.1_ENST00000557981.1_RNA|RP11-272D12.1_ENST00000558742.1_RNA	NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	393					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		TCGAATGAGGCGGGAGAGGCG	0.582																																					p.R393H		Atlas-SNP	.											HCN4,colon,carcinoma,0,1	HCN4	150	.	0			c.G1178A						.						63.0	51.0	55.0					15																	73635757		2198	4297	6495	SO:0001583	missense	10021	exon2			ATGAGGCGGGAGA	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1178G>A	chr15.hg19:g.73635757C>T	ENSP00000261917:p.Arg393His	78.0	0.0		148.0	66.0	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	hg19	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.587141	0.86851	.	.	ENSG00000138622	ENST00000261917	D	0.99591	-6.24	5.34	5.34	0.76211	Ion transport (1);	.	.	.	.	D	0.99746	0.9899	M	0.93420	3.415	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97434	1.0017	9	0.87932	D	0	.	19.4036	0.94640	0.0:1.0:0.0:0.0	.	393	Q9Y3Q4	HCN4_HUMAN	H	393	ENSP00000261917:R393H	ENSP00000261917:R393H	R	-	2	0	HCN4	71422810	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.671000	0.83941	2.657000	0.90304	0.655000	0.94253	CGC	.	.		0.582	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
FAM86A	196483	hgsc.bcm.edu	37	16	5140112	5140112	+	Missense_Mutation	SNP	A	A	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr16:5140112A>T	ENST00000427587.4	-	6	783	c.715T>A	c.(715-717)Ttc>Atc	p.F239I	FAM86A_ENST00000458008.4_Missense_Mutation_p.F205I|FAM86A_ENST00000587133.1_Missense_Mutation_p.F178I	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A	239						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	12						TCTGGCTGGAAGGCAGAGAGC	0.597																																					p.F239I		Atlas-SNP	.											FAM86A,NS,neuroblastoma,0,1	FAM86A	32	.	0			c.T715A						.						33.0	38.0	36.0					16																	5140112		1413	2402	3815	SO:0001583	missense	196483	exon6			GCTGGAAGGCAGA	BC010084	CCDS10529.1, CCDS10530.1, CCDS73823.1	16p13.3	2012-11-07			ENSG00000118894	ENSG00000118894			32221	protein-coding gene	gene with protein product		615263					Standard	NM_201400		Approved	SB153, MGC19636	uc002cyo.2	Q96G04	OTTHUMG00000129527	ENST00000427587.4:c.715T>A	chr16.hg19:g.5140112A>T	ENSP00000398502:p.Phe239Ile	10.0	0.0		10.0	3.0	NM_201400	D3DUF0|Q96S85	Missense_Mutation	SNP	ENST00000427587.4	hg19	CCDS10529.1	.	.	.	.	.	.	.	.	.	.	a	7.916	0.737456	0.15574	.	.	ENSG00000118894	ENST00000458008;ENST00000427587	T;T	0.16457	2.34;2.34	5.02	1.62	0.23740	.	0.452369	0.23165	N	0.051195	T	0.09905	0.0243	L	0.27053	0.805	0.29093	N	0.881992	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.31943	-0.9925	10	0.18276	T	0.48	.	7.9111	0.29791	0.5683:0.0:0.4317:0.0	.	205;239	Q96G04-2;Q96G04	.;FA86A_HUMAN	I	205;239	ENSP00000389710:F205I;ENSP00000398502:F239I	ENSP00000398502:F239I	F	-	1	0	FAM86A	5080113	0.643000	0.27269	1.000000	0.80357	0.172000	0.22775	1.031000	0.30165	0.101000	0.17610	0.370000	0.22315	TTC	.	.		0.597	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	NM_201400	
RLTPR	146206	hgsc.bcm.edu	37	16	67688114	67688114	+	Silent	SNP	G	G	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr16:67688114G>A	ENST00000334583.6	+	30	3511	c.3183G>A	c.(3181-3183)gaG>gaA	p.E1061E	RLTPR_ENST00000545661.1_Silent_p.E1025E	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	1061					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		AGGGCGTGGAGGAATTCTTCT	0.637																																					p.E1061E		Atlas-SNP	.											.	RLTPR	124	.	0			c.G3183A						.						30.0	33.0	32.0					16																	67688114		1949	4120	6069	SO:0001819	synonymous_variant	146206	exon30			CGTGGAGGAATTC	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.3183G>A	chr16.hg19:g.67688114G>A		67.0	0.0		43.0	15.0	NM_001013838	B8X2Z3	Silent	SNP	ENST00000334583.6	hg19	CCDS45513.1																																																																																			.	.		0.637	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838	
OR3A1	4994	hgsc.bcm.edu	37	17	3194961	3194961	+	Missense_Mutation	SNP	T	T	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr17:3194961T>A	ENST00000323404.1	-	1	915	c.916A>T	c.(916-918)Agg>Tgg	p.R306W	RP11-64J4.2_ENST00000573491.1_RNA	NM_002550.2	NP_002541.2	P47881	OR3A1_HUMAN	olfactory receptor, family 3, subfamily A, member 1	306					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|signal transduction (GO:0007165)	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(1)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	20						GTGAGCATCCTCCAGATGGCA	0.473																																					p.R306W	GBM(20;287 516 18743 28660 36594)	Atlas-SNP	.											.	OR3A1	46	.	0			c.A916T						.						84.0	81.0	82.0					17																	3194961		2203	4300	6503	SO:0001583	missense	4994	exon1			GCATCCTCCAGAT	X80391	CCDS11023.1	17p13.3	2012-08-09			ENSG00000180090	ENSG00000180090		"""GPCR / Class A : Olfactory receptors"""	8282	protein-coding gene	gene with protein product						8921386, 8647456	Standard	NM_002550		Approved	OLFRA03, OR40, OR17-40	uc002fvh.1	P47881	OTTHUMG00000090642	ENST00000323404.1:c.916A>T	chr17.hg19:g.3194961T>A	ENSP00000313803:p.Arg306Trp	42.0	0.0		57.0	12.0	NM_002550	Q4VB06|Q6IFM4	Missense_Mutation	SNP	ENST00000323404.1	hg19	CCDS11023.1	.	.	.	.	.	.	.	.	.	.	T	13.42	2.230450	0.39399	.	.	ENSG00000180090	ENST00000323404	T	0.41758	0.99	4.81	1.32	0.21799	.	0.546790	0.16683	N	0.203870	T	0.48241	0.1489	M	0.87180	2.865	0.09310	N	1	B	0.19331	0.035	B	0.15484	0.013	T	0.53725	-0.8398	10	0.87932	D	0	-4.3384	12.8912	0.58071	0.0:0.0:0.2034:0.7966	.	306	P47881	OR3A1_HUMAN	W	306	ENSP00000313803:R306W	ENSP00000313803:R306W	R	-	1	2	OR3A1	3141711	0.000000	0.05858	0.052000	0.19188	0.088000	0.18126	-1.926000	0.01562	0.561000	0.29186	0.533000	0.62120	AGG	.	.		0.473	OR3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207302.2		
HOXB6	3216	hgsc.bcm.edu	37	17	46675276	46675276	+	Silent	SNP	G	G	A	rs577327660		TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr17:46675276G>A	ENST00000484302.2	-	2	859	c.237C>T	c.(235-237)gcC>gcT	p.A79A	HOXB-AS3_ENST00000466037.2_RNA|HOXB6_ENST00000225648.3_Silent_p.A79A|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB6_ENST00000490419.1_5'Flank|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000492897.3_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000460041.1_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000480872.1_RNA			P17509	HXB6_HUMAN	homeobox B6	79					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte homeostasis (GO:0034101)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(1)|lung(4)	7						CGCGGTAGAAGGCCGGCGCCG	0.726													G|||	1	0.000199681	0.0	0.0014	5008	,	,		10490	0.0		0.0	False		,,,				2504	0.0				p.A79A		Atlas-SNP	.											.	HOXB6	13	.	0			c.C237T						.						5.0	6.0	5.0					17																	46675276		2129	4136	6265	SO:0001819	synonymous_variant	3216	exon3			GTAGAAGGCCGGC		CCDS11531.1	17q21.32	2011-06-20	2005-12-22		ENSG00000108511	ENSG00000108511		"""Homeoboxes / ANTP class : HOXL subclass"""	5117	protein-coding gene	gene with protein product		142961	"""homeo box B6"""	HOX2, HOX2B		1973146, 1358459	Standard	XM_005257284		Approved		uc002ins.1	P17509	OTTHUMG00000159912	ENST00000484302.2:c.237C>T	chr17.hg19:g.46675276G>A		148.0	0.0		122.0	70.0	NM_018952	A8K835|D3DTV5|P09068|Q9HB11|Q9UGH2	Silent	SNP	ENST00000484302.2	hg19	CCDS11531.1																																																																																			.	.		0.726	HOXB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358146.2		
CPAMD8	27151	hgsc.bcm.edu	37	19	17014374	17014374	+	Missense_Mutation	SNP	C	C	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr19:17014374C>A	ENST00000443236.1	-	34	4639	c.4608G>T	c.(4606-4608)atG>atT	p.M1536I		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1489						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						ACCTCACCTGCATCAGGCAGC	0.627																																					p.M1536I		Atlas-SNP	.											.	CPAMD8	192	.	0			c.G4608T						.						74.0	89.0	84.0					19																	17014374		2048	4193	6241	SO:0001583	missense	27151	exon34			CACCTGCATCAGG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.4608G>T	chr19.hg19:g.17014374C>A	ENSP00000402505:p.Met1536Ile	128.0	0.0		113.0	26.0	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	hg19	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.94|11.94	1.788366|1.788366	0.31593|0.31593	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000443236|ENST00000291440	.|.	.|.	.|.	3.32|3.32	2.26|2.26	0.28386|0.28386	.|.	.|7739.210000	.|0.00541	.|U	.|0.000222	T|T	0.56217|0.56217	0.1970|0.1970	L|L	0.50993|0.50993	1.605|1.605	0.80722|0.80722	D|D	1|1	.|B	.|0.32781	.|0.384	.|B	.|0.31290	.|0.127	T|T	0.33854|0.33854	-0.9852|-0.9852	5|9	.|0.56958	.|D	.|0.05	.|.	10.2643|10.2643	0.43445|0.43445	0.0:0.8995:0.0:0.1005|0.0:0.8995:0.0:0.1005	.|.	.|1489	.|Q8IZJ3	.|CPMD8_HUMAN	F|I	1547|1536	.|.	.|ENSP00000291440:M1536I	C|M	-|-	2|3	0|0	CPAMD8|CPAMD8	16875374|16875374	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	4.735000|4.735000	0.62051|0.62051	0.417000|0.417000	0.25871|0.25871	0.456000|0.456000	0.33151|0.33151	TGC|ATG	.	.		0.627	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
ZNF714	148206	hgsc.bcm.edu	37	19	21299919	21299921	+	Missense_Mutation	TNP	ATG	ATG	GCA			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A|T|G	A|T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr19:21299919_21299921ATG>GCA	ENST00000596143.1	+	5	774_776	c.449_451ATG>GCA	c.(448-453)gATGaa>gGCAaa	p.150_151DE>GK	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	150					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AAAAAATGTGATGAATCATTTTG	0.291																																					p.D150G|p.D150D|p.E151K		Atlas-SNP	.											.	ZNF714	121	.	0			c.A449G|c.T450C|c.G451A						.																																			SO:0001583	missense	148206	exon5			AATGTGATGAATC|ATGTGATGAATCA|TGTGATGAATCAT	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"""Zinc fingers, C2H2-type"""	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.449_451ATG>GCA	chr19.hg19:g.21299919ATG>GCA	ENSP00000472368:p.D150_E151delinsGK	164.0|168.0|169.0	0.0		250.0|250.0|252.0	41.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation|Silent|Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1																																																																																			.	.		0.291	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515	
MYH14	79784	hgsc.bcm.edu	37	19	50713649	50713649	+	Silent	SNP	C	C	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr19:50713649C>T	ENST00000596571.1	+	1	27	c.27C>T	c.(25-27)ccC>ccT	p.P9P	MYH14_ENST00000601313.1_Silent_p.P9P|MYH14_ENST00000440075.2_Silent_p.P9P|MYH14_ENST00000425460.1_Silent_p.P9P|MYH14_ENST00000598205.1_Silent_p.P9P|MYH14_ENST00000262269.8_Silent_p.P9P|MYH14_ENST00000376970.2_Silent_p.P9P			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	9					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		TGTCGGTGCCCGGGCGGAAGG	0.751																																					p.P9P		Atlas-SNP	.											.	MYH14	261	.	0			c.C27T						.						5.0	5.0	5.0					19																	50713649		1511	3440	4951	SO:0001819	synonymous_variant	79784	exon2			GGTGCCCGGGCGG	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.27C>T	chr19.hg19:g.50713649C>T		154.0	0.0		56.0	11.0	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	hg19	CCDS59411.1																																																																																			.	.		0.751	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
KLK1	3816	hgsc.bcm.edu	37	19	51322506	51322506	+	Missense_Mutation	SNP	C	C	T	rs576085704		TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr19:51322506C>T	ENST00000301420.2	-	5	768	c.733G>A	c.(733-735)Gtc>Atc	p.V245I	CTD-2568A17.5_ENST00000326989.5_lincRNA|KLK1_ENST00000448701.2_Missense_Mutation_p.V143I	NM_002257.2	NP_002248.1	P06870	KLK1_HUMAN	kallikrein 1	245	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			breast(1)|large_intestine(4)|lung(7)|urinary_tract(1)	13		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00399)	Aprotinin(DB06692)	AGCACTCTGACGGCGACAGAA	0.562													C|||	1	0.000199681	0.0008	0.0	5008	,	,		21306	0.0		0.0	False		,,,				2504	0.0				p.V245I		Atlas-SNP	.											.	KLK1	27	.	0			c.G733A						.						134.0	114.0	121.0					19																	51322506		2203	4300	6503	SO:0001583	missense	3816	exon5			CTCTGACGGCGAC	L10038	CCDS12804.1	19q13.3	2008-02-05	2006-10-27			ENSG00000167748	3.4.21.35	"""Kallikreins"""	6357	protein-coding gene	gene with protein product		147910	"""kallikrein 1, renal/pancreas/salivary"""			1684954, 16800724, 16800723	Standard	NM_002257		Approved	Klk6	uc002ptk.1	P06870		ENST00000301420.2:c.733G>A	chr19.hg19:g.51322506C>T	ENSP00000301420:p.Val245Ile	75.0	0.0		96.0	13.0	NM_002257	Q66US9|Q86U61|Q8TCV8|Q9BS53|Q9NQU4|Q9UD19|Q9UMJ1	Missense_Mutation	SNP	ENST00000301420.2	hg19	CCDS12804.1	.	.	.	.	.	.	.	.	.	.	c	12.22	1.872584	0.33069	.	.	ENSG00000167748	ENST00000301420;ENST00000448701	T;T	0.59364	3.3;0.27	3.53	0.196	0.15159	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.35307	0.0927	N	0.10916	0.065	0.09310	N	1	B	0.33379	0.41	B	0.37346	0.247	T	0.31110	-0.9955	9	0.87932	D	0	.	3.1007	0.06325	0.0:0.2592:0.2242:0.5166	.	245	P06870	KLK1_HUMAN	I	245;143	ENSP00000301420:V245I;ENSP00000400994:V143I	ENSP00000301420:V245I	V	-	1	0	KLK1	56014318	0.818000	0.29161	0.000000	0.03702	0.001000	0.01503	0.386000	0.20702	-0.036000	0.13669	-0.502000	0.04539	GTC	.	.		0.562	KLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464135.2	NM_002257	
LILRA3	11026	hgsc.bcm.edu	37	19	54802575	54802575	+	Missense_Mutation	SNP	C	C	G	rs200980681	byFrequency	TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr19:54802575C>G	ENST00000251390.3	-	5	957	c.866G>C	c.(865-867)cGc>cCc	p.R289P	LILRA3_ENST00000391745.1_Missense_Mutation_p.R306P|LILRA3_ENST00000391744.3_Missense_Mutation_p.R225P	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	289	Ig-like C2-type 3.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCCGTAGGAGCGGCTCACAGG	0.662													.|||	8	0.00159744	0.0	0.0072	5008	,	,		10039	0.001		0.002	False		,,,				2504	0.0				p.R289P		Atlas-SNP	.											.	LILRA3	65	.	0			c.G866C						.																																			SO:0001583	missense	11026	exon5			TAGGAGCGGCTCA	U91926		19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.866G>C	chr19.hg19:g.54802575C>G	ENSP00000251390:p.Arg289Pro	8.0	0.0		10.0	5.0	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	hg19	CCDS12887.1	.	.	.	.	.	.	.	.	.	.	C	1.908	-0.451501	0.04572	.	.	ENSG00000170866	ENST00000251390;ENST00000391744;ENST00000391745	T;T;T	0.11277	2.79;2.79;2.79	2.03	-1.81	0.07882	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	3.569410	0.01087	N	0.005100	T	0.03608	0.0103	N	0.01081	-1.03	0.09310	N	1	B;B	0.19331	0.035;0.001	B;B	0.27170	0.077;0.025	T	0.30297	-0.9983	10	0.22109	T	0.4	.	2.9469	0.05849	0.4738:0.368:0.0:0.1583	.	289;289	E7EU74;Q8N6C8	.;LIRA3_HUMAN	P	289;225;306	ENSP00000251390:R289P;ENSP00000375624:R225P;ENSP00000375625:R306P	ENSP00000251390:R289P	R	-	2	0	LILRA3	59494387	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.120000	0.03273	-0.301000	0.08882	-0.238000	0.12139	CGC	.	C|0.999;G|0.001		0.662	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1		
TFAP2C	7022	hgsc.bcm.edu	37	20	55209229	55209229	+	Missense_Mutation	SNP	G	G	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr20:55209229G>T	ENST00000201031.2	+	5	1070	c.827G>T	c.(826-828)cGg>cTg	p.R276L	TFAP2C_ENST00000544508.1_Missense_Mutation_p.R107L	NM_003222.3	NP_003213.1	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma)	276					cell-cell signaling (GO:0007267)|cerebral cortex development (GO:0021987)|dichotomous subdivision of terminal units involved in mammary gland duct morphogenesis (GO:0060598)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|forebrain neuron fate commitment (GO:0021877)|germ-line stem cell maintenance (GO:0030718)|hair follicle development (GO:0001942)|keratinocyte development (GO:0003334)|male gonad development (GO:0008584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermis development (GO:0045682)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sebaceous gland development (GO:0048733)|somatic stem cell maintenance (GO:0035019)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			Colorectal(105;0.229)			AATGGAGGCCGGTCCTTGCGG	0.448																																					p.R276L		Atlas-SNP	.											.	TFAP2C	51	.	0			c.G827T						.						74.0	79.0	78.0					20																	55209229		2203	4300	6503	SO:0001583	missense	7022	exon5			GAGGCCGGTCCTT		CCDS13454.1	20q13.2	2008-07-17	2001-11-28		ENSG00000087510	ENSG00000087510			11744	protein-coding gene	gene with protein product	"""estrogen receptor factor 1"""	601602	"""transcription factor AP-2 gamma (activating enhancer-binding protein 2 gamma)"""			8661133	Standard	NM_003222		Approved	AP2-GAMMA, ERF1, TFAP2G, hAP-2g	uc002xya.3	Q92754	OTTHUMG00000032805	ENST00000201031.2:c.827G>T	chr20.hg19:g.55209229G>T	ENSP00000201031:p.Arg276Leu	94.0	0.0		94.0	4.0	NM_003222	B4DWK3|O00685|O00730|Q86V30|Q8IVB6|Q9P1X2	Missense_Mutation	SNP	ENST00000201031.2	hg19	CCDS13454.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.307258	0.81247	.	.	ENSG00000087510	ENST00000201031;ENST00000544508	D;D	0.97186	-4.28;-4.28	5.3	5.3	0.74995	Transcription factor AP-2, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.98191	0.9402	M	0.89601	3.045	0.80722	D	1	P	0.50819	0.939	P	0.51777	0.679	D	0.99383	1.0923	10	0.87932	D	0	-23.6281	18.9667	0.92700	0.0:0.0:1.0:0.0	.	276	Q92754	AP2C_HUMAN	L	276;107	ENSP00000201031:R276L;ENSP00000442274:R107L	ENSP00000201031:R276L	R	+	2	0	TFAP2C	54642636	1.000000	0.71417	0.997000	0.53966	0.253000	0.25986	9.731000	0.98807	2.480000	0.83734	0.561000	0.74099	CGG	.	.		0.448	TFAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079823.2	NM_003222	
MORC2	22880	hgsc.bcm.edu	37	22	31342353	31342353	+	Missense_Mutation	SNP	A	A	C			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr22:31342353A>C	ENST00000397641.3	-	6	809	c.401T>G	c.(400-402)tTt>tGt	p.F134C	MORC2_ENST00000215862.4_Missense_Mutation_p.F72C			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	134						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						TTCCTCATGAAACGTGCGAGA	0.488																																					p.F72C		Atlas-SNP	.											.	MORC2	78	.	0			c.T215G						.						202.0	156.0	171.0					22																	31342353		2203	4300	6503	SO:0001583	missense	22880	exon7			TCATGAAACGTGC	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 1"", ""zinc finger, CW type with coiled-coil domain 1"""	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.401T>G	chr22.hg19:g.31342353A>C	ENSP00000380763:p.Phe134Cys	52.0	0.0		150.0	42.0	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	hg19		.	.	.	.	.	.	.	.	.	.	A	26.7	4.761248	0.89932	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	D;D	0.94931	-3.56;-3.56	5.15	5.15	0.70609	ATPase-like, ATP-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.97714	0.9250	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98745	1.0718	10	0.87932	D	0	.	15.1388	0.72595	1.0:0.0:0.0:0.0	.	134	Q9Y6X9	MORC2_HUMAN	C	134;72	ENSP00000380763:F134C;ENSP00000215862:F72C	ENSP00000215862:F72C	F	-	2	0	MORC2	29672353	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.761000	0.91691	2.160000	0.67779	0.454000	0.30748	TTT	.	.		0.488	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941	
PLXNB2	23654	hgsc.bcm.edu	37	22	50727540	50727540	+	Missense_Mutation	SNP	T	T	C			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr22:50727540T>C	ENST00000449103.1	-	4	1240	c.1100A>G	c.(1099-1101)gAg>gGg	p.E367G	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Missense_Mutation_p.E367G			O15031	PLXB2_HUMAN	plexin B2	367	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GGGCAGGTGCTCCGAGCCACA	0.697																																					p.E367G		Atlas-SNP	.											.	PLXNB2	172	.	0			c.A1100G						.						9.0	11.0	11.0					22																	50727540		2052	4181	6233	SO:0001583	missense	23654	exon4			AGGTGCTCCGAGC		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.1100A>G	chr22.hg19:g.50727540T>C	ENSP00000409171:p.Glu367Gly	51.0	0.0		47.0	15.0	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	hg19	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.641799	0.87859	.	.	ENSG00000196576	ENST00000449103;ENST00000359337;ENST00000414275;ENST00000411680;ENST00000432455	T;T;T;T	0.04502	3.61;3.61;3.61;3.61	4.58	4.58	0.56647	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.235460	0.29218	N	0.012793	T	0.14141	0.0342	L	0.58354	1.805	0.80722	D	1	D	0.55385	0.971	P	0.60012	0.867	T	0.04268	-1.0964	10	0.29301	T	0.29	.	14.1091	0.65111	0.0:0.0:0.0:1.0	.	367	O15031	PLXB2_HUMAN	G	367;367;367;26;367	ENSP00000409171:E367G;ENSP00000352288:E367G;ENSP00000400679:E26G;ENSP00000392620:E367G	ENSP00000352288:E367G	E	-	2	0	PLXNB2	49069667	1.000000	0.71417	0.999000	0.59377	0.765000	0.43378	5.538000	0.67193	1.928000	0.55862	0.459000	0.35465	GAG	.	.		0.697	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
NLGN4X	57502	hgsc.bcm.edu	37	X	5821285	5821285	+	Missense_Mutation	SNP	G	G	T	rs398124364		TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chrX:5821285G>T	ENST00000381095.3	-	5	2061	c.1434C>A	c.(1432-1434)agC>agA	p.S478R	NLGN4X_ENST00000538097.1_Missense_Mutation_p.S478R|NLGN4X_ENST00000275857.6_Missense_Mutation_p.S478R|NLGN4X_ENST00000381093.2_Missense_Mutation_p.S498R|NLGN4X_ENST00000381092.1_Missense_Mutation_p.S478R	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	478					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						GCTTCATTTCGCTTTGGCAGT	0.607																																					p.S478R		Atlas-SNP	.											.	NLGN4X	191	.	0			c.C1434A						.						67.0	59.0	62.0					X																	5821285		2203	4300	6503	SO:0001583	missense	57502	exon5			CATTTCGCTTTGG	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"""neuroligin 4"""	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1434C>A	chrX.hg19:g.5821285G>T	ENSP00000370485:p.Ser478Arg	352.0	0.0		331.0	95.0	NM_181332	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	hg19	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.735781	0.30774	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	3.93	-1.39	0.08997	Carboxylesterase, type B (1);	.	.	.	.	T	0.65873	0.2733	L	0.51914	1.62	0.48452	D	0.999653	P;P;P	0.45428	0.75;0.858;0.456	P;P;B	0.50405	0.528;0.64;0.393	T	0.62632	-0.6813	9	0.51188	T	0.08	.	11.2547	0.49048	0.8693:0.0:0.1307:0.0	.	535;478;498	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	R	478;498;478;478;478	ENSP00000370485:S478R;ENSP00000370483:S498R;ENSP00000275857:S478R;ENSP00000370482:S478R;ENSP00000439203:S478R	ENSP00000275857:S478R	S	-	3	2	NLGN4X	5831285	0.962000	0.33011	0.734000	0.30879	0.799000	0.45148	0.146000	0.16180	-0.795000	0.04462	-0.881000	0.02953	AGC	.	.		0.607	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742	
RPS6KA6	27330	hgsc.bcm.edu	37	X	83359580	83359580	+	Missense_Mutation	SNP	C	C	T			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chrX:83359580C>T	ENST00000262752.2	-	17	1548	c.1541G>A	c.(1540-1542)tGt>tAt	p.C514Y	RPS6KA6_ENST00000543399.1_Missense_Mutation_p.C514Y|RPS6KA6_ENST00000495332.1_5'UTR	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	514	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						TTCCGAGAAACATTTTTGTTT	0.348																																					p.C514Y		Atlas-SNP	.											.	RPS6KA6	116	.	0			c.G1541A						.						87.0	76.0	80.0					X																	83359580		2202	4297	6499	SO:0001583	missense	27330	exon17			GAGAAACATTTTT	AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"""ribosomal protein S6 kinase, 90kD, polypeptide 6"""			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.1541G>A	chrX.hg19:g.83359580C>T	ENSP00000262752:p.Cys514Tyr	143.0	0.0		329.0	46.0	NM_014496	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	ENST00000262752.2	hg19	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	C	0.799	-0.756075	0.03019	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	T;T	0.38560	1.13;1.13	5.34	4.35	0.52113	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.162448	0.56097	D	0.000028	T	0.15739	0.0379	N	0.10733	0.035	0.32667	N	0.517343	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.29366	-1.0014	10	0.02654	T	1	.	4.045	0.09768	0.2276:0.555:0.0:0.2173	.	514;514	B7ZL90;Q9UK32	.;KS6A6_HUMAN	Y	514	ENSP00000262752:C514Y;ENSP00000440830:C514Y	ENSP00000262752:C514Y	C	-	2	0	RPS6KA6	83246236	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.091000	0.41691	2.205000	0.71048	0.600000	0.82982	TGT	.	.		0.348	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496	
TLL1	7092	hgsc.bcm.edu	37	4	166986896	166986900	+	Frame_Shift_Del	DEL	GCAAA	GCAAA	-	rs374208896|rs112517603	byFrequency	TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	GCAAA	GCAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr4:166986896_166986900delGCAAA	ENST00000061240.2	+	16	2716_2720	c.2069_2073delGCAAA	c.(2068-2073)ggcaaafs	p.GK690fs	TLL1_ENST00000507499.1_Frame_Shift_Del_p.GK713fs	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	690	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		AAACTGCATGGCAAATTCTGTGGCG	0.4																																					p.690_691del		Atlas-Indel,Pindel	.											.	TLL1	194	.	0			c.2068_2072del						.																																			SO:0001589	frameshift_variant	7092	exon16			.	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2069_2073delGCAAA	chr4.hg19:g.166986896_166986900delGCAAA	ENSP00000061240:p.Gly690fs	54.0	0.0		89.0	18.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Frame_Shift_Del	DEL	ENST00000061240.2	hg19	CCDS3811.1																																																																																			.	.		0.400	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1		
SLC38A6	145389	hgsc.bcm.edu	37	14	61550366	61550378	+	Frame_Shift_Del	DEL	GGAGAACCAAACG	GGAGAACCAAACG	-	rs147438249	byFrequency	TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	GGAGAACCAAACG	GGAGAACCAAACG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr14:61550366_61550378delGGAGAACCAAACG	ENST00000354886.2	+	17	1666_1678	c.1502_1514delGGAGAACCAAACG	c.(1501-1515)aggagaaccaaacgtfs	p.RRTKR501fs	SLC38A6_ENST00000456840.2_Frame_Shift_Del_p.GEPNV480fs	NM_001172702.1	NP_001166173.1	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	0					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		agaggcctcaggagaaccaaacgtgtccacacc	0.469																																					p.501_505del		Atlas-Indel,Pindel	.											.	SLC38A6	87	.	0			c.1501_1513del						.																																			SO:0001589	frameshift_variant	145389	exon17			.	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"""Solute carriers"""	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000354886.2:c.1502_1514delGGAGAACCAAACG	chr14.hg19:g.61550366_61550378delGGAGAACCAAACG	ENSP00000346959:p.Arg501fs	49.0	0.0		60.0	12.0	NM_001172702	C9JWA6|Q86SY5	Frame_Shift_Del	DEL	ENST00000354886.2	hg19	CCDS53900.1																																																																																			.	.		0.469	SLC38A6-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
KANSL2	54934	hgsc.bcm.edu	37	12	49075410	49075430	+	Start_Codon_Del	DEL	GTTCATAACCAAAACCTGCGG	GTTCATAACCAAAACCTGCGG	-	rs199711246		TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	GTTCATAACCAAAACCTGCGG	GTTCATAACCAAAACCTGCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr12:49075410_49075430delGTTCATAACCAAAACCTGCGG	ENST00000420613.2	-	0	39_53				KANSL2_ENST00000553086.1_Start_Codon_Del|KANSL2_ENST00000550347.1_In_Frame_Del_p.PQVLVMN179del|KANSL2_ENST00000357861.3_5'UTR	NM_017822.3	NP_060292.3	Q9H9L4	KANL2_HUMAN	KAT8 regulatory NSL complex subunit 2						chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)											TCCGAATCCTGTTCATAACCAAAACCTGCGGGGTCAAACGA	0.529																																					.		Atlas-Indel,Pindel	.											.	.	.	.	0			.						.																																			SO:0001582	initiator_codon_variant	54934	wholegene			.	AK094528	CCDS44869.1	12q13.11	2011-10-31	2011-10-31	2011-10-31	ENSG00000139620	ENSG00000139620			26024	protein-coding gene	gene with protein product		615488	"""chromosome 12 open reading frame 41"""	C12orf41		12477932	Standard	NM_017822		Approved	FLJ20436, NSL2	uc001rrz.2	Q9H9L4	OTTHUMG00000170392		chr12.hg19:g.49075410_49075430delGTTCATAACCAAAACCTGCGG		80.0	0.0		81.0	17.0	NM_017822	Q8N3B5|Q96CV0|Q9NX51	Frame_Shift_Del	DEL	ENST00000420613.2	hg19	CCDS44869.1																																																																																			.	.		0.529	KANSL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408841.1	NM_017822	
TRIM13	10206	hgsc.bcm.edu	37	13	50586334	50586335	+	Frame_Shift_Ins	INS	-	-	A			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr13:50586334_50586335insA	ENST00000378182.3	+	2	996_997	c.258_259insA	c.(259-261)atcfs	p.I87fs	TRIM13_ENST00000478111.1_Intron|TRIM13_ENST00000457662.2_Frame_Shift_Ins_p.I87fs|TRIM13_ENST00000298772.5_Frame_Shift_Ins_p.I90fs|TRIM13_ENST00000356017.4_Frame_Shift_Ins_p.I90fs|TRIM13_ENST00000420995.2_Frame_Shift_Ins_p.I87fs	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13	87					anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		ACAAGATCAAGATCTCTCCCAA	0.446																																					p.K89fs		Atlas-Indel,Pindel	.											.	TRIM13	30	.	0			c.267_268insA						.																																			SO:0001589	frameshift_variant	10206	exon4			.	AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9976	protein-coding gene	gene with protein product		605661	"""ret finger protein 2"", ""tripartite motif-containing 13"""	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.259dupA	chr13.hg19:g.50586335_50586335dupA	ENSP00000367424:p.Ile87fs	48.0	0.0		82.0	19.0	NM_001007278	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	Frame_Shift_Ins	INS	ENST00000378182.3	hg19	CCDS9423.1																																																																																			.	.		0.446	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278	
SIRT6	51548	hgsc.bcm.edu	37	19	4174810	4174811	+	Frame_Shift_Ins	INS	-	-	G			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr19:4174810_4174811insG	ENST00000337491.2	-	8	935_936	c.871_872insC	c.(871-873)cgcfs	p.R291fs	SIRT6_ENST00000601488.1_3'UTR|SIRT6_ENST00000381935.3_Frame_Shift_Ins_p.R219fs|SIRT6_ENST00000305232.6_Frame_Shift_Ins_p.R264fs|SIRT6_ENST00000594279.1_3'UTR	NM_016539.2	NP_057623.2	Q8N6T7	SIR6_HUMAN	sirtuin 6	291	Pro-rich.				histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|protein ADP-ribosylation (GO:0006471)|regulation of double-strand break repair via homologous recombination (GO:0010569)	nuclear telomeric heterochromatin (GO:0005724)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|lung(4)|ovary(1)|skin(1)	8		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.023)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTGGGCGGGCGGGGCAGGGGT	0.708																																					p.R291fs		Atlas-INDEL	.											.	SIRT6	16	.	0			c.872_873insC						.																																			SO:0001589	frameshift_variant	51548	exon8			.	AF233396	CCDS12122.1, CCDS54199.1	19p13.3	2010-06-25	2010-06-25			ENSG00000077463			14934	protein-coding gene	gene with protein product		606211	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 6"", ""sirtuin (silent mating type information regulation 2 homolog) 6 (S. cerevisiae)"""			10873683	Standard	NM_016539		Approved		uc002lzo.3	Q8N6T7		ENST00000337491.2:c.872dupC	chr19.hg19:g.4174814_4174814dupG	ENSP00000337332:p.Arg291fs	35.0	0.0		27.0	10.0	NM_016539	B2RCD0|O75291|Q6IAF5|Q6PK99|Q8NCD2|Q9BSI5|Q9BWP3|Q9NRC7|Q9UQD1	Frame_Shift_Ins	INS	ENST00000337491.2	hg19	CCDS12122.1																																																																																			.	.		0.708	SIRT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457931.2		
GRN	2896	hgsc.bcm.edu	37	17	42429084	42429086	+	In_Frame_Del	DEL	ATA	ATA	-			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	ATA	ATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr17:42429084_42429086delATA	ENST00000053867.3	+	10	1162_1164	c.1100_1102delATA	c.(1099-1104)gataat>gat	p.N368del	GRN_ENST00000589265.1_In_Frame_Del_p.N211del|GRN_ENST00000589923.1_3'UTR	NM_002087.2	NP_002078.1	P28799	GRN_HUMAN	granulin	368					blastocyst hatching (GO:0001835)|cell death (GO:0008219)|embryo implantation (GO:0007566)|positive regulation of epithelial cell proliferation (GO:0050679)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	growth factor activity (GO:0008083)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GTCCCCTGTGATAATGTCAGCAG	0.601																																					p.367_367del		Atlas-Indel,Pindel	.											.	GRN	51	.	0			c.1099_1101del						.																																			SO:0001651	inframe_deletion	2896	exon10			.	M75161	CCDS11483.1	17q21.32	2014-09-17				ENSG00000030582			4601	protein-coding gene	gene with protein product	"""progranulin"""	138945				1417868, 9826678	Standard	XM_005257253		Approved	PCDGF, PGRN, CLN11	uc002igp.1	P28799		ENST00000053867.3:c.1100_1102delATA	chr17.hg19:g.42429084_42429086delATA	ENSP00000053867:p.Asn368del	43.0	0.0		74.0	12.0	NM_002087	D3DX55|P23781|P23782|P23783|P23784|Q53HQ8|Q53Y88|Q540U8|Q9BWE7|Q9H8S1|Q9UCH0	In_Frame_Del	DEL	ENST00000053867.3	hg19	CCDS11483.1																																																																																			.	.		0.601	GRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457766.1	NM_002087	
GMPR2	51292	hgsc.bcm.edu	37	14	24707793	24707798	+	Splice_Site	DEL	TTTAAG	TTTAAG	-			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	TTTAAG	TTTAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr14:24707793_24707798delTTTAAG	ENST00000355299.4	+	10	1318_1322	c.857_861delTTTAAG	c.(856-861)atttaa>a	p.I*286del	GMPR2_ENST00000557854.1_In_Frame_Del_p.FK365del|GMPR2_ENST00000348719.7_In_Frame_Del_p.FK347del|GMPR2_ENST00000420554.2_Splice_Site_p.I*304del|GMPR2_ENST00000456667.3_Splice_Site_p.I*258del|GMPR2_ENST00000559836.1_Splice_Site_p.I*286del|GMPR2_ENST00000399440.2_Splice_Site_p.I*286del|GMPR2_ENST00000559910.1_Splice_Site_p.I*253del|GMPR2_ENST00000559104.1_Splice_Site_p.I*271del	NM_001002000.1	NP_001002000.1	Q9P2T1	GMPR2_HUMAN	guanosine monophosphate reductase 2	286	GMP binding.				GMP metabolic process (GO:0046037)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)	p.A287V(1)		large_intestine(4)|lung(3)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(265;0.0181)		TCCTACTTTAAGAGCCTCAGAGGGAA	0.476																																					.		Atlas-Indel,Pindel	.											.	GMPR2	37	.	1	Substitution - Missense(1)	large_intestine(1)	.						.																																			SO:0001630	splice_region_variant	51292	.			.		CCDS41935.1, CCDS45087.1, CCDS61419.1, CCDS73624.1	14q11.2	2006-11-24							4377	protein-coding gene	gene with protein product		610781					Standard	XM_005267742		Approved		uc001wnw.3	Q9P2T1		ENST00000355299.4:c.858-1TTTAAG>-	chr14.hg19:g.24707793_24707798delTTTAAG		99.0	0.0		148.0	41.0	.	D3DS66|Q567T0|Q6IAJ8|Q86T14	Splice_Site	DEL	ENST00000355299.4	hg19	CCDS41935.1																																																																																			.	.		0.476	GMPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415821.2	NM_016576	In_Frame_Del
HIPK2	28996	hgsc.bcm.edu	37	7	139311420	139311425	+	In_Frame_Del	DEL	TTCTCT	TTCTCT	-			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	TTCTCT	TTCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr7:139311420_139311425delTTCTCT	ENST00000406875.3	-	6	1635_1640	c.1541_1546delAGAGAA	c.(1540-1548)aagagaatc>atc	p.KR514del	HIPK2_ENST00000428878.2_In_Frame_Del_p.KR514del|HIPK2_ENST00000342645.6_In_Frame_Del_p.KR514del	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	514	Interaction with DAXX.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					ATTGGAGTGATTCTCTTGTCAGCATC	0.49																																					p.514_516del		Atlas-Indel,Pindel	.											.	HIPK2	192	.	0			c.1542_1547del						.																																			SO:0001651	inframe_deletion	28996	exon6			.	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"""homeodomain-interacting protein kinase 2"""			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1541_1546delAGAGAA	chr7.hg19:g.139311420_139311425delTTCTCT	ENSP00000385571:p.Lys514_Arg515del	51.0	0.0		139.0	19.0	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	In_Frame_Del	DEL	ENST00000406875.3	hg19																																																																																				.	.		0.490	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740	
BAP1	8314	hgsc.bcm.edu	37	3	52439158	52439167	+	Frame_Shift_Del	DEL	CTAGAAAGGC	CTAGAAAGGC	-			TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	CTAGAAAGGC	CTAGAAAGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr3:52439158_52439167delCTAGAAAGGC	ENST00000460680.1	-	11	1546_1555	c.1075_1084delGCCTTTCTAG	c.(1075-1086)gcctttctagacfs	p.AFLD359fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.AFLD341fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F360L(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TTGTGATTGTCTAGAAAGGCCGGCAGCCGC	0.552			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															p.359_362del	GBM(101;493 1458 7992 21037 25532)	Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	1	Substitution - Missense(1)	kidney(1)	c.1076_1085del						.																																			SO:0001589	frameshift_variant	8314	exon11			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1075_1084delGCCTTTCTAG	chr3.hg19:g.52439158_52439167delCTAGAAAGGC	ENSP00000417132:p.Ala359fs	83.0	0.0		45.0	13.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.552	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		
ATG14	22863	hgsc.bcm.edu	37	14	55878482	55878483	+	Frame_Shift_Ins	INS	-	-	G	rs201727714		TCGA-2Y-A9H2-01A-12D-A382-10	TCGA-2Y-A9H2-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d34332a4-c52c-428f-bef7-95432afb6d1d	466f3a9c-b339-460c-8d5f-563852b7b498	g.chr14:55878482_55878483insG	ENST00000247178.5	-	1	93_94	c.58_59insC	c.(58-60)cggfs	p.R20fs		NM_014924.4	NP_055739.2	Q6ZNE5	BAKOR_HUMAN	autophagy related 14	20					autophagic vacuole assembly (GO:0000045)|endosome to lysosome transport (GO:0008333)|positive regulation of autophagy (GO:0010508)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|pre-autophagosomal structure membrane (GO:0034045)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(2)	13						GGCGAGCGGCCGGGGCCCGCAG	0.693																																					p.R20fs		Atlas-Indel,Pindel	.											.	ATG14	36	.	0			c.59_60insC						.																																			SO:0001589	frameshift_variant	22863	exon1			.	AB020638	CCDS32087.1	14q22.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000126775	ENSG00000126775			19962	protein-coding gene	gene with protein product	"""Barkor"", ""beclin 1-associated autophagy-related key regulator"""	613515	"""KIAA0831"", ""ATG14 autophagy related 14 homolog (S. cerevisiae)"""	KIAA0831		18843052	Standard	NM_014924		Approved	ATG14L	uc001xbx.2	Q6ZNE5	OTTHUMG00000172129	ENST00000247178.5:c.59dupC	chr14.hg19:g.55878486_55878486dupG	ENSP00000247178:p.Arg20fs	204.0	0.0		99.0	44.0	NM_014924	A6NJE4|A8K9U5|B7ZWP5|O94920|Q32MK7|Q32MK8	Frame_Shift_Ins	INS	ENST00000247178.5	hg19	CCDS32087.1																																																																																			.	.		0.693	ATG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416992.1	NM_014924	
